http://2010.igem.org/wiki/index.php?title=Special:Contributions&feed=atom&limit=50&target=Pjwu2010.igem.org - User contributions [en]2024-03-29T12:10:31ZFrom 2010.igem.orgMediaWiki 1.16.5http://2010.igem.org/Template:CalgaryMenuTemplate:CalgaryMenu2010-10-28T03:50:30Z<p>Pjwu: </p>
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</html></div>Pjwuhttp://2010.igem.org/Team:CalgaryTeam:Calgary2010-10-28T03:47:07Z<p>Pjwu: </p>
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<p>Our modelling project consists of two components: a mathematical model done in MATLAB and an animation done in Autodesk <i>Maya</i>. We hope to model the formation of inclusion bodies, which are aggregations of misfolded protein that can occur within cells. Using <i>Maya</i>, we also hope to visually show other students one of the proposed aggregation mechanisms described in the literature.<br />
<a href="https://2010.igem.org/Team:Calgary/Modelling">Read more here...</a></p><br />
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<p>Our outreach project included educating highschool students about iGEM. Outreach also entailed blog entries and podcasts about synthetic life, iGEM and open source as well as genetically modified foods. The blog entry, podcasts and high school presentations allowed the iGEM students to spread knowledge about iGEM to the general public and to potential future scientists. <a href="https://2010.igem.org/Team:Calgary/Community">Read more here...</a></p><br />
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<p class="tabText" style="padding-left:10px;">What new dangers and unintended consequences will synthetic biology pose to us in the future? iGEM Calgary travels to Defence Research and Development Canada Suffield, a major Canadian Military Research facility that specializes in chemo-biological threats. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community/Suffield">Read more...</a></p><br />
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<p class="tabText" style="padding-left:10px;">The University of Calgary, Alberta, and Lethbridge iGEM teams met in Lethbridge at a conference put on by Alberta Innovates Technology Futures to learn important aspects of iGEM. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community/Conferences#lethbridge">Read more...</a></p><br />
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<p class="tabText" style="padding-left:10px;">Have you ever seen an aggregate protein dance? Look out for iGEM Calgary’s rambunctious mascot “Protein Man” at the Jamboree promoting proper protein expression. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Extras#proteinman">Learn more about him...</a></p><br />
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<p class="tabText" style="padding-left:10px;">Team Calgary brings iGEM awareness to the community. The iGEM bake sale was a great success, both in selling cupcakes and educating customers about our team. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community">See what else we've been doing...</a></p><br />
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<p class="tabText" style="padding-left:10px;">Alberta’s very own Jamboree. The three Alberta iGEM teams, the Universities of Alberta, Calgary, and Lethbridge meet to perform a practice project presentation to each other. Experts within their field are also present to give teams challenging questions, and then meet with each team to suggest improvements. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community/Conferences#agem">Read more...</a></p><br />
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<h3>Wetlab</h3><br />
<p>You’re stressing me out! This year, in the wetlab, we have been designing a reporter system to detect problems in protein expression. Our system uses a visual output to allow specificity in determining which step in protein expression problems are occurring.</p><br />
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<h3>Modelling</h3><br />
<p>Our modeling project has focused on simulating and modeling the formation of inclusion bodies, aggregates of protein within the cell. We've been exploring the factors that lead to their formation.</p><br />
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<h3>Community</h3><br />
<p>Our human practices section focused on exploring ethical issues in synthetic biology through an ethics paper as well as a podcast focusing on a few key issues. Our outreach initiatives also allowed the iGEM students to spread knowledge about iGEM to the general public and to potential future scientists through activities such as high school presentations and participation in various research symposiums.</p><br />
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<p>Our modelling project consists of two components: a mathematical model done in MATLAB and an animation done in Autodesk <i>Maya</i>. We hope to model the formation of inclusion bodies, which are aggregations of misfolded protein that can occur within cells. Using <i>Maya</i>, we also hope to visually show other students one of the proposed aggregation mechanisms described in the literature.<br />
<a href="https://2010.igem.org/Team:Calgary/Modelling">Read more here...</a></p><br />
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<p>Our outreach project included educating highschool students about iGEM. Outreach also entailed blog entries and podcasts about synthetic life, iGEM and open source as well as genetically modified foods. The blog entry, podcasts and high school presentations allowed the iGEM students to spread knowledge about iGEM to the general public and to potential future scientists. <a href="https://2010.igem.org/Team:Calgary/Community">Read more here...</a></p><br />
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<p class="tabText" style="padding-left:10px;">What new dangers and unintended consequences will synthetic biology pose to us in the future? iGEM Calgary travels to Defence Research and Development Canada Suffield, a major Canadian Military Research facility that specializes in chemo-biological threats. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community/Suffield">Read more...</a></p><br />
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<p class="tabText" style="padding-left:10px;">The University of Calgary, Alberta, and Lethbridge iGEM teams met in Lethbridge at a conference put on by Alberta Innovates Technology Futures to learn important aspects of iGEM. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community/Conferences#lethbridge">Read more...</a></p><br />
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<p class="tabText" style="padding-left:10px;">Have you ever seen an aggregate protein dance? Look out for iGEM Calgary’s rambunctious mascot “Protein Man” at the Jamboree promoting proper protein expression. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Extras#proteinman">Learn more about him...</a></p><br />
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<p class="tabText" style="padding-left:10px;">Team Calgary brings iGEM awareness to the community. The iGEM bake sale was a great success, both in selling cupcakes and educating customers about our team. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community">See what else we've been doing...</a></p><br />
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<p class="tabText" style="padding-left:10px;">Alberta’s very own Jamboree. The three Alberta iGEM teams, the Universities of Alberta, Calgary, and Lethbridge meet to perform a practice project presentation to each other. Experts within their field are also present to give teams challenging questions, and then meet with each team to suggest improvements. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community/Conferences#agem">Read more...</a></p><br />
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<h3>Wetlab</h3><br />
<p>You’re stressing me out! This year, in the wetlab, we have been designing a reporter system to detect problems in protein expression. Our system uses a visual output to allow specificity in determining which step in protein expression problems are occurring.</p><br />
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<h3>Modelling</h3><br />
<p>Our modeling project has focused on simulating and modeling the formation of inclusion bodies, aggregates of protein within the cell. We've been exploring the factors that lead to their formation.</p><br />
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<h3>Community</h3><br />
<p>Our human practices section focused on exploring ethical issues in synthetic biology through an ethics paper as well as a podcast focusing on a few key issues. Our outreach initiatives also allowed the iGEM students to spread knowledge about iGEM to the general public and to potential future scientists through activities such as high school presentations and participation in various research symposiums.</p><br />
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<p>Our modelling project consists of two components: a mathematical model done in MATLAB and an animation done in Autodesk <i>Maya</i>. We hope to model the formation of inclusion bodies, which are aggregations of misfolded protein that can occur within cells. Using <i>Maya</i>, we also hope to visually show other students one of the proposed aggregation mechanisms described in the literature.<br />
<a href="https://2010.igem.org/Team:Calgary/Modelling">Read more here...</a></p><br />
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<p>Our outreach project included educating highschool students about iGEM. Outreach also entailed blog entries and podcast about synthetic life, iGEM and open source as well as Genetically modified foods. The blog entry, podcasts and high school presentations allowed the iGEM students to spread knowledge about iGEM to the general public and to potential future scientists. <a href="https://2010.igem.org/Team:Calgary/Community">Read more here...</a></p><br />
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<p class="tabText" style="padding-left:10px;">What new dangers and unintended consequences will synthetic biology pose to us in the future? iGEM Calgary travels to Defence Research and Development Canada Suffield, a major Canadian Military Research facility that specializes in chemo-biological threats. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community/Suffield">Read more...</a></p><br />
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<p class="tabText" style="padding-left:10px;">The University of Calgary, Alberta, and Lethbridge iGEM teams met in Lethbridge at a conference put on by Alberta Innovates Technology Futures to learn important aspects of iGEM. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community/Conferences#lethbridge">Read more...</a></p><br />
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<p class="tabText" style="padding-left:10px;">Have you ever seen an aggregate protein dance? Look out for iGEM Calgary’s rambunctious mascot “Protein Man” at the Jamboree promoting proper protein expression. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Extras#proteinman">Learn more about him...</a></p><br />
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<p class="tabText" style="padding-left:10px;">Team Calgary brings iGEM awareness to the community. The iGEM bake sale was a great success, both in selling cupcakes and educating customers about our team. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community">See what else we've been doing...</a></p><br />
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<p class="tabText" style="padding-left:10px;">Alberta’s very own Jamboree. The three Alberta iGEM teams, the Universities of Alberta, Calgary, and Lethbridge meet to perform a practice project presentation to each other. Experts within their field are also present to give teams challenging questions, and then meet with each team to suggest improvements. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community/Conferences#agem">Read more...</a></p><br />
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<h3>Wetlab</h3><br />
<p>You’re stressing me out! This year, in the wetlab, we have been designing a reporter system to detect problems in protein expression. Our system uses a visual output to allow specificity in determining which step in protein expression problems are occurring.</p><br />
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<h3>Modelling</h3><br />
<p>Our modeling project has focused on simulating and modeling the formation of inclusion bodies, aggregates of protein within the cell. We've been exploring the factors that lead to their formation.</p><br />
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<h3>Community</h3><br />
<p>Our human practices section focused on exploring ethical issues in synthetic biology through an ethics paper as well as a podcast focusing on a few key issues. Our outreach initiatives also allowed the iGEM students to spread knowledge about iGEM to the general public and to potential future scientists through activities such as high school presentations and participation in various research symposiums.</p><br />
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<p>Our modelling project consists of two components: a mathematical model done in MATLAB and an animation done in Autodesk <i>Maya</i>. We hope to model the formation of inclusion bodies, which are aggregations of misfolded protein that can occur within cells. Using <i>Maya</i>, we also hope to visually show other students one of the proposed aggregation mechanisms described in the literature.<br />
<a href="https://2010.igem.org/Team:Calgary/Modelling">Read more here...</a></p><br />
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<p>Our outreach project included educating highschool students about iGEM. Outreach also entailed blog entries and podcast about synthetic life, iGEM and open source as well as Genetically modified foods. The blog entry, podcasts and high school presentations allowed the iGEM students to spread knowledge about iGEM to the general public and to potential future scientists. <a href="https://2010.igem.org/Team:Calgary/Community">Read more here...</a></p><br />
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<p class="tabText" style="padding-left:10px;">What new dangers and unintended consequences will synthetic biology pose to us in the future? iGEM Calgary travels to Defence Research and Development Canada Suffield, a major Canadian Military Research facility that specializes in chemo-biological threats. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community/Suffield">Read more...</a></p><br />
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<p class="tabText" style="padding-left:10px;">The University of Calgary, Alberta, and Lethbridge iGEM teams met in Lethbridge at a conference put on by Alberta Innovates Technology Futures to learn important aspects of iGEM. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community/Conferences#lethbridge">Read more...</a></p><br />
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<p class="tabText" style="padding-left:10px;">Have you ever seen an aggregate protein dance? Look out for iGEM Calgary’s rambunctious mascot “Protein Man” at the Jamboree promoting proper protein expression. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Extras#proteinman">Learn more about him...</a></p><br />
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<p class="tabText" style="padding-left:10px;">Team Calgary brings iGEM awareness to the community. The iGEM bake sale was a great success, both in selling cupcakes and educating customers about our team. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community">See what else we've been doing...</a></p><br />
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<p class="tabText" style="padding-left:10px;">Alberta’s very own Jamboree. The three Alberta iGEM teams, the Universities of Alberta, Calgary, and Lethbridge meet to perform a practice project presentation to each other. Experts within their field are also present to give teams challenging questions, and then meet with each team to suggest improvements. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community/Conferences#agem">Read more...</a></p><br />
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<h3>Wetlab</h3><br />
<p>You’re stressing me out! This year, in the wetlab, we have been designing a reporter system to detect problems in protein expression. Our system uses a visual output to allow specificity in determining which step in protein expression problems are occurring.</p><br />
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<p>Our modeling project has focused on simulating and modeling the formation of inclusion bodies, aggregates of protein within the cell. We've been exploring the factors that lead to their formation.</p><br />
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<p>Our human practices section focused on exploring ethical issues in synthetic biology through an ethics paper as well as a podcast focusing on a few key issues. Our outreach initiatives also allowed the iGEM students to spread knowledge about iGEM to the general public and to potential future scientists through activities such as high school presentations and participation in various research symposiums.</p><br />
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<p class="tabText" style="padding-left:10px;">What new dangers and unintended consequences will synthetic biology pose to us in the future? iGEM Calgary travels to Defence Research and Development Canada Suffield, a major Canadian Military Research facility that specializes in chemo-biological threats. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community/Suffield">Read more...</a></p><br />
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<p class="tabText" style="padding-left:10px;">The University of Calgary, Alberta, and Lethbridge iGEM teams met in Lethbridge at a conference put on by Alberta Innovates Technology Futures to learn important aspects of iGEM. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community/Conferences#lethbridge">Read more...</a></p><br />
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<p class="tabText" style="padding-left:10px;">Have you ever seen an aggregate protein dance? Look out for iGEM Calgary’s rambunctious mascot “Protein Man” at the Jamboree promoting proper protein expression. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Extras#proteinman">Learn more about him...</a></p><br />
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<p class="tabText" style="padding-left:10px;">Team Calgary brings iGEM awareness to the community. The iGEM bake sale was a great success, both in selling cupcakes and educating customers about our team. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community">See what else we've been doing...</a></p><br />
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<p class="tabText" style="padding-left:10px;">Alberta’s very own Jamboree. The three Alberta iGEM teams, the Universities of Alberta, Calgary, and Lethbridge meet to perform a practice project presentation to each other. Experts within their field are also present to give teams challenging questions, and then meet with each team to suggest improvements. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community/Conferences#agem">Read more...</a></p><br />
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<p>Our modelling project consists of two components: a mathematical model done in MATLAB and an animation done in Autodesk <i>Maya</i>. We hope to model the formation of inclusion bodies, which are aggregations of misfolded protein that can occur within cells. Using <i>Maya</i>, we also hope to visually show other students one of the proposed aggregation mechanisms described in the literature.<br />
<a href="https://2010.igem.org/Team:Calgary/Modelling">Read more here...</a></p><br />
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<p>Our outreach project included educating highschool students about iGEM. Outreach also entailed blog entries and podcast about synthetic life, iGEM and open source as well as Genetically modified foods. The blog entry, podcasts and high school presentations allowed the iGEM students to spread knowledge about iGEM to the general public and to potential future scientists. <a href="https://2010.igem.org/Team:Calgary/Community">Read more here...</a></p><br />
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<h3>Wetlab</h3><br />
<p>You’re stressing me out! This year, in the wetlab, we have been designing a reporter system to detect problems in protein expression. Our system uses a visual output to allow specificity in determining which step in protein expression problems are occurring.</p><br />
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<h3>Modelling</h3><br />
<p>Our modeling project has focused on simulating and modeling the formation of inclusion bodies, aggregates of protein within the cell. We've been exploring the factors that lead to their formation.</p><br />
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<h3>Community</h3><br />
<p>Our human practices section focused on exploring ethical issues in synthetic biology through an ethics paper as well as a podcast focusing on a few key issues. Our outreach initiatives also allowed the iGEM students to spread knowledge about iGEM to the general public and to potential future scientists through activities such as high school presentations and participation in various research symposiums.</p><br />
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<p>Synthetic biology is a novel, developing science that is introducing new technologies and capabilities to biology. It gives scientists the ability to create novel systems operating in existing organisms, as well as a growing capacity to synthesize fully synthetic life. There are concerns developing however, that this type of research could lead to either the purposeful, or inadvertent creation of harmful organisms or bioweapons. Increased affordability of synthesizing gene sequences, as well as the increased accessibility of synthetic biology are both issues that our increasing these fears. Therefore our team felt that we should gain an expert’s perspective on the dangers of synthetic biology.</p><br />
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<p>Our iGEM team presented the concept of biobricks, the registry of standardized parts, and the iGEM competition to researchers at DRDC Suffield. Defence Research and Development Suffield, or DRDC Suffield, is a Canadian Military Research facility located in southern Alberta. A major focus of DRDC Suffield is addressing chemical and biological threats. It is also the host of the Counter Terrorism Technology Centre, a key component of national defence that uses unique laboratories and testing facilities to help better prepare Canada from chemical, biological, radiological, nuclear, and explosive (CBRNE) threats.</p><br />
<p>Following our presentation we engaged in a roundtable discussion with researchers and experts. As with most scientists, DRDC Suffield scientists acknowledged that synthetic biology, including iGEM projects, have the dual-use capability. This refers to biological research with legitimate scientific purpose, but also has the potential for misuse that would threaten public health, and/or national security. Another danger discussed was the potential to synthesize harmful pathogens from digital genomes, such as smallpox. Although this would be catastrophic if achieved, it was not interpreted as a priority to our security because of the difficulty of “rougue” scientists achieving such a momentous task. A more “real” application of synthetic biology causing dangers to our security was the potential to synthesize biotoxins, or other poisons that could be derived from DNA sequences.</p><br />
<p>Other discussions revolved around the “open source” nature of iGEM. Although the registry was met with a positive response from experts, they were also able to see the concerns with making synthetic biology easier and more accessible. We discussed the dangers of making it easy for amateurs to be dealing with this technology. One of the greatest potentials for dangers that DRDC scientists said would arise from simplifying synthetic biology was the introduction of antibiotic resistance to harmful bacteria, and then being released in to the public.</p><br />
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</html></div>Pjwuhttp://2010.igem.org/Team:Calgary/NotebookTeam:Calgary/Notebook2010-10-28T03:03:07Z<p>Pjwu: </p>
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<li><a href="https://2010.igem.org/Team:Calgary/Notebook/Calendar">Calendar</a></li><br />
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<span id="bodytitle"><h1>Team Notebook</h1></span><br />
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<p>The University of Calgary 2010 iGEM team keeps a record of our summer's work in the Notebook. The Notebook contains daily activities, a log of our brainstorming sessions and meetings, and a handy, detailed reference guide to each lab procedure we have used.</p><br />
<br />
<table><br />
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<td><a href="https://2010.igem.org/Team:Calgary/Notebook/Calendar"><img src="http://i872.photobucket.com/albums/ab287/iGEMCalgary_2010/CalendarIcon.png"></a></img></td><br />
<td><span class="blue"><p>Calendar</p></span><br />
<p>Want to know what we've been up to? Click <span class="blue"><a href="https://2010.igem.org/Team:Calgary/Notebook/Calendar">here</a></span> for a record of each team member's activity over the summer.</p><br />
</td><br />
</tr><br />
<br />
<tr><br />
<td><a href="https://2010.igem.org/Team:Calgary/Notebook/Future_Directions"><img src="http://i872.photobucket.com/albums/ab287/iGEMCalgary_2010/BrainstormIcon.png"></a></img></td><br />
<td><span class="green"><p>Future Directions</p></span><br />
<p>With this project, there are tons of directions that we can head. Click <span class="green"><a href="https://2010.igem.org/Team:Calgary/Notebook/Brainstorming">here</a></span> to see some of the ideas we have in store for the future.</p><br />
</td><br />
</tr><br />
<br />
<tr><br />
<td><a href="https://2010.igem.org/Team:Calgary/Notebook/Safety_And_Protocols"><img src="http://i872.photobucket.com/albums/ab287/iGEMCalgary_2010/ProtocolIcon.png"></a></img></td><br />
<td><span class="purple"><p>Protocols</p></span><br />
<p>So you've looked at our <span class="purple"><a href="https://2010.igem.org/Team:Calgary/Notebook/Calendar">calendar</a></span>. That's all well and good... but what is this "PCR" thing that keeps popping up? If you want to see details for each lab procedure mentioned in our calendar, click <span class="purple"><a href="https://2010.igem.org/Team:Calgary/Notebook/Safety_And_Protocols">here</a></span> for a reference.</p><br />
</td><br />
</tr><br />
<tr><br />
<td><a href="https://2010.igem.org/Team:Calgary/Notebook/Safety"><img src="http://i872.photobucket.com/albums/ab287/iGEMCalgary_2010/SafetyIcon-2.png"></a></img></td><br />
<td><span class="orange"><p>Safety</p></span><br />
<p>To see our completed iGEM safety requirements questionnaire follow this link: <span class="orange"><a href="https://2010.igem.org/Team:Calgary/Notebook/Safety">safety questionnaire</a></span><br />
</p><br />
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</html></div>Pjwuhttp://2010.igem.org/Team:Calgary/NotebookTeam:Calgary/Notebook2010-10-28T02:53:21Z<p>Pjwu: </p>
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<div class="mainbody"><br />
<br />
<span id="bodytitle"><h1>Team Notebook</h1></span><br />
<br />
<p>The University of Calgary 2010 iGEM team keeps a record of our summer's work in the Notebook. The Notebook contains daily activities, a log of our brainstorming sessions and meetings, and a handy, detailed reference guide to each lab procedure we have used.</p><br />
<br />
<table><br />
<tr><br />
<td><a href="https://2010.igem.org/Team:Calgary/Notebook/Calendar"><img src="http://i872.photobucket.com/albums/ab287/iGEMCalgary_2010/CalendarIcon.png"></a></img></td><br />
<td><span class="blue"><p>Calendar</p></span><br />
<p>Want to know what we've been up to? Click <span class="blue"><a href="https://2010.igem.org/Team:Calgary/Notebook/Calendar">here</a></span> for a record of each team member's activity over the summer.</p><br />
</td><br />
</tr><br />
<br />
<tr><br />
<td><a href="https://2010.igem.org/Team:Calgary/Notebook/Future_Directions"><img src="http://i872.photobucket.com/albums/ab287/iGEMCalgary_2010/BrainstormIcon.png"></a></img></td><br />
<td><span class="green"><p>Future Directions</p></span><br />
<p>With this project, there are tons of directions that we can head. Click <span class="green"><a href="https://2010.igem.org/Team:Calgary/Notebook/Brainstorming">here</a></span> to see some of the ideas we have in store for the future.</p><br />
</td><br />
</tr><br />
<br />
<tr><br />
<td><a href="https://2010.igem.org/Team:Calgary/Notebook/Safety_And_Protocols"><img src="http://i872.photobucket.com/albums/ab287/iGEMCalgary_2010/ProtocolIcon.png"></a></img></td><br />
<td><span class="purple"><p>Protocols</p></span><br />
<p>So you've looked at our <span class="purple"><a href="https://2010.igem.org/Team:Calgary/Notebook/Calendar">calendar</a></span>. That's all well and good... but what is this "PCR" thing that keeps popping up? If you want to see details for each lab procedure mentioned in our calendar, click <span class="purple"><a href="https://2010.igem.org/Team:Calgary/Notebook/Safety_And_Protocols">here</a></span> for a reference.</p><br />
</td><br />
</tr><br />
<tr><br />
<td><a href="https://2010.igem.org/Team:Calgary/Notebook/Safety"><img src="http://i872.photobucket.com/albums/ab287/iGEMCalgary_2010/SafetyIcon.png"></a></img></td><br />
<td><span class="yellow"><p>Safety</p></span><br />
<p>To see our completed iGEM safety requirements questionnaire follow this link: <span class="yellow"><a href="https://2010.igem.org/Team:Calgary/Notebook/Safety">safety questionnaire</a></span><br />
</p><br />
</td><br />
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</html></div>Pjwuhttp://2010.igem.org/Team:Calgary/Community/EthicsTeam:Calgary/Community/Ethics2010-10-28T02:40:53Z<p>Pjwu: </p>
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<span id="bodytitle"><h1>Ethics and Human Practices</h1></span><br />
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<h3>Ethics Podcast and Paper</h3><br />
<table><br />
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<td><p>Synthetic Biology is a new and emerging field with many potential benefits. Because the public perception of synthetic biology is still very limited, knowledge and understanding of projects relating to synthetic biology continues to remain limited, as well. Therefore, the iGEM Calgary team believes that it is essential to recognize the ethical implications of our project. We hope to improve the public's understanding of Synthetic Biology and alleviate common concerns with the field. With this aim, our team began working on two major projects for the Ethics and Human Practices component. </p><br />
</td><br />
<td><a href="http://s872.photobucket.com/albums/ab287/iGEMCalgary_2010/?action=view&current=Untitled-8-1.png" target="_blank"><img src="http://i872.photobucket.com/albums/ab287/iGEMCalgary_2010/Untitled-8-1.png" border="0" alt="Photobucket"></a><br />
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<p><br />
One project examines Synthetic Biology from a general perspective, while the other discusses the ethical implications of our project specifically.<br />
In the first project, we have created a series of <a href="https://2010.igem.org/Team:Calgary/Community/Podcasts">podcasts</a> regarding various issues relating to Synthetic Biology. In the podcasts, members of our group have an open discussion about issues such as the concept of synthetic life and the nature of open-source science. This allowed us to reflect on the potentials of Synthetic Biology, and hence, enrich our understanding about this field. We also wrote a paper where we discuss the ethical, economical and social implications of our project. This allowed us to understand our project from different perspectives. The significance of this paper is that it allowed us, as a team, to reflect on the potential benefits and risks that our project can entail. <br />
Apart from working on these two projects over the summer, we have also incorporated an outreach program into our Ethics portion. We have presented to several high schools, with the aim of increasing awareness of Synthetic Biology to high-school students. As a team, we believe that high school students will be the generation that will be increasingly exposed to this field.</p><br />
<br />
<a title="View iGEM Project Ethics Paper on Scribd" href="http://www.scribd.com/doc/40288018/iGEM-Project-Ethics-Paper" style="margin: 12px auto 6px auto; font-family: Helvetica,Arial,Sans-serif; font-style: normal; font-variant: normal; font-weight: normal; font-size: 14px; line-height: normal; font-size-adjust: none; font-stretch: normal; -x-system-font: none; display: block; text-decoration: underline;">iGEM Project Ethics Paper</a> <object id="doc_909203733605803" name="doc_909203733605803" height="600" width="100%" type="application/x-shockwave-flash" data="http://d1.scribdassets.com/ScribdViewer.swf" style="outline:none;" > <param name="movie" value="http://d1.scribdassets.com/ScribdViewer.swf"> <param name="wmode" value="opaque"> <param name="bgcolor" value="#ffffff"> <param name="allowFullScreen" value="true"> <param name="allowScriptAccess" value="always"> <param name="FlashVars" value="document_id=40288018&access_key=key-13j3j0z0xvcjvq8dwi2n&page=1&viewMode=list"> <embed id="doc_909203733605803" name="doc_909203733605803" src="http://d1.scribdassets.com/ScribdViewer.swf?document_id=40288018&access_key=key-13j3j0z0xvcjvq8dwi2n&page=1&viewMode=list" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" height="600" width="100%" wmode="opaque" bgcolor="#ffffff"></embed> </object> <br />
<br />
<h3>High School Presentations</h3><br />
<br />
<p> Synthetic Biology is a new emerging field of Science and the general public are still unfamiliar about its potentials. High school students are an important generation who should become aware of this fascinating approach to science. This is not just to increase public awareness but also because high school students are the ones who will be most exposed to Synthetic Biology in the upcoming years. With that intention, we went to several high schools to introduce Synthetic Biology and its potentials. We discussed with the students about the three components of projects related to Synthetic Biology in iGEM: Wetlab, Modelling and Human Practice. We emphasized on the interdisciplinary characteristic of projects in iGEM that are related to Synthetic Biology. With this, we hope that students of next generations are more interested in Synthetic Biology. In addition, we hope to empower the students with the growing techniques and perspectives of looking at biological functions. </p><br />
<br />
<h3>Research Symposiums</h3><br />
<br />
<p> <br />
This year our iGEM team participated in a few research sympoisums. This was a great way to raise more awareness for iGEM at our own Univeristy while getting to practice presenting our work to varied audiences.</p><br />
<h4>BHSc Research Symposium</h4><br />
<p>On October 7th we presented an oral presentation as well as a poster rpesentation at the Bachelor of Health Sciences Research Symposium. This was a great way to get more people from the Faculty of Medicine interested in iGEM. There was a mix of undergradutae students, researchers and professors in attendance, so this was a great place to show off what we did this Summer.</p><br />
<h4>USRP Research Symposium</h4><br />
<p>On October 7th we also had the opportunity to present a poster at the USRP Markin Research Symposium at the University of Calgary. This was a great opportunity to get the word out about iGEM and our project to a wider audience at our university. There were students and faculty mambers from across all faculties ad it was good practice trying to explain our project to people with very little biological background.</p><br />
<h4>Student’s Union Research Symposium</h4><br />
<p>Still to come we have the Univeristy of Calgary’s Student’s Union Research Symposium in late November. This will be a good platform to start recruitment for next year’s team as this symposium attracts students and faculty from across the university. This will also be a great wrap-up to our iGEM season a couple of weeks after the actual iGEM Jamboree.</p><br />
<h3>Bake Sale</h3><br />
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<a href="http://s872.photobucket.com/albums/ab287/iGEMCalgary_2010/?action=view&current=TabMenuBackSale-1.png" target="_blank"><img src="http://i872.photobucket.com/albums/ab287/iGEMCalgary_2010/TabMenuBackSale-1.png" border="0" alt="Photobucket"></a></td></tr><br />
<tr><td><br />
<p> This year, the purpose of the bake sale included two aspects: firstly, it was to raise awareness about Synthetic Biology in our Health Sciences department and secondly, it was a fundraising activity to have the financial support to complete the Wetlab portion of our project.</p><br />
<br />
<p><br />
The Bake Sale was a great way to interact with the undergraduate and graduate students in the Health Sciences department of the University of Calgary. Many researchers were interested in finding out more about Synthetic Biology in the small time of interaction during the fundraising. <br />
</p><br />
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</html></div>Pjwuhttp://2010.igem.org/Team:Calgary/Community/EthicsTeam:Calgary/Community/Ethics2010-10-28T02:31:07Z<p>Pjwu: </p>
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<li><a href="https://2010.igem.org/Team:Calgary/Community/Ethics">Human Practices</a></li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Community/Gallery">Photo Gallery</a></li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Community/Conferences">Conferences</a></li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Community/Suffield">DRDC Suffield</a></li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Community/Podcasts">Podcasts</a></li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Community/Blog">Visit Our Blog!</a></li><br />
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<span id="bodytitle"><h1>Ethics and Human Practices</h1></span><br />
<br />
<h3>Ethics Podcast and Paper</h3><br />
<table><br />
<tr><br />
<td><p>Synthetic Biology is a new and emerging field with many potential benefits. Because the public perception of synthetic biology is still very limited, knowledge and understanding of projects relating to synthetic biology continues to remain limited, as well. Therefore, the iGEM Calgary team believes that it is essential to recognize the ethical implications of our project. We hope to improve the public's understanding of Synthetic Biology and alleviate common concerns with the field. With this aim, our team began working on two major projects for the Ethics and Human Practices component. </p><br />
</td><br />
<td><a href="http://s872.photobucket.com/albums/ab287/iGEMCalgary_2010/?action=view&current=Untitled-8-1.png" target="_blank"><img src="http://i872.photobucket.com/albums/ab287/iGEMCalgary_2010/Untitled-8-1.png" border="0" alt="Photobucket"></a><br />
<br />
</td><br />
</tr><br />
</table><br />
<p><br />
One project examines Synthetic Biology from a general perspective, while the other discusses the ethical implications of our project specifically.<br />
In the first project, we have created a series of <a href="https://2010.igem.org/Team:Calgary/Community/Podcasts">podcasts</a> regarding various issues relating to Synthetic Biology. In the podcasts, members of our group have an open discussion about issues such as the concept of synthetic life and the nature of open-source science. This allowed us to reflect on the potentials of Synthetic Biology, and hence, enrich our understanding about this field. We also wrote a paper where we discuss the ethical, economical and social implications of our project. This allowed us to understand our project from different perspectives. The significance of this paper is that it allowed us, as a team, to reflect on the potential benefits and risks that our project can entail. <br />
Apart from working on these two projects over the summer, we have also incorporated an outreach program into our Ethics portion. We have presented to several high schools, with the aim of increasing awareness of Synthetic Biology to high-school students. As a team, we believe that high school students will be the generation that will be increasingly exposed to this field.</p><br />
<br />
<a title="View iGEM Project Ethics Paper on Scribd" href="http://www.scribd.com/doc/40288018/iGEM-Project-Ethics-Paper" style="margin: 12px auto 6px auto; font-family: Helvetica,Arial,Sans-serif; font-style: normal; font-variant: normal; font-weight: normal; font-size: 14px; line-height: normal; font-size-adjust: none; font-stretch: normal; -x-system-font: none; display: block; text-decoration: underline;">iGEM Project Ethics Paper</a> <object id="doc_909203733605803" name="doc_909203733605803" height="600" width="100%" type="application/x-shockwave-flash" data="http://d1.scribdassets.com/ScribdViewer.swf" style="outline:none;" > <param name="movie" value="http://d1.scribdassets.com/ScribdViewer.swf"> <param name="wmode" value="opaque"> <param name="bgcolor" value="#ffffff"> <param name="allowFullScreen" value="true"> <param name="allowScriptAccess" value="always"> <param name="FlashVars" value="document_id=40288018&access_key=key-13j3j0z0xvcjvq8dwi2n&page=1&viewMode=list"> <embed id="doc_909203733605803" name="doc_909203733605803" src="http://d1.scribdassets.com/ScribdViewer.swf?document_id=40288018&access_key=key-13j3j0z0xvcjvq8dwi2n&page=1&viewMode=list" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" height="600" width="100%" wmode="opaque" bgcolor="#ffffff"></embed> </object> <br />
<br />
<h3>High School Presentations</h3><br />
<br />
<p> Synthetic Biology is a new emerging field of Science and the general public are still unfamiliar about its potentials. High school students are an important generation who should become aware of this fascinating approach to science. This is not just to increase public awareness but also because high school students are the ones who will be most exposed to Synthetic Biology in the upcoming years. With that intention, we went to several high schools to introduce Synthetic Biology and its potentials. We discussed with the students about the three components of projects related to Synthetic Biology in iGEM: Wetlab, Modelling and Human Practice. We emphasized on the interdisciplinary characteristic of projects in iGEM that are related to Synthetic Biology. With this, we hope that students of next generations are more interested in Synthetic Biology. In addition, we hope to empower the students with the growing techniques and perspectives of looking at biological functions. </p><br />
<br />
<h3>Research Symposiums</h3><br />
<br />
<p> <br />
This year our iGEM team participated in a few research sympoisums. This was a great way to raise more awareness for iGEM at our own Univeristy while getting to practice presenting our work to varied audiences.</p><br />
<br/><br />
<h4>BHSc Research Symposium</h4><br />
<p>On October 7th we presented an oral presentation as well as a poster rpesentation at the Bachelor of Health Sciences Research Symposium. This was a great way to get more people from the Faculty of Medicine interested in iGEM. There was a mix of undergradutae students, researchers and professors in attendance, so this was a great place to show off what we did this Summer.</p><br />
<br/><br/><br />
<h4>USRP Research Symposium</h4><br />
<p>On October 7th we also had the opportunity to present a poster at the USRP Markin Research Symposium at the University of Calgary. This was a great opportunity to get the word out about iGEM and our project to a wider audience at our university. There were students and faculty mambers from across all faculties ad it was good practice trying to explain our project to people with very little biological background.</p><br />
<br/></br><br />
<h4>Student’s Union Research Symposium</h4><br />
<p>Still to come we have the Univeristy of Calgary’s Student’s Union Research Symposium in late November. This will be a good platform to start recruitment for next year’s team as this symposium attracts students and faculty from across the university. This will also be a great wrap-up to our iGEM season a couple of weeks after the actual iGEM Jamboree.</p><br />
<h3>Bake Sale</h3><br />
<table><br />
<tr><br />
<td><br />
<br />
<a href="http://s872.photobucket.com/albums/ab287/iGEMCalgary_2010/?action=view&current=TabMenuBackSale-1.png" target="_blank"><img src="http://i872.photobucket.com/albums/ab287/iGEMCalgary_2010/TabMenuBackSale-1.png" border="0" alt="Photobucket"></a></td></tr><br />
<tr><td><br />
<p> This year, the purpose of the bake sale included two aspects: firstly, it was to raise awareness about Synthetic Biology in our Health Sciences department and secondly, it was a fundraising activity to have the financial support to complete the Wetlab portion of our project.</p><br />
<br />
<p><br />
The Bake Sale was a great way to interact with the undergraduate and graduate students in the Health Sciences department of the University of Calgary. Many researchers were interested in finding out more about Synthetic Biology in the small time of interaction during the fundraising. <br />
</p><br />
</td></tr></table><br />
</div><br />
<br />
</div><br />
<br />
</body><br />
</html></div>Pjwuhttp://2010.igem.org/Team:Calgary/Community/EthicsTeam:Calgary/Community/Ethics2010-10-28T02:28:51Z<p>Pjwu: </p>
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<h1>Community</h1><br />
<br />
<ul><br />
<li><a href="https://2010.igem.org/Team:Calgary/Community/Ethics">Human Practices</a></li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Community/Gallery">Photo Gallery</a></li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Community/Conferences">Conferences</a></li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Community/Suffield">DRDC Suffield</a></li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Community/Podcasts">Podcasts</a></li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Community/Blog">Visit Our Blog!</a></li><br />
</ul><br />
<br />
</div><br />
<br />
<div class="mainbody"><br />
<br />
<span id="bodytitle"><h1>Ethics and Human Practices</h1></span><br />
<br />
<h3>Ethics Podcast and Paper</h3><br />
<table><br />
<tr><br />
<td><p>Synthetic Biology is a new and emerging field with many potential benefits. Because the public perception of synthetic biology is still very limited, knowledge and understanding of projects relating to synthetic biology continues to remain limited, as well. Therefore, the iGEM Calgary team believes that it is essential to recognize the ethical implications of our project. We hope to improve the public's understanding of Synthetic Biology and alleviate common concerns with the field. With this aim, our team began working on two major projects for the Ethics and Human Practices component. </p><br />
</td><br />
<br />
<td><br />
<img src="http://i872.photobucket.com/albums/ab287/iGEMCalgary_2010/Untitled-8.png?t=1288232737"></img><br />
<br />
</td><br />
</tr><br />
</table><br />
<p><br />
One project examines Synthetic Biology from a general perspective, while the other discusses the ethical implications of our project specifically.<br />
In the first project, we have created a series of <a href="https://2010.igem.org/Team:Calgary/Community/Podcasts">podcasts</a> regarding various issues relating to Synthetic Biology. In the podcasts, members of our group have an open discussion about issues such as the concept of synthetic life and the nature of open-source science. This allowed us to reflect on the potentials of Synthetic Biology, and hence, enrich our understanding about this field. We also wrote a paper where we discuss the ethical, economical and social implications of our project. This allowed us to understand our project from different perspectives. The significance of this paper is that it allowed us, as a team, to reflect on the potential benefits and risks that our project can entail. <br />
Apart from working on these two projects over the summer, we have also incorporated an outreach program into our Ethics portion. We have presented to several high schools, with the aim of increasing awareness of Synthetic Biology to high-school students. As a team, we believe that high school students will be the generation that will be increasingly exposed to this field.</p><br />
<br />
<a title="View iGEM Project Ethics Paper on Scribd" href="http://www.scribd.com/doc/40288018/iGEM-Project-Ethics-Paper" style="margin: 12px auto 6px auto; font-family: Helvetica,Arial,Sans-serif; font-style: normal; font-variant: normal; font-weight: normal; font-size: 14px; line-height: normal; font-size-adjust: none; font-stretch: normal; -x-system-font: none; display: block; text-decoration: underline;">iGEM Project Ethics Paper</a> <object id="doc_909203733605803" name="doc_909203733605803" height="600" width="100%" type="application/x-shockwave-flash" data="http://d1.scribdassets.com/ScribdViewer.swf" style="outline:none;" > <param name="movie" value="http://d1.scribdassets.com/ScribdViewer.swf"> <param name="wmode" value="opaque"> <param name="bgcolor" value="#ffffff"> <param name="allowFullScreen" value="true"> <param name="allowScriptAccess" value="always"> <param name="FlashVars" value="document_id=40288018&access_key=key-13j3j0z0xvcjvq8dwi2n&page=1&viewMode=list"> <embed id="doc_909203733605803" name="doc_909203733605803" src="http://d1.scribdassets.com/ScribdViewer.swf?document_id=40288018&access_key=key-13j3j0z0xvcjvq8dwi2n&page=1&viewMode=list" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" height="600" width="100%" wmode="opaque" bgcolor="#ffffff"></embed> </object> <br />
<br />
<h3>High School Presentations</h3><br />
<br />
<p> Synthetic Biology is a new emerging field of Science and the general public are still unfamiliar about its potentials. High school students are an important generation who should become aware of this fascinating approach to science. This is not just to increase public awareness but also because high school students are the ones who will be most exposed to Synthetic Biology in the upcoming years. With that intention, we went to several high schools to introduce Synthetic Biology and its potentials. We discussed with the students about the three components of projects related to Synthetic Biology in iGEM: Wetlab, Modelling and Human Practice. We emphasized on the interdisciplinary characteristic of projects in iGEM that are related to Synthetic Biology. With this, we hope that students of next generations are more interested in Synthetic Biology. In addition, we hope to empower the students with the growing techniques and perspectives of looking at biological functions. </p><br />
<br />
<h3>Research Symposiums</h3><br />
<br />
<p> <br />
This year our iGEM team participated in a few research sympoisums. This was a great way to raise more awareness for iGEM at our own Univeristy while getting to practice presenting our work to varied audiences.</p><br />
<br/><br />
<h4>BHSc Research Symposium</h4><br />
<p>On October 7th we presented an oral presentation as well as a poster rpesentation at the Bachelor of Health Sciences Research Symposium. This was a great way to get more people from the Faculty of Medicine interested in iGEM. There was a mix of undergradutae students, researchers and professors in attendance, so this was a great place to show off what we did this Summer.</p><br />
<br/><br/><br />
<h4>USRP Research Symposium</h4><br />
<p>On October 7th we also had the opportunity to present a poster at the USRP Markin Research Symposium at the University of Calgary. This was a great opportunity to get the word out about iGEM and our project to a wider audience at our university. There were students and faculty mambers from across all faculties ad it was good practice trying to explain our project to people with very little biological background.</p><br />
<br/></br><br />
<h4>Student’s Union Research Symposium</h4><br />
<p>Still to come we have the Univeristy of Calgary’s Student’s Union Research Symposium in late November. This will be a good platform to start recruitment for next year’s team as this symposium attracts students and faculty from across the university. This will also be a great wrap-up to our iGEM season a couple of weeks after the actual iGEM Jamboree.</p><br />
<h3>Bake Sale</h3><br />
<table><br />
<tr><br />
<td><br />
<br />
<a href="http://s872.photobucket.com/albums/ab287/iGEMCalgary_2010/?action=view&current=TabMenuBackSale-1.png" target="_blank"><img src="http://i872.photobucket.com/albums/ab287/iGEMCalgary_2010/TabMenuBackSale-1.png" border="0" alt="Photobucket"></a></td></tr><br />
<tr><td><br />
<p> This year, the purpose of the bake sale included two aspects: firstly, it was to raise awareness about Synthetic Biology in our Health Sciences department and secondly, it was a fundraising activity to have the financial support to complete the Wetlab portion of our project.</p><br />
<br />
<p><br />
The Bake Sale was a great way to interact with the undergraduate and graduate students in the Health Sciences department of the University of Calgary. Many researchers were interested in finding out more about Synthetic Biology in the small time of interaction during the fundraising. <br />
</p><br />
</td></tr></table><br />
</div><br />
<br />
</div><br />
<br />
</body><br />
</html></div>Pjwuhttp://2010.igem.org/Team:Calgary/ExtrasTeam:Calgary/Extras2010-10-28T02:22:18Z<p>Pjwu: Undo revision 204311 by H.dastidar (Talk)</p>
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<h1>Extras</h1><br />
<br />
<ul><br />
<li><a href="#tshirt">T-Shirts</a></li><br />
<li><a href="#proteinman">The Protein Man</a></li><br />
</ul><br />
<br />
<br />
<br />
</div><br />
<br />
<div class="mainbody"><br />
<br />
<span id="bodytitle"><h1>Extras</h1></span><br />
<br />
<h2>T-Shirts</h2><br />
<p>T-shirts were printed by Apparel Ink. T-shirts were printed in yellow. Photos of T-shirt coming soon!<br />
<li>6455 Macleod Trail South</li><br />
<li>Calgary,AB. T2H 0K8</li><br />
<li>Ph:403-255-1150</li><br />
</p><br />
<img class="autodlogo" src="http://i872.photobucket.com/albums/ab287/iGEMCalgary_2010/FinalT-shirt.png"></img><br />
<br />
<a name="proteinman"></a><br />
<h2>The Protein Man!</h2><br />
<br />
<br />
<br />
<p>Hey iGEM-ers,</p><br />
<p><br />
This is Protein Man checking in! I hope the iGEM competition is not stressing you out too much! Remember, stress causes protein misfolding and my job is to promote proper protein expression. I will be the mascot of the 2010 iGEM Calgary team, whose project is about stress detection in our favourite bug E. coli or any other bugs that y’all might be using for your project.</p><br />
<p><br />
<br />
I wish you all good luck and keep an eye out for me at the iGEM jamboree and ladies you can aggregate around me to relive your stress.</p><br />
<br />
<p>Checking out,</p><br />
<p><br />
Protein man!</p><br />
<br />
<img style= "width: 600px;" src="http://i872.photobucket.com/albums/ab287/iGEMCalgary_2010/proteinman-01.png"></img><br />
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</html></div>Pjwuhttp://2010.igem.org/Team:Calgary/Community/ConferencesTeam:Calgary/Community/Conferences2010-10-28T02:18:45Z<p>Pjwu: </p>
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<h1>Community</h1><br />
<br />
<ul><br />
<li><a href="https://2010.igem.org/Team:Calgary/Community/Ethics">Human Practices</a></li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Community/Gallery">Photo Gallery</a></li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Community/Conferences">Conferences</a></li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Community/Suffield">DRDC Suffield</a></li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Community/Podcasts">Podcasts</a></li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Community/Blog">Visit Our Blog!</a></li><br />
</ul><br />
<br />
</div><br />
<br />
<div class="mainbody"><br />
<br />
<span id="bodytitle"><h1>Conferences</h1></span><br />
<br />
<a name="springworkshop"></a><br />
<h3>Spring Workshop</h3><br />
<br />
<p>The iGEM spring workshop was organized by iGEM headquarters on May 29-30. These workshops were organized in many different continents including Europe, North America and Asia. This year, the Canadian workshop was organized at the University of Calgary. The main purpose of the iGEM workshop was to provide new iGEM students with background about synthetic biology and iGEM in general. There were workshops that covered general concepts ranging from synthetic biology to biobricks, wiki design, using the registry of standard parts, submitting parts and the iGEM Jamboree.</p><br />
<br />
<p>Speakers included:</p><br />
<br />
<p><u>Tom Knight</u></p><br />
<br />
<p>One of the founders of synthetic biology, Tom Knight was responsible for designing the standard BioBrick system and co-pioneering the standard digestion and ligation cloning method (also known as BioBrick cloning method) that is used widely in synthetic biology and iGEM. Tom Knight presented a little bit of history of iGEM and the pioneering of standard biological parts that came about from a group of engineers, including himself and Drew Endy. Tom Knight also gave an overview of the BioBrick cloning method, including some tips and tricks that he had encountered over the years that he has been involved in the field of synthetic biology.</p><br />
<br />
<p><u>Megan Lizarazo</u></p><br />
<p>Megan Lizarazo is the iGEM Research Technician. She handles most of the shipping and receiving of parts, as well as communicating with and updating all the teams about iGEM related events. During the workshop Megan provided valuable information about how to send DNA parts to the registry.<br />
</p><br />
<br />
<p><u>Barry Canton</u></p><br />
<p>Barry Canton works in the Drew Endy Lab. He is a previous iGEM alumni. Barry Canton talked about Wiki creation, uploading parts information, and also taught us about different tips and tricks regarding the wiki. This presentation also included building a wiki for Team:Example which ended up looking quite... <a href="https://2010.igem.org/wiki/index.php?title=Team:Example&oldid=5571">interesting</a>, thanks to the contributions of every member there.<br />
</p><br />
<br />
<p><u>Randy Retberg</u></p><br />
<p>Randy Retberg is the director of iGEM competition. He is primarily an engineer who has worked for well-known companies such as Sun, IBM, etc. Randy Retberg presented on the general notion of synthetic biology and iGEM. He also talked about future of iGEM and synthetic biology.</p><br />
<br />
<a name="lethbridge"></a><br />
<h3>Lethbridge Conference</h3><br />
<br />
<a href="http://s872.photobucket.com/albums/ab287/iGEMCalgary_2010/?action=view&current=TabMenuLethbridgeWorkshop-1.png" target="_blank"><img src="http://i872.photobucket.com/albums/ab287/iGEMCalgary_2010/TabMenuLethbridgeWorkshop-1.png" border="0" alt="Photobucket"></a><br />
<br />
<p>On June 26th and 27th, Alberta Innovates Technology Futures had invited us to attend their student workshop in Lethbridge, Alberta. Throughout the weekend we were given insight on several areas of our iGEM project. These included marketing, media relations, presentation skills and project ideas and troubleshooting.</p><br />
<br />
<p>Presenters included:</p><br />
<br />
<p><u>Joey Hundert – Marketing/Sponsorship</u></p><br />
<p>The first guest speaker at Lethbridge was Joey Hundert. Joey was an amazing resource because of his expertise in entrepreneurship specifically on the field of sustainable development. He broadened our understanding on approaching companies for sponsorship, especially when marketing to companies about the new and innovative field of synthetic biology. This was incredibly useful for our group as none of the undergraduates had prior experiences with marketing and sponsorship.</p><br />
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<p><u>Erin Prefontaine and Bob Cooney - Painless Publicity</u></p><br />
<p>The next presentation was a joint presentation by Erin and Bob. Erin is the Communication Officer of Alberta Innovates Technology Futures, and Bob is the Communications Officer of the University of Lethbridge. They offered an insightful presentation on the precautions necessary when speaking to the media. They provided us with advices on how to approach the media while remaining careful with the choice of our words. Our aim is not to scare the public, but to show them why we're are doing what we are doing and what the benefits to the public are, from our findings. They also suggested we contact Grady Simmons, who is involved with the media relations for the University of Calgary.</p><br />
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<p><u>Anne Marie Downey - Communication</u></p><br />
<p>On June 28th, our first speaker was Anne Marie Downey. She was a gracious, talented guest speaker who gave us constructive ideas regarding presentation skills. Some of the keypoints of the presentation were communication skills, developing the content in PowerPoints, the purpose of using visuals and managing the response of the audience. During her presentation, every team practiced their short “Elevator Pitch” to explain their project to the general public while the audience analyzed and suggested ways to improve this Elevator Pitch of the projects. Her presentation was extremely beneficial for the team, which was evident in the improvement of our own presentations. We did short summary descriptions of our project as we moved from one member to the other, and received constructive feedback from Anne Marie and also other students of the University of Lethbridge and the University of Alberta. We were also given a “Communication That Works” booklet to help us in the future with Presentation Skills. </p> <br />
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<p><u>Andrew Hessel</u></p><br />
<p>Andrew Hessel was the iGEM Ambassador at MIT and currently the Co-Chair of Bioinformatics and Biotechnology at Singularity University. He was the last presenter of the day, but just as useful as the other speaker sessions we had. He gave us suggestions on various subjects: Wet lab, marketing and promotion to name a few. He strongly suggested that we approach Oil Sands Companies for sponsorship.<br />
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<p>The Alberta Genetically Engineered Machines competition (aGEM) is an Alberta-wide competition held every year since 2007. During aGEM, the Alberta teams (Universities of Calgary, Alberta, and Lethbridge) present their projects in front of respected and qualified judges who provide feedback and meet the teams one-on-one to suggest future improvement before iGEM comes around. This year, team Calgary met with ex-iGEMer Justin Pahara and was helped with their presentation in general. Other judges such as Andrew Hessel also provided valuable feedback on the team’s website, presentation and future direction. Thank you Alberta Innovates Technology Futures, for such a great opportunity. <br />
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<p class="tabText" style="padding-left:10px;">What new dangers and unintended consequences will synthetic biology pose to us in the future? iGEM Calgary travels to Defence Research and Development Canada Suffield, a major Canadian Military Research facility that specializes in chemo-biological threats. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community/Suffield">Read more...</a></p><br />
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<p class="tabText" style="padding-left:10px;">The University of Calgary, Alberta, and Lethbridge iGEM teams met in Lethbridge at a conference put on by Alberta Innovates Technology Futures to learn important aspects of iGEM. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community/Conferences#lethbridge">Read more...</a></p><br />
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<p class="tabText" style="padding-left:10px;">Have you ever seen an aggregate protein dance? Look out for iGEM Calgary’s rambunctious mascot “Protein Man” at the Jamboree promoting proper protein expression. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Extras#proteinman">Learn more about him...</a></p><br />
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<p class="tabText" style="padding-left:10px;">Team Calgary brings iGEM awareness to the community. The iGEM bake sale was a great success, both in selling cupcakes and educating customers about our team. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community">See what else we've been doing...</a></p><br />
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<p class="tabText" style="padding-left:10px;">Alberta’s very own Jamboree. The three Alberta iGEM teams, the Universities of Alberta, Calgary, and Lethbridge meet to perform a practice project presentation to each other. Experts within their field are also present to give teams challenging questions, and then meet with each team to suggest improvements. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community/Conferences#agem">Read more...</a></p><br />
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<p>Our modelling project consists of two components: a mathematical model done in MATLAB and an animation done in Autodesk <i>Maya</i>. We hope to model the formation of inclusion bodies, which are aggregations of misfolded protein that can occur within cells. Using <i>Maya</i>, we also hope to visually show other students one of the proposed aggregation mechanisms described in the literature.<br />
<a href="https://2010.igem.org/Team:Calgary/Modelling">Read more here...</a></p><br />
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<p>Our outreach project included educating highschool students about iGEM. Outreach also entailed blog entries and podcast about synthetic life, iGEM and open source as well as Genetically modified foods. The blog entry, podcasts and high school presentations allowed the iGEM students to spread knowledge about iGEM to the general public and to potential future scientists. <a href="https://2010.igem.org/Team:Calgary/Community">Read more here...</a></p><br />
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<h3>Wetlab</h3><br />
<p>You’re stressing me out! This year, in the wetlab, we have been designing a reporter system to detect problems in protein expression. Our system uses a visual output to allow specificity in determining which step in protein expression problems are occurring.</p><br />
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<h3>Modelling</h3><br />
<p>Our modeling project has focused on simulating and modeling the formation of inclusion bodies, aggregates of protein within the cell. We've been exploring the factors that lead to their formation.</p><br />
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<h3>Community</h3><br />
<p>Our human practices section focused on exploring ethical issues in synthetic biology through an ethics paper as well as a podcast focusing on a few key issues. Our outreach initiatives also allowed the iGEM students to spread knowledge about iGEM to the general public and to potential future scientists through activities such as high school presentations and participation in various research symposiums.</p><br />
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<p>As part of our Ethics and Human Practices project, we created a series of podcasts that analyze the benefits and consequences of the new and emerging field of Synthetic Biology. Currently, our series of podcasts consists of three episodes: Synthetic Life, The Consequences of Open Source Biology and Genetically Modified Foods. We have covered content in these podcasts and targeted them at the general public in the hopes of raising awareness, clearing up misconceptions, and educating others about the field of Synthetic Biology. We felt this was necessary after reading some of the reactions the public had in regards to Craig Venter’s ‘creation’ of synthetic life this summer. The podcasts offer unbiased and easy to understand subject matter presented in a very interactive manner.<br />
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<h3>Synthetic Life</h3><br />
<p>With the creation of Craig Venter’s first synthetic genome, inserted into bacteria, media outlets did a very poor job of publicizing this news, often overemphasizing and exaggerating the original findings of the Venter lab. This put a lot of fear in the public’s eye in regards to Synthetic Biology. This podcast covers Venter’s Synthetic Bacteria and analyzes his findings from a scientific and unbiased perspective.</p><br />
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<p><a href="http://www.wikiwikiwebworks.ca/SyntheticLifePodcast.mp3" target="_blank">Listen to it here!</a> - <a href="https://2010.igem.org/Team:Calgary/Community/Podcasts/Transcripts#synthlife" target="_blank">Transcript here</a></p><br />
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<h3>The Consequences of Open-Source Biology</h3><br />
<p>In this podcast, we begin with the structure, foundations and the history of iGEM and the Registry of Parts. We transition to focus on our project and what we aim to do with it. The podcast is wrapped up with our experiences from our visit to DRDC Suffield and the opinions of experts in the field.</p><br />
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<p><a href="http://www.wikiwikiwebworks.ca/OpenSourcePodcast.mp3" target="_blank">Listen to it here!</a> - <a href="https://2010.igem.org/Team:Calgary/Community/Podcasts/Transcripts#opensource" target="_blank">Transcript here</a></p><br />
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<h3>Genetically Modified Foods</h3><br />
<p>The advantages and disadvantages of genetically modified foods are discussed. The role that Synthetic Biology plays in genetically modified foods is also analyzed.</p><br />
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<p><a href="http://www.wikiwikiwebworks.ca/GMFoodPodcast.mp3" target="_blank">Listen to it here!</a> - <a href="https://2010.igem.org/Team:Calgary/Community/Podcasts/Transcripts#gm" target="_blank">Transcript here</a></p><br />
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<a name="synthlife"></a><br />
<h1>Synthetic Life</h1><br />
<p><b>Alex:</b> Hi my name’s Alex Grigg, and this is my teammate Dev Vyas. And we would like to welcome you to the first episode of Synthetic Ethics. So Dev, I’m sure your familiar with synthetic biology, but what about our listeners who still don’t quite get what synthetic biology is?</p><br />
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<p><b>Dev:</b> Well synthetic biology is an emerging science with vast potential and opportunity. It can be described as the combination of science and engineering. What synthetic biologists do is create new organic systems operating within living organisms. It even has the potential to create life from scratch.</p><br />
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<p><b>Alex:</b> I’m going to stop you right there, because today we are discussing the ethics of synthetic life, a topic which draws some of the most excitement, and controversy to our field. So, if I were to tell you that a colossal achievement that has been compared to other scientific milestones such as the sequencing of the human genome, and the cloning of the sheep Dolly happened just a few months ago, what would you think I was talking about?</p><br />
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<p><b>Dev:</b> Does it have anything to do with Bald Bearded scientists?</p><br />
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<p><b>Alex:</b> Good guess Dev! Although I think every scientific milestone can be somehow attributed to the Bald and Bearded. The particular accomplishment to which I’m referring is the creation of synthia, the first synthetic, self-replicating life.</p><br />
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<p><b>Dev:</b> That’s right, in 2008 a team of scientists at the J. Craig Venter Institute headed up by Drs. Craig Venter, our bald and bearded scientist, Hamilton Smith, and Clyde Hutchison were able to create a small bacterial genome, and by May 2010 it was announced that they had successfully used a synthetic genome of the bacterium mycroplasma mycocides to create a bacteria that could sustain, and replicate itself.</p><br />
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<p><b>Alex:</b> Alright, lets take a step back and talk about how such an achievement was attained. It all started with the chemical synthesis of DNA fragments of 1078 base pairs. These cassettes each had overlaps of 80 base pairs, which allowed them to be recombined in yeast. 10 of these cassettes were recombined into 10kb cassettes of DNA, which were then recombined again into 100kb pieces that could be used to create the final synthetic genome of mycroplasma myocides which is 1.08 million basepairs long. Venter and his team also included what are called “watermarks” in the genome which are sequences that allow us to differentiate this synthetic genome, from the naturally occurring genome. But what’d they do next with the genome?</p><br />
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<p><b>Dev:</b> Well, M. mycoide genomes were transplanted into restriction-minus Mycoplasma capricolum recipient cells. These cells, containing only the synthetic genome that they had created, were able to self-replicate.</p><br />
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<p><b>Alex:</b> This Sounds like great news! Craig Venter and his team has proven that we are able to create life, Imagine the possibilities. We could potentially create organisms which we have never before observed.</p><br />
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<p><b>Dev:</b> Well I for one think “We're all doomed! Doooooooooooommmmmmmmmmmmeeeeeeeeeddd!!!”</p><br />
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<p><b>Alex:</b> Wow Really? Why?</p><br />
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<p><b>Dev:</b> To be honest I don’t really think we’re all doomed, but that is a comment taken from a story in the guardian in which many of the reader’s voice concerns about synthetic life, and show that there is a lot of fear taken from news of this achievement. Another commenter, posting under the name CruyffTurn had a concern when he read that the synthetic organism had included watermarks so that we can keep track of it. He said: “So, what you really mean if the organism somehow manages to escape in to the environment, subsequently mutating in to some evil virulent pathogen, killing billions, we can be safe in the knowledge that we will know where it came from. Amazing piece of scientific work though.”</p><br />
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<p><b>Alex:</b> Well do you think that there’s a possibility that this synthetic mycroplasma myocide will mutate into a some sort of superbug that will kill billions?</p><br />
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<p><b>Dev:</b> I’m actually not that concerned. What people need to understand is that the bug that Craig Venter synthesized is essentially the same as a bug that came to us naturally, through Darwinian evolution. The DNA is fully synthetic, but the sequence itself is natural, and so is the cell in which they inserted the genome so that it can replicate and carry out protein synthesis.</p><br />
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<p><b>Alex:</b> Well it seems to me that we aren’t doomed at all, all they made was an naturally occurring germ. But, another commenter said “I want to be excited by this news, but it scares the bejeezus out of me...”</p><br />
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<p><b>Dev:</b> So what else are they scared of?</p><br />
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<p><b>Alex:</b> Well I know a lot of fear stems from the possibility of synthesizing organisms which would be extremely harmful to humans if they were released.</p><br />
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<p><b>Dev:</b> Ok, I think that is a legitimate concern. So what kind of organisms would that be?</p> <br />
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<p><b>Alex:</b> Well one example of a synthetic organism that could cause massive casualties is smallpox. Digital genomes of smallpox are present online, and could potentially be created chemically using a similar process that Craig Venter used. In June 2006 a reporter for the guardian obtained a small sequence of smallpox DNA delivered to his home from a gene synthesis company. Now that sounds scary.</p><br />
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<p><b>Dev:</b> Well what kind of company would send the smallpox genome to a residential address? Even if it is piece by piece.</p><br />
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<p><b>Alex:</b> This reporter was able to achieve this from a major gene synthesis company through the lack of screening technology and safeguards that are present at these gene synthesis companies. As the price of synthesizing genes gets more and more affordable, efficient safeguards which screen both the content being ordered, and who is ordering them needs to be put in place in order to ensure that gene sequencing isn’t used by would-be terrorists.</p><br />
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<p><b>Dev:</b> Why isn’t there anything already in place to help gene synthesis companies from sending out sequences that contain harmful genes?</p><br />
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<p><b>Alex:</b> Actually there is. The International Gene Synthesis Consortium is an organization consisting of 5 major gene synthesis companies, and makes up over 80% of commercial gene synthesis capacity world-wide. These companies have agreed to screen synthetic gene orders to identify pathogen sequences and other potentially dangerous sequences, screen customers by requiring identification, and keep records for at least 8 years of customers, sequences, and delivery information. They also do not send to post office boxes, which seems like a no brainer to me.</p><br />
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<p><b>Dev:</b> Ok, so we can all feel a little safer knowing that random people can’t just order sequences containing harmful genes, but the idea that some disgruntled scientist can synthesize killer bugs in his basement is a little far-fetched.</p><br />
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<p><b>Alex:</b> Yeah people need to understand that this kind of work requires more than a few test tubes. What kind of things would a disgruntled scientists need if he wanted to synthesize an evil organism?</p><br />
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<p><b>Dev:</b> Well besides the need for precise chemical synthesis of gene fragments from somewhere such as a gene synthesis company, synthesizing self-replicating life requires high-throughput sequencing facilities so that you can be sure you have the right sequence, sophisticated designing strategy, and multiple steps of quality control. Among other things.</p><br />
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<p><b>Alex:</b> So this sort of thing couldn’t be done alone in your garage.</p><br />
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<p><b>Dev:</b> Assuming your garage isn’t extremely well equipped.</p><br />
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<p><b>Alex:</b> But people aren’t just worried about their safety in the sense that harmful organisms could be created, there is also a lot of concern revolving around the ethical implications of our newfound capacity to chemically create life. There’s a lot of use of the phrase “playing god”.</p><br />
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<p><b>Dev:</b> But is this a real worry? I mean it’s not like we can now create new organisms or animals.</p><br />
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<p><b>Alex:</b> Well there is a concern that as we further this technology, we will be able to create organisms that did not come to us through natural Darwinian evolution, and even gain the ability to use this technology to genetically design humans.</p><br />
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<p><b>Dev:</b> That sounds almost like something out of science fiction.</p><br />
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<p><b>Alex:</b> At this stage in the game, it sort of is, but that doesn’t mean that we shouldn’t be aware of the ethical risks associated with the advancement of our capability to synthesize life. The Vatican’s response to the creation of replicating synthetic life by Craig Venter and his team was actually fairly positive. “If it is used toward the good, to treat pathologies, we can only be positive” the Vatican’s top bioethics official, Monsignor Rino Fisichella, told Italian state-run television news programme TG Uno. The head of the Italian Catholic bishop’s conference Cardinal Angelo Bagnasco said that “intelligence can never be without responsibility”</p><br />
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<p><b>Dev:</b> Well I think that that properly sums up the attitude that we should have towards instances like this. The advent of synthetic life represents a momentous step forward in mankind’s ability to combat many of the problems facing us, but we need to ensure that those tools are not abused so as to cause harmful results.</p><br />
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<p>OUTRO</p><br />
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<p><b>Alex:</b> Well thanks for joining us while we explore the ethical issues associated with synthetic biology. If your looking for more news and exciting stories within synthetic biology, check out our blog at http://igemcalgary2010.blogspot.com, or if you want to learn more about our team and the work we are doing check out our wiki at https://2010.igem.org/Team:Calgary</p><br />
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<h1>Open Source Biology</h1><br />
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<p><b>Introduction: </b> Welcome to Synthetic Ethics from the University of Calgary’s iGEM team.</p><br />
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<p><b>Alex: </b> Hello and welcome to synthetic ethics from the University of Calgary’s iGEM team. My name is Alex Grigg, and this is my iGEM teammate Dev Vyas. Let’s give out listeners a little information on what iGEM is all about. </p><br />
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<p><b>Dev: </b> Sure Alex, iGEM is an undergraduate synthetic biology competition in which undergraduate students like ourselves work over the summer to design and develop a project. This year 128 teams from all over the globe are participating. </p><br />
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<p><b>Alex:</b> Yes, and the project is pretty much completely open ended, past project have ranged from detecting arsenic in drinking water, to beer that fights cancer, to bacterial art using fluorescence proteins. </p><br />
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<p><b>Dev: </b> There’s a number of streams that you can choose to work in, including Food or Energy, Environment, Health or medicine, manufacturing, new application, foundational advance, and information processing. </p><br />
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<p><b>Alex: </b> So should we let the listeners hear a little about what we were working on in the wet-lab? </p><br />
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<p><b>Dev: </b> Yeah sure, this year we were constructing a biological toolkit that can detect problems with protein expression within E. Coli. Our vision for our circuit is a kit on two plasmids, which researchers could implant a gene of interest coding for the protein they want to be expressed in E. Coli, and determine where problems are occurring. </p><br />
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<p><b>Alex: </b> Yep, One circuit we built would confirm that the protein is being translated and transcribed, and the other circuit could tell if a protein is being mislfolded. It detects protein misfolding in the periplasm, and cytoplasm, and will give us a simple visual output of fluorescence proteins. </p><br />
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<p><b>Dev: </b> At the end of all this work the teams all meet at M.I.T to present their projects, and judges determine which teams deserve medals. </p><br />
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<p><b>Alex: </b> So what kind of criteria do we need to meet in order to achieve one of these medals? </p><br />
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<p><b>Dev: </b> Well the criteria are rather extensive, and you don’t need to meet all this criteria in order to achieve a bronze or silver medal. For one, your team needs to describe your project on your team wiki, you can view ours at https://2010.igem.org/Team:Calgary. Both Calgary and Team needs to be capitalized. We also need to present a poster, and talk at the jamboree, and we need to submit a new bio brick to the Registry of Parts. </p><br />
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<p><b>Alex: </b> Yeah that’s right, all the genetic sequences that code for the parts that we create our projects with have been standardized into something we call a biobrick. Every biobrick has the same prefix and suffix made of restriction sites. This allows every biobrick to be put together into a “circuit” that we can then transform into a host such as e coli, which will then use those sequences to carry out their function. </p><br />
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<p><b>Dev: </b> O.K. so every bio brick can be cut, and then put together using the same enzymes and sites? </p><br />
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<p><b>Alex: </b> Yep, Biobricks have been likened to lego bricks, every piece has the same sized holes on the bottom and top so that you can easily put them together and build whatever you and your team have dreamt up. </p><br />
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<p><b>Dev: </b> Well that makes it sound pretty easy to create these biological circuits; it wouldn’t be very hard to teach anyone how to put these systems together. </p><br />
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<p><b>Alex:</b> iGEM is making synthetic biology much easier to access, opening it to thousands of undergraduate students. And the creation of standardized biobricks isn’t the only aspect of iGEM that is making synthetic biology easier and more accessible; it also has created the Registry of Standard Biological Parts.</p><br />
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<p><b>Dev:</b> Yeah the Registry of Standard Biological Parts is a collection of these interchangeable biobrick parts that are made available to iGEM teams and certain academic labs. It runs on a “get some, give some” basis, meaning that everyone who benefits from being able to access this collection of parts to create integrated biological systems, will also then contribute to the registry by providing information on the parts they use, and submit new parts which contain the biobrick prefix and suffix.</p><br />
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<p><b>Alex:</b> So how many parts does this registry have?</p><br />
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<p><b>Dev:</b> Well the registry was created in 2003 at M.I.T, by 2004 it had accumulated about 100 parts such as protein coding sequences, and devices built from these parts. This is because assembly of parts into devices and systems can then be put back into the registry so that others can use it to improve their own projects. Now with the growth of iGEM, the registry contains 2000 defined parts, 700 of which can be ordered.</p><br />
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<p><b>Alex:</b> So what kind of parts does it contain now?</p><br />
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<p><b>Dev:</b> Well the fact that people can now access the registry, and be completely creative with their projects has given the registry a vast array of parts with many different functions. You can affect the motility of a bacteria, use sequences that can use cell-cell signaling and quorum sensing so that cells can talk to each other, and there are many others even including sequences that makes bacteria produce scents such as banana. The best part of the registry is that each contributor can build on the work of others. If you go to http://partsregistry.org you can browse every part for yourself.<p><br />
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<p><b>Alex:</b> Yeah, and although most parts are made for use within e. coli, the registry is also growing in the types of organismal hosts that parts are made for. Bacillus subtilis, bacteriophage T7, and even yeast which is a eukaryote have parts made for them within the registry. But Dev this is the synthetic ethics podcast, and I can already see the concerns that are associated with making synthetic biological systems.</p><br />
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<p><b>Dev:</b> Yep the registry would be an example of what is known as “open source biology”. This is a term coined by one of iGEM’s founders, Drew Endy. This is the idea that biology can be developed using open intellectual property models just like open source software, like the firefox browser, or linux.</p><br />
<br />
<p><b>Alex:</b> Well I think the benefits of open source biology in this context are very apparent. It supports the belief the idea that biology develops best when ideas, data, and resources are shared openly. </p><br />
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<p><b>Dev:</b> But I think to many of our listeners, the dangers of making synthetic biology not only easier to access, but also creating a large collection of easily accessed parts is also very apparent. </p><br />
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<p><b>Alex:</b> Making biology convenient and available to more and more people, and inviting the general public to start coming up with ideas not only maximizes the amount of creativity and cooperation within synthetic biology. There is the risk that people accessing this technology such as hackers, amateurs, and even terrorists could develop malicious systems.</p><br />
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<p><b>Dev:</b> Yeah our iGEM team went on a visit to DRDC Suffield. Which stands for Defence Research and Development Canada. DRDC Suffield specializes in chemical and biological threats. When we were there we explained the iGEM philosophy of standardization and the cooperation of teams through the registry of parts. In a round table discussion with experts we got to hear their concerns having to do with iGEM.</p><br />
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<p><b>Alex:</b> I remember that they expressed concern with making synthetic biology easier to access. Some of their largest concerns with that is someone could potentially either on purpose or on accident release antibiotic resistant bacteria into the environment causing an epidemic. Other concerns had to do with the potential to engineer a host that will more efficiently create biotoxin, which a terrorist or disgruntled scientist could use in an attack. So the threat of a bioweapon that can’t be found in nature is real. </p><br />
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<p><b>Dev:</b> But does that mean that open-source biology is contributing to that danger? Drew Endy seems to believe that keeping synthetic biology transparent and open is the best way for us to monitor labs for malicious activity. He said “The only way the (expletive deleted) doesn't hit the fan is if everybody engineering biology does so in the open. We're co-opting the idea from open-source software that 'many eyes lead to few bugs.' In other words, I don't trust you not to make any mistakes the next time you program a piece of DNA. You shouldn't trust me."</p><br />
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<p><b>Alex:</b> Alright, so I guess the argument can be made that open source science allows science to self-monitor for unethical or dangerous practices. But this system wouldn’t work for do-it-yourself biologists who work with no federal funding. Synthetic biology may therefore necessitate a new model for addressing ethical and policy issues because of the complexity of the biological systems being manipulated.</p><br />
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<p><b>Outro:</b> Well thanks for joining us while we explore the ethical issues associated with synthetic biology. If your looking for more news and exciting stories within synthetic biology, check out our blog at igemcalgary2010.blogspot.com or if you want to learn more about our team and the work we are doing check out our wiki at https://2010.igem.org/Team:Calgary.</p><br />
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<a name="gm"></a><br />
<h1>Genetically Modified Foods</h1><br />
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<p><b>Alex:</b> Hi my name is Alex Grigg, and I’m here with my teammate Dev Vyas, and this is the third of our synthetic biology ethics podcast. Today we’re talking about a heavily debated topic within synthetic biology, which is genetically modified foods.</p><br />
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<p><b>Dev:</b> "There will be a significant challenge for agriculture and the science that will be required to provide a healthy, nutritious and adequate food supply in coming decades for a rapidly growing population,"</p><br />
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<p><b>Alex:</b> Wow Dev that’s pretty profound, did you come up with that?</p><br />
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<p><b>Dev:</b> No that’s actually a quote from University of Idaho animal scientist Rod Hill in an article in science daily. But it’s a popular opinion that as our population and demand for food rises, we’ll need to find new ways to increase our food production using technologies such as those present within synthetic biology.</p><br />
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<p><b>Alex:</b> Yeah although synthetic biology is still in its infancy as a science; genetically modified foods have been around on the market for human consumption since 1994. A genetically modified food is any food that comes from an organism that has had genes either inserted into it’s nucleus, or deleted from it’s genome. Techniques used in synthetic biology such as gene synthesis have the potential to have a drastic effect on the foods that we consume. </p><br />
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<p><b>Dev:</b> Yeah, genetically modified food most commonly refers to crops created for human or animal consumption using the latest molecular biology techniques. New methods of farming, as well as manipulating current food sources to be grown more efficiently are both possible approaches that could solve the growing demand for food.</p><br />
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<p><b>Alex:</b> Genetically modified food can be modified to have an array of advantages of over naturally occurring sources such as herbicide tolerance, pest resistance, disease resistance, drought tolerance, and increased nutrition.</p><br />
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<p><b>Dev:</b> And these foods are already available on the market. The first commercially available food that was available is the flavr savr tomato. This tomato was modified so that the ripening process was slowed down, and therefore it would have a long shelf life. This was achieved by the introduction of an antisense gene that interfered with an enzyme that accelerated the ripening process. </p><br />
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<p><b>Alex:</b> One of the most common examples of using genetically modified food is the use of Bacillus thuringiensis, or B.T, genes in corn and other crops. As of 2003, 62 million hectares of B.T gene containing crops were planted worldwide. These genes produce the Cry toxin, which binds to the cell membrane of insect cells within its gut. This causes the cells to lyse, and kills the insect. </p><br />
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<p><b>Alex:</b> So it’s great that the tomatoes can last longer, and corn can produce it’s own pesticides, but is it safe to eat? I mean can we have unintended effects when modifying the genetic make up of these foods?</p><br />
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<p><b>Dev:</b> Well the FDA approved the consumption of the Flavr Savr tomato in 1994 stating that it is as safe as tomatoes bred by conventional means, but production ceased in 1997 due to production costs. But there are a lot of concerns about the safety of genetically modified food. </p><br />
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<p><b>Alex:</b> Yeah these foods have sometimes been referred to as “Franeknstein foods”, A major concern about modifying food is inadvertently triggering an allergic reaction. Specific proteins in milk, eggs, wheat, fish, tree nuts, peanuts, soybeans, and shellfish cause over 90% of food allergies, and if one of these proteins was used in a genetically modified food it could unknowingly trigger an allergic reaction.</p> <br />
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<p><b>Dev:</b> This scenario is unlikely though because of safeguards that are already in place from organizations such as the FDA. Producers of genetically modified food must prove that they have not incorporated any allergenic substance into their product. If they are unable to prove this, a label will be put on the product to alert consumers of the risk. </p><br />
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<p><b>Alex:</b> But governmental organizations aren’t always successful in properly managing genetically modified organisms. There was an example of this in genetically modified trees in China. China has planted over one million genetically modified trees that were designed to contain genes that would make the trees resistant to insects and pests. Because the trees are not classified as crops, China's Ministry of Agriculture has no control over genetically modified trees and they are allowed to plant without having to meet the same standards as food. It was then determined that the trees "are so widely planted in northern China that pollen and seed dispersal cannot be prevented".</p><br />
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<p><b>Dev:</b> So what other dangers are there if this were to happen to a genetically modified crop? </p><br />
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<p><b>Alex:</b> One of the dangers that I’ve heard about is the potential for genes to be “leaked” to the naturally occurring form of organism, or even genes being transferred into bacteria in the human gut. </p><br />
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<p><b>Dev:</b> And there is some legitimacy in this concern. Researchers from the University of Newcastle upon Tyne proved that in an experiment on intestinal bacteria that DNA plasmids can be taken up by these gut cells. This only happened in one in every 300 cells though, and another experiment confirmed that some transgenes in GM foods might survive passage through the small intestine. In this experiment, 19 volunteers ate a burger and milkshake containing genetically modified soya. 7 of the volunteers have had their colons previously removed, which allowed them to examine ileostomoy bags to look for gene transfer in the gut. It was found that 3.7% of the DNA had survived, and some of it had been transferred to bacteria in the gut.</p><br />
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<p><b>Alex:</b> Yeah that’s true, but they were unable to isolate the precise bacteria that had taken up the DNA because of the small amount that was transferred. Also, when they examined the stools of the volunteers, no evidence of the DNA was found, showing that although it may be capable of surviving the small intestine, it was completely destroyed in the large intestine. The fact that the DNA survived shouldn’t be very unsettling either, unmodified DNA from soya is degraded exactly the same as the DNA from the modified strain.</p><br />
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<p><b>Dev:</b> Well it’s good to know that if we consume anything that has been genetically modified, it is unlikely that genes that, for example contain antibiotic resistance, are very unlikely to be transferred to bacteria within the gut. But in April 2001, a poll conducted by PBS with over 21,000 respondents indicated that 65% of those polled said that we should not grow genetically modified food. So there is still a lot of controversy involved in consuming genetically modified products.</p><br />
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<p><b>Alex:</b> Yeah, there is also a worry that genetically modified foods are worse for the environment. In 2003 there was a trial which used three modified types of crops, and compared it to its effect on wildlife with the naturally occurring type of crop. In order to test the effect on wildlife on this farm, researchers monitored weeds, weed seeds, and collected beetles and other insects in traps.</p><br />
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<p><b>Dev:</b> The results of this study found that in two of three plots, weeds didn’t grow near as well. When comparing the genetically modified corn with the natural type, it was actually found that there were more weeds growing, and that it actually had the potential to increase the biodiversity on farms.</p><br />
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<p><b>Alex:</b> So what are governments doing about controlling genetically modified foods? If people think that it somehow harmful to either them, or a risk to the environment can they avoid it?</p><br />
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<p><b>Dev:</b> Well in Canada, if the nutritional value or composition of the food has been changed, or if there is an allergen present in the food, the food must be labeled to indicate this. Though it doesn’t have to indicate if the food has been genetically modified, because we have adopted a standard for voluntary labeling of genetically modified products.</p><br />
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<p><b>Alex:</b> Yeah, but this isn’t the case for all countries, the U.K takes a much more stringent approach. Since September 1998, U.K all foods, additives, and flavorings that contain more than 1% GM content have to be labeled. In April 2000, the new UK Food Safety Agency extended that provision to all GM foods, additives, and flavorings, including those on the market before 1998. The UK also requires that all restaurant meals with GM foods be labeled. </p><br />
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<p><b>Dev:</b> Synthetic biology may have the potential to help make these products, and even help relieve some of the controversy surrounding the use of genetically modified foods. The use of transgenes, which is DNA from another organism introduced in a crop causes a lot of concerns because of fears that it could be leaked.</p><br />
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<p><b>Alex:</b> Yeah, but new technology is already helping this field become less controversial. Marker assisted selection is an example of this. This allows us to use genetic markers to locate genes affecting traits such as meat quality, or disease resistance. Because this involves the use of existing DNA within the organism, and not transgenic DNA, there is the possibility that this will created modified food that will be less controversial. The public's acceptance or rejection of new technologies that could determine future food supplies will be crucial for the direction of synthetic biology.</p><br />
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<p><b>Dev:</b> Well thanks for joining us while we explore the ethical issues associated with synthetic biology. If your looking for more news and exciting stories within synthetic biology, check out our blog at igemcalgary2010.blogspot.com, or if you want to learn more about our team and the work we are doing check out our wiki at https://2010.igem.org/Team:Calgary,</p><br />
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<h1>Synthetic Life</h1><br />
<p><b>Alex:</b> Hi my name’s Alex Grigg, and this is my teammate Dev Yvas. And we would like to welcome you to the first episode of Synthetic Ethics. So Dev, I’m sure your familiar with synthetic biology, but what about our listeners who still don’t quite get what synthetic biology is?</p><br />
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<p><b>Dev:</b> Well synthetic biology is an emerging science with vast potential and opportunity. It can be described as the combination of science and engineering. What synthetic biologists do is create new organic systems operating within living organisms. It even has the potential to create life from scratch.</p><br />
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<p><b>Alex:</b> I’m going to stop you right there, because today we are discussing the ethics of synthetic life, a topic which draws some of the most excitement, and controversy to our field. So, if I were to tell you that a colossal achievement that has been compared to other scientific milestones such as the sequencing of the human genome, and the cloning of the sheep Dolly happened just a few months ago, what would you think I was talking about?</p><br />
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<p><b>Dev:</b> Does it have anything to do with Bald Bearded scientists?</p><br />
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<p><b>Alex:</b> Good guess Dev! Although I think every scientific milestone can be somehow attributed to the Bald and Bearded. The particular accomplishment to which I’m referring is the creation of synthia, the first synthetic, self-replicating life.</p><br />
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<p><b>Dev:</b> That’s right, in 2008 a team of scientists at the J. Craig Venter Institute headed up by Drs. Craig Venter, our bald and bearded scientist, Hamilton Smith, and Clyde Hutchison were able to create a small bacterial genome, and by May 2010 it was announced that they had successfully used a synthetic genome of the bacterium mycroplasma mycocides to create a bacteria that could sustain, and replicate itself.</p><br />
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<p><b>Alex:</b> Alright, lets take a step back and talk about how such an achievement was attained. It all started with the chemical synthesis of DNA fragments of 1078 base pairs. These cassettes each had overlaps of 80 base pairs, which allowed them to be recombined in yeast. 10 of these cassettes were recombined into 10kb cassettes of DNA, which were then recombined again into 100kb pieces that could be used to create the final synthetic genome of mycroplasma myocides which is 1.08 million basepairs long. Venter and his team also included what are called “watermarks” in the genome which are sequences that allow us to differentiate this synthetic genome, from the naturally occurring genome. But what’d they do next with the genome?</p><br />
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<p><b>Dev:</b> Well, M. mycoide genomes were transplanted into restriction-minus Mycoplasma capricolum recipient cells. These cells, containing only the synthetic genome that they had created, were able to self-replicate.</p><br />
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<p><b>Alex:</b> This Sounds like great news! Craig Venter and his team has proven that we are able to create life, Imagine the possibilities. We could potentially create organisms which we have never before observed.</p><br />
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<p><b>Dev:</b> Well I for one think “We're all doomed! Doooooooooooommmmmmmmmmmmeeeeeeeeeddd!!!”</p><br />
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<p><b>Alex:</b> Wow Really? Why?</p><br />
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<p><b>Dev:</b> To be honest I don’t really think we’re all doomed, but that is a comment taken from a story in the guardian in which many of the reader’s voice concerns about synthetic life, and show that there is a lot of fear taken from news of this achievement. Another commenter, posting under the name CruyffTurn had a concern when he read that the synthetic organism had included watermarks so that we can keep track of it. He said: “So, what you really mean if the organism somehow manages to escape in to the environment, subsequently mutating in to some evil virulent pathogen, killing billions, we can be safe in the knowledge that we will know where it came from. Amazing piece of scientific work though.”</p><br />
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<p><b>Alex:</b> Well do you think that there’s a possibility that this synthetic mycroplasma myocide will mutate into a some sort of superbug that will kill billions?</p><br />
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<p><b>Dev:</b> I’m actually not that concerned. What people need to understand is that the bug that Craig Venter synthesized is essentially the same as a bug that came to us naturally, through Darwinian evolution. The DNA is fully synthetic, but the sequence itself is natural, and so is the cell in which they inserted the genome so that it can replicate and carry out protein synthesis.</p><br />
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<p><b>Alex:</b> Well it seems to me that we aren’t doomed at all, all they made was an naturally occurring germ. But, another commenter said “I want to be excited by this news, but it scares the bejeezus out of me...”</p><br />
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<p><b>Dev:</b> So what else are they scared of?</p><br />
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<p><b>Alex:</b> Well I know a lot of fear stems from the possibility of synthesizing organisms which would be extremely harmful to humans if they were released.</p><br />
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<p><b>Dev:</b> Ok, I think that is a legitimate concern. So what kind of organisms would that be?</p> <br />
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<p><b>Alex:</b> Well one example of a synthetic organism that could cause massive casualties is smallpox. Digital genomes of smallpox are present online, and could potentially be created chemically using a similar process that Craig Venter used. In June 2006 a reporter for the guardian obtained a small sequence of smallpox DNA delivered to his home from a gene synthesis company. Now that sounds scary.</p><br />
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<p><b>Dev:</b> Well what kind of company would send the smallpox genome to a residential address? Even if it is piece by piece.</p><br />
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<p><b>Alex:</b> This reporter was able to achieve this from a major gene synthesis company through the lack of screening technology and safeguards that are present at these gene synthesis companies. As the price of synthesizing genes gets more and more affordable, efficient safeguards which screen both the content being ordered, and who is ordering them needs to be put in place in order to ensure that gene sequencing isn’t used by would-be terrorists.</p><br />
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<p><b>Dev:</b> Why isn’t there anything already in place to help gene synthesis companies from sending out sequences that contain harmful genes?</p><br />
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<p><b>Alex:</b> Actually there is. The International Gene Synthesis Consortium is an organization consisting of 5 major gene synthesis companies, and makes up over 80% of commercial gene synthesis capacity world-wide. These companies have agreed to screen synthetic gene orders to identify pathogen sequences and other potentially dangerous sequences, screen customers by requiring identification, and keep records for at least 8 years of customers, sequences, and delivery information. They also do not send to post office boxes, which seems like a no brainer to me.</p><br />
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<p><b>Dev:</b> Ok, so we can all feel a little safer knowing that random people can’t just order sequences containing harmful genes, but the idea that some disgruntled scientist can synthesize killer bugs in his basement is a little far-fetched.</p><br />
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<p><b>Alex:</b> Yeah people need to understand that this kind of work requires more than a few test tubes. What kind of things would a disgruntled scientists need if he wanted to synthesize an evil organism?</p><br />
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<p><b>Dev:</b> Well besides the need for precise chemical synthesis of gene fragments from somewhere such as a gene synthesis company, synthesizing self-replicating life requires high-throughput sequencing facilities so that you can be sure you have the right sequence, sophisticated designing strategy, and multiple steps of quality control. Among other things.</p><br />
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<p><b>Alex:</b> So this sort of thing couldn’t be done alone in your garage.</p><br />
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<p><b>Dev:</b> Assuming your garage isn’t extremely well equipped.</p><br />
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<p><b>Alex:</b> But people aren’t just worried about their safety in the sense that harmful organisms could be created, there is also a lot of concern revolving around the ethical implications of our newfound capacity to chemically create life. There’s a lot of use of the phrase “playing god”.</p><br />
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<p><b>Dev:</b> But is this a real worry? I mean it’s not like we can now create new organisms or animals.</p><br />
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<p><b>Alex:</b> Well there is a concern that as we further this technology, we will be able to create organisms that did not come to us through natural Darwinian evolution, and even gain the ability to use this technology to genetically design humans.</p><br />
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<p><b>Dev:</b> That sounds almost like something out of science fiction.</p><br />
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<p><b>Alex:</b> At this stage in the game, it sort of is, but that doesn’t mean that we shouldn’t be aware of the ethical risks associated with the advancement of our capability to synthesize life. The Vatican’s response to the creation of replicating synthetic life by Craig Venter and his team was actually fairly positive. “If it is used toward the good, to treat pathologies, we can only be positive” the Vatican’s top bioethics official, Monsignor Rino Fisichella, told Italian state-run television news programme TG Uno. The head of the Italian Catholic bishop’s conference Cardinal Angelo Bagnasco said that “intelligence can never be without responsibility”</p><br />
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<p><b>Dev:</b> Well I think that that properly sums up the attitude that we should have towards instances like this. The advent of synthetic life represents a momentous step forward in mankind’s ability to combat many of the problems facing us, but we need to ensure that those tools are not abused so as to cause harmful results.</p><br />
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<p>OUTRO</p><br />
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<p><b>Alex:</b> Well thanks for joining us while we explore the ethical issues associated with synthetic biology. If your looking for more news and exciting stories within synthetic biology, check out our blog at http://igemcalgary2010.blogspot.com, or if you want to learn more about our team and the work we are doing check out our wiki at https://2010.igem.org/Team:Calgary</p><br />
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<h1>Open Source Biology</h1><br />
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<p><b>Introduction: </b> Welcome to Synthetic Ethics from the University of Calgary’s iGEM team.</p><br />
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<p><b>Alex: </b> Hello and welcome to synthetic ethics from the University of Calgary’s iGEM team. My name is Alex Grigg, and this is my iGEM teammate Dev Vyas. Let’s give out listeners a little information on what iGEM is all about. </p><br />
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<p><b>Dev: </b> Sure Alex, iGEM is an undergraduate synthetic biology competition in which undergraduate students like ourselves work over the summer to design and develop a project. This year 128 teams from all over the globe are participating. </p><br />
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<p><b>Alex:</b> Yes, and the project is pretty much completely open ended, past project have ranged from detecting arsenic in drinking water, to beer that fights cancer, to bacterial art using fluorescence proteins. </p><br />
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<p><b>Dev: </b> There’s a number of streams that you can choose to work in, including Food or Energy, Environment, Health or medicine, manufacturing, new application, foundational advance, and information processing. </p><br />
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<p><b>Alex: </b> So should we let the listeners hear a little about what we were working on in the wet-lab? </p><br />
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<p><b>Dev: </b> Yeah sure, this year we were constructing a biological toolkit that can detect problems with protein expression within E. Coli. Our vision for our circuit is a kit on two plasmids, which researchers could implant a gene of interest coding for the protein they want to be expressed in E. Coli, and determine where problems are occurring. </p><br />
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<p><b>Alex: </b> Yep, One circuit we built would confirm that the protein is being translated and transcribed, and the other circuit could tell if a protein is being mislfolded. It detects protein misfolding in the periplasm, and cytoplasm, and will give us a simple visual output of fluorescence proteins. </p><br />
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<p><b>Dev: </b> At the end of all this work the teams all meet at M.I.T to present their projects, and judges determine which teams deserve medals. </p><br />
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<p><b>Alex: </b> So what kind of criteria do we need to meet in order to achieve one of these medals? </p><br />
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<p><b>Dev: </b> Well the criteria are rather extensive, and you don’t need to meet all this criteria in order to achieve a bronze or silver medal. For one, your team needs to describe your project on your team wiki, you can view ours at https://2010.igem.org/Team:Calgary. Both Calgary and Team needs to be capitalized. We also need to present a poster, and talk at the jamboree, and we need to submit a new bio brick to the Registry of Parts. </p><br />
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<p><b>Alex: </b> Yeah that’s right, all the genetic sequences that code for the parts that we create our projects with have been standardized into something we call a biobrick. Every biobrick has the same prefix and suffix made of restriction sites. This allows every biobrick to be put together into a “circuit” that we can then transform into a host such as e coli, which will then use those sequences to carry out their function. </p><br />
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<p><b>Dev: </b> O.K. so every bio brick can be cut, and then put together using the same enzymes and sites? </p><br />
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<p><b>Alex: </b> Yep, Biobricks have been likened to lego bricks, every piece has the same sized holes on the bottom and top so that you can easily put them together and build whatever you and your team have dreamt up. </p><br />
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<p><b>Dev: </b> Well that makes it sound pretty easy to create these biological circuits; it wouldn’t be very hard to teach anyone how to put these systems together. </p><br />
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<p><b>Alex:</b> iGEM is making synthetic biology much easier to access, opening it to thousands of undergraduate students. And the creation of standardized biobricks isn’t the only aspect of iGEM that is making synthetic biology easier and more accessible; it also has created the Registry of Standard Biological Parts.</p><br />
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<p><b>Dev:</b> Yeah the Registry of Standard Biological Parts is a collection of these interchangeable biobrick parts that are made available to iGEM teams and certain academic labs. It runs on a “get some, give some” basis, meaning that everyone who benefits from being able to access this collection of parts to create integrated biological systems, will also then contribute to the registry by providing information on the parts they use, and submit new parts which contain the biobrick prefix and suffix.</p><br />
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<p><b>Alex:</b> So how many parts does this registry have?</p><br />
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<p><b>Dev:</b> Well the registry was created in 2003 at M.I.T, by 2004 it had accumulated about 100 parts such as protein coding sequences, and devices built from these parts. This is because assembly of parts into devices and systems can then be put back into the registry so that others can use it to improve their own projects. Now with the growth of iGEM, the registry contains 2000 defined parts, 700 of which can be ordered.</p><br />
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<p><b>Alex:</b> So what kind of parts does it contain now?</p><br />
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<p><b>Dev:</b> Well the fact that people can now access the registry, and be completely creative with their projects has given the registry a vast array of parts with many different functions. You can affect the motility of a bacteria, use sequences that can use cell-cell signaling and quorum sensing so that cells can talk to each other, and there are many others even including sequences that makes bacteria produce scents such as banana. The best part of the registry is that each contributor can build on the work of others. If you go to http://partsregistry.org you can browse every part for yourself.<p><br />
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<p><b>Alex:</b> Yeah, and although most parts are made for use within e. coli, the registry is also growing in the types of organismal hosts that parts are made for. Bacillus subtilis, bacteriophage T7, and even yeast which is a eukaryote have parts made for them within the registry. But Dev this is the synthetic ethics podcast, and I can already see the concerns that are associated with making synthetic biological systems.</p><br />
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<p><b>Dev:</b> Yep the registry would be an example of what is known as “open source biology”. This is a term coined by one of iGEM’s founders, Drew Endy. This is the idea that biology can be developed using open intellectual property models just like open source software, like the firefox browser, or linux.</p><br />
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<p><b>Alex:</b> Well I think the benefits of open source biology in this context are very apparent. It supports the belief the idea that biology develops best when ideas, data, and resources are shared openly. </p><br />
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<p><b>Dev:</b> But I think to many of our listeners, the dangers of making synthetic biology not only easier to access, but also creating a large collection of easily accessed parts is also very apparent. </p><br />
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<p><b>Alex:</b> Making biology convenient and available to more and more people, and inviting the general public to start coming up with ideas not only maximizes the amount of creativity and cooperation within synthetic biology. There is the risk that people accessing this technology such as hackers, amateurs, and even terrorists could develop malicious systems.</p><br />
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<p><b>Dev:</b> Yeah our iGEM team went on a visit to DRDC Suffield. Which stands for Defence Research and Development Canada. DRDC Suffield specializes in chemical and biological threats. When we were there we explained the iGEM philosophy of standardization and the cooperation of teams through the registry of parts. In a round table discussion with experts we got to hear their concerns having to do with iGEM.</p><br />
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<p><b>Alex:</b> I remember that they expressed concern with making synthetic biology easier to access. Some of their largest concerns with that is someone could potentially either on purpose or on accident release antibiotic resistant bacteria into the environment causing an epidemic. Other concerns had to do with the potential to engineer a host that will more efficiently create biotoxin, which a terrorist or disgruntled scientist could use in an attack. So the threat of a bioweapon that can’t be found in nature is real. </p><br />
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<p><b>Dev:</b> But does that mean that open-source biology is contributing to that danger? Drew Endy seems to believe that keeping synthetic biology transparent and open is the best way for us to monitor labs for malicious activity. He said “The only way the (expletive deleted) doesn't hit the fan is if everybody engineering biology does so in the open. We're co-opting the idea from open-source software that 'many eyes lead to few bugs.' In other words, I don't trust you not to make any mistakes the next time you program a piece of DNA. You shouldn't trust me."</p><br />
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<p><b>Alex:</b> Alright, so I guess the argument can be made that open source science allows science to self-monitor for unethical or dangerous practices. But this system wouldn’t work for do-it-yourself biologists who work with no federal funding. Synthetic biology may therefore necessitate a new model for addressing ethical and policy issues because of the complexity of the biological systems being manipulated.</p><br />
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<p><b>Outro:</b> Well thanks for joining us while we explore the ethical issues associated with synthetic biology. If your looking for more news and exciting stories within synthetic biology, check out our blog at igemcalgary2010.blogspot.com or if you want to learn more about our team and the work we are doing check out our wiki at https://2010.igem.org/Team:Calgary.</p><br />
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<h1>Genetically Modified Foods</h1><br />
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<p><b>Alex:</b> Hi my name is Alex Grigg, and I’m here with my teammate Dev Vyas, and this is the third of our synthetic biology ethics podcast. Today we’re talking about a heavily debated topic within synthetic biology, which is genetically modified foods.</p><br />
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<p><b>Dev:</b> "There will be a significant challenge for agriculture and the science that will be required to provide a healthy, nutritious and adequate food supply in coming decades for a rapidly growing population,"</p><br />
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<p><b>Alex:</b> Wow Dev that’s pretty profound, did you come up with that?</p><br />
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<p><b>Dev:</b> No that’s actually a quote from University of Idaho animal scientist Rod Hill in an article in science daily. But it’s a popular opinion that as our population and demand for food rises, we’ll need to find new ways to increase our food production using technologies such as those present within synthetic biology.</p><br />
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<p><b>Alex:</b> Yeah although synthetic biology is still in its infancy as a science; genetically modified foods have been around on the market for human consumption since 1994. A genetically modified food is any food that comes from an organism that has had genes either inserted into it’s nucleus, or deleted from it’s genome. Techniques used in synthetic biology such as gene synthesis have the potential to have a drastic effect on the foods that we consume. </p><br />
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<p><b>Dev:</b> Yeah, genetically modified food most commonly refers to crops created for human or animal consumption using the latest molecular biology techniques. New methods of farming, as well as manipulating current food sources to be grown more efficiently are both possible approaches that could solve the growing demand for food.</p><br />
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<p><b>Alex:</b> Genetically modified food can be modified to have an array of advantages of over naturally occurring sources such as herbicide tolerance, pest resistance, disease resistance, drought tolerance, and increased nutrition.</p><br />
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<p><b>Dev:</b> And these foods are already available on the market. The first commercially available food that was available is the flavr savr tomato. This tomato was modified so that the ripening process was slowed down, and therefore it would have a long shelf life. This was achieved by the introduction of an antisense gene that interfered with an enzyme that accelerated the ripening process. </p><br />
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<p><b>Alex:</b> One of the most common examples of using genetically modified food is the use of Bacillus thuringiensis, or B.T, genes in corn and other crops. As of 2003, 62 million hectares of B.T gene containing crops were planted worldwide. These genes produce the Cry toxin, which binds to the cell membrane of insect cells within its gut. This causes the cells to lyse, and kills the insect. </p><br />
<br />
<p><b>Alex:</b> So it’s great that the tomatoes can last longer, and corn can produce it’s own pesticides, but is it safe to eat? I mean can we have unintended effects when modifying the genetic make up of these foods?</p><br />
<br />
<p><b>Dev:</b> Well the FDA approved the consumption of the Flavr Savr tomato in 1994 stating that it is as safe as tomatoes bred by conventional means, but production ceased in 1997 due to production costs. But there are a lot of concerns about the safety of genetically modified food. </p><br />
<br />
<p><b>Alex:</b> Yeah these foods have sometimes been referred to as “Franeknstein foods”, A major concern about modifying food is inadvertently triggering an allergic reaction. Specific proteins in milk, eggs, wheat, fish, tree nuts, peanuts, soybeans, and shellfish cause over 90% of food allergies, and if one of these proteins was used in a genetically modified food it could unknowingly trigger an allergic reaction.</p> <br />
<br />
<p><b>Dev:</b> This scenario is unlikely though because of safeguards that are already in place from organizations such as the FDA. Producers of genetically modified food must prove that they have not incorporated any allergenic substance into their product. If they are unable to prove this, a label will be put on the product to alert consumers of the risk. </p><br />
<br />
<p><b>Alex:</b> But governmental organizations aren’t always successful in properly managing genetically modified organisms. There was an example of this in genetically modified trees in China. China has planted over one million genetically modified trees that were designed to contain genes that would make the trees resistant to insects and pests. Because the trees are not classified as crops, China's Ministry of Agriculture has no control over genetically modified trees and they are allowed to plant without having to meet the same standards as food. It was then determined that the trees "are so widely planted in northern China that pollen and seed dispersal cannot be prevented".</p><br />
<br />
<p><b>Dev:</b> So what other dangers are there if this were to happen to a genetically modified crop? </p><br />
<br />
<p><b>Alex:</b> One of the dangers that I’ve heard about is the potential for genes to be “leaked” to the naturally occurring form of organism, or even genes being transferred into bacteria in the human gut. </p><br />
<br />
<p><b>Dev:</b> And there is some legitimacy in this concern. Researchers from the University of Newcastle upon Tyne proved that in an experiment on intestinal bacteria that DNA plasmids can be taken up by these gut cells. This only happened in one in every 300 cells though, and another experiment confirmed that some transgenes in GM foods might survive passage through the small intestine. In this experiment, 19 volunteers ate a burger and milkshake containing genetically modified soya. 7 of the volunteers have had their colons previously removed, which allowed them to examine ileostomoy bags to look for gene transfer in the gut. It was found that 3.7% of the DNA had survived, and some of it had been transferred to bacteria in the gut.</p><br />
<br />
<p><b>Alex:</b> Yeah that’s true, but they were unable to isolate the precise bacteria that had taken up the DNA because of the small amount that was transferred. Also, when they examined the stools of the volunteers, no evidence of the DNA was found, showing that although it may be capable of surviving the small intestine, it was completely destroyed in the large intestine. The fact that the DNA survived shouldn’t be very unsettling either, unmodified DNA from soya is degraded exactly the same as the DNA from the modified strain.</p><br />
<br />
<p><b>Dev:</b> Well it’s good to know that if we consume anything that has been genetically modified, it is unlikely that genes that, for example contain antibiotic resistance, are very unlikely to be transferred to bacteria within the gut. But in April 2001, a poll conducted by PBS with over 21,000 respondents indicated that 65% of those polled said that we should not grow genetically modified food. So there is still a lot of controversy involved in consuming genetically modified products.</p><br />
<br />
<p><b>Alex:</b> Yeah, there is also a worry that genetically modified foods are worse for the environment. In 2003 there was a trial which used three modified types of crops, and compared it to its effect on wildlife with the naturally occurring type of crop. In order to test the effect on wildlife on this farm, researchers monitored weeds, weed seeds, and collected beetles and other insects in traps.</p><br />
<br />
<p><b>Dev:</b> The results of this study found that in two of three plots, weeds didn’t grow near as well. When comparing the genetically modified corn with the natural type, it was actually found that there were more weeds growing, and that it actually had the potential to increase the biodiversity on farms.</p><br />
<br />
<p><b>Alex:</b> So what are governments doing about controlling genetically modified foods? If people think that it somehow harmful to either them, or a risk to the environment can they avoid it?</p><br />
<br />
<p><b>Dev:</b> Well in Canada, if the nutritional value or composition of the food has been changed, or if there is an allergen present in the food, the food must be labeled to indicate this. Though it doesn’t have to indicate if the food has been genetically modified, because we have adopted a standard for voluntary labeling of genetically modified products.</p><br />
<br />
<p><b>Alex:</b> Yeah, but this isn’t the case for all countries, the U.K takes a much more stringent approach. Since September 1998, U.K all foods, additives, and flavorings that contain more than 1% GM content have to be labeled. In April 2000, the new UK Food Safety Agency extended that provision to all GM foods, additives, and flavorings, including those on the market before 1998. The UK also requires that all restaurant meals with GM foods be labeled. </p><br />
<br />
<p><b>Dev:</b> Synthetic biology may have the potential to help make these products, and even help relieve some of the controversy surrounding the use of genetically modified foods. The use of transgenes, which is DNA from another organism introduced in a crop causes a lot of concerns because of fears that it could be leaked.</p><br />
<br />
<p><b>Alex:</b> Yeah, but new technology is already helping this field become less controversial. Marker assisted selection is an example of this. This allows us to use genetic markers to locate genes affecting traits such as meat quality, or disease resistance. Because this involves the use of existing DNA within the organism, and not transgenic DNA, there is the possibility that this will created modified food that will be less controversial. The public's acceptance or rejection of new technologies that could determine future food supplies will be crucial for the direction of synthetic biology.</p><br />
<br />
<p><b>Dev:</b> Well thanks for joining us while we explore the ethical issues associated with synthetic biology. If your looking for more news and exciting stories within synthetic biology, check out our blog at igemcalgary2010.blogspot.com, or if you want to learn more about our team and the work we are doing check out our wiki at https://2010.igem.org/Team:Calgary,</p><br />
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This is Protein Man checking in! I hope the iGEM competition is not stressing you out too much! Remember, stress causes protein misfolding and my job is to promote proper protein expression. I will be the mascot of the 2010 iGEM Calgary team, whose project is about stress detection in our favourite bug E. coli or any other bugs that y’all might be using for your project.</p><br />
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<br />
I wish you all good luck and keep an eye out for me at the iGEM jamboree and ladies you can aggregate around me to relive your stress.</p><br />
<br />
<p>Checking out,</p><br />
<p><br />
Protein man!</p><br />
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<p><br />
<br />
I wish you all good luck and keep an eye out for me at the iGEM jamboree and ladies you can aggregate around me to relive your stress.</p><br />
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<p>Checking out,</p><br />
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Protein man!</p><br />
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<p><br />
<br />
I wish you all good luck and keep an eye out for me at the iGEM jamboree and ladies you can aggregate around me to relive your stress.</p><br />
<br />
<p>Checking out,</p><br />
<p><br />
Protein man!</p><br />
<br />
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<p class="tabText" style="padding-left:10px;">What new dangers and unintended consequences will synthetic biology pose to us in the future? iGEM Calgary travels to Defence Research and Development Canada Suffield, a major Canadian Military Research facility that specializes in chemo-biological threats. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community/Suffield">Read more...</a></p><br />
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<p class="tabText" style="padding-left:10px;">The University of Calgary, Alberta, and Lethbridge iGEM teams met in Lethbridge at a conference put on by Alberta Innovates Technology Futures to learn important aspects of iGEM. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community/Conferences#lethbridge">Read more...</a></p><br />
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<p class="tabText" style="padding-left:10px;">Have you ever seen an aggregate protein dance? Look out for iGEM Calgary’s rambunctious mascot “Protein Man” at the Jamboree promoting proper protein expression. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Extras#proteinman">Learn more about him...</a></p><br />
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<p class="tabText" style="padding-left:10px;">Team Calgary brings iGEM awareness to the community. The iGEM bake sale was a great success, both in selling cupcakes and educating customers about our team. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community">See what else we've been doing...</a></p><br />
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<p class="tabText" style="padding-left:10px;">Alberta’s very own Jamboree. The three Alberta iGEM teams, the Universities of Alberta, Calgary, and Lethbridge meet to perform a practice project presentation to each other. Experts within their field are also present to give teams challenging questions, and then meet with each team to suggest improvements. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community/Conferences#agem">Read more...</a></p><br />
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<p>Our modelling project consists of two components: a mathematical model done in MATLAB and an animation done in Autodesk <i>Maya</i>. We hope to model the formation of inclusion bodies, which are aggregations of misfolded protein that can occur within cells. Using <i>Maya</i>, we also hope to visually show other students one of the proposed aggregation mechanisms described in the literature.<br />
<a href="https://2010.igem.org/Team:Calgary/Modelling">Read more here...</a></p><br />
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<p>Our outreach project included educating highschool students about iGEM. Outreach also entailed blog entries and podcast about synthetic life, iGEM and open source as well as Genetically modified foods. The blog entry, podcasts and high school presentations allowed the iGEM students to spread knowledge about iGEM to the general public and to potential future scientists. <a href="https://2010.igem.org/Team:Calgary/Community">Read more here...</a></p><br />
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<h3>Wetlab</h3><br />
<p>You’re stressing me out! This year, in the wetlab, we have been designing a reporter system to detect problems in protein expression. Our system uses a visual output to allow specificity in determining which step in protein expression problems are occurring.</p><br />
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<h3>Modelling</h3><br />
<p>Our modeling project has focused on simulating and modeling the formation of inclusion bodies, aggregates of protein within the cell. We've been exploring the factors that lead to their formation.</p><br />
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<h3>Community</h3><br />
<p>Our human practices section focused on exploring ethical issues in synthetic biology through an ethics paper as well as a podcast focusing on a few key issues. Our outreach initiatives also allowed the iGEM students to spread knowledge about iGEM to the general public and to potential future scientists through activities such as high school presentations and participation in various research symposiums.</p><br />
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</html></div>Pjwuhttp://2010.igem.org/Team:Calgary/Modelling/MayaTeam:Calgary/Modelling/Maya2010-10-28T01:07:27Z<p>Pjwu: </p>
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<h1>Modelling</h1><br />
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<li><a href="https://2010.igem.org/Team:Calgary/Modelling/MATLAB">MATLAB Models</a></li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Modelling/Maya">Maya Animation</a></li><br />
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<p>As a side animation project, we are using <i>Maya</i>, a 3D graphics and animation program provided to us by Autodesk, who is a sponsor of iGEM this year. We intended to create an animation visualizing what the process of inclusion body formation might look like. The basis of this animation can be found in literature (Roberts, 2007).</p><br />
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<p>We believe this animation will help students in iGEM visualize and understand the process behind inclusion body formation. A dynamic visual catches people's attention and shows things as they happen, rather than showing static intermediate images on a diagram.</p><br />
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<p>This is what we are showing:<br />
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<li>A misfolded protein forms, exposing hydrophobic side chains. (0:00)</li><br />
<li>A nucleus of aggregation is formed by a collection of these misfolded proteins sticking together. (0:01)</li><br />
<li>More misfolded protein become attracted to the nucleus, attempting to "cover up" hydrophobic ends. (0:02 - 0:13)</li><br />
<li>Smaller clumps stick together into larger clumps. (0:14 - 0:23)<br />
<li>This process continues until a large inclusion body forms in the cell, large enough to be visible. (0:23 - 0:38)</li><br />
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<h2>References</h2><br />
<p>Roberts, C.J. (2007). Non-Native Protein Aggregation Kinetics. <i>Biotechnology and Bioengineering 98</i>(5), 927-938.</p><br />
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</html></div>Pjwuhttp://2010.igem.org/Team:Calgary/Modelling/MATLABTeam:Calgary/Modelling/MATLAB2010-10-28T01:04:50Z<p>Pjwu: </p>
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<span id="bodytitle"><h1 id="MATLAB">MATLAB</h1></span><br />
<h2 style="color:#0066CC">Matrix Laboratory Software </h2><br />
<p>The protein production simulation was produced using the Matrix Laboratory software, MATLAB produced by MathWorks. Specifically this project uses the Simbiology application, which is a collection of computational tools for simulating biological processes. The power of this tool lies in its ability to build multi species and reaction models, then simulate how the species will interact.<br />
</p><br /><br />
<br />
<br />
<h2 id="Protein" style="color:#0066CC">Protein Production Abstraction</h2><br />
<p>Our proposed model relies on an abstraction of the process of protein production, taking into account the formation of incorrectly folded intermediates and the presence of aggregated misfolded protein. Our proposed model is shown below</p> <br />
<table><br />
<tr><td valign="top"><img style="margin-right:5px;" src="https://static.igem.org/mediawiki/2010/2/24/Model_flow_chart.png" title="MATLAB Model Network" /></td><br />
<td align="justify"><p><b>Figure 1.</b> The proposed path consists of a number of species. The first one identified is "natal peptide" this species represents the initial amount of amino acid chain being produced by the ribosome. It is the "starting" amount of potential protein/misfolded protein/inclusion body present in the system.</p><br />
<p>The second species identified is the "unstable protein" this references proteins that have not reached their fully stable conformations yet or have been destabilized by environmental conditions. Unstable protein has the potential to be degraded by cellular proteases which results in the "degraded protein" species. Additionally unstable proteins have the potential to clump together to form the "inclusion body" species. The inclusion body species is also degraded by proteases so the degraded protein species is also a potential result.</p><br />
<p>The final species is the stable functional protein form. This stable form is also degraded by proteases but in very very small amounts</p> <br />
</td></tr><br />
</table><br /><br />
<br />
<br />
<h2 id="Relationships" style="color:#0066CC">Relationship Equations</h2><br />
<p>In order to begin investigating the factors that may affect the final state of the natal peptide it first becomes important to define how each of the species in the system interact. This is where the MATLAB software becomes useful. The proposed model pathway can be represented in the MATLAB Simbiology Toolbox.</p><br />
<table><br />
<tr><br />
<td valign="top" align="justify"><b>Figure 2.</b> Each of the blue circles correspond to the species identified in the previous section, while the yellow circles define the reaction that occurs between the two species. The Simbiology software uses these defined reactions to determine the amounts of each species present in the system as the species interact over a period of time. The results of the simulation are described in a later section<br />
</td><br />
<td><br />
<img style="margin-left:5px; width:409px; height:347px;" src="https://static.igem.org/mediawiki/2010/1/12/Matlab_network.png" title="MATLAB Diagram View" /><br />
</td><br />
</tr><br />
</table><br /><br />
<p>The reactions present in the system are described by the following equations</p><br /><br />
<table><br />
<tr><td style="width:250px; margin-right:5px;" valign="top"><em>natal peptide -> unstable protein</em></td><br />
<td><p>This reaction is an irreversible reaction where all of the natal peptide present becomes unstable protein with a rate constant of 1. This reflects the assumption that all of the initial amino acid sequence will at some point be present as unstable protein capable of being degraded or forming inclusion bodies</p><p></p></td></tr><br />
<tr><td style="width:250px; margin-right:5px;" valign="top"><em>unstable protein + inclusion body <-> 2 inclusion body</em></td><br />
<td><p>This reaction is a reversible reaction that defines how unstable proteins form into inclusion bodies. The simulation assumes that there is a baseline very small concentration of inclusion body present. This base value may interact with unstable protein to form more inclusion bodies resulting in a positive feed back that begins to form higher concentrations of inclusion bodies. The rate constant at which this process occurs is dependent on a number of factors discussed in a later section. Inclusion body formation represents a potential outcome of the protein expression system</p><p></p></td></tr><br />
<tr><td style="width:175px; margin-right:5px;" valign="top"><em>unstable protein -> degraded protein</em></td><br />
<td><p>This reaction represents unstable protein being degraded by proteases. This reaction follows the Henri-Michaelis-Menten equilibrium process. In this process there is a pseudo equilibrium present that is determined to be one way, as degraded protein does not return to its pre degraded state. The constant for this reaction is a set value that is relative to the particular protease. For simplicity a single value was selected to represent this impact. Once the unstable protein has been degraded it is removed from the simulation system and can not form inclusion bodies or functional proteins. As a result degraded protein represents one of the potential "outcomes" of a protein expression experiment</p><p></p></td></tr><br />
<tr><td style="width:175px; margin-right:5px;" valign="top"><em>inclusion body -> degraded protein</em></td><br />
<td><p>Our system assumes that inclusion bodies are degraded by the same process as unstable proteins, but that the rate of degradation is slower than that of a single unstable protein. This is proposed to be the result of the protease being unable to access individual proteins of the inclusion body for degradation. As a result the process is considerably slower than the degradation of straight unstable proteins. The difference is reflected in the rate constant for each of the two reactions</p><p></p></td></tr><br />
<tr><td style="width:250px; margin-right:5px;" valign="top"><em>unstable protein <-> functional protein</em></td><br />
<td><p>This reaction represents the process of the unstable protein becoming stable functional protein. The reaction is reversible as different environmental conditions, discussed later on, can determine whether or not the protein is in a stable state or unstable state.</p><p></p></td><br />
</tr></table><br />
<br /><br />
<br />
<br />
<h2 id="Factors" style="color:#0066CC">Factors Under Investigation</h2><br />
<p> For the purpose of our model there were two categories of factors that we investigated. These categories are Environmental factors and sequence factors. It is important to note that these divisions are arbitrary and don't necessarily exist in reality. Specifically these categories were created for the convenience of organizing the factors being investigated and determining how to best evaluate their impact.</p><br />
<h3>Environmental factors</h3><br />
<p>The collection of factors refers to those features of the cells environment that will have an impact on the stability of proteins being produced. When we use the term environment we are referring to both the external temperature at which the cell is growing, the pH of its environment and the concentration of protein within cellular compartments. These factors are not determined by features of the protein being produced but will still affect the likelihood of inclusion body formation and/or protein instability.<br />
</p><br />
<h4 style="color:#003366">Defining environmental impact on protein stability</h4><br />
<p>We have assumed that environmental conditions affect inclusion body formation by altering the equilibrium of the following equation:</p><br />
<br />
<div style="width:450px; margin-left:auto; margin-right:auto;"><b>Functional Protein <-> Unstable Protein <-> Inclusion Body </b></div><br /><br />
<br />
<p>A publication by Brandt et al supports this concept as they showed that isolated protein in a solution can be converted back and forth from its stable form and inclusion body form based on temperature and pH. Specifically that high temperatures and strongly basic pH will encourage the formation of inclusion bodies. This means that equilibrium constant increases as the formation of inclusion bodies has become more favourable</p><br />
<br />
<h4 style="color:#003366">Critical Assumption</h4><br />
<p>From this information we have assumed that altering the environmental conditions of temperature, pH and protein concentration will have a quantifiable effect on the rate constants for the above equation. Currently the exact impact of these factors hasn't been determined. The results section only describes rate constants determined for convenience based on qualitative understanding of the processes.<br />
</p><br />
<br />
<h3>Sequence Dependent Factors</h3> <br />
<p>For these factors we have tried to look at the features of the mRNA and amino acid sequence that could impact the likelihood of inclusion body formation. As a general rule sequence factors were selected based on how the particular feature affects the time taken for the sequence to reach its fully folded stable confirmation. The reason for this based on the assumption that if the protein has more intermediate stages or is more thermodynamically stable in a non folded confirmation then there is more time for the unstable proteins to interact and begin the formation of inclusion bodies.</p><br />
<br />
<h4 style="color:#003366">Critical Assumption</h4><br />
<p>Sequence features such as scarce amino acids ( Tryptohphan ), mRNA structural features that inhibit translation time through the ribosome and the ratio of hydrophobic amino acids to charged amino acids all have a quantifiable effect on the rate constant at which unstable protein becomes stable protein.</p><br />
<br />
<p>This evidence has been indirectly supported from the literature and discussions with researchers in the field. However at this point the precise impact of these factors is still under investigation. As such for the results section, hypothesized relationships alone have been used.</p><br /><br />
<br />
<br />
<br />
<br />
<h2 id="Results" style="color:#0066CC">Result Cases</h2><br />
<p>The result cases represent the preliminary testing of the model to see if the model simulation can be used to analyze the protein production process under different conditions. The rate constants used for each of the cases were selected for convenience in order to determine if relevant results could be obtained. This means that the rate constants used in the models do not directly correspond to biological data. However the relationships between the different rate constants are representative of biological data. It is important to note that this data is very preliminary and only demonstrates that the modelling approach we have taken can be used to investigate the factors affecting protein misfolding.<br />
</p><br />
<br />
<h3>Result Case 1: Successful Expression of Stable Protein</h3><br />
<p>In this case the initial amount of peptide produced is very stable and the equilibrium favours the fast formation of stable correctly folded protein ( red line). Unstable protein is still produced in this scenario, but is quickly degraded by and does not form inclusion bodies. Additionally the unstable protein is not exposing significant hydrophobic amino acids. This also helps prevent the formation of inclusion bodies.</p><br />
<img style="margin-left:-15px; width:682px; height:394px" src="https://static.igem.org/mediawiki/2010/b/bf/Stable_production.png" /><br /><br />
<table><br />
<p><b>Figure 3. </b>In this figure the concentration units are arbitrarily mM and the time value is in seconds. These units were selected for convenience and are not assumed to be accurate for the process being modelled. This issue is discussed in more detail in the conclusion section</p><br />
<tr><br />
<td valign="top" style="width:175px"><p><em>Natal peptide(blue line)</em></p><p></p></td><br />
<td valign="top"><p>An initial arbitrary amount of natal peptide ( 10 M ) is produced in the cell</p><p></p></td><br />
</tr><br />
<br />
<tr><br />
<td valign="top"><em>Unstable Protein (green line)</em><p></p></td><br />
<td valign="top"><p>There is still a peak in unstable protein, as this species will still be present. But this amount will be degraded quickly.</p><p></p></td><br />
</tr><br />
<br />
<tr><br />
<td valign="top"><em>Functional Protein (red line)</em><p></p></td><br />
<td valign="top"><p>In this scenario the natal peptide is quickly driven towards stable protein.</p><p></p></td><br />
</tr><br />
<br />
<tr><br />
<td valign="top"><p><em>Inclusion Body (light blue line) </em></p><p></p></td><br />
<td valign="top"><p>In this scenario very few inclusion bodies are produced as there is not enough unstable protein present to induce nucleation</p><p></p></td><br />
</tr><br />
<br />
<tr><br />
<td valign="top"><em>Degraded Protein (purple line)</em><p></p></td><br />
<td valign="top"><p>Unstable protein and inclusion bodies are degraded. In this model unstable protein is degraded faster than inclusion bodies due to the size difference</p><p></p></td><br />
</tr><br />
</table><br />
<br /><br />
<br />
<h3>Result Case 2: High hydrophobic to charged amino acid ratio with a protein having many unstable intermediates </h3><br />
<p><br />
In this case the produced peptide is highly unstable and is composed of significantly more hydrophobic amino acids than charged amino acids. This indicates that in the unstable form a significant amount of the exposed amino acids will be hydrophobic. This state of unstable protein will strongly drive towards inclusion body formation.<br />
</p><br />
<img style="margin-left:-15px; width:682px; height:394px" src="https://static.igem.org/mediawiki/2010/a/a7/Highly_unstable.png" /><br />
<p><b>Figure 5. </b>In this figure the concentration units are arbitrarily mM and the time value is in seconds. These units were selected for convenience and are not assumed to be accurate for the process being modelled. This issue is discussed in more detail in the conclusion section</p><br />
<table><br />
<tr><br />
<td valign="top" style="width:175px"><p><em>Natal Peptide(blue line)</em></p><p></p></td><br />
<td valign="top"><p>An initial arbitrary amount of natal peptide ( 10 mM ) is produced in the cell</p><p></p></td><br />
</tr><br />
<br />
<tr><br />
<td valign="top"><em>Unstable Protein (green line)</em><p></p></td><br />
<td valign="top"><p>A high hydropathy value increases the time required for the protein to fold into its correct shape. This means more unstable protein will be present in the equilibrium. The green line on the graph represents this value. The peak on the graph represents the point of nucleation whereby the concentration of unstable protein reaches a peak that rapidly increases the drive to inclusion bodies.</p><p></p></td><br />
</tr><br />
<br />
<tr><br />
<td valign="top"><em>Functional Protein (red line)</em><p></p></td><br />
<td valign="top"><p>The increased hydropathy content decreases the presence of functional protein.</p><p></p></td><br />
</tr><br />
<br />
<tr><br />
<td valign="top"><p><em>Inclusion Body (light blue line) </em></p><p></p></td><br />
<td valign="top"><p>The concentration of inclusion body increases rapidly when the concentration of unstable protein reaches the point of nucleation ( peak of the green line )</p><p></p></td><br />
</tr><br />
<br />
<tr><br />
<td valign="top"><em>Degraded Protein (purple line)</em><p></p></td><br />
<td valign="top"><p>Unstable protein and inclusion bodies are degraded. In this model unstable protein is degraded faster than inclusion bodies due to the size difference</p><p></p></td><br />
</tr><br />
</table><br />
<br /><br />
<br />
<br />
<br />
<h3>Result Case 3: Over Produced Protein at High Temperature</h3><br />
<p>In this scenario the protein is highly stable and drives strongly towards it’s stable functional conformation. However the over production of the peptide means there are high concentrations of unstable protein present, and the higher temperature increases the kinetic movement of the unstable protein. This causes the unstable proteins to collide more frequently and form inclusion bodies before they have a chance to become stable protein. Since the protein is highly stable the nucleation point, the peak of the green line, occurs at a higher concentration and greater time value than that of the unstable protein in the previous case.</p><br /><br />
<img style="margin-left:-15px; width:682px; height:394px" src="https://static.igem.org/mediawiki/2010/3/31/Hightemp_stable.png" /><br /> <br />
<p><b>Figure 5. </b>In this figure the concentration units are arbitrarily mM and the time value is in seconds. These units were selected for convenience and are not assumed to be accurate for the process being modelled. This issue is discussed in more detail in the conclusion section</p><br />
<table><br />
<tr><br />
<td valign="top" style="width:175px"><p><em>Natal Peptide(blue line)</em></p><p></p></td><br />
<td valign="top"><p>An initial arbitrary amount of natal peptide ( 10 mM ) is produced in the cell</p><p></p></td><br />
</tr><br />
<br />
<tr><br />
<td valign="top"><em>Unstable Protein (green line)</em><p></p></td><br />
<td valign="top"><p>The highly stable protein produced in this scenario spends very little time in the unstable form. It is quickly converted to stable protein or driven into an inclusion body. In this scenario the concentration and temperature causes the equilibrium to favor inclusion bodies over the functional protein.</p><p></p></td><br />
</tr><br />
<br />
<tr><br />
<td valign="top"><em>Functional Protein (red line)</em><p></p></td><br />
<td valign="top"><p>In this scenario the functional protein is very stable and favored. However the concentration of unstable intermediate causes the intermediate proteins to be caught up in inclusion bodies prior to formation of correctly folded protein.</p><p></p></td><br />
</tr><br />
<br />
<tr><br />
<td valign="top"><p><em>Inclusion Body (light blue line) </em></p><p></p></td><br />
<td valign="top"><p>The concentration of inclusion body increases rapidly when the concentration of unstable protein reaches the point of nucleation ( peak of the green line ). This point is reached more slowly than in the previous scenario as the protein is more stable, and a certain concentration must be met before nucleation occurs.</p><p></p></td><br />
</tr><br />
<br />
<tr><br />
<td valign="top"><em>Degraded Protein (purple line)</em><p></p></td><br />
<td valign="top"><p>Unstable protein and inclusion bodies are degraded. In this model unstable protein is degraded faster than inclusion bodies due to the size difference</p><p></p></td><br />
</tr><br />
</table><br />
<br /><br />
<br />
<h2 id="Conclusions" style="color:#0066CC">Conclusions</h2><br />
<p> <br />
There are a number of immediate problems with this model approach that affect the accuracy of the results. The first and most significant is that the values for the amounts of species and the kinetic constants were selected for convenience. This means they were selected such that their relative relationships would allow us to determine if the model could be made to match the behaviour seen in the literature. As a result the the outputs of the simulation can not be taken as "real" because they do not use true values. The second major issue is the equilibrium equations proposed for each of the reactions are abstractions and may not be the best ways of relating the species. The third major issue is that there aren't any clearly defined relationships between each of the factors being investigated and misfiling. Therefore the relationship between factors such as temperature and sequence features such as hydrophobic/charged amino acids are accounted for in a qualitative way only.<br />
</p><br />
<p>Accounting for these caveats this model was still a success in a number of ways. The results demonstrate that the MATLAB Simbiology software can be used to simulate the process of inclusion body formation. The graphs obtained match closely, albeit in a qualitative way, the process of inclusion body formation as it is described in the literature. Lastly, this approach has provided us with a framework that can be used to study the factors affecting protein misfolding and aggregation. <br />
</p><br /><br />
<br />
<h2 id="Future" style="color:#0066CC">Future Directions</h2><br />
<p>The most necessary future direction is to find a "test" protein and apply the principles of the model to determine if the simulation results match with literature results. If this can be shown more test proteins can be evaluated with the model and the model can be made more general. The second future direction is to explore the concept of "cut off" values. From the equilibrium graphs in the results section it is clear that there is some amount of inclusion body present, some amount of unstable protein and some amount of stable functional protein. This implies that there will always be a ratio between the three different species and also that even when inclusion body is present some functional protein will be too. A cut off value would be the ratio of functional protein to non functional such that functional protein can still be obtained. The final future direction is to develop a way to account for the four different categories of inclusion bodies that are seen in the literature values. <br />
</p><br />
<br />
<h2 id="Future" style="color:#0066CC">References</h2><br />
<br />
<p>Ashbaugh, H. S., & Hatch, H. W. (2008). Natively unfolded protein stability as a coil-to-globule transition in charge/hydropathy space. Journal of the American Chemical Society, 130(29), 9536-9542. </p><br />
<br />
<p><br />
Roberts, C. J. (2007). Non-native protein aggregation kinetics. Biotechnology and Bioengineering, 98(5), 927-938. </p><br />
<br />
<p>Wang, W., Nema, S., & Teagarden, D. (2010). Protein aggregation--pathways and influencing factors. International Journal of Pharmaceutics, 390(2), 89-99. </p><br />
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</div><br />
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</html></div>Pjwuhttp://2010.igem.org/Team:Calgary/Modelling/MATLABTeam:Calgary/Modelling/MATLAB2010-10-28T01:03:20Z<p>Pjwu: </p>
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<h1>Modelling</h1><br />
<br />
<ul><br />
<li><a href="https://2010.igem.org/Team:Calgary/Modelling/MATLAB">MATLAB Models</a><br />
<ul><br />
<li><a href="#MATLAB">Matrix Laboratory Software</a></li><br />
<li><a href="#Protein">Protein Production Abstraction</a></li><br />
<li><a href="#Relationships">Relationship Equations</a></li><br />
<li><a href="#Factors">Factors Under Investigation</a></li><br />
<li><a href="#Results">Result Cases</a></li><br />
<li><a href="#Conclusions">Conclusions</a></li><br />
<li><a href="#Future">Future Directions</a></li><br />
</ul><br />
</li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Modelling/Maya">Maya Animations</a></li><br />
<ul><br />
<br />
<br />
<br />
</div><br />
<br />
<div class="mainbody"><br />
<br />
<span id="bodytitle"><h1 id="MATLAB">MATLAB</h1></span><br />
<h2 style="color:#0066CC">Matrix Laboratory Software </h2><br />
<p>The protein production simulation was produced using the Matrix Laboratory software, MATLAB produced by MathWorks. Specifically this project uses the Simbiology application, which is a collection of computational tools for simulating biological processes. The power of this tool lies in its ability to build multi species and reaction models, then simulate how the species will interact.<br />
</p><br /><br />
<br />
<br />
<h2 id="Protein" style="color:#0066CC">Protein Production Abstraction</h2><br />
<p>Our proposed model relies on an abstraction of the process of protein production, taking into account the formation of incorrectly folded intermediates and the presence of aggregated misfolded protein. Our proposed model is shown below</p> <br />
<table><br />
<tr><td valign="top"><img style="margin-right:5px;" src="https://static.igem.org/mediawiki/2010/2/24/Model_flow_chart.png" title="MATLAB Model Network" /></td><br />
<td align="justify"><p><b>Figure 1.</b> The proposed path consists of a number of species. The first one identified is "natal peptide" this species represents the initial amount of amino acid chain being produced by the ribosome. It is the "starting" amount of potential protein/misfolded protein/inclusion body present in the system.</p><br />
<p>The second species identified is the "unstable protein" this references proteins that have not reached their fully stable conformations yet or have been destabilized by environmental conditions. Unstable protein has the potential to be degraded by cellular proteases which results in the "degraded protein" species. Additionally unstable proteins have the potential to clump together to form the "inclusion body" species. The inclusion body species is also degraded by proteases so the degraded protein species is also a potential result.</p><br />
<p>The final species is the stable functional protein form. This stable form is also degraded by proteases but in very very small amounts</p> <br />
</td></tr><br />
</table><br /><br />
<br />
<br />
<h2 id="Relationships" style="color:#0066CC">Relationship Equations</h2><br />
<p>In order to begin investigating the factors that may affect the final state of the natal peptide it first becomes important to define how each of the species in the system interact. This is where the MATLAB software becomes useful. The proposed model pathway can be represented in the MATLAB Simbiology Toolbox.</p><br />
<table><br />
<tr><br />
<td valign="top" align="justify"><b>Figure 2.</b> Each of the blue circles correspond to the species identified in the previous section, while the yellow circles define the reaction that occurs between the two species. The Simbiology software uses these defined reactions to determine the amounts of each species present in the system as the species interact over a period of time. The results of the simulation are described in a later section<br />
</td><br />
<td><br />
<img style="margin-left:5px; width:409px; height:347px;" src="https://static.igem.org/mediawiki/2010/1/12/Matlab_network.png" title="MATLAB Diagram View" /><br />
</td><br />
</tr><br />
</table><br /><br />
<p>The reactions present in the system are described by the following equations</p><br /><br />
<table><br />
<tr><td style="width:250px; margin-right:5px;" valign="top"><em>natal peptide -> unstable protein</em></td><br />
<td><p>This reaction is an irreversible reaction where all of the natal peptide present becomes unstable protein with a rate constant of 1. This reflects the assumption that all of the initial amino acid sequence will at some point be present as unstable protein capable of being degraded or forming inclusion bodies</p><p></p></td></tr><br />
<tr><td style="width:250px; margin-right:5px;" valign="top"><em>unstable protein + inclusion body <-> 2 inclusion body</em></td><br />
<td><p>This reaction is a reversible reaction that defines how unstable proteins form into inclusion bodies. The simulation assumes that there is a baseline very small concentration of inclusion body present. This base value may interact with unstable protein to form more inclusion bodies resulting in a positive feed back that begins to form higher concentrations of inclusion bodies. The rate constant at which this process occurs is dependent on a number of factors discussed in a later section. Inclusion body formation represents a potential outcome of the protein expression system</p><p></p></td></tr><br />
<tr><td style="width:175px; margin-right:5px;" valign="top"><em>unstable protein -> degraded protein</em></td><br />
<td><p>This reaction represents unstable protein being degraded by proteases. This reaction follows the Henri-Michaelis-Menten equilibrium process. In this process there is a pseudo equilibrium present that is determined to be one way, as degraded protein does not return to its pre degraded state. The constant for this reaction is a set value that is relative to the particular protease. For simplicity a single value was selected to represent this impact. Once the unstable protein has been degraded it is removed from the simulation system and can not form inclusion bodies or functional proteins. As a result degraded protein represents one of the potential "outcomes" of a protein expression experiment</p><p></p></td></tr><br />
<tr><td style="width:175px; margin-right:5px;" valign="top"><em>inclusion body -> degraded protein</em></td><br />
<td><p>Our system assumes that inclusion bodies are degraded by the same process as unstable proteins, but that the rate of degradation is slower than that of a single unstable protein. This is proposed to be the result of the protease being unable to access individual proteins of the inclusion body for degradation. As a result the process is considerably slower than the degradation of straight unstable proteins. The difference is reflected in the rate constant for each of the two reactions</p><p></p></td></tr><br />
<tr><td style="width:250px; margin-right:5px;" valign="top"><em>unstable protein <-> functional protein</em></td><br />
<td><p>This reaction represents the process of the unstable protein becoming stable functional protein. The reaction is reversible as different environmental conditions, discussed later on, can determine whether or not the protein is in a stable state or unstable state.</p><p></p></td><br />
</tr></table><br />
<br /><br />
<br />
<br />
<h2 id="Factors" style="color:#0066CC">Factors Under Investigation</h2><br />
<p> For the purpose of our model there were two categories of factors that we investigated. These categories are Environmental factors and sequence factors. It is important to note that these divisions are arbitrary and don't necessarily exist in reality. Specifically these categories were created for the convenience of organizing the factors being investigated and determining how to best evaluate their impact.</p><br />
<h3>Environmental factors</h3><br />
<p>The collection of factors refers to those features of the cells environment that will have an impact on the stability of proteins being produced. When we use the term environment we are referring to both the external temperature at which the cell is growing, the pH of its environment and the concentration of protein within cellular compartments. These factors are not determined by features of the protein being produced but will still affect the likelihood of inclusion body formation and/or protein instability.<br />
</p><br />
<h4 style="color:#003366">Defining environmental impact on protein stability</h4><br />
<p>We have assumed that environmental conditions affect inclusion body formation by altering the equilibrium of the following equation:</p><br />
<br />
<div style="width:450px; margin-left:auto; margin-right:auto;"><b>Functional Protein <-> Unstable Protein <-> Inclusion Body </b></div><br /><br />
<br />
<p>A publication by Brandt et al supports this concept as they showed that isolated protein in a solution can be converted back and forth from its stable form and inclusion body form based on temperature and pH. Specifically that high temperatures and strongly basic pH will encourage the formation of inclusion bodies. This means that equilibrium constant increases as the formation of inclusion bodies has become more favourable</p><br />
<br />
<h4 style="color:#003366">Critical Assumption</h4><br />
<p>From this information we have assumed that altering the environmental conditions of temperature, pH and protein concentration will have a quantifiable effect on the rate constants for the above equation. Currently the exact impact of these factors hasn't been determined. The results section only describes rate constants determined for convenience based on qualitative understanding of the processes.<br />
</p><br />
<br />
<h3>Sequence Dependent Factors</h3> <br />
<p>For these factors we have tried to look at the features of the mRNA and amino acid sequence that could impact the likelihood of inclusion body formation. As a general rule sequence factors were selected based on how the particular feature affects the time taken for the sequence to reach its fully folded stable confirmation. The reason for this based on the assumption that if the protein has more intermediate stages or is more thermodynamically stable in a non folded confirmation then there is more time for the unstable proteins to interact and begin the formation of inclusion bodies.</p><br />
<br />
<h4 style="color:#003366">Critical Assumption</h4><br />
<p>Sequence features such as scarce amino acids ( Tryptohphan ), mRNA structural features that inhibit translation time through the ribosome and the ratio of hydrophobic amino acids to charged amino acids all have a quantifiable effect on the rate constant at which unstable protein becomes stable protein.</p><br />
<br />
<p>This evidence has been indirectly supported from the literature and discussions with researchers in the field. However at this point the precise impact of these factors is still under investigation. As such for the results section, hypothesized relationships alone have been used.</p><br /><br />
<br />
<br />
<br />
<br />
<h2 id="Results" style="color:#0066CC">Result Cases</h2><br />
<p>The result cases represent the preliminary testing of the model to see if the model simulation can be used to analyze the protein production process under different conditions. The rate constants used for each of the cases were selected for convenience in order to determine if relevant results could be obtained. This means that the rate constants used in the models do not directly correspond to biological data. However the relationships between the different rate constants are representative of biological data. It is important to note that this data is very preliminary and only demonstrates that the modelling approach we have taken can be used to investigate the factors affecting protein misfolding.<br />
</p><br />
<br />
<h3>Result Case 1: Successful Expression of Stable Protein</h3><br />
<p>In this case the initial amount of peptide produced is very stable and the equilibrium favours the fast formation of stable correctly folded protein ( red line). Unstable protein is still produced in this scenario, but is quickly degraded by and does not form inclusion bodies. Additionally the unstable protein is not exposing significant hydrophobic amino acids. This also helps prevent the formation of inclusion bodies.</p><br />
<img style="margin-left:-15px; width:682px; height:394px" src="https://static.igem.org/mediawiki/2010/b/bf/Stable_production.png" /><br /><br />
<table><br />
<p><b>Figure 3. </b>In this figure the concentration units are arbitrarily mM and the time value is in seconds. These units were selected for convenience and are not assumed to be accurate for the process being modelled. This issue is discussed in more detail in the conclusion section</p><br />
<tr><br />
<td valign="top" style="width:175px"><p><em>Natal peptide(blue line)</em></p><p></p></td><br />
<td valign="top"><p>An initial arbitrary amount of natal peptide ( 10 M ) is produced in the cell</p><p></p></td><br />
</tr><br />
<br />
<tr><br />
<td valign="top"><em>Unstable Protein (green line)</em><p></p></td><br />
<td valign="top"><p>There is still a peak in unstable protein, as this species will still be present. But this amount will be degraded quickly.</p><p></p></td><br />
</tr><br />
<br />
<tr><br />
<td valign="top"><em>Functional Protein (red line)</em><p></p></td><br />
<td valign="top"><p>In this scenario the natal peptide is quickly driven towards stable protein.</p><p></p></td><br />
</tr><br />
<br />
<tr><br />
<td valign="top"><p><em>Inclusion Body (light blue line) </em></p><p></p></td><br />
<td valign="top"><p>In this scenario very few inclusion bodies are produced as there is not enough unstable protein present to induce nucleation</p><p></p></td><br />
</tr><br />
<br />
<tr><br />
<td valign="top"><em>Degraded Protein (purple line)</em><p></p></td><br />
<td valign="top"><p>Unstable protein and inclusion bodies are degraded. In this model unstable protein is degraded faster than inclusion bodies due to the size difference</p><p></p></td><br />
</tr><br />
</table><br />
<br /><br />
<br />
<h3>Result Case 2: High hydrophobic to charged amino acid ratio with a protein having many unstable intermediates </h3><br />
<p><br />
In this case the produced peptide is highly unstable and is composed of significantly more hydrophobic amino acids than charged amino acids. This indicates that in the unstable form a significant amount of the exposed amino acids will be hydrophobic. This state of unstable protein will strongly drive towards inclusion body formation.<br />
</p><br />
<img style="margin-left:-15px; width:682px; height:394px" src="https://static.igem.org/mediawiki/2010/a/a7/Highly_unstable.png" /><br />
<p><b>Figure 5. </b>In this figure the concentration units are arbitrarily mM and the time value is in seconds. These units were selected for convenience and are not assumed to be accurate for the process being modelled. This issue is discussed in more detail in the conclusion section</p><br />
<table><br />
<tr><br />
<td valign="top" style="width:175px"><p><em>Natal Peptide(blue line)</em></p><p></p></td><br />
<td valign="top"><p>An initial arbitrary amount of natal peptide ( 10 mM ) is produced in the cell</p><p></p></td><br />
</tr><br />
<br />
<tr><br />
<td valign="top"><em>Unstable Protein (green line)</em><p></p></td><br />
<td valign="top"><p>A high hydropathy value increases the time required for the protein to fold into its correct shape. This means more unstable protein will be present in the equilibrium. The green line on the graph represents this value. The peak on the graph represents the point of nucleation whereby the concentration of unstable protein reaches a peak that rapidly increases the drive to inclusion bodies.</p><p></p></td><br />
</tr><br />
<br />
<tr><br />
<td valign="top"><em>Functional Protein (red line)</em><p></p></td><br />
<td valign="top"><p>The increased hydropathy content decreases the presence of functional protein.</p><p></p></td><br />
</tr><br />
<br />
<tr><br />
<td valign="top"><p><em>Inclusion Body (light blue line) </em></p><p></p></td><br />
<td valign="top"><p>The concentration of inclusion body increases rapidly when the concentration of unstable protein reaches the point of nucleation ( peak of the green line )</p><p></p></td><br />
</tr><br />
<br />
<tr><br />
<td valign="top"><em>Degraded Protein (purple line)</em><p></p></td><br />
<td valign="top"><p>Unstable protein and inclusion bodies are degraded. In this model unstable protein is degraded faster than inclusion bodies due to the size difference</p><p></p></td><br />
</tr><br />
</table><br />
<br /><br />
<br />
<br />
<br />
<h3>Result Case 3: Over Produced Protein at High Temperature</h3><br />
<p>In this scenario the protein is highly stable and drives strongly towards it’s stable functional conformation. However the over production of the peptide means there are high concentrations of unstable protein present, and the higher temperature increases the kinetic movement of the unstable protein. This causes the unstable proteins to collide more frequently and form inclusion bodies before they have a chance to become stable protein. Since the protein is highly stable the nucleation point, the peak of the green line, occurs at a higher concentration and greater time value than that of the unstable protein in the previous case.</p><br /><br />
<img style="margin-left:-15px; width:682px; height:394px" src="https://static.igem.org/mediawiki/2010/3/31/Hightemp_stable.png" /><br /> <br />
<p><b>Figure 5. </b>In this figure the concentration units are arbitrarily mM and the time value is in seconds. These units were selected for convenience and are not assumed to be accurate for the process being modelled. This issue is discussed in more detail in the conclusion section</p><br />
<table><br />
<tr><br />
<td valign="top" style="width:175px"><p><em>Natal Peptide(blue line)</em></p><p></p></td><br />
<td valign="top"><p>An initial arbitrary amount of natal peptide ( 10 mM ) is produced in the cell</p><p></p></td><br />
</tr><br />
<br />
<tr><br />
<td valign="top"><em>Unstable Protein (green line)</em><p></p></td><br />
<td valign="top"><p>The highly stable protein produced in this scenario spends very little time in the unstable form. It is quickly converted to stable protein or driven into an inclusion body. In this scenario the concentration and temperature causes the equilibrium to favor inclusion bodies over the functional protein.</p><p></p></td><br />
</tr><br />
<br />
<tr><br />
<td valign="top"><em>Functional Protein (red line)</em><p></p></td><br />
<td valign="top"><p>In this scenario the functional protein is very stable and favored. However the concentration of unstable intermediate causes the intermediate proteins to be caught up in inclusion bodies prior to formation of correctly folded protein.</p><p></p></td><br />
</tr><br />
<br />
<tr><br />
<td valign="top"><p><em>Inclusion Body (light blue line) </em></p><p></p></td><br />
<td valign="top"><p>The concentration of inclusion body increases rapidly when the concentration of unstable protein reaches the point of nucleation ( peak of the green line ). This point is reached more slowly than in the previous scenario as the protein is more stable, and a certain concentration must be met before nucleation occurs.</p><p></p></td><br />
</tr><br />
<br />
<tr><br />
<td valign="top"><em>Degraded Protein (purple line)</em><p></p></td><br />
<td valign="top"><p>Unstable protein and inclusion bodies are degraded. In this model unstable protein is degraded faster than inclusion bodies due to the size difference</p><p></p></td><br />
</tr><br />
</table><br />
<br /><br />
<br />
<h2 id="Conclusions" style="color:#0066CC">Conclusions</h2><br />
<p> <br />
There are a number of immediate problems with this model approach that affect the accuracy of the results. The first and most significant is that the values for the amounts of species and the kinetic constants were selected for convenience. This means they were selected such that their relative relationships would allow us to determine if the model could be made to match the behaviour seen in the literature. As a result the the outputs of the simulation can not be taken as "real" because they do not use true values. The second major issue is the equilibrium equations proposed for each of the reactions are abstractions and may not be the best ways of relating the species. The third major issue is that there aren't any clearly defined relationships between each of the factors being investigated and misfiling. Therefore the relationship between factors such as temperature and sequence features such as hydrophobic/charged amino acids are accounted for in a qualitative way only.<br />
</p><br />
<p>Accounting for these caveats this model was still a success in a number of ways. The results demonstrate that the MATLAB Simbiology software can be used to simulate the process of inclusion body formation. The graphs obtained match closely, albeit in a qualitative way, the process of inclusion body formation as it is described in the literature. Lastly, this approach has provided us with a framework that can be used to study the factors affecting protein misfolding and aggregation. <br />
</p><br /><br />
<br />
<h2 id="Future" style="color:#0066CC">Future Directions</h2><br />
<p>The most necessary future direction is to find a "test" protein and apply the principles of the model to determine if the simulation results match with literature results. If this can be shown more test proteins can be evaluated with the model and the model can be made more general. The second future direction is to explore the concept of "cut off" values. From the equilibrium graphs in the results section it is clear that there is some amount of inclusion body present, some amount of unstable protein and some amount of stable functional protein. This implies that there will always be a ratio between the three different species and also that even when inclusion body is present some functional protein will be too. A cut off value would be the ratio of functional protein to non functional such that functional protein can still be obtained. The final future direction is to develop a way to account for the four different categories of inclusion bodies that are seen in the literature values. <br />
</p><br />
<br />
<h2 id="Future" style="color:#0066CC">References</h2><br />
<br />
<p>Ashbaugh, H. S., & Hatch, H. W. (2008). Natively unfolded protein stability as a coil-to-globule transition in charge/hydropathy space. Journal of the American Chemical Society, 130(29), 9536-9542. </p><br />
<br />
<p><br />
Roberts, C. J. (2007). Non-native protein aggregation kinetics. Biotechnology and Bioengineering, 98(5), 927-938. </p><br />
<br />
<p>Wang, W., Nema, S., & Teagarden, D. (2010). Protein aggregation--pathways and influencing factors. International Journal of Pharmaceutics, 390(2), 89-99. </p><br />
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<p>The term “model” can refer to a number of different concepts depending on the context in which it is used. These vary from complex sets of mathematical equations to attractive, but often overally thin, people walking down runways. For our purposes though we are using the term to mean: An approach for abstracting a complex process such that aspects of the process can be explored for greater understanding.</p><br /> <br />
<p>For our modeling project we have chosen to explore the processes of protein mis-folding and inclusion body formation. These two processes are interrelated to each other and exploring them complements nicely with the wet lab part of our project.</p><br /><br />
<p>The goals of the modelling project were to:<br /><br />
<ul><br />
<li>Develop an understanding of the sequence of steps that occur as a proteins form inclusion bodies</li><br />
<li>Investigate the factors impacting the formation of misfolded proteins and inclusion bodies</li><br />
<li>Attempt to quantize the affects that different factors have on the likely hood of inclusion body formation</li><br />
<li>Use the developed models to drive hypothesis to be investigated in future wet lab experiments</li><br />
</ul><br />
</p><br /><br />
<p>To achieve those goals two different models were developed. The first model uses MATLAB software to simulate the process of protein production. Qualitative and quantitative data about the protein production process were incorporated into this model to explore how different factors would affect the process. For the second model we have generated a visualization of the process of inclusion body formation. <br />
</p><br /><br />
<p>More detailed information about each of the models can be found in their respective sections</p><br />
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<p>As a side animation project, we are using <i>Maya</i>, a 3D graphics and animation program provided to us by Autodesk, who is a sponsor of iGEM this year. We intended to create an animation visualizing what the process of inclusion body formation might look like. The basis of this animation can be found in literature (Roberts, 2007).</p><br />
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<img src="http://i872.photobucket.com/albums/ab287/iGEMCalgary_2010/MayaFigure.png"></img><br />
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<p>We believe this animation will help students in iGEM visualize and understand the process behind inclusion body formation. A dynamic visual catches people's attention and shows things as they happen, rather than showing static intermediate images on a diagram.</p><br />
<br />
<p>This is what we are showing:<br />
<ol><br />
<li>A misfolded protein forms, exposing hydrophobic side chains. (0:00)</li><br />
<li>A nucleus of aggregation is formed by a collection of these misfolded proteins sticking together. (0:01)</li><br />
<li>More misfolded protein become attracted to the nucleus, attempting to "cover up" hydrophobic ends. (0:02 - 0:13)</li><br />
<li>Smaller clumps stick together into larger clumps. (0:14 - 0:23)<br />
<li>This process continues until a large inclusion body forms in the cell, large enough to be visible. (0:23 - 0:38)</li><br />
</ol></p><br />
<br/><br />
<br />
<object width="480" height="385"><param name="movie" value="http://www.youtube.com/v/IouuHDjVpbo?fs=1&amp;hl=en_US"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/IouuHDjVpbo?fs=1&amp;hl=en_US" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="480" height="385"></embed></object><br />
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<p>Roberts, C.J. (2007). Non-Native Protein Aggregation Kinetics. <i>Biotechnology and Bioengineering 98</i>(5), 927-938.</p><br />
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<p>This year, iGEM Calgary created a blog that updated with information regarding synthetic biology news, features of other iGEM projects as well as updates of our own team and our project. Our goal was to improve the public image of synthetic biology and showcase the many cool and interesting things that the field can bring. In this way, we hope to reach out to the community and hopefully alleviate some skepticism behind synthetic biology.</p><br />
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<li><a href="https://2010.igem.org/Team:Calgary/Community/Ethics">Human Practices</a></li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Community/Gallery">Photo Gallery</a></li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Community/Conferences">Conferences</a></li><br />
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<span id="bodytitle"><h1>Our Blog</h1></span><br />
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<p>This year, iGEM Calgary created a blog that updated with information regarding synthetic biology news, features of other iGEM projects as well as updates of our own team and our project. Our goal was to improve the public image of synthetic biology and showcase the many cool and interesting things that the field can bring. In this way, we hope to reach out to the community and hopefully alleviate some skepticism behind synthetic biology.</p><br />
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<a href="http://igemcalgary2010.blogspot.com" target="_blank">Check Out Our Blog!</a><br />
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<p>As part of our Ethics and Human Practices project, we created a series of podcasts that analyze the benefits and consequences of the new and emerging field of Synthetic Biology. Currently, our series of podcasts consists of three episodes: Synthetic Life, The Consequences of Open Source Biology and Genetically Modified Foods. We have covered content in these podcasts and targeted them at the general public in the hopes of raising awareness, clearing up misconceptions, and educating others about the field of Synthetic Biology. We felt this was necessary after reading some of the reactions the public had in regards to Craig Venter’s ‘creation’ of synthetic life this summer. The podcasts offer unbiased and easy to understand subject matter presented in a very interactive manner.<br />
</p><br />
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<h3>Synthetic Life</h3><br />
<p>With the creation of Craig Venter’s first synthetic genome, inserted into bacteria, media outlets did a very poor job of publicizing this news, often overemphasizing and exaggerating the original findings of the Venter lab. This put a lot of fear in the public’s eye in regards to Synthetic Biology. This podcast covers Venter’s Synthetic Bacteria and analyzes his findings from a scientific and unbiased perspective.</p><br />
<br />
<p><a href="http://www.wikiwikiwebworks.ca/SyntheticLifePodcast.mp3" target="_blank">Listen to it here!</a> - <a href="https://2010.igem.org/Team:Calgary/Community/Podcasts/Transcripts#synthlife">Transcript here</a></p><br />
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<h3>The Consequences of Open-Source Biology</h3><br />
<p>In this podcast, we begin with the structure, foundations and the history of iGEM and the Registry of Parts. We transition to focus on our project and what we aim to do with it. The podcast is wrapped up with our experiences from our visit to DRDC Suffield and the opinions of experts in the field.</p><br />
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<p><a href="http://www.wikiwikiwebworks.ca/OpenSourcePodcast.mp3" target="_blank">Listen to it here!</a> - <a href="https://2010.igem.org/Team:Calgary/Community/Podcasts/Transcripts#opensource">Transcript here</a></p><br />
<br />
<h3>Genetically Modified Foods</h3><br />
<p>The advantages and disadvantages of genetically modified foods are discussed. The role that Synthetic Biology plays in genetically modified foods is also analyzed.</p><br />
<br />
<p><a href="http://www.wikiwikiwebworks.ca/GMFoodPodcast.mp3" target="_blank">Listen to it here!</a> - <a href="https://2010.igem.org/Team:Calgary/Community/Podcasts/Transcripts#gm">Transcript here</a></p><br />
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<span id="bodytitle"><h1>Conferences</h1></span><br />
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<h3>Spring Workshop</h3><br />
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<p>The iGEM spring workshop was organized by iGEM headquarters on May 29-30. These workshops were organized in many different continents including Europe, North America and Asia. This year, the Canadian workshop was organized at the University of Calgary. The main purpose of the iGEM workshop was to provide new iGEM students with background about synthetic biology and iGEM in general. There were workshops that covered general concepts ranging from synthetic biology to biobricks, wiki design, using the registry of standard parts, submitting parts and the iGEM Jamboree.</p><br />
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<p>Speakers included:</p><br />
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<p><u>Tom Knight</u></p><br />
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<p>One of the founders of synthetic biology, Tom Knight was responsible for designing the standard BioBrick system and co-pioneering the standard digestion and ligation cloning method (also known as BioBrick cloning method) that is used widely in synthetic biology and iGEM. Tom Knight presented a little bit of history of iGEM and the pioneering of standard biological parts that came about from a group of engineers, including himself and Drew Endy. Tom Knight also gave an overview of the BioBrick cloning method, including some tips and tricks that he had encountered over the years that he has been involved in the field of synthetic biology.</p><br />
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<p><u>Megan Lizarazo</u></p><br />
<p>Megan Lizarazo is the iGEM Research Technician. She handles most of the shipping and receiving of parts, as well as communicating with and updating all the teams about iGEM related events. During the workshop Megan provided valuable information about how to send DNA parts to the registry.<br />
</p><br />
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<p><u>Barry Canton</u></p><br />
<p>Barry Canton works in the Drew Endy Lab. He is a previous iGEM alumni. Barry Canton talked about Wiki creation, uploading parts information, and also taught us about different tips and tricks regarding the wiki. This presentation also included building a wiki for Team:Example which ended up looking quite... <a href="https://2010.igem.org/wiki/index.php?title=Team:Example&oldid=5571">interesting</a>, thanks to the contributions of every member there.<br />
</p><br />
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<p><u>Randy Retberg</u></p><br />
<p>Randy Retberg is the director of iGEM competition. He is primarily an engineer who has worked for well-known companies such as Sun, IBM, etc. Randy Retberg presented on the general notion of synthetic biology and iGEM. He also talked about future of iGEM and synthetic biology.</p><br />
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<h3>Lethbridge Conference</h3><br />
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<a href="http://s872.photobucket.com/albums/ab287/iGEMCalgary_2010/?action=view&current=TabMenuLethbridgeWorkshop-1.png" target="_blank"><img src="http://i872.photobucket.com/albums/ab287/iGEMCalgary_2010/TabMenuLethbridgeWorkshop-1.png" border="0" alt="Photobucket"></a><br />
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<p>On June 26th and 27th, Alberta Innovates Technology Futures had invited us to attend their student workshop in Lethbridge, Alberta. Throughout the weekend we were given insight on several areas of our iGEM project. These included marketing, media relations, presentation skills and project ideas and troubleshooting.</p><br />
<br />
<p>Presenters included:</p><br />
<br />
<p><u>Joey Hundert – Marketing/Sponsorship</u></p><br />
<p>The first guest speaker at Lethbridge was Joey Hundert. Joey was an amazing resource because of his expertise in entrepreneurship specifically on the field of sustainable development. He broadened our understanding on approaching companies for sponsorship, especially when marketing to companies about the new and innovative field of synthetic biology. This was incredibly useful for our group as none of the undergraduates had prior experiences with marketing and sponsorship.</p><br />
<br />
<p><u>Erin Prefontaine and Bob Cooney - Painless Publicity</u></p><br />
<p>The next presentation was a joint presentation by Erin and Bob. Erin is the Communication Officer of Alberta Innovates Technology Futures, and Bob is the Communications Officer of the University of Lethbridge. They offered an insightful presentation on the precautions necessary when speaking to the media. They provided us with advices on how to approach the media while remaining careful with the choice of our words. Our aim is not to scare the public, but to show them why we're are doing what we are doing and what the benefits to the public are, from our findings. They also suggested we contact Grady Simmons, who is involved with the media relations for the University of Calgary.</p><br />
<br />
<p><u>Anne Marie Downey - Communication</u></p><br />
<p>On June 28th, our first speaker was Anne Marie Downey. She was a gracious, talented guest speaker who gave us constructive ideas regarding presentation skills. Some of the keypoints of the presentation were communication skills, developing the content in PowerPoints, the purpose of using visuals and managing the response of the audience. During her presentation, every team practiced their short “Elevator Pitch” to explain their project to the general public while the audience analyzed and suggested ways to improve this Elevator Pitch of the projects. Her presentation was extremely beneficial for the team, which was evident in the improvement of our own presentations. We did short summary descriptions of our project as we moved from one member to the other, and received constructive feedback from Anne Marie and also other students of the University of Lethbridge and the University of Alberta. We were also given a “Communication That Works” booklet to help us in the future with Presentation Skills. </p> <br />
<br />
<p><u>Andrew Hessel</u></p><br />
<p>Andrew Hessel was the iGEM Ambassador at MIT and currently the Co-Chair of Bioinformatics and Biotechnology at Singularity University. He was the last presenter of the day, but just as useful as the other speaker sessions we had. He gave us suggestions on various subjects: Wet lab, marketing and promotion to name a few. He strongly suggested that we approach Oil Sands Companies for sponsorship.<br />
</p><br />
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<h3>aGEM</h3><br />
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<p>The Alberta Genetically Engineered Machines competition (aGEM) is an Alberta-wide competition held every year since 2007. During aGEM, the Alberta teams (Universities of Calgary, Alberta, and Lethbridge) present their projects in front of respected and qualified judges who provide feedback and meet the teams one-on-one to suggest future improvement before iGEM comes around. This year, team Calgary met with ex-iGEMer Justin Pahara and was helped with their presentation in general. Other judges such as Andrew Hessel also provided valuable feedback on the team’s website, presentation and future direction. Thank you Alberta Innovates Technology Futures, for such a great opportunity. <br />
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<p>Here is a collection of the various photos, activities, and hijinks our team got into over the summer.</p><br />
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<span id="bodytitle"><h1>Ethics and Human Practices</h1></span><br />
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<h3>Ethics Podcast and Paper</h3><br />
<table><br />
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<td><p>Synthetic Biology is a new and emerging field with many potential benefits. Because the public perception of synthetic biology is still very limited, knowledge and understanding of projects relating to synthetic biology continues to remain limited, as well. Therefore, the iGEM Calgary team believes that it is essential to recognize the ethical implications of our project. We hope to improve the public's understanding of Synthetic Biology and alleviate common concerns with the field. With this aim, our team began working on two major projects for the Ethics and Human Practices component. </p><br />
</td><br />
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<p><br />
One project examines Synthetic Biology from a general perspective, while the other discusses the ethical implications of our project specifically.<br />
In the first project, we have created a series of <a href="https://2010.igem.org/Team:Calgary/Community/Podcasts">podcasts</a> regarding various issues relating to Synthetic Biology. In the podcasts, members of our group have an open discussion about issues such as the concept of synthetic life and the nature of open-source science. This allowed us to reflect on the potentials of Synthetic Biology, and hence, enrich our understanding about this field. We also wrote a paper where we discuss the ethical, economical and social implications of our project. This allowed us to understand our project from different perspectives. The significance of this paper is that it allowed us, as a team, to reflect on the potential benefits and risks that our project can entail. <br />
Apart from working on these two projects over the summer, we have also incorporated an outreach program into our Ethics portion. We have presented to several high schools, with the aim of increasing awareness of Synthetic Biology to high-school students. As a team, we believe that high school students will be the generation that will be increasingly exposed to this field.</p><br />
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<br />
<h3>High School Presentations</h3><br />
<br />
<p> Synthetic Biology is a new emerging field of Science and the general public are still unfamiliar about its potentials. High school students are an important generation who should become aware of this fascinating approach to science. This is not just to increase public awareness but also because high school students are the ones who will be most exposed to Synthetic Biology in the upcoming years. With that intention, we went to several high schools to introduce Synthetic Biology and its potentials. We discussed with the students about the three components of projects related to Synthetic Biology in iGEM: Wetlab, Modelling and Human Practice. We emphasized on the interdisciplinary characteristic of projects in iGEM that are related to Synthetic Biology. With this, we hope that students of next generations are more interested in Synthetic Biology. In addition, we hope to empower the students with the growing techniques and perspectives of looking at biological functions. </p><br />
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<h3>Research Symposiums</h3><br />
<br />
<p> <br />
This year our iGEM team participated in a few research sympoisums. This was a great way to raise more awareness for iGEM at our own Univeristy while getting to practice presenting our work to varied audiences.<br />
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''BHSc Research Symposium''<Br><br />
On October 7th we presented an oral presentation as well as a poster rpesentation at the Bachelor of Health Scinecs research symposium. This was a great way to get more people from the faculty of medicine interested in iGEM. There was a mix of undergradutae students, researchers and professors in attendance, so this was a great place to show pff what we did this Summer.<br />
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'''USRP Research Symposium'''<Br><br />
On October 7th we also had the opportunity to present a poster at the USRP Markin Research Symposium at the University of Calgary. This was a great opportunity to get the word out about iGEM and our project to a wider audience at our university. There were students and faculty mambers from across all faculties ad it was good practice trying to explain our project to people with very little biological background.<br />
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'''Student’s Union Research Symposium'''<Br><br />
Still to come we have the Univeristy of Calgary’s Student’s Union Research Symposium in late November. This will be a good platform to start recruitment for next year’s team as this symposium attracts students and faculty from across the university. This will also be a great wrap-up to our iGEM season a couple of weeks after the actual iGEM Jamboree.</p><br />
<h3>Bake Sale</h3><br />
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<p> This year, the purpose of the bake sale included two aspects: firstly, it was to raise awareness about Synthetic Biology in our Health Sciences department and secondly, it was a fundraising activity to have the financial support to complete the Wetlab portion of our project.</p><br />
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The Bake Sale was a great way to interact with the undergraduate and graduate students in the Health Sciences department of the University of Calgary. Many researchers were interested in finding out more about Synthetic Biology in the small time of interaction during the fundraising. <br />
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<p class="tabText" style="padding-left:10px;">What new dangers and unintended consequences will synthetic biology pose to us in the future? iGEM Calgary travels to Defence Research and Development Canada Suffield, a major Canadian Military Research facility that specializes in chemo-biological threats. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community/Suffield">Read more...</a></p><br />
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<p class="tabText" style="padding-left:10px;">The University of Calgary, Alberta, and Lethbridge iGEM teams met in Lethbridge at a conference put on by Alberta Innovates Technology Futures to learn important aspects of iGEM. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community/Conferences#lethbridge">Read more...</a></p><br />
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<p class="tabText" style="padding-left:10px;">Have you ever seen an aggregate protein dance? Look out for iGEM Calgary’s rambunctious mascot “Protein Man” at the Jamboree promoting proper protein expression. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Extras/Protein_Man">Learn more about him...</a></p><br />
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<p class="tabText" style="padding-left:10px;">Team Calgary brings iGEM awareness to the community. The iGEM bake sale was a great success, both in selling cupcakes and educating customers about our team. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community">See what else we've been doing...</a></p><br />
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<p class="tabText" style="padding-left:10px;">Alberta’s very own Jamboree. The three Alberta iGEM teams, the Universities of Alberta, Calgary, and Lethbridge meet to perform a practice project presentation to each other. Experts within their field are also present to give teams challenging questions, and then meet with each team to suggest improvements. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community/Conferences#agem">Read more...</a></p><br />
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<p>Our modelling project consists of two components: a mathematical model done in MATLAB and an animation done in Autodesk <i>Maya</i>. We hope to model the formation of inclusion bodies, which are aggregations of misfolded protein that can occur within cells. Using <i>Maya</i>, we also hope to visually show other students one of the proposed aggregation mechanisms described in the literature.<br />
<a href="https://2010.igem.org/Team:Calgary/Modelling">Read more here...</a></p><br />
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<p>Our outreach project included educating highschool students about iGEM. Outreach also entailed blog entries and podcast about synthetic life, iGEM and open source as well as Genetically modified foods. The blog entry, podcasts and high school presentations allowed the iGEM students to spread knowledge about iGEM to the general public and to potential future scientists. <a href="https://2010.igem.org/Team:Calgary/Community">Read more here...</a></p><br />
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<h3>Wetlab</h3><br />
<p>You’re stressing me out! This year, in the wetlab, we have been designing a reporter system to detect problems in protein expression. Our system uses a visual output to allow specificity in determining which step in protein expression problems are occurring.</p><br />
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<h3>Modelling</h3><br />
<p>Our modeling project has focused on simulating and modeling the formation of inclusion bodies, aggregates of protein within the cell. We've been exploring the factors that lead to their formation.</p><br />
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<h3>Community</h3><br />
<p>Our human practices section focused on exploring ethical issues in synthetic biology through an ethics paper as well as a podcast focusing on a few key issues. Our outreach initiatives also allowed the iGEM students to spread knowledge about iGEM to the general public and to potential future scientists through activities such as high school presentations and participation in various research symposiums.</p><br />
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<p>This year the target of our community section is to inform the public about the potentials of synthetic biology. From preliminary assessments iGEM Calgary has discovered that the major outlet of synthetic biology news usually comes from misinformed media sources. Although there are some great sources such as the 2009 New Yorker article titled “A Life if it’s Own”, there are numerous other articles that fail to capture the true understanding of what synthetic biology actually entails. Because of this iGEM Calgary has decided to appeal to one of the most cost effective and efficient method of how the word of synthetic biology could be spread, by creating a series of podcasts. In addition, several members on the team have given seminars in high schools around Calgary as well as appear in a local newspaper.</p> <br />
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<p>In terms of looking at the ethics of the 2010 project, Raida Khwaja has written a paper regarding the political, social and economic implications of the protein expression toolkit. <br />
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<p>As part of our Ethics and Human Practices project, we created a series of podcasts that analyze the benefits and consequences of the new and emerging field of Synthetic Biology. Currently, our series of podcasts consists of three episodes: Synthetic Life, The Consequences of Open Source Biology and Genetically Modified Foods. We have covered content in these podcasts and targeted them at the general public in the hopes of raising awareness, clearing up misconceptions, and educating others about the field of Synthetic Biology. We felt this was necessary after reading some of the reactions the public had in regards to Craig Venter’s ‘creation’ of synthetic life this summer. The podcasts offer unbiased and easy to understand subject matter presented in a very interactive manner.<br />
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<h3>Synthetic Life</h3><br />
<p>With the creation of Craig Venter’s first synthetic genome, inserted into bacteria, media outlets did a very poor job of publicizing this news, often overemphasizing and exaggerating the original findings of the Venter lab. This put a lot of fear in the public’s eye in regards to Synthetic Biology. This podcast covers Venter’s Synthetic Bacteria and analyzes his findings from a scientific and unbiased perspective.</p><br />
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<p><a href="http://www.wikiwikiwebworks.ca/SyntheticLifePodcast.mp3" target="_blank">Listen to it here!</a> - <a href="https://2010.igem.org/Team:Calgary/Community/Podcasts/Transcripts#synthlife">Transcript here</a></p><br />
<br />
<h3>The Consequences of Open-Source Biology</h3><br />
<p>In this podcast, we begin with the structure, foundations and the history of iGEM and the Registry of Parts. We transition to focus on our project and what we aim to do with it. The podcast is wrapped up with our experiences from our visit to DRDC Suffield and the opinions of experts in the field.</p><br />
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<p><a href="http://www.wikiwikiwebworks.ca/OpenSourcePodcast.mp3" target="_blank">Listen to it here!</a> - <a href="https://2010.igem.org/Team:Calgary/Community/Podcasts/Transcripts#opensource">Transcript here</a></p><br />
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<h3>Genetically Modified Foods</h3><br />
<p>The advantages and disadvantages of genetically modified foods are discussed. The role that Synthetic Biology plays in genetically modified foods is also analyzed.</p><br />
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<p><a href="http://www.wikiwikiwebworks.ca/GMFoodPodcast.mp3" target="_blank">Listen to it here!</a> - <a href="https://2010.igem.org/Team:Calgary/Community/Podcasts/Transcripts#gm">Transcript here</a></p><br />
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</html></div>Pjwuhttp://2010.igem.org/Team:Calgary/Community/Podcasts/TranscriptsTeam:Calgary/Community/Podcasts/Transcripts2010-10-28T00:07:14Z<p>Pjwu: New page: {{CalgaryMenu}} <html> <body> <h1>Synthetic Life</h1> <p>Alex: Hi my name’s Alex Grigg, and this is my teammate Dev Yvas. And we would like to welcome you to the first episode of Synt...</p>
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<p>Alex: Hi my name’s Alex Grigg, and this is my teammate Dev Yvas. And we would like to welcome you to the first episode of Synthetic Ethics. So Dev, I’m sure your familiar with synthetic biology, but what about our listeners who still don’t quite get what synthetic biology is?</p><br />
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<p>Dev: Well synthetic biology is an emerging science with vast potential and opportunity. It can be described as the combination of science and engineering. What synthetic biologists do is create new organic systems operating within living organisms. It even has the potential to create life from scratch.</p><br />
<br />
<p>Alex: I’m going to stop you right there, because today we are discussing the ethics of synthetic life, a topic which draws some of the most excitement, and controversy to our field. So, if I were to tell you that a colossal achievement that has been compared to other scientific milestones such as the sequencing of the human genome, and the cloning of the sheep Dolly happened just a few months ago, what would you think I was talking about?</p><br />
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<p>Dev: Does it have anything to do with Bald Bearded scientists?</p><br />
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<p>Alex: Good guess Dev! Although I think every scientific milestone can be somehow attributed to the Bald and Bearded. The particular accomplishment to which I’m referring is the creation of synthia, the first synthetic, self-replicating life.</p><br />
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<p>Dev: That’s right, in 2008 a team of scientists at the J. Craig Venter Institute headed up by Drs. Craig Venter, our bald and bearded scientist, Hamilton Smith, and Clyde Hutchison were able to create a small bacterial genome, and by May 2010 it was announced that they had successfully used a synthetic genome of the bacterium mycroplasma mycocides to create a bacteria that could sustain, and replicate itself.</p><br />
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<p>Alex: Alright, lets take a step back and talk about how such an achievement was attained. It all started with the chemical synthesis of DNA fragments of 1078 base pairs. These cassettes each had overlaps of 80 base pairs, which allowed them to be recombined in yeast. 10 of these cassettes were recombined into 10kb cassettes of DNA, which were then recombined again into 100kb pieces that could be used to create the final synthetic genome of mycroplasma myocides which is 1.08 million basepairs long. Venter and his team also included what are called “watermarks” in the genome which are sequences that allow us to differentiate this synthetic genome, from the naturally occurring genome. But what’d they do next with the genome?</p><br />
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<p>Dev: Well, M. mycoide genomes were transplanted into restriction-minus Mycoplasma capricolum recipient cells. These cells, containing only the synthetic genome that they had created, were able to self-replicate.</p><br />
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<p>Alex: This Sounds like great news! Craig Venter and his team has proven that we are able to create life, Imagine the possibilities. We could potentially create organisms which we have never before observed.</p><br />
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<p>Dev: Well I for one think “We're all doomed! Doooooooooooommmmmmmmmmmmeeeeeeeeeddd!!!”</p><br />
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<p>Alex: Wow Really? Why?</p><br />
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<p>Dev: To be honest I don’t really think we’re all doomed, but that is a comment taken from a story in the guardian in which many of the reader’s voice concerns about synthetic life, and show that there is a lot of fear taken from news of this achievement. Another commenter, posting under the name CruyffTurn had a concern when he read that the synthetic organism had included watermarks so that we can keep track of it. He said: “So, what you really mean if the organism somehow manages to escape in to the environment, subsequently mutating in to some evil virulent pathogen, killing billions, we can be safe in the knowledge that we will know where it came from. Amazing piece of scientific work though.”</p><br />
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<p>Alex: Well do you think that there’s a possibility that this synthetic mycroplasma myocide will mutate into a some sort of superbug that will kill billions?</p><br />
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<p>Dev: I’m actually not that concerned. What people need to understand is that the bug that Craig Venter synthesized is essentially the same as a bug that came to us naturally, through Darwinian evolution. The DNA is fully synthetic, but the sequence itself is natural, and so is the cell in which they inserted the genome so that it can replicate and carry out protein synthesis.</p><br />
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<p>Alex: Well it seems to me that we aren’t doomed at all, all they made was an naturally occurring germ. But, another commenter said “I want to be excited by this news, but it scares the bejeezus out of me...”</p><br />
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<p>Dev: So what else are they scared of?</p><br />
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<p>Alex: Well I know a lot of fear stems from the possibility of synthesizing organisms which would be extremely harmful to humans if they were released.</p><br />
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<p>Dev: Ok, I think that is a legitimate concern. So what kind of organisms would that be?</p> <br />
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<p>Alex: Well one example of a synthetic organism that could cause massive casualties is smallpox. Digital genomes of smallpox are present online, and could potentially be created chemically using a similar process that Craig Venter used. In June 2006 a reporter for the guardian obtained a small sequence of smallpox DNA delivered to his home from a gene synthesis company. Now that sounds scary.</p><br />
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<p>Dev: Well what kind of company would send the smallpox genome to a residential address? Even if it is piece by piece.</p><br />
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<p>Alex: This reporter was able to achieve this from a major gene synthesis company through the lack of screening technology and safeguards that are present at these gene synthesis companies. As the price of synthesizing genes gets more and more affordable, efficient safeguards which screen both the content being ordered, and who is ordering them needs to be put in place in order to ensure that gene sequencing isn’t used by would-be terrorists.</p><br />
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<p>Dev: Why isn’t there anything already in place to help gene synthesis companies from sending out sequences that contain harmful genes?</p><br />
<br />
<p>Alex: Actually there is. The International Gene Synthesis Consortium is an organization consisting of 5 major gene synthesis companies, and makes up over 80% of commercial gene synthesis capacity world-wide. These companies have agreed to screen synthetic gene orders to identify pathogen sequences and other potentially dangerous sequences, screen customers by requiring identification, and keep records for at least 8 years of customers, sequences, and delivery information. They also do not send to post office boxes, which seems like a no brainer to me.</p><br />
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<p>Dev: Ok, so we can all feel a little safer knowing that random people can’t just order sequences containing harmful genes, but the idea that some disgruntled scientist can synthesize killer bugs in his basement is a little far-fetched.</p><br />
<br />
<p>Alex: Yeah people need to understand that this kind of work requires more than a few test tubes. What kind of things would a disgruntled scientists need if he wanted to synthesize an evil organism?</p><br />
<br />
<p>Dev: Well besides the need for precise chemical synthesis of gene fragments from somewhere such as a gene synthesis company, synthesizing self-replicating life requires high-throughput sequencing facilities so that you can be sure you have the right sequence, sophisticated designing strategy, and multiple steps of quality control. Among other things.</p><br />
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<p>Alex: So this sort of thing couldn’t be done alone in your garage.</p><br />
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<p>Dev: Assuming your garage isn’t extremely well equipped.</p><br />
<br />
<p>Alex: But people aren’t just worried about their safety in the sense that harmful organisms could be created, there is also a lot of concern revolving around the ethical implications of our newfound capacity to chemically create life. There’s a lot of use of the phrase “playing god”.</p><br />
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<p>Dev: But is this a real worry? I mean it’s not like we can now create new organisms or animals.</p><br />
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<p>Alex: Well there is a concern that as we further this technology, we will be able to create organisms that did not come to us through natural Darwinian evolution, and even gain the ability to use this technology to genetically design humans.</p><br />
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<p>Dev: That sounds almost like something out of science fiction.</p><br />
<br />
<p>Alex: At this stage in the game, it sort of is, but that doesn’t mean that we shouldn’t be aware of the ethical risks associated with the advancement of our capability to synthesize life. The Vatican’s response to the creation of replicating synthetic life by Craig Venter and his team was actually fairly positive. “If it is used toward the good, to treat pathologies, we can only be positive” the Vatican’s top bioethics official, Monsignor Rino Fisichella, told Italian state-run television news programme TG Uno. The head of the Italian Catholic bishop’s conference Cardinal Angelo Bagnasco said that “intelligence can never be without responsibility”</p><br />
<br />
<p>Dev: Well I think that that properly sums up the attitude that we should have towards instances like this. The advent of synthetic life represents a momentous step forward in mankind’s ability to combat many of the problems facing us, but we need to ensure that those tools are not abused so as to cause harmful results.</p><br />
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<p>OUTRO</p><br />
<br />
<p>Alex: Well thanks for joining us while we explore the ethical issues associated with synthetic biology. If your looking for more news and exciting stories within synthetic biology, check out our blog at (BLOG ADRESS), or if you want to learn more about our team and the work we are doing check out our wiki at https://2010.igem.org/Team:Calgary</p><br />
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<p>As part of our Ethics and Human Practices project, we created a series of podcasts that analyze the benefits and consequences of the new and emerging field of Synthetic Biology. Currently, our series of podcasts consists of three episodes: Synthetic Life, The Consequences of Open Source Biology and Genetically Modified Foods. We have covered content in these podcasts and targeted them at the general public in the hopes of raising awareness, clearing up misconceptions, and educating others about the field of Synthetic Biology. We felt this was necessary after reading some of the reactions the public had in regards to Craig Venter’s ‘creation’ of synthetic life this summer. The podcasts offer unbiased and easy to understand subject matter presented in a very interactive manner.<br />
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<p>With the creation of Craig Venter’s first synthetic genome, inserted into bacteria, media outlets did a very poor job of publicizing this news, often overemphasizing and exaggerating the original findings of the Venter lab. This put a lot of fear in the public’s eye in regards to Synthetic Biology. This podcast covers Venter’s Synthetic Bacteria and analyzes his findings from a scientific and unbiased perspective.</p><br />
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<p><a href="http://www.wikiwikiwebworks.ca/SyntheticLifePodcast.mp3" target="_blank">Listen to it here!</a> - <a href="https://2010.igem.org/Team:Calgary/Community/Podcasts/Transcripts#synthlife">Transcript here</a></p><br />
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<p>In this podcast, we begin with the structure, foundations and the history of iGEM and the Registry of Parts. We transition to focus on our project and what we aim to do with it. The podcast is wrapped up with our experiences from our visit to DRDC Suffield and the opinions of experts in the field.</p><br />
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<p><a href="http://www.wikiwikiwebworks.ca/OpenSourcePodcast.mp3" target="_blank">Listen to it here!</a> - <a href="https://2010.igem.org/Team:Calgary/Community/Podcasts/Transcripts#opensource">Transcript here</a></p><br />
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<p>The advantages and disadvantages of genetically modified foods are discussed. The role that Synthetic Biology plays in genetically modified foods is also analyzed.</p><br />
<br />
<p><a href="http://www.wikiwikiwebworks.ca/GMFoodPodcast.mp3" target="_blank">Listen to it here!</a> - <a href="https://2010.igem.org/Team:Calgary/Community/Podcasts/Transcripts#gm">Transcript here</a></p><br />
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<p>With the creation of Craig Venter’s first synthetic genome, inserted into bacteria, media outlets did a very poor job of publicizing this news, often overemphasizing and exaggerating the original findings of the Venter lab. This put a lot of fear in the public’s eye in regards to Synthetic Biology. This podcast covers Venter’s Synthetic Bacteria and analyzes his findings from a scientific and unbiased perspective.</p><br />
<br />
<embed type=”application/x-shockwave-flash” flashvars=”audioUrl=http://www.wikiwikiwebworks.ca/SyntheticLifePodcast.mp3” src=”http://www.google.com/reader/ui/3523697345-audio-player.swf” width=”400″ height=”27″ quality=”best”></embed><br />
<br />
<h3>The Consequences of Open-Source Biology</h3><br />
<p>In this podcast, we begin with the structure, foundations and the history of iGEM and the Registry of Parts. We transition to focus on our project and what we aim to do with it. The podcast is wrapped up with our experiences from our visit to DRDC Suffield and the opinions of experts in the field.</p><br />
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<embed type=”application/x-shockwave-flash” flashvars=”audioUrl=http://www.wikiwikiwebworks.ca/OpenSourcePodcast.mp3” src=”http://www.google.com/reader/ui/3523697345-audio-player.swf” width=”400″ height=”27″ quality=”best”></embed><br />
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<p>The advantages and disadvantages of genetically modified foods are discussed. The role that Synthetic Biology plays in genetically modified foods is also analyzed.</p><br />
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</html></div>Pjwuhttp://2010.igem.org/Team:Calgary/Project/AchievementsTeam:Calgary/Project/Achievements2010-10-27T23:19:57Z<p>Pjwu: </p>
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<h1>Project Descriptions</h1><br />
<br />
<br />
<ul><br />
<li><a href="https://2010.igem.org/Team:Calgary/Project/Transcription">Transcription/Translation Reporter Circuit</a></li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Project/misfolding_overview">Protein Misfolding Reporters</a><br />
<ul><br />
<li><a href="https://2010.igem.org/Team:Calgary/Project/IbpAB">Cytoplasmic Stress Detectors</a></li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Project/CpxP">Periplasmic Stress Detectors</a></li><br />
</ul><br />
</li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Project/Controls">Testing Our System</a></li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Project/Achievements">Achievements</a></li><br />
</ul><br />
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<br />
<span id="bodytitle"><h1>Achievements</h1></span><br />
<br />
<p><br />
<h2 style="color:#0066CC">Bronze medal requirements</h2><br />
<ul><br />
<li>Register the team</li><br />
<br />
<li>Successfully complete and submit a project summary form</li><br />
<br />
<li>Create a Wiki which includes all the details of the project</li><br />
<br />
<li>Present a presentation and a poster at the iGEM Jamboree</li><br />
<br />
<li>Enter information detailing at least one new standard BioBrick Part or Device in the Registry of Parts </li><br />
<br />
<li>Data was entered for 11 new biobrick parts</li><br />
<br />
<li>Submit DNA for at least one new BioBrick Part or Device to the Registry of Parts</li><br />
<br />
<br />
<li>We designed and submitted DNA for three new biobrick parts</li><br />
</ul><br />
<ul><br />
<li><p>Cytoplasmic maltose binding protein (malESS)</li><br />
<li>IbpAb/ fxsA fusion promoter</li><br />
<li> CpxP Promoter </li></ul><br />
<br />
<p>We also built the following new constructs:</p><br />
<br />
<br />
<ul><br />
<br />
<li>ibpAB reporter BBa_K339011</li><br />
<li>CpxR reporter BBa_K339007</li><br />
<li>DegP reporter BBa_K339008</li><br />
<li>MalE generator BBa_K339004</li><br />
<li>MalE31 generator BBa_K339005</li><br />
<li>CpxR Promoter with RFP Reporter and Arabinose Inducible MalE31 BBa_K339009 </li></ul><br />
<br />
All of these parts were verified via restriction digests and PCR, and then finally sequenced.<br />
<br />
<h2 style="color:#0066CC">Silver medal Requirements</h2><br />
<br />
<ul><h3>Demonstrate that one of your parts works as expected</h3><br />
<br />
<li>Through our characterization data, we showed that several of our parts worked as expected. Click here for more information.<br />
<br />
<p>The CpxR reporter was found to report on misfolding protein. We characterized this promoter with varying concentrations of folding and misfolding proteins produced which we assumed is correlated to arabinose concentrations due to the use of AraC promoter. We also tested this promoter with NlpE, an outer membrane lipoprotein that literature has found activates the Cpx pathway. Finally, we tested this promoter in varying temperature to produce a heat shock response.</p></li><br />
<h3>Characterize the operation of at least one new BioBrick Part or Device and enter this information on the Parts or Device page via the Registry of Parts</h3><br />
<br />
<li>Both MalE and MalE31 also worked as expected, malE folding in the periplasm and malE31 showing a misfolding response. This was indicated through testing with a reporter from another lab (Raivio) (for more info click here) as well as tetsing with our cpxR reporter click here.</li><br />
<br />
<li>We characterized the cpxR reporter, malE31, MalE and IbpAB. See characterization data here.</li></ul><br />
<br />
<h2 style="color:#0066CC">Gold Medal requirements</h2><br />
<br />
<ul><h3>Characterize or improve an existing BioBrick Part or Device and enter this information back on the Registry.</h3> <br />
<br />
<li>we entered new DNA as well as new sequences for malE and malE31.</li><br />
<li>we entered characterization data for the CpxR promoter.</li><br />
<br />
<h3>Help another iGEM team by, for example, characterizing a part, debugging a construct, or modeling or simulating their system. </h3><br />
<br />
<li>We tested out a part for Lethbridge. We characterized it for possible misfolding in the cytoplasm. Results can be found here.</li><br />
<br />
<li>We also attended a regional workshop as well as a mock iGEM event with the University of Alberta as well as the University of Lethbridge. Here we helped each their out with our projects by practicing our presentations for each other, giving suggestions, future directions as well as troubleshooting</li><br />
<br />
<li>Finally our team filled out surveys for the following teams:</li><br />
<br />
<br />
<li>This year we chose to approach ethics by making a podscasts covering a few different ethical issues pertaining to synthetic biology. We felt tat this would be a novel way to increase awareness about the field of synthetic biology while having a discussion of important issues. We felt that this would be a much more accessible way for the public to gain a better understanding of what the real fears in synthetic biology is as well as to dispel some of the misleading impressions given by media sources.</li><br />
</ul><br />
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</html></div>Pjwuhttp://2010.igem.org/Team:Calgary/ProjectTeam:Calgary/Project2010-10-27T23:12:25Z<p>Pjwu: </p>
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<h1>Project Descriptions</h1><br />
<br />
<br />
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<li><a href="https://2010.igem.org/Team:Calgary/Project/Transcription">Transcription/Translation Reporter Circuit</a></li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Project/misfolding_overview">Protein Misfolding Reporters</a><br />
<ul><br />
<li><a href="https://2010.igem.org/Team:Calgary/Project/IbpAB">Cytoplasmic Stress Detectors</a></li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Project/CpxP">Periplasmic Stress Detectors</a></li><br />
</ul><br />
</li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Project/Controls">Testing Our System</a></li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Project/Achievements">Achievements</a></li><br />
</ul><br />
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<span id="bodytitle"><h1>The Project</h1></span><br />
<br />
<h2 style="color:#0066CC">Overview</h2><br />
<p>Many synthetic biology projects involve the expression of recombinant proteins in microorganisms such as <i>E. coli</i>. The problems encountered with many synthetic biology projects often involve problems with protein expression. It is often very difficult to recognize the problem and pinpoint where it lies. The goal of the University of Calgary 2010 iGEM team is to build a protein expression "troubleshooting kit". This kit will contain two systems with which target genes can be inserted. In the resulting cell growth, fluorescent protein production will be used to determine whether there is a problem with protein expression as well as indicate where the protein expression is failing.</p><br />
<br />
<br />
<p><br />
Protein expression happens in three steps: the transcription of cell DNA to mRNA, the translation of mRNA into an amino acid sequence, and the folding of that amino acid sequence into a protein.</p><br />
<img src="http://i872.photobucket.com/albums/ab287/iGEMCalgary_2010/CentralDogma.png"></img><br />
<br />
<br /><br />
<br />
<h2 style="color:#0066CC">Sites of Failure</h2><br />
<p><br />
Protein expression can fail at any point along these three steps. Our system uses two circuits to detect at which step possible errors have occured. The first circuit has a fluorescent reporter (GFP) that is produced when DNA is transcribed into mRNA and another (RFP) that is produced when mRNA is translated into a functional protein. When both reporter proteins are expressed in the cell, it indicates both transcription and translation are occurring. The second circuit involves reporter systems that are activated as a result of protein misfolding. Two native stress-activated promoters from <i>E. coli</i> were engineered upstream to fluorescent reporters that will respond to periplasmic and cytoplasmic protein misfolding. If the protein of interest misfolds in either area of the cell, one of the promoters will be activated and the corresponding fluorescence will be observed.<br />
</p><br />
<br />
<h3>Transcription</h3><br />
<table><br />
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</td><br />
<td><br />
<br />
<p>Transcription is the process by which the cell makes messenger RNA (mRNA) from DNA using RNA polymerase. The mRNA sequence is complementary to the DNA sequence that is being transcribed and uses adenine, cytosine, guanine, and uracil nucleotides (uracil replacing thymine). This mRNA sequence is later used as a template for the amino acid sequence.</p><br />
<br />
</td><br />
</tr><br />
</table><br /><br />
<br />
<br />
<h3>Translation</h3><br />
<table><br />
<tr><br />
<td><br />
<img style="width:200px;" src="http://i872.photobucket.com/albums/ab287/iGEMCalgary_2010/DogmaTranslation.png"></img><br />
</td><br />
<td><br />
<p>Translation is the process by which the cell forms a polypeptide chain using the mRNA sequence produced during transcription as a template. A ribosome translates the mRNA in three-nucleotide segments which each code for a diffferent amino acid. This polypeptide chain later folds into a functional protein conformation. </p><br />
</td><br />
</tr><br />
</table><br /><br />
<br />
<h3>Folding</h3><br />
<table><br />
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<td><br />
<img style="width:200px;" src="http://i872.photobucket.com/albums/ab287/iGEMCalgary_2010/DogmaFolding.png"></img><br />
</td><br />
<td><br />
<p>Protein folding is the process by which a polypeptide chain folds into a functional protein. Amino acids in proteins have a property pertaining to water in which some have high afinity with water (hydrophilic) and some only repel water (hydrophobic). Due to the cells typically containing high quantities of water, the amino acid chain folds in order to hide the hydrophobic amino acids from the cell content. To increase the probability of a successful conformation being made, chaperone proteins are often used by the cell.</p><br />
</td><br />
</tr><br />
</table><br /><br />
<br />
<h2 style="color:#0066CC">Our circuit and conventional transcriptional and translational tests</h2><br />
<p>The problem faced by many researchers today is difficulty in locating which step of the protein expression process is malfunctioning. iGEM teams are additionally constrained by a deadline. Our Toolkit has made it possible to pinpoint the exact process in which errors are occurring (transcription, translation, cytoplasmic protein folding or periplasmic protein folding), over the period of a few days.</p><br />
<br />
<h3>Overview of Conventional Methods</h3> <br />
<p>The most commonly used tests for transcription and translation are the Northern and Western Blot respectively. Northern Blot can be used to detect transcription because it relies on the isolation of mRNA. mRNA is typically extracted from a sample using oligo (dT) – cellulose chromatography. Essentially, this method exploits the poly-A tail characteristic of mRNA. In living cells, there are three types of naturally occurring RNA: rRNA, tRNA and mRNA. mRNA has a segment of (~250) Adenine nucleotides on the 3’ end that enhances both the lifetime and translatability of mRNA. The sample can be ran through a column containing oligo dT or deoxyribose Thymine nucleotides. These thymine nucleotides act as a sort of ‘primer’ such as primers in a PCR binding with the Poly-A tail. This ‘double stranded’ mRNA complex can be eluted out with a slight pH fluctuation. The isolated mRNA is then ran on a gel allowing it to segregate by size, and then blotted onto a nylon membrane. A positively charged nylon membrane is often more effective as the negatively charged nucleic acids have a higher affinity for it. The blotted membrane is then transferred to a transfer buffer containing RNA probes complimentary to the RNA sequence of interest. RNA is very unstable and is often degraded by factors such as high temperatures therefore the blotting process needs occur in the presence of formamide which helps lower the probe-RNA interaction temperature. Formamide is highly corrosive to the skin and an extreme teratogen. The membrane can then be examined under UV light, which will allow the RNA-probe complexes to fluoresce. This indicates that the DNA sequence of interest is being translated. </p><br />
<br />
<h3>Discussion of Disadvantages of Conventional Methods</h3><br />
<p>From this procedure, we can see that there are limitations and disadvantages of using Northern Blot. Firstly, it is an extremely selective procedure. Concentrations of buffers, solvents and probes need to be optimal for the reaction to occur. Additionally, primer and probe sequences need to be exact. The entire Northen Blot procedure can take up to 8 days, which can be big issue for iGEM teams with stringent deadlines. Another major limitation is due the unstability of RNA, if RNA samples are even slightly degraded, the quality of the data and the ability to quantitate expression are severely compromised. For example, even a single cleavage in 20% of 4 kb target molecules will decrease the returned signal by 20%. Thus, RNase-free reagents and techniques are essential. The obvious final disadvatage is that Northern requires the use of harmful chemicals that need to be handled carefully.</p><br />
<br />
<h3>Advantages of Our Circuit</h3> <br />
<p>Our transcription/translation circuit has many advantages over the Norther Blot. For one, it does not require the user to handle RNA and therefore it eliminates concerns regarding mRNA degradation. Another advantage would be that it does not require the use of harmful and carcinogenic chemicals, as it is just a simple construction of two DNA sequences that can then be transformed into cells. Our system also eliminates the specificity of primers and probes by eliminating the use of them together.</p><br />
<br />
<p>Our project is broken up into three smaller sections. Click any of the links on the side to learn more about each individual section.</p><br />
</div><br />
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<h1>Project Descriptions</h1><br />
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<ul><br />
<li><a href="https://2010.igem.org/Team:Calgary/Project/Transcription">Transcription/Translation Reporter Circuit</a></li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Project/misfolding_overview">Protein Misfolding Reporters</a><br />
<ul><br />
<li><a href="https://2010.igem.org/Team:Calgary/Project/IbpAB">Cytoplasmic Stress Detectors</a></li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Project/CpxP">Periplasmic Stress Detectors</a></li><br />
</ul><br />
</li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Project/Controls">Testing Our System</a></li><br />
<li><a href="https://2010.igem.org/Team:Calgary/Project/Achievements">Achievements</a></li><br />
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<span id="bodytitle"><h1>The Project</h1></span><br />
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<h2 style="color:#0066CC">Overview</h2><br />
<p>Many synthetic biology projects involve the expression of recombinant proteins in microorganisms such as <i>E. coli</i>. The problems encountered with many synthetic biology projects often involve problems with protein expression. It is often very difficult to recognize the problem and pinpoint where it lies. The goal of the University of Calgary 2010 iGEM team is to build a protein expression "troubleshooting kit". This kit will contain two systems with which target genes can be inserted. In the resulting cell growth, fluorescent protein production will be used to determine whether there is a problem with protein expression as well as indicate where the protein expression is failing.</p><br />
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<br />
<p><br />
Protein expression happens in three steps: the transcription of cell DNA to mRNA, the translation of mRNA into an amino acid sequence, and the folding of that amino acid sequence into a protein.</p><br />
<img src="http://i872.photobucket.com/albums/ab287/iGEMCalgary_2010/CentralDogma.png"></img><br />
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<h2 style="color:#0066CC">Sites of Failure</h2><br />
<p><br />
Protein expression can fail at any point along these three steps. Our system uses two circuits to detect at which step possible errors have occured. The first circuit has a fluorescent reporter (GFP) that is produced when DNA is transcribed into mRNA and another (RFP) that is produced when mRNA is translated into a functional protein. When both reporter proteins are expressed in the cell, it indicates both transcription and translation are occurring. The second circuit involves reporter systems that are activated as a result of protein misfolding. Two native stress-activated promoters from <i>E. coli</i> were engineered upstream to fluorescent reporters that will respond to periplasmic and cytoplasmic protein misfolding. If the protein of interest misfolds in either area of the cell, one of the promoters will be activated and the corresponding fluorescence will be observed.<br />
</p><br />
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<h3>Transcription</h3><br />
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<p>Transcription is the process by which the cell makes messenger RNA (mRNA) from DNA using RNA polymerase. The mRNA sequence is complementary to the DNA sequence that is being transcribed and uses adenine, cytosine, guanine, and uracil nucleotides (uracil replacing thymine). This mRNA sequence is later used as a template for the amino acid sequence.</p><br />
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<h3>Translation</h3><br />
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<p>Translation is the process by which the cell forms a polypeptide chain using the mRNA sequence produced during transcription as a template. A ribosome translates the mRNA in three-nucleotide segments which each code for a diffferent amino acid. This polypeptide chain later folds into a functional protein conformation. </p><br />
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<h3>Folding</h3><br />
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<p>Protein folding is the process by which a polypeptide chain folds into a functional protein. Amino acids in proteins have a property pertaining to water in which some have high afinity with water (hydrophilic) and some only repel water (hydrophobic). Due to the cells typically containing high quantities of water, the amino acid chain folds in order to hide the hydrophobic amino acids from the cell content. To increase the probability of a successful conformation being made, chaperone proteins are often used by the cell.</p><br />
</td><br />
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<h2 style="color:#0066CC">Our circuit and conventional transcriptional and translational tests</h2><br />
<p>The problem faced by many researchers today is difficulty in locating which step of the protein expression process is malfunctioning. iGEM teams are additionally constrained by a deadline. Our Toolkit has made it possible to pinpoint the exact process in which errors are occurring (transcription, translation, cytoplasmic protein folding or periplasmic protein folding), over the period of a few days.</p><br />
<br />
<h3>Overview of Conventional Methods</h3> <br />
<p>The most commonly used tests for transcription and translation are the Northern and Western Blot respectively. Northern Blot can be used to detect transcription because it relies on the isolation of mRNA. mRNA is typically extracted from a sample using oligo (dT) – cellulose chromatography. Essentially, this method exploits the poly-A tail characteristic of mRNA. In living cells, there are three types of naturally occurring RNA: rRNA, tRNA and mRNA. mRNA has a segment of (~250) Adenine nucleotides on the 3’ end that enhances both the lifetime and translatability of mRNA. The sample can be ran through a column containing oligo dT or deoxyribose Thymine nucleotides. These thymine nucleotides act as a sort of ‘primer’ such as primers in a PCR binding with the Poly-A tail. This ‘double stranded’ mRNA complex can be eluted out with a slight pH fluctuation. The isolated mRNA is then ran on a gel allowing it to segregate by size, and then blotted onto a nylon membrane. A positively charged nylon membrane is often more effective as the negatively charged nucleic acids have a higher affinity for it. The blotted membrane is then transferred to a transfer buffer containing RNA probes complimentary to the RNA sequence of interest. RNA is very unstable and is often degraded by factors such as high temperatures therefore the blotting process needs occur in the presence of formamide which helps lower the probe-RNA interaction temperature. Formamide is highly corrosive to the skin and an extreme teratogen. The membrane can then be examined under UV light, which will allow the RNA-probe complexes to fluoresce. This indicates that the DNA sequence of interest is being translated. </p><br />
<br />
<h3>Discussion of Disadvantages of Conventional Methods</h3><br />
<p>From this procedure, we can see that there are limitations and disadvantages of using Northern Blot. Firstly, it is an extremely selective procedure. Concentrations of buffers, solvents and probes need to be optimal for the reaction to occur. Additionally, primer and probe sequences need to be exact. The entire Northen Blot procedure can take up to 8 days, which can be big issue for iGEM teams with stringent deadlines. Another major limitation is due the unstability of RNA, if RNA samples are even slightly degraded, the quality of the data and the ability to quantitate expression are severely compromised. For example, even a single cleavage in 20% of 4 kb target molecules will decrease the returned signal by 20%. Thus, RNase-free reagents and techniques are essential. The obvious final disadvatage is that Northern requires the use of harmful chemicals that need to be handled carefully.</p><br />
<br />
<h3>Advantages of Our Circuit</h3> <br />
<p>Our transcription/translation circuit has many advantages over the Norther Blot. For one, it does not require the user to handle RNA and therefore it eliminates concerns regarding mRNA degradation. Another advantage would be that it does not require the use of harmful and carcinogenic chemicals, as it is just a simple construction of two DNA sequences that can then be transformed into cells. Our system also eliminates the specificity of primers and probes by eliminating the use of them together.</p><br />
<br />
<p>Our project is broken up into three smaller sections. Click any of the links on the side to learn more about each individual section.</p><br />
</div><br />
<br />
</div><br />
<br />
</body><br />
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<p class="tabText" style="padding-left:10px;">What new dangers and unintended consequences will synthetic biology pose to us in the future? iGEM Calgary travels to Defence Research and Development Canada Suffield, a major Canadian Military Research facility that specializes in chemo-biological threats. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community/Suffield">Read more...</a></p><br />
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<p class="tabText" style="padding-left:10px;">The University of Calgary, Alberta, and Lethbridge iGEM teams met in Lethbridge at a conference put on by Alberta Innovates Technology Futures to learn important aspects of iGEM. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community/Conferences#lethbridge">Read more...</a></p><br />
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<p class="tabText" style="padding-left:10px;">Have you ever seen an aggregate protein dance? Look out for iGEM Calgary’s rambunctious mascot “Protein Man” at the Jamboree promoting proper protein expression. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Extras/Protein_Man">Learn more about him...</a></p><br />
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<p class="tabText" style="padding-left:10px;">Team Calgary brings iGEM awareness to the community. The iGEM bake sale was a great success, both in selling cupcakes and educating customers about our team. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community">See what else we've been doing...</a></p><br />
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<p class="tabText" style="padding-left:10px;">Alberta’s very own Jamboree. The three Alberta iGEM teams, the Universities of Alberta, Calgary, and Lethbridge meet to perform a practice project presentation to each other. Experts within their field are also present to give teams challenging questions, and then meet with each team to suggest improvements. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community/Conferences#agem">Read more...</a></p><br />
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<p>Our modelling project consists of two components: a mathematical model done in MATLAB and an animation done in Autodesk <i>Maya</i>. We hope to model the formation of inclusion bodies, which are aggregations of misfolded protein that can occur within cells. Using <i>Maya</i>, we also hope to visually show other students one of the proposed aggregation mechanisms described in the literature.<br />
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<p>Our outreach project included educating highschool students about iGEM. Outreach also entailed blog entries and podcast about synthetic life, iGEM and open source as well as Genetically modified foods. The blog entry, podcasts and high school presentations allowed the iGEM students to spread knowledge about iGEM to the general public and to potential future scientists. <a href="https://2010.igem.org/Team:Calgary/Community">Read more here...</a></p><br />
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<h3>Wetlab</h3><br />
<p>You’re stressing me out! This year, in the wetlab, we have been designing a reporter system to detect problems in protein expression. Our system uses a visual output to allow ppecificy in determing which step in protein expression the problem is ccuring at</p><br />
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<h3>Modelling</h3><br />
<p>Our modeling project has focused on modeling and simultaing the formation of inclusion bdes, aggregates of protein within the cell, exploring the factors that lead to heri ormation</p><br />
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<h3>Community</h3><br />
<p>Our human practices section focused on exploring ethical issues in synthetic biology through an ethics paper as well as a podcast focusing on a few key issues. We also presented our project at a variety of high schools and research symposiums.</p><br />
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<p class="tabText" style="padding-left:10px;">What new dangers and unintended consequences will synthetic biology pose to us in the future? iGEM Calgary travels to Defence Research and Development Canada Suffield, a major Canadian Military Research facility that specializes in chemo-biological threats. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community/Suffield">Read more...</a></p><br />
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<p class="tabText" style="padding-left:10px;">The University of Calgary, Alberta, and Lethbridge iGEM teams met in Lethbridge at a conference put on by Alberta Innovates Technology Futures to learn important aspects of iGEM. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community/Conferences#lethbridge">Read more...</a></p><br />
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<p class="tabText" style="padding-left:10px;">Have you ever seen an aggregate protein dance? Look out for iGEM Calgary’s rambunctious mascot “Protein Man” at the Jamboree promoting proper protein expression. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Extras/Protein_Man">Learn more about him...</a></p><br />
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<p class="tabText" style="padding-left:10px;">Team Calgary brings iGEM awareness to the community. The iGEM bake sale was a great success, both in selling cupcakes and educating customers about our team. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community">See what else we've been doing...</a></p><br />
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<p class="tabText" style="padding-left:10px;">Alberta’s very own Jamboree. The three Alberta iGEM teams, the Universities of Alberta, Calgary, and Lethbridge meet to perform a practice project presentation to each other. Experts within their field are also present to give teams challenging questions, and then meet with each team to suggest improvements. <a class="tabLink" href="https://2010.igem.org/Team:Calgary/Community/Conferences#agem">Read more...</a></p><br />
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<h3>Wetlab</h3><br />
<p>You’re stressing me out! This year, in the wetlab, we have been designing a reporter system to detect problems in protein expression. Our system uses a visual output to allow ppecificy in determing which step in protein expression the problem is ccuring at</p><br />
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<h3>Modelling</h3><br />
<p>Our modeling project has focused on modeling and simultaing the formation of inclusion bdes, aggregates of protein within the cell, exploring the factors that lead to heri ormation</p><br />
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<h3>Community</h3><br />
<p>Our human practices section focused on exploring ethical issues in synthetic biology through an ethics paper as well as a podcast focusing on a few key issues. We also presented our project at a variety of high schools and research symposiums.</p><br />
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<p>Our modelling project consists of two components: a mathematical model done in MATLAB and an animation done in Autodesk <i>Maya</i>. We hope to model the formation of inclusion bodies, which are aggregations of misfolded protein that can occur within cells. Using <i>Maya</i>, we also hope to visually show other students one of the proposed aggregation mechanisms described in the literature.<br />
<a href="https://2010.igem.org/Team:Calgary/Modelling">Read more here...</a></p><br />
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<p>Our outreach project included educating highschool students about iGEM. Outreach also entailed blog entries and podcast about synthetic life, iGEM and open source as well as Genetically modified foods. The blog entry, podcasts and high school presentations allowed the iGEM students to spread knowledge about iGEM to the general public and to potential future scientists. <a href="https://2010.igem.org/Team:Calgary/Community">Read more here...</a></p><br />
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<p>Synthetic biology is a novel, developing science that is introducing new technologies and capabilities to biology. It gives scientists the ability to create novel systems operating in existing organisms, as well as a growing capacity to synthesize fully synthetic life. There are concerns developing however, that this type of research could lead to either the purposeful, or inadvertent creation of harmful organisms or bioweapons. Increased affordability of synthesizing gene sequences, as well as the increased accessibility of synthetic biology are both issues that our increasing these fears. Therefore our team felt that we should gain an expert’s perspective on the danger’s of synthetic biology.</p><br />
<p>Our iGEM team presented the concept of biobricks, the registry of standardized parts, and the iGEM competition to researchers at DRDC Suffield. Defence Research and Development Suffield, or DRDC Suffield, is a Canadian Military Research facility located in southern Alberta. A major focus of DRDC Suffield is addressing chemical and biological threats. It is also the host of the Counter Terrorism Technology Centre, a key component of national defence that uses unique laboratories and testing facilities to help better prepare Canada from chemical, biological, radiological, nuclear, and explosive (CBRNE) threats.</p><br />
<p>Following our presentation we engaged in a roundtable discussion with researchers and experts. As with most scientists, DRDC Suffield scientists acknowledged that synthetic biology, including iGEM projects, have the dual-use capability. This refers to biological research with legitimate scientific purpose, but also has the potential for misuse that would threaten public health, and/or national security. Another danger discussed was the potential to synthesize harmful pathogens from digital genomes, such as smallpox. Although this would be catastrophic if achieved, it was not interpreted as a priority to our security because of the difficulty of “rougue” scientists achieving such a momentous task. A more “real” application of synthetic biology causing dangers to our security was the potential to synthesize biotoxins, or other poisons that could be derived from DNA sequences.</p><br />
<p>Other discussions revolved around the “open source” nature of iGEM. Although the registry was met with a positive response from experts, they were also able to see the concerns with making synthetic biology easier and more accessible. We discussed the dangers of making it easy for amateurs to be dealing with this technology. Some of the greatest potentials for dangers that DRDC scientists said would arise from synthetic biology were the introduction of antibiotic resistance to harmful bacteria, and then being released in to the public.</p><br />
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