http://2009.igem.org/wiki/index.php?title=Special:Contributions&feed=atom&limit=20&target=Ahatch&year=&month=2009.igem.org - User contributions [en]2024-03-28T21:42:10ZFrom 2009.igem.orgMediaWiki 1.16.5http://2009.igem.org/File:USU_NMR_spectra.pngFile:USU NMR spectra.png2010-10-27T06:01:39Z<p>Ahatch: </p>
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<div></div>Ahatchhttp://2009.igem.org/File:USU_BBa_K390501_Part.pngFile:USU BBa K390501 Part.png2010-10-27T05:55:25Z<p>Ahatch: </p>
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<div></div>Ahatchhttp://2009.igem.org/Team:Utah_State/ETHICSTeam:Utah State/ETHICS2009-10-22T03:41:52Z<p>Ahatch: </p>
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<td id="nav"><a href="https://2009.igem.org/Team:Utah_State"><font size = 4>HOME</font></a></td><br />
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<td id="nav"><a href="https://2009.igem.org/Team:Utah_State/Team"><font size = 4>ABOUT US</font></a></td><br />
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<td id="nav"><a href="https://2009.igem.org/Team:Utah_State/Project"><font size = 4>PROJECT</font></a></td><br />
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<td id="nav"><a href="https://2009.igem.org/Team:Utah_State/Parts"><font size = 4>BIOBRICKS</font></a></td><br />
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<td id="nav"><a href="https://2009.igem.org/Team:Utah_State/Modeling"><font size = 4>MODELING</font></a></td><br />
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<td id="nav"><a href="https://2009.igem.org/Team:Utah_State/Notebook"><font size = 4>NOTEBOOK</font></a></td><br />
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<td width="172" id="ana"><span class="currentPage"><font size = 4>ETHICS</font></span><br />
<a href="#intro">Introduction</a><br /><br />
<a href="#synbio">Synthetic Biology</a><br /><br />
<a href="#team">Team Education</a><br /><br />
<a href="#public">Public Education</a><br/><br />
<a href="#conclusions">Conclusions</a><br/><br />
<a href="#references">Referencess</a><br />
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<b>Synthetic Biology:<br />
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<font size="5" face="Century Gothic, Arial, San Serif" color =green>Education in an Emerging Field</font><br><br />
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The iGEM competition is devoted to the advancement of synthetic biology, specifically in standardized parts-based research. It welcomes participants from institutions of higher education from around the world. Just as important as contributing to the understanding of molecular biology based engineering is contributing to a framework which allows applications of this knowledge to be implemented in a manner that serves society. As we address human practices on our wiki we give a brief overview of synthetic biology, list areas in human practice commonly recognized as needing address, pose questions for discussion associated with those areas, and outline two ways the iGEM community can take fundamental actions. These actions involve a broader education of iGEM participants, and the dissemination of knowledge in our educational and public communities.<br />
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Synthetic Biology and Human Practices<br />
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Synthetic biology has been hailed by some as the next technological revolution. It has been said that standard biological parts “will be for the 21st century what screws and bolts were to the 19th, or transistors and resistors to the 20th (Endy quoted in Parens, Johnston, and Moses, 2009).” Members in the field have visions of using synthetic biology to develop new applications in the areas of environment, health, and industry, as well as learning to understand the fundamental components of life itself. Significant progress has already been made evidenced by the ever increasing size of the registry of parts with applications in the areas listed above. With time other applications will likely arise.<br />
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<p class="class">As with any new technology, there exist potential benefits and potential areas of concern. There must be a balance between the desire to bring innovative and beneficial products to market and prevent potential harm to public health and the environment (Rodemeyer, 2009). Following are some of the issues that are commonly indicated as areas that must be addressed. </p><br />
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<li>Biosafety: How can research personnel, the environment, and society be protected from intended or accidental exposure to developed products? </li><br />
<li>Biosecurity: What measures should be taken to ensure that products of synthetic biology are not used in a malevolent manner?</li><br />
<li>Property Rights: What is the best way to share information to ensure that the field progresses rapidly, that opportunities to contribute are distributed fairly, and that contributors to the field are fairly compensated? Is it ethical to have a patent on life?</li><br />
<li>Governance: What is the best way to implement policy that governs the field of synthetic biology? Is there a need for outside oversight or is self-governance sufficient? What challenges would arise if governing policy varied from country to country?</li><br />
<li>Mankind and Nature: What roles should humans play in manipulating nature? Who should decide to what extent manipulation of life is acceptable?</li><br />
<li>Public Perception and Involvement: Public involvement often is a deciding factor in funding and regulation. How should synthetic biology disseminate knowledge to the public and hear and address public concerns?</li><br />
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Efforts have been made to foster discussion about these areas and various measures to address them have been suggested (Maurer et al., 2006; Garfinkel et al., 2007). As synthetic biology is still in its youth, actions taken now and continued efforts to address these concerns in the future will enable the field to progress with minimal hindrance. “Procrastination bears a risk. A productive dialogue may become more difficult as synthetic biology evolves and stakeholders become divided in their opinions about benefits and risks (Rejeski, 2009a).” As the iGEM jamboree is the largest gathering related to synthetic biology in the world, we propose that initiative taken here will have a significant impact on the world. The “current and future leaders of the field” are participating in these gatherings (2009.igem.org/About). </p><br />
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iGEM and Education<br />
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<p class = "class2"><b>Broader Education of iGEM Participants </b></p><br />
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Establishing governing policy for synthetic biology is complex and difficult to address (Rodemeyer, 2009). Problems can arise from limited jurisdiction of a governing body (Marchant & Pope, 2009) or the expense and cumbersome nature of monitoring activity (Rodemeyer, 2009) among other difficulties. Whatever policy is decided upon, the ultimate difficulty comes in enforcing the policy.<br />
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In preparation for the Synthetic Biology 2.0 conference in 2006, Laurie Zoloth addressing “ethics training” stated:<br />
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What is needed is a lab culture which is strong enough and decent enough to teach and model impeccably honest moral science citizenship in the as yet small academic field of synthetic biology… Ethics education cannot be done with websites or software—there is a need for individual moral agency, and for this task, serious questions about the complexities of good and evil, difficult moral choices, the nature of the love of country, the nature of obligation to the other and the limits of the search for knowledge, all must be read about and studied with the same seriousness that young scientists give to understanding siRNA or nanobiobarcodes. </p><br><br />
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<p class ="class">As the current and future leaders of the field of synthetic biology participate in these conferences, time before the conference and during the conference should be devoted to establishing appropriate human practices and ensuring that these practices are taught and implemented. The nature of iGEM and its multidisciplinary approach to a successful team is conducive to researching and establishing appropriate human practices. In order to qualify for a gold medal, teams are encouraged to address appropriate human practices as part of their project. Due to the difficult nature of the questions concerning human practices, we propose more could be done by iGEM participants. Possible additional measures include: </p><br><br />
<ul class="circle"><br />
<li>A new track focused solely on researching proper human practices, performing risk assessment, or researching public perception.</li><br />
<li>A portion of the conference set aside to relaying current best practices, or bringing before the community options for current best practices for discussion and acceptance.</li><br />
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<p class ="class">As ensuring that proper policy is implemented and followed is important for the development of this or any field, these increased measures could help to ensure that policy becomes international and observed. Again, iGEM participants largely represent the future of the field. As policy is accepted within the iGEM community, enforcing the policy is simplified because it would be regularly taught and more widely accepted.</p><br />
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Public Education<br />
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<p class = "class">Hart Researchers learned in a U.S. survey in 2009 that about 80% of the population had heard little or nothing about synthetic biology. Given the young age of the field, and based on a report about media coverage in the U.S. and Europe (Pauwels & Ifrim, 2008) we assume that there has been similar public exposure around the world. Some fields of study with great potential have been hindered as a result of not having adequate democratic involvement with the public for example genetically modified foods (Parens et al., 2009) or stem cell research (Marchant & Pope, 2009). The Hart researchers also found that there is a broad consensus that “more should be done to inform the American public.” 90% of adults surveyed agreed with that statement and 73 % “strongly agreed.”</p> <br />
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<p class = "class"> In an address to the National Academy of Sciences, David Rejeski (2009b) suggested that there is a lack of good science reporters. Media, for various reasons, is prone to embellish and to present information that catches attention, but is not necessarily accurate. This leads to inaccurate initial assessments of synthetic biology. Once an initial assessment has been made, the feelings rarely change, but rather become stronger (Kahan et al., 2009). Addressing public perception, Tucker and Zilinskas (2006) wrote: </p><br />
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<p class="margin">Although it is often difficult to persuade scientists to leave the laboratory for even a few hours to participate in a public discussion of their work and its implications for society, such efforts should be encouraged because they generate good will and may help to prevent a future political backlash that could cripple the emerging field of synthetic biology. </p><br />
<br><br />
<p class = "class">With more than 100 teams participating in iGEM coming from around the world, we represent a tremendous asset in disseminating accurate knowledge to the public. We propose two measures that could be taken by iGEM teams to increase public education. </p><br />
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<ul class="circle"><br />
<li>In order to qualify for a gold medal a team should make an effort to have accurately released in a school newspaper or website, an article about synthetic biology and the school’s involvement with iGEM.</li><br />
<li>Encourage iGEM teams to host or give a presentation addressing synthetic biology open to the school and public. The presentation should also be open to accepting questions and addressing concerns.</li></ul><br />
<br><br />
<p class = "class">Efforts to honestly present information to the public will lead to public trust and a market that welcomes innovations from the field. Interaction with the public in this fashion will also help to establish guidelines as to what research is considered acceptable and will aid in establishing regulatory frameworks. </p><br />
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Conclusions<br />
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<p class = "class">The teams participating in iGEM can play an invaluable role in establishing policy regarding human practices and in acting as a liaison between the community of synthetic biology and the public. The multidisciplinary aspect of iGEM is conducive to progress in these two areas. With a concerted effort we can help ensure that synthetic biology continues to progress and reach its potential. </p><br />
<p class = "class">Our team has taken specific measures to follow our suggested proposals. In the education of our team, we discussed the potential benefits of a standard secretion system but also discussed the potential of our designed secretion pathways to be used in a malevolent manner. As a team we acknowledge the importance of high moral accountability and commitment to safety and security. Additionally, in an effort to foster the sharing of information in our community, upon completion of the jamboree we will submit an article to be released in our school newspaper and in our College of Engineering website. This winter we are also hosting a lecture by Drew Endy addressing synthetic biology which will be open to the public. We hope to act as ambassadors to foster support and excitement in our own community.</p><br />
<p class = "class">Finally, our biosafety committee on campus has approved our project and considered possible safety risks to our team members and the environment. It has been determined, that in our stage of research, basic laboratory precautions are sufficient to address our team safety including; wearing gloves, wearing eyeware, using a safety hood, and properly disposing of biowastes. The biobrick components we have made this year are pose no known harm to human or animal safety. Potentially, a secretion pathway could be used to secrete toxic proteins. The secretion products that we have been intererested in are not known to be harmful. </p><br />
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References<br />
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<ul class="circle"><br />
<li>Garfinkel M, Endy D, Epstein GL, Friedman RM (2007) Synthetic genomics – options for governance. http://www.synbioproject.org/topics/synbio101/bibliography/governance </li><br />
<li>Hart Research (2009) Nanotechnology, synthetic biology, & public opinion: What does the public think?. http://www.synbioproject.org/events/archive/6380/ </li><br />
<li>Kahan DM, Braman D, Mandel GN (2009, Feb. 20) Risk and culture: Is synthetic biology different? Harvard Law School Program on Risk Regulation Research Paper No. 09-2; Yale Law School, Public Law Working Paper No. 190. http://ssrn.com/abstract=1347165 </li><br />
<li>Marchant GE, Pope LL (2009) The problems with forbidding science. Sci Eng Ethics 15:375-394 </li><br />
<li>Maurer SM, et al.(2006) From understanding to action: Community-based options for improving safety and security in synthetic biology. http://gspp.berkeley.edu/iths/UC%20White%20Paper.pdf </li><br />
<li>Parens E, et al.(2009) Ethical issues in synthetic biology: An overview of the debates. http://www.synbioproject.org/library/publications/archive/synbio3/ </li><br />
<li>Pauwels E, Ifrim I (2008) Trends in American and European Press Coverage of Synthetic Biology. http://www.synbioproject.org/library/publications/archive/why_scientists_should_care/ </li><br />
<li>Rejeski D (2009a) Foreword-New life old bottles: Regulating first-generation products of synthetic biology. http://www.synbioproject.org/library/publications/archive/synbio2/ </li><br />
<li>Rejeski D (2009b) Public perceptions on the technological frontier. Given at National Academy of Sciences July 10, 2009. Audio Retrieved from http://www.synbioproject.org/process/assets/files/6372/_draft/rejeski.ppt#268,1, </li><br />
<li>Rodemeyer M (2009) New life old bottles: Regulating first-generation products of synthetic biology. http://www.synbioproject.org/library/publications/archive/synbio2/ </li><br />
<li>Tucker JB, Zilinskas RA (2006) The promise and perils of synthetic biology. The New Atlantis 12:25-45. </li><br />
<li>Zoloth L (2006) Ethical issues in synthetic biology: Security and regulation of experiments of concern. http://gspp.berkeley.edu/iths/UC%20White%20Paper.pdf </li><br />
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</head></div>Ahatchhttp://2009.igem.org/Team:Utah_State/ETHICSTeam:Utah State/ETHICS2009-10-22T03:40:28Z<p>Ahatch: </p>
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<td width="172" id="ana"><span class="currentPage"><font size = 4>ETHICS</font></span><br />
<a href="#intro">Introduction</a><br /><br />
<a href="#synbio">Synthetic Biology</a><br /><br />
<a href="#team">Team Education</a><br /><br />
<a href="#public">Public Education</a><br/><br />
<a href="#conclusions">Conclusions</a><br/><br />
<a href="#references">Referencess</a><br />
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<b>Synthetic Biology:<br />
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<font size="5" face="Century Gothic, Arial, San Serif" color =green>Education in an Emerging Field</font><br><br />
<HR><br />
<p class="class"> <br />
The iGEM competition is devoted to the advancement of synthetic biology, specifically in standardized parts-based research. It welcomes participants from institutions of higher education from around the world. Just as important as contributing to the understanding of molecular biology based engineering is contributing to a framework which allows applications of this knowledge to be implemented in a manner that serves society. As we address human practices on our wiki we give a brief overview of synthetic biology, list areas in human practice commonly recognized as needing address, pose questions for discussion associated with those areas, and outline two ways the iGEM community can take fundamental actions. These actions involve a broader education of iGEM participants, and the dissemination of knowledge in our educational and public communities.<br />
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Synthetic Biology and Human Practices<br />
</font></b></i> <br />
<p class="class"><br />
Synthetic biology has been hailed by some as the next technological revolution. It has been said that standard biological parts “will be for the 21st century what screws and bolts were to the 19th, or transistors and resistors to the 20th (Endy quoted in Parens, Johnston, and Moses, 2009).” Members in the field have visions of using synthetic biology to develop new applications in the areas of environment, health, and industry, as well as learning to understand the fundamental components of life itself. Significant progress has already been made evidenced by the ever increasing size of the registry of parts with applications in the areas listed above. With time other applications will likely arise.<br />
<br><br />
<p class="class">As with any new technology, there exist potential benefits and potential areas of concern. There must be a balance between the desire to bring innovative and beneficial products to market and prevent potential harm to public health and the environment (Rodemeyer, 2009). Following are some of the issues that are commonly indicated as areas that must be addressed. </p><br />
</p><br><br />
<ul class="circle"><br />
<li>Biosafety: How can research personnel, the environment, and society be protected from intended or accidental exposure to developed products? </li><br />
<li>Biosecurity: What measures should be taken to ensure that products of synthetic biology are not used in a malevolent manner?</li><br />
<li>Property Rights: What is the best way to share information to ensure that the field progresses rapidly, that opportunities to contribute are distributed fairly, and that contributors to the field are fairly compensated? Is it ethical to have a patent on life?</li><br />
<li>Governance: What is the best way to implement policy that governs the field of synthetic biology? Is there a need for outside oversight or is self-governance sufficient? What challenges would arise if governing policy varied from country to country?</li><br />
<li>Mankind and Nature: What roles should humans play in manipulating nature? Who should decide to what extent manipulation of life is acceptable?</li><br />
<li>Public Perception and Involvement: Public involvement often is a deciding factor in funding and regulation. How should synthetic biology disseminate knowledge to the public and hear and address public concerns?</li><br />
</ul></font><br><br />
<p class="class"><br />
Efforts have been made to foster discussion about these areas and various measures to address them have been suggested (Maurer et al., 2006; Garfinkel et al., 2007). As synthetic biology is still in its youth, actions taken now and continued efforts to address these concerns in the future will enable the field to progress with minimal hindrance. “Procrastination bears a risk. A productive dialogue may become more difficult as synthetic biology evolves and stakeholders become divided in their opinions about benefits and risks (Rejeski, 2009a).” As the iGEM jamboree is the largest gathering related to synthetic biology in the world, we propose that initiative taken here will have a significant impact on the world. The “current and future leaders of the field” are participating in these gatherings (2009.igem.org/About). </p><br />
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iGEM and Education<br />
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<p class = "class2"><b>Broader Education of iGEM Participants </b></p><br />
<p class="class"><br />
Establishing governing policy for synthetic biology is complex and difficult to address (Rodemeyer, 2009). Problems can arise from limited jurisdiction of a governing body (Marchant & Pope, 2009) or the expense and cumbersome nature of monitoring activity (Rodemeyer, 2009) among other difficulties. Whatever policy is decided upon, the ultimate difficulty comes in enforcing the policy.<br />
</p><br />
<p class="class"><br />
In preparation for the Synthetic Biology 2.0 conference in 2006, Laurie Zoloth addressing “ethics training” stated:<br />
</p><br><br />
<p class="margin"><br />
What is needed is a lab culture which is strong enough and decent enough to teach and model impeccably honest moral science citizenship in the as yet small academic field of synthetic biology… Ethics education cannot be done with websites or software—there is a need for individual moral agency, and for this task, serious questions about the complexities of good and evil, difficult moral choices, the nature of the love of country, the nature of obligation to the other and the limits of the search for knowledge, all must be read about and studied with the same seriousness that young scientists give to understanding siRNA or nanobiobarcodes. </p><br><br />
<br />
<p class ="class">As the current and future leaders of the field of synthetic biology participate in these conferences, time before the conference and during the conference should be devoted to establishing appropriate human practices and ensuring that these practices are taught and implemented. The nature of iGEM and its multidisciplinary approach to a successful team is conducive to researching and establishing appropriate human practices. In order to qualify for a gold medal, teams are encouraged to address appropriate human practices as part of their project. Due to the difficult nature of the questions concerning human practices, we propose more could be done by iGEM participants. Possible additional measures include: </p><br><br />
<ul class="circle"><br />
<li>A new track focused solely on researching proper human practices, performing risk assessment, or researching public perception.</li><br />
<li>A portion of the conference set aside to relaying current best practices, or bringing before the community options for current best practices for discussion and acceptance.</li><br />
</ul><br><br />
<br />
<p class ="class">As ensuring that proper policy is implemented and followed is important for the development of this or any field, these increased measures could help to ensure that policy becomes international and observed. Again, iGEM participants largely represent the future of the field. As policy is accepted within the iGEM community, enforcing the policy is simplified because it would be regularly taught and more widely accepted.</p><br />
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Public Education<br />
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<p class = "class">Hart Researchers learned in a U.S. survey in 2009 that about 80% of the population had heard little or nothing about synthetic biology. Given the young age of the field, and based on a report about media coverage in the U.S. and Europe (Pauwels & Ifrim, 2008) we assume that there has been similar public exposure around the world. Some fields of study with great potential have been hindered as a result of not having adequate democratic involvement with the public for example genetically modified foods (Parens et al., 2009) or stem cell research (Marchant & Pope, 2009). The Hart researchers also found that there is a broad consensus that “more should be done to inform the American public.” 90% of adults surveyed agreed with that statement and 73 % “strongly agreed.”</p> <br />
<br />
<p class = "class"> In an address to the National Academy of Sciences, David Rejeski (2009b) suggested that there is a lack of good science reporters. Media, for various reasons, is prone to embellish and to present information that catches attention, but is not necessarily accurate. This leads to inaccurate initial assessments of synthetic biology. Once an initial assessment has been made, the feelings rarely change, but rather become stronger (Kahan et al., 2009). Addressing public perception, Tucker and Zilinskas (2006) wrote: </p><br />
<br><br />
<p class="margin">Although it is often difficult to persuade scientists to leave the laboratory for even a few hours to participate in a public discussion of their work and its implications for society, such efforts should be encouraged because they generate good will and may help to prevent a future political backlash that could cripple the emerging field of synthetic biology. </p><br />
<br><br />
<p class = "class">With more than 100 teams participating in iGEM coming from around the world, we represent a tremendous asset in disseminating accurate knowledge to the public. We propose two measures that could be taken by iGEM teams to increase public education. </p><br />
<br><br />
<ul class="circle"><br />
<li>In order to qualify for a gold medal a team should make an effort to have accurately released in a school newspaper or website, an article about synthetic biology and the school’s involvement with iGEM.</li><br />
<li>Encourage iGEM teams to host or give a presentation addressing synthetic biology open to the school and public. The presentation should also be open to accepting questions and addressing concerns.</li></ul><br />
<br><br />
<p class = "class">Efforts to honestly present information to the public will lead to public trust and a market that welcomes innovations from the field. Interaction with the public in this fashion will also help to establish guidelines as to what research is considered acceptable and will aid in establishing regulatory frameworks. </p><br />
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Conclusions<br />
</font></b></i> <br />
<p class = "class">The teams participating in iGEM can play an invaluable role in establishing policy regarding human practices and in acting as a liaison between the community of synthetic biology and the public. The multidisciplinary aspect of iGEM is conducive to progress in these two areas. With a concerted effort we can help ensure that synthetic biology continues to progress and reach its potential. </p><br />
<p class = "class">Our team has taken specific measures to follow our suggested proposals. In the education of our team, we discussed the potential benefits of a standard secretion system but also discussed the potential of our designed secretion pathways to be used in a malevolent manner. As a team we acknowledge the importance of high moral accountability and commitment to safety and security. Additionally, in an effort to foster the sharing of information in our community, upon completion of the jamboree we will submit an article to be released in our school newspaper and in our College of Engineering website. This winter we are also hosting a lecture by Drew Endy addressing synthetic biology which will be open to the public. We hope to act as ambassadors to foster support and excitement in our own community.</p><br />
<p class = "class">Finally, our biosafety committee on campus has approved our project and considered possible safety risks to our team members and the environment. It has been determined, that in our stage of research, basic laboratory precautions are sufficient to address our team safety including, wearing gloves, wearing eyeware, using a safety hood, and properly disposing of biowastes. The biobrick components we have made this year are pose no known harm to human or animal safety. Potentially, a secretion pathway could be used to secrete toxic proteins. The secretion products that we have been interersted in are not known to be harmful. </p><br />
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References<br />
</font></b></i> <hr><br />
<br />
<ul class="circle"><br />
<li>Garfinkel M, Endy D, Epstein GL, Friedman RM (2007) Synthetic genomics – options for governance. http://www.synbioproject.org/topics/synbio101/bibliography/governance </li><br />
<li>Hart Research (2009) Nanotechnology, synthetic biology, & public opinion: What does the public think?. http://www.synbioproject.org/events/archive/6380/ </li><br />
<li>Kahan DM, Braman D, Mandel GN (2009, Feb. 20) Risk and culture: Is synthetic biology different? Harvard Law School Program on Risk Regulation Research Paper No. 09-2; Yale Law School, Public Law Working Paper No. 190. http://ssrn.com/abstract=1347165 </li><br />
<li>Marchant GE, Pope LL (2009) The problems with forbidding science. Sci Eng Ethics 15:375-394 </li><br />
<li>Maurer SM, et al.(2006) From understanding to action: Community-based options for improving safety and security in synthetic biology. http://gspp.berkeley.edu/iths/UC%20White%20Paper.pdf </li><br />
<li>Parens E, et al.(2009) Ethical issues in synthetic biology: An overview of the debates. http://www.synbioproject.org/library/publications/archive/synbio3/ </li><br />
<li>Pauwels E, Ifrim I (2008) Trends in American and European Press Coverage of Synthetic Biology. http://www.synbioproject.org/library/publications/archive/why_scientists_should_care/ </li><br />
<li>Rejeski D (2009a) Foreword-New life old bottles: Regulating first-generation products of synthetic biology. http://www.synbioproject.org/library/publications/archive/synbio2/ </li><br />
<li>Rejeski D (2009b) Public perceptions on the technological frontier. Given at National Academy of Sciences July 10, 2009. Audio Retrieved from http://www.synbioproject.org/process/assets/files/6372/_draft/rejeski.ppt#268,1, </li><br />
<li>Rodemeyer M (2009) New life old bottles: Regulating first-generation products of synthetic biology. http://www.synbioproject.org/library/publications/archive/synbio2/ </li><br />
<li>Tucker JB, Zilinskas RA (2006) The promise and perils of synthetic biology. The New Atlantis 12:25-45. </li><br />
<li>Zoloth L (2006) Ethical issues in synthetic biology: Security and regulation of experiments of concern. http://gspp.berkeley.edu/iths/UC%20White%20Paper.pdf </li><br />
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</head></div>Ahatchhttp://2009.igem.org/Team:Utah_State/ETHICSTeam:Utah State/ETHICS2009-10-22T03:21:58Z<p>Ahatch: </p>
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<td id="nav"><a href="https://2009.igem.org/Team:Utah_State"><font size = 4>HOME</font></a></td><br />
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<td id="nav"><a href="https://2009.igem.org/Team:Utah_State/Team"><font size = 4>ABOUT US</font></a></td><br />
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<td id="nav"><a href="https://2009.igem.org/Team:Utah_State/Project"><font size = 4>PROJECT</font></a></td><br />
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<td width="172" id="ana"><span class="currentPage"><font size = 4>ETHICS</font></span><br />
<a href="#intro">Introduction</a><br /><br />
<a href="#synbio">Synthetic Biology</a><br /><br />
<a href="#team">Team Education</a><br /><br />
<a href="#public">Public Education</a><br/><br />
<a href="#conclusions">Conclusions</a><br/><br />
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<b>Synthetic Biology:<br />
</b></font><br />
<font size="5" face="Century Gothic, Arial, San Serif" color =green>Education in an Emerging Field</font><br><br />
<HR><br />
<p class="class"> <br />
The iGEM competition is devoted to the advancement of synthetic biology, specifically in standardized parts-based research. It welcomes participants from institutions of higher education from around the world. Just as important as contributing to the understanding of molecular biology based engineering is contributing to a framework which allows applications of this knowledge to be implemented in a manner that serves society. As we address human practices on our wiki we give a brief overview of synthetic biology, list areas in human practice commonly recognized as needing address, pose questions for discussion associated with those areas, and outline two ways the iGEM community can take fundamental actions. These actions involve a broader education of iGEM participants, and the dissemination of knowledge in our educational and public communities.<br />
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Synthetic Biology and Human Practices<br />
</font></b></i> <br />
<p class="class"><br />
Synthetic biology has been hailed by some as the next technological revolution. It has been said that standard biological parts “will be for the 21st century what screws and bolts were to the 19th, or transistors and resistors to the 20th (Endy quoted in Parens, Johnston, and Moses, 2009).” Members in the field have visions of using synthetic biology to develop new applications in the areas of environment, health, and industry, as well as learning to understand the fundamental components of life itself. Significant progress has already been made evidenced by the ever increasing size of the registry of parts with applications in the areas listed above. With time other applications will likely arise.<br />
<br><br />
<p class="class">As with any new technology, there exist potential benefits and potential areas of concern. There must be a balance between the desire to bring innovative and beneficial products to market and prevent potential harm to public health and the environment (Rodemeyer, 2009). Following are some of the issues that are commonly indicated as areas that must be addressed. </p><br />
</p><br><br />
<ul class="circle"><br />
<li>Biosafety: How can research personnel, the environment, and society be protected from intended or accidental exposure to developed products? </li><br />
<li>Biosecurity: What measures should be taken to ensure that products of synthetic biology are not used in a malevolent manner?</li><br />
<li>Property Rights: What is the best way to share information to ensure that the field progresses rapidly, that opportunities to contribute are distributed fairly, and that contributors to the field are fairly compensated? Is it ethical to have a patent on life?</li><br />
<li>Governance: What is the best way to implement policy that governs the field of synthetic biology? Is there a need for outside oversight or is self-governance sufficient? What challenges would arise if governing policy varied from country to country?</li><br />
<li>Mankind and Nature: What roles should humans play in manipulating nature? Who should decide to what extent manipulation of life is acceptable?</li><br />
<li>Public Perception and Involvement: Public involvement often is a deciding factor in funding and regulation. How should synthetic biology disseminate knowledge to the public and hear and address public concerns?</li><br />
</ul></font><br><br />
<p class="class"><br />
Efforts have been made to foster discussion about these areas and various measures to address them have been suggested (Maurer et al., 2006; Garfinkel et al., 2007). As synthetic biology is still in its youth, actions taken now and continued efforts to address these concerns in the future will enable the field to progress with minimal hindrance. “Procrastination bears a risk. A productive dialogue may become more difficult as synthetic biology evolves and stakeholders become divided in their opinions about benefits and risks (Rejeski, 2009a).” As the iGEM jamboree is the largest gathering related to synthetic biology in the world, we propose that initiative taken here will have a significant impact on the world. The “current and future leaders of the field” are participating in these gatherings (2009.igem.org/About). </p><br />
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iGEM and Education<br />
</font></b></i> <br />
<p class = "class2"><b>Broader Education of iGEM Participants </b></p><br />
<p class="class"><br />
Establishing governing policy for synthetic biology is complex and difficult to address (Rodemeyer, 2009). Problems can arise from limited jurisdiction of a governing body (Marchant & Pope, 2009) or the expense and cumbersome nature of monitoring activity (Rodemeyer, 2009) among other difficulties. Whatever policy is decided upon, the ultimate difficulty comes in enforcing the policy.<br />
</p><br />
<p class="class"><br />
In preparation for the Synthetic Biology 2.0 conference in 2006, Laurie Zoloth addressing “ethics training” stated:<br />
</p><br><br />
<p class="margin"><br />
What is needed is a lab culture which is strong enough and decent enough to teach and model impeccably honest moral science citizenship in the as yet small academic field of synthetic biology… Ethics education cannot be done with websites or software—there is a need for individual moral agency, and for this task, serious questions about the complexities of good and evil, difficult moral choices, the nature of the love of country, the nature of obligation to the other and the limits of the search for knowledge, all must be read about and studied with the same seriousness that young scientists give to understanding siRNA or nanobiobarcodes. </p><br><br />
<br />
<p class ="class">As the current and future leaders of the field of synthetic biology participate in these conferences, time before the conference and during the conference should be devoted to establishing appropriate human practices and ensuring that these practices are taught and implemented. The nature of iGEM and its multidisciplinary approach to a successful team is conducive to researching and establishing appropriate human practices. In order to qualify for a gold medal, teams are encouraged to address appropriate human practices as part of their project. Due to the difficult nature of the questions concerning human practices, we propose more could be done by iGEM participants. Possible additional measures include: </p><br><br />
<ul class="circle"><br />
<li>A new track focused solely on researching proper human practices, performing risk assessment, or researching public perception.</li><br />
<li>A portion of the conference set aside to relaying current best practices, or bringing before the community options for current best practices for discussion and acceptance.</li><br />
</ul><br><br />
<br />
<p class ="class">As ensuring that proper policy is implemented and followed is important for the development of this or any field, these increased measures could help to ensure that policy becomes international and observed. Again, iGEM participants largely represent the future of the field. As policy is accepted within the iGEM community, enforcing the policy is simplified because it would be regularly taught and more widely accepted.</p><br />
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Public Education<br />
</b></p><br />
<p class = "class">Hart Researchers learned in a U.S. survey in 2009 that about 80% of the population had heard little or nothing about synthetic biology. Given the young age of the field, and based on a report about media coverage in the U.S. and Europe (Pauwels & Ifrim, 2008) we assume that there has been similar public exposure around the world. Some fields of study with great potential have been hindered as a result of not having adequate democratic involvement with the public for example genetically modified foods (Parens et al., 2009) or stem cell research (Marchant & Pope, 2009). The Hart researchers also found that there is a broad consensus that “more should be done to inform the American public.” 90% of adults surveyed agreed with that statement and 73 % “strongly agreed.”</p> <br />
<br />
<p class = "class"> In an address to the National Academy of Sciences, David Rejeski (2009b) suggested that there is a lack of good science reporters. Media, for various reasons, is prone to embellish and to present information that catches attention, but is not necessarily accurate. This leads to inaccurate initial assessments of synthetic biology. Once an initial assessment has been made, the feelings rarely change, but rather become stronger (Kahan et al., 2009). Addressing public perception, Tucker and Zilinskas (2006) wrote: </p><br />
<br><br />
<p class="margin">Although it is often difficult to persuade scientists to leave the laboratory for even a few hours to participate in a public discussion of their work and its implications for society, such efforts should be encouraged because they generate good will and may help to prevent a future political backlash that could cripple the emerging field of synthetic biology. </p><br />
<br><br />
<p class = "class">With more than 100 teams participating in iGEM coming from around the world, we represent a tremendous asset in disseminating accurate knowledge to the public. We propose two measures that could be taken by iGEM teams to increase public education. </p><br />
<br><br />
<ul class="circle"><br />
<li>In order to qualify for a gold medal a team should make an effort to have accurately released in a school newspaper or website, an article about synthetic biology and the school’s involvement with iGEM.</li><br />
<li>Encourage iGEM teams to host or give a presentation addressing synthetic biology open to the school and public. The presentation should also be open to accepting questions and addressing concerns.</li></ul><br />
<br><br />
<p class = "class">Efforts to honestly present information to the public will lead to public trust and a market that welcomes innovations from the field. Interaction with the public in this fashion will also help to establish guidelines as to what research is considered acceptable and will aid in establishing regulatory frameworks. </p><br />
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Conclusions<br />
</font></b></i> <br />
<p class = "class">The teams participating in iGEM can play an invaluable role in establishing policy regarding human practices and in acting as a liaison between the community of synthetic biology and the public. The multidisciplinary aspect of iGEM is conducive to progress in these two areas. With a concerted effort we can help ensure that synthetic biology continues to progress and reach its potential. </p><br />
<p class = "class">Our team has taken specific measures to follow our suggested proposals. In the education of our team, we discussed the potential benefits of a standard secretion system but also discussed the potential of our designed secretion pathways to be used in a malevolent manner. As a team we acknowledge the importance of high moral accountability and commitment to safety and security. Additionally, in an effort to foster the sharing of information in our community, upon completion of the jamboree we will submit an article to be released in our school newspaper and in our College of Engineering website. This winter we are also hosting a lecture by Drew Endy addressing synthetic biology which will be open to the public. We hope to act as ambassadors to foster support and excitement in our own community.</p><br />
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References<br />
</font></b></i> <hr><br />
<br />
<ul class="circle"><br />
<li>Garfinkel M, Endy D, Epstein GL, Friedman RM (2007) Synthetic genomics – options for governance. http://www.synbioproject.org/topics/synbio101/bibliography/governance </li><br />
<li>Hart Research (2009) Nanotechnology, synthetic biology, & public opinion: What does the public think?. http://www.synbioproject.org/events/archive/6380/ </li><br />
<li>Kahan DM, Braman D, Mandel GN (2009, Feb. 20) Risk and culture: Is synthetic biology different? Harvard Law School Program on Risk Regulation Research Paper No. 09-2; Yale Law School, Public Law Working Paper No. 190. http://ssrn.com/abstract=1347165 </li><br />
<li>Marchant GE, Pope LL (2009) The problems with forbidding science. Sci Eng Ethics 15:375-394 </li><br />
<li>Maurer SM, et al.(2006) From understanding to action: Community-based options for improving safety and security in synthetic biology. http://gspp.berkeley.edu/iths/UC%20White%20Paper.pdf </li><br />
<li>Parens E, et al.(2009) Ethical issues in synthetic biology: An overview of the debates. http://www.synbioproject.org/library/publications/archive/synbio3/ </li><br />
<li>Pauwels E, Ifrim I (2008) Trends in American and European Press Coverage of Synthetic Biology. http://www.synbioproject.org/library/publications/archive/why_scientists_should_care/ </li><br />
<li>Rejeski D (2009a) Foreword-New life old bottles: Regulating first-generation products of synthetic biology. http://www.synbioproject.org/library/publications/archive/synbio2/ </li><br />
<li>Rejeski D (2009b) Public perceptions on the technological frontier. Given at National Academy of Sciences July 10, 2009. Audio Retrieved from http://www.synbioproject.org/process/assets/files/6372/_draft/rejeski.ppt#268,1, </li><br />
<li>Rodemeyer M (2009) New life old bottles: Regulating first-generation products of synthetic biology. http://www.synbioproject.org/library/publications/archive/synbio2/ </li><br />
<li>Tucker JB, Zilinskas RA (2006) The promise and perils of synthetic biology. The New Atlantis 12:25-45. </li><br />
<li>Zoloth L (2006) Ethical issues in synthetic biology: Security and regulation of experiments of concern. http://gspp.berkeley.edu/iths/UC%20White%20Paper.pdf </li><br />
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</head></div>Ahatchhttp://2009.igem.org/Team:Utah_State/ETHICSTeam:Utah State/ETHICS2009-10-22T03:14:00Z<p>Ahatch: </p>
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<td id="nav"><a href="https://2009.igem.org/Team:Utah_State"><font size = 4>HOME</font></a></td><br />
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<td id="nav"><a href="https://2009.igem.org/Team:Utah_State/Team"><font size = 4>ABOUT US</font></a></td><br />
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<td id="nav"><a href="https://2009.igem.org/Team:Utah_State/Project"><font size = 4>PROJECT</font></a></td><br />
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<td id="nav"><a href="https://2009.igem.org/Team:Utah_State/Parts"><font size = 4>BIOBRICKS</font></a></td><br />
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<td id="nav"><a href="https://2009.igem.org/Team:Utah_State/Modeling"><font size = 4>MODELING</font></a></td><br />
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<td width="172" id="ana"><span class="currentPage"><font size = 4>ETHICS</font></span><br />
<a href="#intro">Introduction</a><br /><br />
<a href="#synbio">Synthetic Biology</a><br /><br />
<a href="#team">Team Education</a><br /><br />
<a href="#public">Public Education</a><br/><br />
<a href="#conclusions">Conclusions</a><br/><br />
<a href="#references">Referencess</a><br />
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<td id="nav"><a href="https://2009.igem.org/Team:Utah_State/Achievements"><font size = 4>JUDGING</font></a></td><br />
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<b>Synthetic Biology:<br />
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<font size="5" face="Century Gothic, Arial, San Serif" color =green>Education in an Emerging Field</font><br><br />
<HR><br />
<p class="class"> <br />
The iGEM competition is devoted to the advancement of synthetic biology, specifically in standardized parts-based research. It welcomes participants from institutions of higher education from around the world. Just as important as contributing to the understanding of molecular biology based engineering is contributing to a framework which allows applications of this knowledge to be implemented in a manner that serves society. As we address human practices on our wiki we give a brief overview of synthetic biology, list areas in human practice commonly recognized as needing address, pose questions for discussion associated with those areas, and outline two ways the iGEM community can take fundamental actions. These actions involve a broader education of iGEM participants, and the dissemination of knowledge in our educational and public communities.<br />
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Synthetic Biology and Human Practices<br />
</font></b></i> <br />
<p class="class"><br />
Synthetic biology has been hailed by some as the next technological revolution. It has been said that standard biological parts “will be for the 21st century what screws and bolts were to the 19th, or transistors and resistors to the 20th (Endy quoted in Parens, Johnston, and Moses, 2009).” Members in the field have visions of using synthetic biology to develop new applications in the areas of environment, health, and industry, as well as learning to understand the fundamental components of life itself. Significant progress has already been made evidenced by the ever increasing size of the registry of parts with applications in the areas listed above. With time other applications will likely arise.<br />
<br><br />
<p class="class">As with any new technology, there exist potential benefits and potential areas of concern. There must be a balance between the desire to bring innovative and beneficial products to market and prevent potential harm to public health and the environment (Rodemeyer, 2009). Following are some of the issues that are commonly indicated as areas that must be addressed. </p><br />
</p><br><br />
<ul class="circle"><br />
<li>Biosafety: How can research personnel, the environment, and society be protected from intended or accidental exposure to developed products? </li><br />
<li>Biosecurity: What measures should be taken to ensure that products of synthetic biology are not used in a malevolent manner?</li><br />
<li>Property Rights: What is the best way to share information to ensure that the field progresses rapidly, that opportunities to contribute are distributed fairly, and that contributors to the field are fairly compensated? Is it ethical to have a patent on life?</li><br />
<li>Governance: What is the best way to implement policy that governs the field of synthetic biology? Is there a need for outside oversight or is self-governance sufficient? What challenges would arise if governing policy varied from country to country?</li><br />
<li>Mankind and Nature: What roles should humans play in manipulating nature? Who should decide to what extent manipulation of life is acceptable?</li><br />
<li>Public Perception and Involvement: Public involvement often is a deciding factor in funding and regulation. How should synthetic biology disseminate knowledge to the public and hear and address public concerns?</li><br />
</ul></font><br><br />
<p class="class"><br />
Efforts have been made to foster discussion about these areas and various measures to address them have been suggested (Maurer et al., 2006; Garfinkel et al., 2007). As synthetic biology is still in its youth, actions taken now and continued efforts to address these concerns in the future will enable the field to progress with minimal hindrance. “Procrastination bears a risk. A productive dialogue may become more difficult as synthetic biology evolves and stakeholders become divided in their opinions about benefits and risks (Rejeski, 2009a).” As the iGEM jamboree is the largest gathering related to synthetic biology in the world, we propose that initiative taken here will have a significant impact on the world. The “current and future leaders of the field” are participating in these gatherings (2009.igem.org/About). </p><br />
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iGEM and Education<br />
</font></b></i> <br />
<p class = "class2"><b>Broader Education of iGEM Participants </b></p><br />
<p class="class"><br />
Establishing governing policy for synthetic biology is complex and difficult to address (Rodemeyer, 2009). Problems can arise from limited jurisdiction of a governing body (Marchant & Pope, 2009) or the expense and cumbersome nature of monitoring activity (Rodemeyer, 2009) among other difficulties. Whatever policy is decided upon, the ultimate difficulty comes in enforcing the policy.<br />
</p><br />
<p class="class"><br />
In preparation for the Synthetic Biology 2.0 conference in 2006, Laurie Zoloth addressing “ethics training” stated:<br />
</p><br><br />
<p class="margin"><br />
What is needed is a lab culture which is strong enough and decent enough to teach and model impeccably honest moral science citizenship in the as yet small academic field of synthetic biology… Ethics education cannot be done with websites or software—there is a need for individual moral agency, and for this task, serious questions about the complexities of good and evil, difficult moral choices, the nature of the love of country, the nature of obligation to the other and the limits of the search for knowledge, all must be read about and studied with the same seriousness that young scientists give to understanding siRNA or nanobiobarcodes. </p><br><br />
<br />
<p class ="class">As the current and future leaders of the field of synthetic biology participate in these conferences, time before the conference and during the conference should be devoted to establishing appropriate human practices and ensuring that these practices are taught and implemented. The nature of iGEM and its multidisciplinary approach to a successful team is conducive to researching and establishing appropriate human practices. In order to qualify for a gold medal, teams are encouraged to address appropriate human practices as part of their project. Due to the difficult nature of the questions concerning human practices, we propose more could be done by iGEM participants. Possible additional measures include: </p><br><br />
<ul class="circle"><br />
<li>A new track focused solely on researching proper human practices, performing risk assessment, or researching public perception.</li><br />
<li>A portion of the conference set aside to relaying current best practices, or bringing before the community options for current best practices for discussion and acceptance.</li><br />
</ul><br><br />
<br />
<p class ="class">As ensuring that proper policy is implemented and followed is important for the development of this or any field, these increased measures could help to ensure that policy becomes international and observed. Again, iGEM participants largely represent the future of the field. As policy is accepted within the iGEM community, enforcing the policy is simplified because it would be regularly taught and more widely accepted.</p><br />
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Public Education<br />
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<p class = "class">Hart Researchers learned in a U.S. survey in 2009 that about 80% of the population had heard little or nothing about synthetic biology. Given the young age of the field, and based on a report about media coverage in the U.S. and Europe (Pauwels & Ifrim, 2008) we assume that there has been similar public exposure around the world. Some fields of study with great potential have been hindered as a result of not having adequate democratic involvement with the public for example genetically modified foods (Parens et al., 2009) or stem cell research (Marchant & Pope, 2009). The Hart researchers also found that there is a broad consensus that “more should be done to inform the American public.” 90% of adults surveyed agreed with that statement and 73 % “strongly agreed.”</p> <br />
<br />
<p class = "class"> In an address to the National Academy of Sciences, David Rejeski (2009b) suggested that there is a lack of good science reporters. Media, for various reasons, is prone to embellish and to present information that catches attention, but is not necessarily accurate. This leads to inaccurate initial assessments of synthetic biology. Once an initial assessment has been made, the feelings rarely change, but rather become stronger (Kahan et al., 2009). Addressing public perception, Tucker and Zilinskas (2006) wrote: </p><br />
<br><br />
<p class="margin">Although it is often difficult to persuade scientists to leave the laboratory for even a few hours to participate in a public discussion of their work and its implications for society, such efforts should be encouraged because they generate good will and may help to prevent a future political backlash that could cripple the emerging field of synthetic biology. </p><br />
<br><br />
<p class = "class">With more than 100 teams participating in iGEM coming from around the world, we represent a tremendous asset in disseminating accurate knowledge to the public. We propose two measures that could be taken by iGEM teams to increase public education. </p><br />
<br><br />
<ul class="circle"><br />
<li>In order to qualify for a gold medal a team should make an effort to have accurately released in a school newspaper or website, an article about synthetic biology and the school’s involvement with iGEM.</li><br />
<li>Encourage iGEM teams to host or give a presentation addressing synthetic biology open to the school and public. The presentation should also be open to accepting questions and addressing concerns.</li></ul><br />
<br><br />
<p class = "class">Efforts to honestly present information to the public will lead to public trust and a market that welcomes innovations from the field. Interaction with the public in this fashion will also help to establish guidelines as to what research is considered acceptable and will aid in establishing regulatory frameworks. </p><br />
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Conclusions<br />
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<p class = "class">The teams participating in iGEM can play an invaluable role in establishing policy regarding human practices and in acting as a liaison between the community of synthetic biology and the public. The multidisciplinary aspect of iGEM is conducive to progress in these two areas. With a concerted effort we can help ensure that synthetic biology continues to progress and reach its potential. </p><br />
<p class = "class">Our team has taken specific measures to follow our suggested proposals. In the education of our team, we discussed the potential benefits of a standard secretion system but also discussed the potential of our designed secretion pathways to be used in a malevolent manner. As a team we acknowledge the importance of high moral accountability and commitment to safety and security. Additionally, in an effort to foster the sharing of information in our community, upon completion of the jamboree we will submit an article to be released in our school newspaper and in the college of engineering website. This winter we are also hosting a lecture by Drew Endy addressing synthetic biology which will be open to the public. We hope to act as ambassadors to foster support and excitement in our own community.</p><br />
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References<br />
</font></b></i> <hr><br />
<br />
<ul class="circle"><br />
<li>Garfinkel M, Endy D, Epstein GL, Friedman RM (2007) Synthetic genomics – options for governance. http://www.synbioproject.org/topics/synbio101/bibliography/governance </li><br />
<li>Hart Research (2009) Nanotechnology, synthetic biology, & public opinion: What does the public think?. http://www.synbioproject.org/events/archive/6380/ </li><br />
<li>Kahan DM, Braman D, Mandel GN (2009, Feb. 20) Risk and culture: Is synthetic biology different? Harvard Law School Program on Risk Regulation Research Paper No. 09-2; Yale Law School, Public Law Working Paper No. 190. http://ssrn.com/abstract=1347165 </li><br />
<li>Marchant GE, Pope LL (2009) The problems with forbidding science. Sci Eng Ethics 15:375-394 </li><br />
<li>Maurer SM, et al.(2006) From understanding to action: Community-based options for improving safety and security in synthetic biology. http://gspp.berkeley.edu/iths/UC%20White%20Paper.pdf </li><br />
<li>Parens E, et al.(2009) Ethical issues in synthetic biology: An overview of the debates. http://www.synbioproject.org/library/publications/archive/synbio3/ </li><br />
<li>Pauwels E, Ifrim I (2008) Trends in American and European Press Coverage of Synthetic Biology. http://www.synbioproject.org/library/publications/archive/why_scientists_should_care/ </li><br />
<li>Rejeski D (2009a) Foreword-New life old bottles: Regulating first-generation products of synthetic biology. http://www.synbioproject.org/library/publications/archive/synbio2/ </li><br />
<li>Rejeski D (2009b) Public perceptions on the technological frontier. Given at National Academy of Sciences July 10, 2009. Audio Retrieved from http://www.synbioproject.org/process/assets/files/6372/_draft/rejeski.ppt#268,1, </li><br />
<li>Rodemeyer M (2009) New life old bottles: Regulating first-generation products of synthetic biology. http://www.synbioproject.org/library/publications/archive/synbio2/ </li><br />
<li>Tucker JB, Zilinskas RA (2006) The promise and perils of synthetic biology. The New Atlantis 12:25-45. </li><br />
<li>Zoloth L (2006) Ethical issues in synthetic biology: Security and regulation of experiments of concern. http://gspp.berkeley.edu/iths/UC%20White%20Paper.pdf </li><br />
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</head></div>Ahatchhttp://2009.igem.org/Team:Utah_State/ModelingTeam:Utah State/Modeling2009-10-21T23:24:07Z<p>Ahatch: </p>
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<td id="nav"><a href="https://2009.igem.org/Team:Utah_State"><font size = 4>HOME</font></a></td><br />
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<td id="nav"><a href="https://2009.igem.org/Team:Utah_State/Team"><font size = 4>ABOUT US</font></a></td><br />
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<td width="172" id="ana"><span class="currentPage"><font size = 4>MODELING</font></span><br />
<a href="#parameters">Parameters</a><br /><br />
<a href="#simulations">Simulations</a><br /><br />
<a href="#references">References</a><br />
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<b><i>Modeling Secretion Mechanisms</b></i></font><br />
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<p class = "class"> <br />
There are currently few guidelines for selecting which signal peptide (which determine the secretion pathway taken) should be used for a given recombinant protein (Choi, 2004). The construction of models that evaluate protein secretion may provide a useful framework for studying and attempting to predict factors that affect secretion efficiency. Models of the Sec and Tat translocation pathways were made using MATLAB’s Simbiology toolbox. They were evaluated using the embedded ordinary differential equation solver in the software. Assumptions were made for both models due to lack of time scale information for individual steps for these translocation mechanisms. However, both provide a flexible framework that can become more detailed as additional information is found in literature or discovered in the laboratory. Within both models, a protein is first generated and then carried out of the cytoplasm to the periplasm. Only protein species were tracked, as species involved with making the protein are currently not as useful to monitor.<br />
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Model Parameters<br />
</font></b></i> <br />
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In both models, parameters for the manufacture of protein were the same and found using averaged values for <i>E. coli</i>. The average length of an mRNA for <i>E. coli</i> is 1100 nucleotides and an <i>E. coli</i> cell transcribes at an average rate of 70 nucleotides per second. A simple rate calculation determines that a strand of mRNA is made approximately every 15.7 seconds. This value was then used to yield a first order reaction rate of (1/15.7) 1/second. The translation rate was found in a similar manner. Given an average protein size in <i>E. coli</i> as 360 amino acids and the average translation rate is 40 amino acids per second, the first order translation rate constant is (1/9) 1/s (Institute for Biomolecular Design, 2008). To initiate the model, the concentration of the gene was set at 1, which was locked at that value over the course of the simulation. The median half life for mRNA was found to be 3.7 minutes, after which it will degrade (Milo, n. d.). For the Tat-dependent mechanism, the protein is fully folded prior to translocation (Mergulhão, 2005). For this folding time, a place holder value of 10 minutes was used as an approximate order of magnitude, although the value can easily be changed depending on parameters of the protein in question. Degradation of protein was modeled as the average time it takes the cell to reproduce, which is given as half an hour (Institute for Biomolecular Design, 2008).<br />
</P><br />
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In addition to the discussed values regarding the manufacture of protein, parameters for the Sec and Tat pathway are required. A literature review yielded no specific rate constants or time parameters for the individual steps involved with either process. However, one article stated that the Sec and Tat pathways take a few seconds and a few minutes, respectively, to translocate protein to the periplasmic space (Mergulhão, 2005). Accordingly, the Sec and Tat pathways were modeled to require 3 seconds and 3 minutes for protein translocation, respectively. First order rate constants were determined by taking the inverse of these values in seconds. Images of the model diagrams are seen below. The different pathways after the formation of protein can be activated and deactivated as more detailed information comes available about the translocation and secretion processes. The Sec secretion pathway also includes the SRP secretion pathway as a possible option. The constructed models for the Sec and Tat pathways are given as Figures 1 and 2, respectively.<br />
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<b>Figure 1.</b> Sec Pathway Model Diagram<br />
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<b>Figure 2.</b> Tat Pathway Model Diagram<br />
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<p class = "class">Simulations for the Sec pathways were run for 5400 seconds (1.5 hours), which allowed the number of periplasmic to reach approximately steady state. The simulation for the Sec pathway secretion model is shown below as Figure 3. <br />
Protein generated by the <i>E. coli</i> cell reaches steady state quickly, as it is both produced and translocated in to the periplasm rapidly. The periplasmic protein reaches approximately 90 proteins upon achieving steady state. The long settling time and high number of periplasmic protein are a result of the long protein degradation time.</p><br />
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<br><br />
<div align="center"><img src="https://static.igem.org/mediawiki/2009/b/b4/Model3.png" align = "middle" height="400" style="padding:.5px; border-style:solid; border-color:#999" alt="Figure 3"> </div><br />
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<b>Figure 3.</b> Simulation of protein production and translocation by the Sec pathway<br />
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<br />
<p class= "class">Simulations for the Tat pathway were run for 3600 seconds (1 hour). The shorter length of simulation relative to the Sec model is used despite having significantly longer protein translocation time because the time-consuming folding step limits the reaction. The results of the ordinary differential equation simulation are shown below in Figure 4. The amount of periplasmic protein is lower than cytoplasmic and folded protein values upon reaching steady state. This is due to the rate-limiting folding step, which also leads to an expected high concentration of folded protein as well.<br />
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<div align="center"><img src="https://static.igem.org/mediawiki/2009/b/b2/Model4.png" align = "middle" height="400" style="padding:.5px; border-style:solid; border-color:#999" alt="Figure 4"> </div><br />
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<b>Figure 4.</b> Simulation of protein production, folding, and translocation by the Tat pathway<br />
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<br />
<p class = "class"> The accuracy of models, such as those constructed, will increase as more knowledge about the time step parameters for each of the mechanisms is determined. These improvements will allow for a better comparison of the two secretion methods, which can lead to better signal peptide selection (and corresponding pathway selection) for the protein in question. Future work could also include incorporating promoter strength into the model to affect transcription rates to provide a more accurate depiction of what is happening inside the cell. Better correlation between these parameters and the model will result in a more useful aid in when studying protein secretion. <br />
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References<br />
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<li>Institute for Biomolecular Design (2008, August 1) CyberCell Database. Retrieved October 2009. http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi<br />
<li>Choi JH, Lee SY (2004) Secretory and extracellular production of recombinant proteins using <i>Escherichia coli</i>. Appl Microbiol Biotechnol 64:625-635</li><br />
<li>Mergulhão FJM, Summers DK, Montier GA (2005) Recombinant protein secretion in <i>Escherichia coli</i>. Biotechnol Adv 23:177-202</li><br />
<li>Milo R (n.d.) BioNumbers: The Database of Useful Biological Numbers. Retrieved October 2009. http://bionumbers.hms.harvard.edu/default.aspx</li><br />
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<td id="nav"><a href="https://2009.igem.org/Team:Utah_State"><font size = 4>HOME</font></a></td><br />
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<td id="nav"><a href="https://2009.igem.org/Team:Utah_State/Team"><font size = 4>ABOUT US</font></a></td><br />
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<td id="nav"><a href="https://2009.igem.org/Team:Utah_State/Project"><font size = 4>PROJECT</font></a></td><br />
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<td id="nav"><a href="https://2009.igem.org/Team:Utah_State/Experiments"><font size = 4>EXPERIMENTS</font></a></td><br />
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<td width="172" id="ana"><span class="currentPage"><font size = 4>BIOBRICKS</font></span><br />
<a href="#tested">Tested</a><br/><br />
<a href="#submitted">Submitted </a><br /><br />
<a href="#designed">Designed</a><br /><br />
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<td id="nav"><a href="https://2009.igem.org/Team:Utah_State/Modeling"><font size = 4>MODELING</font></a></td><br />
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<td id="nav"><a href="https://2009.igem.org/Team:Utah_State/Notebook"><font size = 4>NOTEBOOK</font></a></td><br />
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<td id="nav"><a href="https://2009.igem.org/Team:Utah_State/ETHICS"><font size = 4>ETHICS</font></a></td><br />
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<td id="nav"><a href="https://2009.igem.org/Team:Utah_State/Achievements"><font size = 4>JUDGING</font></a></td><br />
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<td id="nav"><a href="https://2009.igem.org/Team:Utah_State/Contact"><font size = 4>CONTACT</font></a></td><br />
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<b><i>BioBricks</b></i></font><br />
<p class="class">The USU iGEM team has successfully constructed 49 BioBrick parts and devices. Of these, we have had the time to show the functionality of 6 BioBricks, and had 42 of them sequenced and shown to be correct. Check out our <a href="http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2009&group=Utah_State/"><font color=#009900>BioBrick Registry</font></b></a> page to see all of these parts and to find more detailed information about them.<br />
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<a href="https://2009.igem.org/Team:Utah_State"><br />
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<td id="nav"><a href="https://2009.igem.org/Team:Utah_State"><font size = 4>HOME</font></a></td><br />
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<td width="172" id="ana"><span class="currentPage"><font size = 4>ABOUT US</font></span><br />
<a href="#team">The Team</a><br /><br />
<a href="#advisors">Advisors</a><br /><br />
<a href="#faculty">Faculty Support</a><br /><br />
<a href="#USU">Utah State University</a><br /><br />
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<b><i>Team USU</i></b></font><br />
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<p> <font size="2.5" face=" Tahoma, Helvetica, Arial" color =#000000><br />
This is Utah State University's second year participating in the iGEM competition. Our team has grown in the past year and includes high school, undergraduate, and graduate students, along with outstanding faculty advisors. Though there have been many challenges throughout this project, participation in the iGEM competition has been a great learning experience for all involved on the team. Below, you can meet each member of our team and find more information about Utah State University and Logan, Utah. </font></p><br />
<br />
<div align="center"><img src="https://static.igem.org/mediawiki/2009/e/ee/Teamusu.png"" align = "middle" height="400" style="padding:.5px; border-style:solid; border-color:#999" alt="Team USU" /> </div><br />
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<img src="https://static.igem.org/mediawiki/2009/f/fc/Garrett_Hinton_cropped.jpg" align = "right" height="150" style="padding:.5px; border-style:solid; border-color:#999" alt="Garrett Hinton"/> <br />
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<b><br />
GARRETT HINTON<br />
</b></font><p class="margin"><br />
Garrett Hinton is a Senior at Sky View High School in Smithfield, UT. He began his research experience at USU in 2006 as he was starting his freshman year in high school. He was a member of the USU iGEM team in 2008, and is excited to be involved again this year. For this project, Garrett performed various lab procedures, including DNA purification, gel electrophoresis, restriction enzyme digestions, ligations, and more. Additionally, he helped out in the lab by making medias and monitoring experiments. Outside of the lab, Garrett likes basketball and ping pong.<br />
</p><br/><br/><br />
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<img src="https://static.igem.org/mediawiki/2009/b/b3/Jody_Jerez_cropped.jpg" align = "right" height="150" style="padding:.5px; border-style:solid; border-color:#999" alt="Jody Jerez"/> <br />
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JODY JEREZ<br />
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<p class="margin">Jody Jerez is a senior at InTech Collegiate High School in North Logan, Utah. She has been interested in biological engineering and decided to participate in iGEM to learn more about it. This is her first year participating in iGEM and she has learned a lot and enjoys what she was able to do for the team. Jody contributed by doing general laboratory procedures in the lab, as well as adding content to the wiki. Other than learning more about biological engineering, Jody enjoys hiking, dancing, and rock climbing.<br />
</p><br /><br /><br /><br />
<br />
<br />
<img src="https://static.igem.org/mediawiki/2009/3/39/Jeff_Karren_cropped.jpg" align = "right" height="150" style="padding:.5px; border-style:solid; border-color:#999" alt="Jeff Karren"/> <br />
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<br />
<b><br />
JEFF KARREN<br />
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<p class="margin"><br />
Jeff is also a senior at InTech Collegiate High School. He first learned about iGEM and synthetic biology when USU's Biological Engineering gave a presentation at his school. Although Jeff helped primarily with the team wiki, especially the protocol page, he did help with some work in the lab as well, particularly in the initial stages of the project. He has enjoyed learning about synthetic biology, and is excited for the Jamboree. Jeff is on his high school robotics team, plays the pipe organ, hikes, and swing dances. <br />
</p><br /><br /><br /><br />
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<img src="https://static.igem.org/mediawiki/2009/5/56/Tyrell_Rupp_cropped.jpg" align = "right" height="150" style="padding:.5px; border-style:solid; border-color:#999" alt="Tyrell Rupp"/> <br />
<font size="2" face="Helvetica, Arial, San Serif" color =#231f20><br />
<b><br />
TYREL RUPP<br />
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<p class="margin">Tyrel is a senior at a Sky View High School near USU. In the spring of 2009 he was exposed to synthetic biological engineering through an internship class. Ty spent the summer working for the Synthetic Biomanufacturing Center, which lead to his participation in iGEM. Over the past few months, he has learned a lot about synthetic biology and the research process. Among other things, Ty enjoys mountain biking and snowboarding in the mountain ranges above USU. For iGEM, Ty has helped carry out basic laboratory procedures and contributed some to the team’s wiki design. <br />
</p><br /><br /><br /><br />
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<img src="https://static.igem.org/mediawiki/2009/c/c2/Hyun-jin_Kim_cropped.jpg" align = "right" height="150" style="padding:.5px; border-style:solid; border-color:#999" alt="Tyrell Rupp"/> <br />
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<b><br />
HYUN-JIN KIM<br />
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<p class="margin">Hyun-Jin is a freshman at Intech Collegiate High School. He started at the lab from summer and is now very proficient in most laboratory procedures used in the Synthetic Biomanufacturing Lab. In example, he makes media, isolates plasmid DNA using the CTAB method, and carries out transformations of <i> E. coli</i>. He is from Gwangju, South Korea and is excited to be involved with the iGEM 2009 project. He enjoys football, Frisbee and basketball.<br />
</p><br /><br /><br /><br /><br />
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<img src="https://static.igem.org/mediawiki/2009/7/79/Sean_Bedingfield_cropped.jpg" align = "right" height="150" style="padding:.5px; border-style:solid; border-color:#999" alt="Sean Bedingfield"/> <br />
<font size="2" face="Helvetica, Arial, San Serif" color =#231f20><br />
<b><br />
SEAN BEDINGFIELD<br />
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<p class="margin">Sean Bedingfield is a Utah State Research Fellow in his freshman year. His personal research is focused on effective expression of the LacOperon gene for the production of particular proteins. Sean is an avid hiker, pheasant hunter, and cook. Sean’s contributions to the project include assisting with tri-parental mating, researching<br />
secretion systems of different bacteria, transforming competent <i>E. coli</i>, and getting the team T-shirts made. <br />
</p><br /><br /><br /><br /><br />
<br />
<img src="https://static.igem.org/mediawiki/2009/1/1d/Cole_Peterson_cropped.jpg" align = "right" height="150" style="padding:.5px; border-style:solid; border-color:#999" alt="Cole Peterson"/> <br />
<font size="2" face="Helvetica, Arial, San Serif" color =#231f20><br />
<b><br />
COLE PETERSON<br />
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<p class="margin">Cole is a sophomore in Biological Engineering, and this is his first year participating in iGEM. He spent the summer enthusiastically working on USU’s iGEM project. When not in school or in the lab he likes running, cycling, hiking, rock climbing and skiing. Cole spent the majority of his time in the lab modifying and testing multiple broad-host range vectors, as well as performing general laboratory tasks and procedures.<br />
</p><br /><br /><br /><br /><br /><br />
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<img src="https://static.igem.org/mediawiki/2009/3/37/Alex_Hatch_cropped.jpg" align = "right" height="150" style="padding:.5px; border-style:solid; border-color:#999" alt="Alex Hatch"/> <br />
<font size="2" face="Helvetica, Arial, San Serif" color =#231f20><br />
<b><br />
ALEX HATCH<br />
</b></font><br />
<p class="margin">Alex Hatch is a junior in Biological Engineering at Utah State University. His personal research has dealt with microbial diversity in TCE bioremediation and currently algal diversity in wastewater treatment and biofuel production. He is participating with iGEM for the first time this year and has enjoyed the opportunity to be introduced to this emerging field. He is pursuing a career in medicine and plans to attend medical school upon graduation. He loves to spend time with his young family, wife Laura and son Graham. Together they like to spend time outside, read together, and build forts out of furniture and blankets. Alex has helped in general laboratory activities and was responsible for addressing human practices in synthetic biology on the Wiki.</p><br />
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<br />
<br />
<img src="https://static.igem.org/mediawiki/2009/e/ea/Rachel_Jackson_cropped.jpg" align = "right" height="150" style="padding:.5px; border-style:solid; border-color:#999" alt="Rachel Porter"/> <br />
<font size="2" face="Helvetica, Arial, San Serif" color =#231f20><br />
<b><br />
RACHEL PORTER<br />
</b></font><br />
<p class="margin">Rachel is in her third year at Utah State University majoring in Biological Engineering. She is interested in genetic and biomedical engineering research and would like to pursue a masters degree in biomedical engineering. She enjoys participating in iGEM because it is interesting and helps her apply the concepts she has learned in classes. She hopes to work in a research laboratory after graduation. Originally from Salt Lake City, Utah, her hobbies include playing volleyball, mountain biking, hiking, camping, and almost anything outdoors. <br />
<br /><br /><br /></p><br />
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<br />
<img src="https://static.igem.org/mediawiki/2009/b/b7/Trent_Mortensen_cropped.jpg" align = "right" height="150" style="padding:.5px; border-style:solid; border-color:#999" alt="Trent Mortensen"/> <br />
<font size="2" face="Helvetica, Arial, San Serif" color =#231f20><br />
<b><br />
TRENT MORTENSEN<br />
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<p class="margin">Trent is a finishing senior in Biological Engineering at Utah State University. His personal research is focused on the antimycobacterial properties of the St. John’s Wort herb. Trent participated in the 2008 Utah State iGEM project and is participating once again because of the excellent experience he had last year. He is looking into a career in the biomedical field in the area of disease and injury research and treatment and feels that Synthetic Biology has enormous potential for advancing this field. Trent enjoys hiking, fishing, and snowmobiling in the nearby mountains. He also enjoys playing basketball, racquetball, and ultimate. For this year’s project, Trent aided in laboratory work, team coordination, gathering materials for the Wiki, and preparation of the presentation materials. </p><br />
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<img src=" https://static.igem.org/mediawiki/2009/3/32/Brad_Henrie_cropped.jpg" align = "right" height="150" style="padding:.5px; border-style:solid; border-color:#999" alt="Brad Henrie" /> <br />
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BRAD HENRIE<br />
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<p class="margin">Brad is a graduate student in the Biological and Irrigation Engineering at Utah State University. His personal research is centered around analyzing an unknown microbial community, and characterizing it's genetic phylogeny. Brad is participating in the iGEM competition for the first time, and has enjoyed being a part of the group. He has a passion for caving, and tries to go as often as the team would let him. Other than that, he enjoys rock climbing, camping, the occasional computer game, and is excited for the duck hunting season. Brad was primarily responsible for culturing the cyanobacteria, and conducting the tri-parental mating procedure, and generally helped out around the lab.<br />
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<img src="https://static.igem.org/mediawiki/2009/7/7f/Libbie_Linton_cropped.jpg" align = "right" height="150" style="padding:.5px; border-style:solid; border-color:#999" alt="Libbie Linton" /> <br />
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LIBBIE LINTON<br />
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<p class="margin">Libbie is a Masters student in Biological Engineering. Like a few others on this year's team, Libbie was also a member of the 2008 iGEM team. She is glad to be back for a second year, this time as an advisor. Her Masters' work is in investigating different ways to improve PHA production economics. She is hoping to complete her thesis within the next few months, followed by finding employment in bioprocess/biochemical engineering. In her spare time, Libbie is a musician. She also enjoys beating fellow iGEM teammate Trent Mortensen in racquetball, as well as playing with her 6 month old puppy, Rooster. For this years' iGEM team, Libbie advised on topics related to bioplastic production, secretion systems and mechanisms, and general laboratory procedures. She was also involved in coordinating efforts with the wiki. <br />
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<img src="https://static.igem.org/mediawiki/2008/7/7f/JH.jpg" align = "right" height="158" style="padding:.5px; border-style:solid; border-color:#999" alt="Junling Huo" /> <br />
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JUNLING HUO<br />
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<p class="margin">Junling Huo is a PhD student in Biological Engineering at USU. His dissertation research is focused on design a gene expression system for Rhodobacter sphaeroides, which is a photosynthetic bacteria. This gene expression system will include BioBrick compatible promoters, Ribosome Binding Sites (RBS), and terminators. The planned promoters and RBS will have different activities. Terminators will be either bidirectional or unidirectional. He hopes to complete his dissertation in the next year or so, and continuing doing research. He was also a member of 2008 USU iGEM team, and is happy to serve as an advisor again this year.<br />
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Our faculty advisors are Dr. Ronald C. Sims, Dean H. Scott Hinton, and Dr. Charles D. Miller. We would like to thank them for all of their help and guidance throughout the project. To view their professional biographies, please refer to our <a href="http://www.bie.usu.edu/"><b><font color =#009900>department website</font></b></a>:<br />
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<b><i>Utah State University</i></b></font><br />
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Located in <a href="http://www.loganutah.org/"><b><font color=#009900>Logan, Utah</font></b></a>, about 80 miles north of Salt Lake City, Utah State University sits just outside the mouth of Logan Canyon. The city, founded in 1859, has a population of approximately 47,000 and boasts a rich heritage. Whether on campus, historic Main Street, down in the “island”, or up the canyon, there is always something to do. <br />
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Originally founded in 1888 as the Agricultural College of Utah, the school officially became a university in 1957. As the state's land-and space-grant university, USU conducts world-class research in many disciplines and has several projects in conjunction with the Department of Defense and NASA. USU’s research program is second in age only to MIT in the United States. USU's <a href="http://www.sdl.usu.edu/index-noflash.html"><b><font color =#009900>Space Dynamics Laboratory</font></b></a> has put more experiments into space than any university in the world and is ranked first in the United States for funding for aerospace research. <br />
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<p class="class">The <a href="http://www.engineering.usu.edu"><b><font color=#009900>engineering</font></b></a> program at Utah State is known for its excellence, with a 96% first-time pass rate on the national engineering exam compared to a national average of 55%. Beyond the Logan campus, Utah State's Extension programs extend academic resources and support throughout the entire state of Utah, having extension locations in each of Utah's 29 counties.</p><br />
<p class="class"><a href="http://www.bie.usu.edu/"><b><font color =#009900>Biological and Irrigation Engineering</font></b></a> is a relatively small department at Utah State, with about 30 faculty and 120 undergraduate and graduate students. This great student-to-teacher ratio helps students succeed in their classes. The Biological Engineering Program teaches students to manipulate biological systems for useful purposes, understand scientific literature, and to work well and communicate effectively with others, both in the field of Biological Engineering and out. In the first years of the program, students learn the basics of biology, chemistry, physics, and mathematics. This knowledge base is then broadened by a study of liberal arts and humanities including literature, philosophy, political science, art, and music classes. Students finally delve into technical engineering courses, many chosen personally by students to apply to their particular areas of interest. These courses develop practical problem-solving abilities, increasing sensitivity to the economic, social, and legal dimensions of technical problems. Students leave the program well-qualified for their careers, with an understanding of the importance of social and professional ethics and responsibility to accompany their technical learning. After graduation, students will apply their knowledge to a wide range of careers, from genetic engineering to design of prosthetic devices for amputees.</p><br />
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<a href="http://www.bie.usu.edu/"><img src="https://static.igem.org/mediawiki/2009/2/29/Logan_canyon.jpg" align = "middle" height="217" style="float:left;" alt="Logan Canyon"/> </a><br />
<a href="http://www.engineering.usu.edu/"><img src="https://static.igem.org/mediawiki/2009/a/aa/USU_Campus.jpg" align = "middle" height="217" style="float:left;"alt="Campus"/></a><br />
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<td width="172" id="ana"><span class="currentPage"><font size = 4>ABOUT US</font></span><br />
<a href="#team">The Team</a><br /><br />
<a href="#advisors">Advisors</a><br /><br />
<a href="#faculty">Faculty Support</a><br /><br />
<a href="#USU">Utah State University</a><br /><br />
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<b><i>Team USU</i></b></font><br />
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This is Utah State University's second year participating in the iGEM competition. Our team has grown in the past year and includes high school, undergraduate, and graduate students, along with outstanding faculty advisors. Though there have been many challenges throughout this project, participation in the iGEM competition has been a great learning experience for all involved on the team. Below, you can meet each member of our team and find more information about Utah State University and Logan, Utah. </font></p><br />
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GARRETT HINTON<br />
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Garrett Hinton is a Senior at Sky View High School in Smithfield, UT. He began his research experience at USU in 2006 as he was starting his freshman year in high school. He was a member of the USU iGEM team in 2008, and is excited to be involved again this year. For this project, Garrett performed various lab procedures, including DNA purification, gel electrophoresis, restriction enzyme digestions, ligations, and more. Additionally, he helped out in the lab by making medias and monitoring experiments. Outside of the lab, Garrett likes basketball and ping pong.<br />
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<img src="https://static.igem.org/mediawiki/2009/b/b3/Jody_Jerez_cropped.jpg" align = "right" height="150" style="padding:.5px; border-style:solid; border-color:#999" alt="Jody Jerez"/> <br />
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JODY JEREZ<br />
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<p class="margin">Jody Jerez is a senior at InTech Collegiate High School in North Logan, Utah. She has been interested in biological engineering and decided to participate in iGEM to learn more about it. This is her first year participating in iGEM and she has learned a lot and enjoys what she was able to do for the team. Jody contributed by doing general laboratory procedures in the lab, as well as adding content to the wiki. Other than learning more about biological engineering, Jody enjoys hiking, dancing, and rock climbing.<br />
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<img src="https://static.igem.org/mediawiki/2009/3/39/Jeff_Karren_cropped.jpg" align = "right" height="150" style="padding:.5px; border-style:solid; border-color:#999" alt="Jeff Karren"/> <br />
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JEFF KARREN<br />
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Jeff is also a senior at InTech Collegiate High School. He first learned about iGEM and synthetic biology when USU's Biological Engineering gave a presentation at his school. Although Jeff helped primarily with the team wiki, especially the protocol page, he did help with some work in the lab as well, particularly in the initial stages of the project. He has enjoyed learning about synthetic biology, and is excited for the Jamboree. Jeff is on his high school robotics team, plays the pipe organ, hikes, and swing dances. <br />
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<img src="https://static.igem.org/mediawiki/2009/5/56/Tyrell_Rupp_cropped.jpg" align = "right" height="150" style="padding:.5px; border-style:solid; border-color:#999" alt="Tyrell Rupp"/> <br />
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TYREL RUPP<br />
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<p class="margin">Tyrel is a senior at a Sky View High School near USU. In the spring of 2009 he was exposed to synthetic biological engineering through an internship class. Ty spent the summer working for the Synthetic Biomanufacturing Center, which lead to his participation in iGEM. Over the past few months, he has learned a lot about synthetic biology and the research process. Among other things, Ty enjoys mountain biking and snowboarding in the mountain ranges above USU. For iGEM, Ty has helped carry out basic laboratory procedures and contributed some to the team’s wiki design. <br />
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<img src="https://static.igem.org/mediawiki/2009/c/c2/Hyun-jin_Kim_cropped.jpg" align = "right" height="150" style="padding:.5px; border-style:solid; border-color:#999" alt="Tyrell Rupp"/> <br />
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HYUN-JIN KIM<br />
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<p class="margin">Hyun-Jin is a freshman at Intech Collegiate High School. He started at the lab from summer and is now very proficient in most laboratory procedures used in the Synthetic Biomanufacturing Lab. In example, he makes media, isolates plasmid DNA using the CTAB method, and carries out transformations of <i> E. coli</i>. He is from Gwangju, South Korea and is excited to be involved with the iGEM 2009 project. He enjoys football, Frisbee and basketball.<br />
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<img src="https://static.igem.org/mediawiki/2009/7/79/Sean_Bedingfield_cropped.jpg" align = "right" height="150" style="padding:.5px; border-style:solid; border-color:#999" alt="Sean Bedingfield"/> <br />
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SEAN BEDINGFIELD<br />
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<p class="margin">Sean Bedingfield is a Utah State Research Fellow in his freshman year. His personal research is focused on effective expression of the LacOperon gene for the production of particular proteins. Sean is an avid hiker, pheasant hunter, and cook. Sean’s contributions to the project include assisting with tri-parental mating, researching<br />
secretion systems of different bacteria, transforming competent <i>E. coli</i>, and getting the team T-shirts made. <br />
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<img src="https://static.igem.org/mediawiki/2009/1/1d/Cole_Peterson_cropped.jpg" align = "right" height="150" style="padding:.5px; border-style:solid; border-color:#999" alt="Cole Peterson"/> <br />
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COLE PETERSON<br />
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<p class="margin">Cole is a sophomore in Biological Engineering, and this is his first year participating in iGEM. He spent the summer enthusiastically working on USU’s iGEM project. When not in school or in the lab he likes running, cycling, hiking, rock climbing and skiing. Cole spent the majority of his time in the lab modifying and testing multiple broad-host range vectors, as well as performing general laboratory tasks and procedures.<br />
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<img src="https://static.igem.org/mediawiki/2009/3/37/Alex_Hatch_cropped.jpg" align = "right" height="150" style="padding:.5px; border-style:solid; border-color:#999" alt="Alex Hatch"/> <br />
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ALEX HATCH<br />
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<p class="margin">Alex Hatch is a junior in Biological Engineering at Utah State University. His personal research has dealt with microbial diversity in TCE bioremediation and currently algal diversity in wastewater treatment and biofuel production. He is participating with iGEM for the first time this year and has enjoyed the opportunity to be introduced to this emerging field. He is pursuing a career in medicine and plans to attend medical school upon graduation. He loves to spend time with his young family, wife Laura and son Graham. Together they like to spend time outside, read together, and build forts out of furniture and blankets. Alex has helped in general laboratory activities and was responsible for addressing human practices in synthetic biology on the Wiki.</p><br />
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<img src="https://static.igem.org/mediawiki/2009/e/ea/Rachel_Jackson_cropped.jpg" align = "right" height="150" style="padding:.5px; border-style:solid; border-color:#999" alt="Rachel Porter"/> <br />
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RACHEL PORTER<br />
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<p class="margin">Rachel is in her third year at Utah State University majoring in Biological Engineering. She is interested in genetic and biomedical engineering research and would like to pursue a masters degree in biomedical engineering. She enjoys participating in iGEM because it is interesting and helps her apply the concepts she has learned in classes. She hopes to work in a research laboratory after graduation. Originally from Salt Lake City, Utah, her hobbies include playing volleyball, mountain biking, hiking, camping, and almost anything outdoors. <br />
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<img src="https://static.igem.org/mediawiki/2009/b/b7/Trent_Mortensen_cropped.jpg" align = "right" height="150" style="padding:.5px; border-style:solid; border-color:#999" alt="Trent Mortensen"/> <br />
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TRENT MORTENSEN<br />
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<p class="margin">Trent is a finishing senior in Biological Engineering at Utah State University. His personal research is focused on the antimycobacterial properties of the St. John’s Wort herb. Trent participated in the 2008 Utah State iGEM project and is participating once again because of the excellent experience he had last year. He is looking into a career in the biomedical field in the area of disease and injury research and treatment and feels that Synthetic Biology has enormous potential for advancing this field. Trent enjoys hiking, fishing, and snowmobiling in the nearby mountains. He also enjoys playing basketball, racquetball, and ultimate. For this year’s project, Trent aided in laboratory work, team coordination, gathering materials for the Wiki, and preparation of the presentation materials. </p><br />
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<img src=" https://static.igem.org/mediawiki/2009/3/32/Brad_Henrie_cropped.jpg" align = "right" height="150" style="padding:.5px; border-style:solid; border-color:#999" alt="Brad Henrie" /> <br />
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BRAD HENRIE<br />
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<p class="margin">Brad is a graduate student in the Biological and Irrigation Engineering at Utah State University. His personal research is centered around analyzing an unknown microbial community, and characterizing it's genetic phylogeny. Brad is participating in the iGEM competition for the first time, and has enjoyed being a part of the group. He has a passion for caving, and tries to go as often as the team would let him. Other than that, he enjoys rock climbing, camping, the occasional computer game, and is excited for the duck hunting season. Brad was primarily responsible for culturing the cyanobacteria, and conducting the tri-parental mating procedure, and generally helped out around the lab.<br />
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<img src="https://static.igem.org/mediawiki/2009/7/7f/Libbie_Linton_cropped.jpg" align = "right" height="150" style="padding:.5px; border-style:solid; border-color:#999" alt="Libbie Linton" /> <br />
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LIBBIE LINTON<br />
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<p class="margin">Libbie is a Masters student in Biological Engineering. Like a few others on this year's team, Libbie was also a member of the 2008 iGEM team. She is glad to be back for a second year, this time as an advisor. Her Masters' work is in investigating different ways to improve PHA production economics. She is hoping to complete her thesis within the next few months, followed by finding employment in bioprocess/biochemical engineering. In her spare time, Libbie is a musician. She also enjoys beating fellow iGEM teammate Trent Mortensen in racquetball, as well as playing with her 6 month old puppy, Rooster. For this years' iGEM team, Libbie advised on topics related to bioplastic production, secretion systems and mechanisms, and general laboratory procedures. She was also involved in coordinating efforts with the wiki. <br />
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<img src="https://static.igem.org/mediawiki/2008/7/7f/JH.jpg" align = "right" height="158" style="padding:.5px; border-style:solid; border-color:#999" alt="Junling Huo" /> <br />
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JUNLING HUO<br />
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<p class="margin">Junling Huo is a PhD student in Biological Engineering at USU. His dissertation research is focused on design a gene expression system for Rhodobacter sphaeroides, which is a photosynthetic bacteria. This gene expression system will include BioBrick compatible promoters, Ribosome Binding Sites (RBS), and terminators. The planned promoters and RBS will have different activities. Terminators will be either bidirectional or unidirectional. He hopes to complete his dissertation in the next year or so, and continuing doing research. He was also a member of 2008 USU iGEM team, and is happy to serve as an advisor again this year.<br />
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Our faculty advisors are Dr. Ronald C. Sims, Dean H. Scott Hinton, and Dr. Charles D. Miller. We would like to thank them for all of their help and guidance throughout the project. To view their professional biographies, please refer to our <a href="http://www.bie.usu.edu/"><b><font color =#009900>department website</font></b></a>:<br />
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<b><i>Utah State University</i></b></font><br />
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<p class="class"><br />
Located in <a href="http://www.loganutah.org/"><b><font color=#009900>Logan, Utah</font></b></a>, about 80 miles north of Salt Lake City, Utah State University sits just outside the mouth of Logan Canyon. The city, founded in 1859, has a population of approximately 47,000 and boasts a rich heritage. Whether on campus, historic Main Street, down in the “island”, or up the canyon, there is always something to do. <br />
</p><br />
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Originally founded in 1888 as the Agricultural College of Utah, the school officially became a university in 1957. As the state's land-and space-grant university, USU conducts world-class research in many disciplines and has several projects in conjunction with the Department of Defense and NASA. USU’s research program is second in age only to MIT in the United States. USU's <a href="http://www.sdl.usu.edu/index-noflash.html"><b><font color =#009900>Space Dynamics Laboratory</font></b></a> has put more experiments into space than any university in the world and is ranked first in the United States for funding for aerospace research. <br />
</p><br />
<p class="class">The <a href="http://www.engineering.usu.edu"><b><font color=#009900>engineering</font></b></a> program at Utah State is known for its excellence, with a 96% first-time pass rate on the national engineering exam compared to a national average of 55%. Beyond the Logan campus, Utah State's Extension programs extend academic resources and support throughout the entire state of Utah, having extension locations in each of Utah's 29 counties.</p><br />
<p class="class"><a href="http://www.bie.usu.edu/"><b><font color =#009900>Biological and Irrigation Engineering</font></b></a> is a relatively small department at Utah State, with about 30 faculty and 120 undergraduate and graduate students. This great student-to-teacher ratio helps students succeed in their classes. The Biological Engineering Program teaches students to manipulate biological systems for useful purposes, understand scientific literature, and to work well with and communicate effectively with others, both in the field of Biological Engineering and out. In the first years of the program, students learn the basics of biology, chemistry, physics, and mathematics. This knowledge base is then broadened by a study of liberal arts and humanities including literature, philosophy, political science, art, and music classes. Students finally delve into technical engineering courses, many chosen personally by students to apply to their particular areas of interest. These courses develop practical problem-solving abilities, increasing sensitivity to the economic, social, and legal dimensions of technical problems. Students leave the program well-qualified for their careers, with an understanding of the importance of social and professional ethics and responsibility to accompany their technical learning. After graduation, students will apply their knowledge to a wide range of careers, from genetic engineering to design of prosthetic devices for amputees.</p><br />
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<a href="http://www.bie.usu.edu/"><img src="https://static.igem.org/mediawiki/2009/2/29/Logan_canyon.jpg" align = "middle" height="217" style="float:left;" alt="Logan Canyon"/> </a><br />
<a href="http://www.engineering.usu.edu/"><img src="https://static.igem.org/mediawiki/2009/a/aa/USU_Campus.jpg" align = "middle" height="217" style="float:left;"alt="Campus"/></a><br />
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<td id="nav"><a href="https://2009.igem.org/Team:Utah_State"><font size = 4>HOME</font></a></td><br />
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<td id="nav"><a href="https://2009.igem.org/Team:Utah_State/Team"><font size = 4>ABOUT US</font></a></td><br />
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<b><i>Contact Us</b></i></font><br />
<HR><br />
<p class="class"><br />
We would like to hear your questions and comments! Please send us an email and come talk to us at the Jamboree! Thanks for your interest in USU iGEM 2009. Be sure to also check out the links to our sponsors web pages - we have greatly appreciated their help. </p><br />
<br />
<ul class="circle"><br />
<li>Dr. Charles Miller: charles.miller@engineering.usu.edu </li><br />
<li>The USU iGEM Team: iGEMUSU@gmail.com </li></ul><br />
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<a href="http://www.engineering.usu.edu/"><img src="https://static.igem.org/mediawiki/2009/2/25/CollegeofEng.png" align = "middle" height="100" style="float:center;" alt="COE"></a><br />
<a href="http://www.bie.usu.edu/"><img src="https://static.igem.org/mediawiki/2009/9/9c/BIEpicture.png" align = "middle" height="100" style="float:center;" alt="BIE"> </div><br />
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<div></div>Ahatchhttp://2009.igem.org/Team:Utah_State/TeamTeam:Utah State/Team2009-09-24T07:34:07Z<p>Ahatch: </p>
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!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State|<font color="#ffffff">Home</font>]]<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State/Team|<font color="#A9A9A9">The Team</font>]]<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State/Project|<font color="#ffffff">The Project</font>]]<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State/Parts|<font color="#ffffff">Parts</font>]]<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State/Notebook|<font color="#ffffff">Notebook</font>]]<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State/Protocols|<font color="#ffffff">Protocols</font>]]<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State/Links|<font color="#ffffff">Links</font>]]<br />
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{|align="justify"<br />
|Utah State University is participating for the second time in the iGEM Competition. The Department of Biological and Irrigation Engineering and the College of Engineering at Utah State University are the primary supporters of our team. We thank them for providing such a tremendous opportunity.<br />
|-<br />
|Our team is a combination of local high school students, undergraduates and graduates from the Department of Biological and Irrigation Engineering, and our outstanding faculty advisors.<br />
|-<br />
|align="center"|[[Team:Utah_State | Team Example 2]]<br />
|}<br />
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<br />
== '''Who we are''' ==<br />
{|border = "0"<br />
|-<br />
|rowspan="3"|<br />
<br />
'''FACULTY ADVISORS:'''<br />
*'''Scott Hinton''': Dean of the College of Engineering, USU<br />
*'''Dr. Charles Miller''': Department of Biological and Irrigation Engineering, USU<br />
*'''Dr. Ronald C. Sims''': Department of Biological and Irrigation Engineering, USU<br />
<br />
'''GRADUATE STUDENTS:''' <br />
*'''Brad Henrie''': Department of Biological and Irrigation Engineering, USU <br />
*'''Elisabeth Linton''': Department of Biological and Irrigation Engineering, USU <br />
*'''Trent Mortensen''': Department of Biological and Irrigation Engineering, USU <br />
<br />
'''UNDERGRADUATE STUDENTS:'''<br />
*'''Amanda Feldt''': Department of Biological and Irrigation Engineering, USU<br />
*'''Alex Hatch''': Department of Biological and Irrigation Engineering, USU<br />
*'''Rachel Nicole Porter Jackson''': Department of Biological and Irrigation Engineering, USU <br />
*'''Cole Peterson''': Department of Biological and Irrigation Engineering, USU<br />
<br />
'''HIGH SCHOOL STUDENTS:'''<br />
*'''Sean Bedingfield''': Sky View High School<br />
*'''Garrett Hinton''': Sky View High School<br />
*'''Jody Jerez''': InTech Collegiate High School<br />
*'''Jeff Karren''': InTech Collegiate High School <br />
*'''Hyunjin Kim''': InTech Collegiate High School<br />
*'''Tyrel Rupp''': Sky View High School<br />
|<br />
<gallery><br />
Image:Dean_Hinton.jpg|Dean Scott Hinton<br />
Image:Ron_Sims.jpg|Dr. Ron Sims<br />
Image:Miller1.png|Charles Miller<br />
Image:Brad's_temp_iGEM_picture.JPG|Brad Henrie<br />
Image:LibbieL.jpg|Elisabeth Linton<br />
Image:Trent Mortensen iGEM.jpg|Trent Mortensen<br />
Image:RachelJacksonigem.jpg|Rachel Nicole Porter Jackson<br />
Image:AlexPicture.jpg|Alex Hatch<br />
Image:DSCN3548.JPG|Cole Peterson<br />
Image:SeanBedingfield.jpg|Sean Bedingfield<br />
Image:Jody.JPG|Jody Jerez<br />
Image:Jeff Karren.jpg|Jeff Karren<br />
Image:Jins.JPG|Hyun-Jin Kim<br />
Image:Tyruppsprofile.JPG|Tyrel Rupp</gallery><br />
|}<br />
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== '''More About Us'''==<br />
<br />
*'''Trent Mortensen''' is a master's student in Biological Engineering. His main research direction is biomedical in nature, studying the antimycobacterial properties of the St. John's Wort herb. He was on the 2008 Utah State iGEM team and is working as a graduate advisor for the 2009 team.<br />
<br />
*'''Elisabeth Linton''' is a Biological Engineering student. Her research is focused on polyhydroxyalkanoates. For the iGEM team, Libbie helped in project determination and planning, as well as literature review and topic research. She also carried out work in the laboratory like restriction enzyme digestions, gel electrophoresis, DNA isolation, and bacterial transformations. She was also responsible for coordinating efforts and organizing the wiki.<br />
<br />
*'''Rachel Nicole Porter Jackson''' is in her third year at Utah State University majoring in Biological Engineering. For the iGEM project, she helped to carry out some of the lab work, work on the logo, and contribute to the wiki. In the lab, she helped isolate and purify DNA, prepare and run electrophoresis gels, and culture cells.<br />
<br />
*'''Matthew Sims''' is a Senior attending Logan High School. This is his first year participating in laboratory research at Utah State University. He plans to go to college next fall and continue his studies in molecular biology and biochemistry. He helped during the summer months to carry out many experiments and obtain and analyze data.<br />
<br />
*'''Garrett Hinton''' is a senior at Sky View High School in Smithfield, Utah. He was heavily involved in the project discussion meetings, as well as the background literature research. Garrett spent many hours working on this project and carried out a substantial portion of the laboratory work.<br />
<br />
*'''Sean Bedingfield''' is a freshman at Utah State University majoring in Biological Engineering/pre-med. He has been involved with some lab work and research into the systems of various bacteria for the project.<br />
<br />
*'''Hyunjin Kim''' is a freshmen at InTech Collegiate High School. He is from Gwangju, South Korea. He has followed his father, who is a visiting professor, to Logan, Utah and got interested at the iGEM project and joined the team. He is now learning many skills in the laboratory by his helpers.<br />
<br />
*'''Jeff Karren''' is a senior at InTech Collegiate High School, and hails from Logan, Utah. As one of several InTech students selected to participate in internships with USU's biological engineering department, he had the opportunity to join the iGEM team at USU. He has specialized mostly in helping with the wiki, but has assisted in some lab work, including using CTAB to isolate DNA plasmids.<br />
<br />
*'''Tyrel Rupp''' is a senior at Sky View High School in Smithfield, Utah. This is his first year involved in iGEM. As well as being an excellent pipetter, he is skilled in many of the laboratory arts such as electrophoresis and DNA transformation.<br />
<br />
*'''Alex Hatch''' is a junior at Utah State University with a major in Biological Engineering and a pre-med emphasis. He's a Utah native. Currently he's working on research dealing with microbial diversity in bioremediation, with a developing interest in synthetic biology.<br />
<br />
== '''Logan and USU''' ==<br />
[[Image:USU_Campus.jpg|right|450px]]<br />
[[Image:USU1.gif|left|508px]]<br />
[[Image:Logo_horizontal.gif]]<br />
<br />
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<b><a href="http://www.usu.edu/">Utah State University</a></b> is located in Logan, Utah. Logan is about 80 miles north of Salt Lake City, Utah. The city of Logan is located in the heart of Cache Valley near the western slopes of the Bear River Mountains, the northernmost branch of the Wasatch Range. The city has a population of approximately 47,000. Logan was established in 1859 and has a rich heritage and wonderful culture. The city of Logan has been stated to be among the safest cities in America.<br><br />
<br><br />
Utah State University was established in 1888 as the Agricultural College of Utah. Its name was later changed to Utah State Agricultural College and finally became Utah State University (USU) in 1957. As the land-grant university in Utah, USU conducts world-class research in a variety of agricultural and natural resource disciplines, and has several projects in conjunction with the Department of Defense and NASA. Utah State University also conducts extensive aerospace research. The main campus is located in Logan, Utah. Beyond the Logan campus, Utah State's Extension programs extend academic resources and support throughout the entire state of Utah, having extension locations in each of Utah's 29 counties.<br><br />
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[[Image:600px-Sant_Blgd.jpg|right|frame|''The Sant Building is home to the new USU synthetic biology laboratory'']]<br />
[[Image:Utah_State.jpg]]<br />
[[Image:USUheader.gif]]</div>Ahatchhttp://2009.igem.org/Team:Utah_State/TeamTeam:Utah State/Team2009-09-24T07:28:32Z<p>Ahatch: </p>
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<div>{|style="font color="#CC3300"; background-color:#212223; cellpadding="3" cellspacing="5" border="2" bordercolor="#cd0000"border-spacing:6px; text-align:center" width="960px"<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State|<font color="#ffffff">Home</font>]]<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State/Team|<font color="#A9A9A9">The Team</font>]]<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State/Project|<font color="#ffffff">The Project</font>]]<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State/Parts|<font color="#ffffff">Parts</font>]]<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State/Notebook|<font color="#ffffff">Notebook</font>]]<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State/Protocols|<font color="#ffffff">Protocols</font>]]<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State/Links|<font color="#ffffff">Links</font>]]<br />
|}<br />
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{|align="justify"<br />
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Utah State University is participating for the second time in the iGEM Competition. The Department of Biological and Irrigation Engineering and the College of Engineering at Utah State University are the primary supporters of our team. We thank them for providing such a tremendous opportunity.<br />
<br />
<br />
Our team is a combination of local high school students, undergraduates and graduates from the Department of Biological and Irrigation Engineering, and our outstanding faculty advisors.<br />
<br />
|<br />
|align="center"|[[Team:Utah_State | Team Example 2]]<br />
|}<br />
<br />
<br />
== '''Who we are''' ==<br />
{|border = "0"<br />
|-<br />
|rowspan="3"|<br />
<br />
'''FACULTY ADVISORS:'''<br />
*'''Scott Hinton''': Dean of the College of Engineering, USU<br />
*'''Dr. Charles Miller''': Department of Biological and Irrigation Engineering, USU<br />
*'''Dr. Ronald C. Sims''': Department of Biological and Irrigation Engineering, USU<br />
<br />
'''GRADUATE STUDENTS:''' <br />
*'''Brad Henrie''': Department of Biological and Irrigation Engineering, USU <br />
*'''Elisabeth Linton''': Department of Biological and Irrigation Engineering, USU <br />
*'''Trent Mortensen''': Department of Biological and Irrigation Engineering, USU <br />
<br />
'''UNDERGRADUATE STUDENTS:'''<br />
*'''Amanda Feldt''': Department of Biological and Irrigation Engineering, USU<br />
*'''Alex Hatch''': Department of Biological and Irrigation Engineering, USU<br />
*'''Rachel Nicole Porter Jackson''': Department of Biological and Irrigation Engineering, USU <br />
*'''Cole Peterson''': Department of Biological and Irrigation Engineering, USU<br />
<br />
'''HIGH SCHOOL STUDENTS:'''<br />
*'''Sean Bedingfield''': Sky View High School<br />
*'''Garrett Hinton''': Sky View High School<br />
*'''Jody Jerez''': InTech Collegiate High School<br />
*'''Jeff Karren''': InTech Collegiate High School <br />
*'''Hyunjin Kim''': InTech Collegiate High School<br />
*'''Tyrel Rupp''': Sky View High School<br />
|<br />
<gallery><br />
Image:Dean_Hinton.jpg|Dean Scott Hinton<br />
Image:Ron_Sims.jpg|Dr. Ron Sims<br />
Image:Miller1.png|Charles Miller<br />
Image:Brad's_temp_iGEM_picture.JPG|Brad Henrie<br />
Image:LibbieL.jpg|Elisabeth Linton<br />
Image:Trent Mortensen iGEM.jpg|Trent Mortensen<br />
Image:RachelJacksonigem.jpg|Rachel Nicole Porter Jackson<br />
Image:AlexPicture.jpg|Alex Hatch<br />
Image:DSCN3548.JPG|Cole Peterson<br />
Image:SeanBedingfield.jpg|Sean Bedingfield<br />
Image:Jody.JPG|Jody Jerez<br />
Image:Jeff Karren.jpg|Jeff Karren<br />
Image:Jins.JPG|Hyun-Jin Kim<br />
Image:Tyruppsprofile.JPG|Tyrel Rupp</gallery><br />
|}<br />
<br />
== '''More About Us'''==<br />
<br />
*'''Trent Mortensen''' is a master's student in Biological Engineering. His main research direction is biomedical in nature, studying the antimycobacterial properties of the St. John's Wort herb. He was on the 2008 Utah State iGEM team and is working as a graduate advisor for the 2009 team.<br />
<br />
*'''Elisabeth Linton''' is a Biological Engineering student. Her research is focused on polyhydroxyalkanoates. For the iGEM team, Libbie helped in project determination and planning, as well as literature review and topic research. She also carried out work in the laboratory like restriction enzyme digestions, gel electrophoresis, DNA isolation, and bacterial transformations. She was also responsible for coordinating efforts and organizing the wiki.<br />
<br />
*'''Rachel Nicole Porter Jackson''' is in her third year at Utah State University majoring in Biological Engineering. For the iGEM project, she helped to carry out some of the lab work, work on the logo, and contribute to the wiki. In the lab, she helped isolate and purify DNA, prepare and run electrophoresis gels, and culture cells.<br />
<br />
*'''Matthew Sims''' is a Senior attending Logan High School. This is his first year participating in laboratory research at Utah State University. He plans to go to college next fall and continue his studies in molecular biology and biochemistry. He helped during the summer months to carry out many experiments and obtain and analyze data.<br />
<br />
*'''Garrett Hinton''' is a senior at Sky View High School in Smithfield, Utah. He was heavily involved in the project discussion meetings, as well as the background literature research. Garrett spent many hours working on this project and carried out a substantial portion of the laboratory work.<br />
<br />
*'''Sean Bedingfield''' is a freshman at Utah State University majoring in Biological Engineering/pre-med. He has been involved with some lab work and research into the systems of various bacteria for the project.<br />
<br />
*'''Hyunjin Kim''' is a freshmen at InTech Collegiate High School. He is from Gwangju, South Korea. He has followed his father, who is a visiting professor, to Logan, Utah and got interested at the iGEM project and joined the team. He is now learning many skills in the laboratory by his helpers.<br />
<br />
*'''Jeff Karren''' is a senior at InTech Collegiate High School, and hails from Logan, Utah. As one of several InTech students selected to participate in internships with USU's biological engineering department, he had the opportunity to join the iGEM team at USU. He has specialized mostly in helping with the wiki, but has assisted in some lab work, including using CTAB to isolate DNA plasmids.<br />
<br />
*'''Tyrel Rupp''' is a senior at Sky View High School in Smithfield, Utah. This is his first year involved in iGEM. As well as being an excellent pipetter, he is skilled in many of the laboratory arts such as electrophoresis and DNA transformation.<br />
<br />
*'''Alex Hatch''' is a junior at Utah State University with a major in Biological Engineering and a pre-med emphasis. He's a Utah native. Currently he's working on research dealing with microbial diversity in bioremediation, with a developing interest in synthetic biology.<br />
<br />
== '''Logan and USU''' ==<br />
[[Image:USU_Campus.jpg|right|450px]]<br />
[[Image:USU1.gif|left|508px]]<br />
[[Image:Logo_horizontal.gif]]<br />
<br />
<html><br />
<style type="text/css"><br />
<br />
</style> <br />
<b><a href="http://www.usu.edu/">Utah State University</a></b> is located in Logan, Utah. Logan is about 80 miles north of Salt Lake City, Utah. The city of Logan is located in the heart of Cache Valley near the western slopes of the Bear River Mountains, the northernmost branch of the Wasatch Range. The city has a population of approximately 47,000. Logan was established in 1859 and has a rich heritage and wonderful culture. The city of Logan has been stated to be among the safest cities in America.<br><br />
<br><br />
Utah State University was established in 1888 as the Agricultural College of Utah. Its name was later changed to Utah State Agricultural College and finally became Utah State University (USU) in 1957. As the land-grant university in Utah, USU conducts world-class research in a variety of agricultural and natural resource disciplines, and has several projects in conjunction with the Department of Defense and NASA. Utah State University also conducts extensive aerospace research. The main campus is located in Logan, Utah. Beyond the Logan campus, Utah State's Extension programs extend academic resources and support throughout the entire state of Utah, having extension locations in each of Utah's 29 counties.<br><br />
<br />
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</html><br />
<br />
[[Image:600px-Sant_Blgd.jpg|right|frame|''The Sant Building is home to the new USU synthetic biology laboratory'']]<br />
[[Image:Utah_State.jpg]]<br />
[[Image:USUheader.gif]]</div>Ahatchhttp://2009.igem.org/Team:Utah_State/NotebookTeam:Utah State/Notebook2009-09-24T06:54:06Z<p>Ahatch: </p>
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!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State|<font color="#ffffff">Home</font>]]<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State/Team|<font color="#ffffff">The Team</font>]]<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State/Project|<font color="#ffffff">The Project</font>]]<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State/Parts|<font color="#ffffff">Parts</font>]]<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State/Notebook|<font color="#A9A9A9">Notebook</font>]]<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State/Protocols|<font color="#ffffff">Protocols</font>]]<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State/Links|<font color="#ffffff">Links</font>]]<br />
|}<br />
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<!--- The Mission, Experiments ---><br />
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==Team Meetings==<br />
----<br />
;''May 12''<br />
:Introduction to iGEM and to team members. Reviewed last years competition. Overview of the iGEM website.<br />
*Plan-Become familiar with website, review team projects from previous years, create user accounts.<br />
<br />
;''June 23''<br />
:Discussed University of Hawaii team project from 2008. Watched their presentation and discussed their project goals. Decided as a group to continue their project where they left off, after having made contact with them.<br />
*Plan-Request constructs and parts from team Hawaii. Have conference call with last year's Hawaii team. Literature search.<br />
<br />
;''June 30''<br />
:Team introduction to working with a wiki. Waiting for constructs. <br />
*Plan-Contribute name, brief autobiographical description, and picture to wiki.<br />
<br />
;''August ?''<br />
:Project Progress Check.<br />
::Broad-Host Vector: After PCR, ligation attempts, gel observations, it appears that the Broad-Host Vector in the catalog is not functioning nor is it the anticipated length. Intend to take a known broad-host vector, perform an enzyme digestion and test ability of vector to carry red flourescent protein sequence. <br />
<br />
;''September 3''<br />
<br />
;''September 10''<br />
:Finalized team roster and travel information. Reviewed judging criteria, our current standing as far as BioBricks designed, what could still be designed and feasibly tested. Discussed the track in which we would compete. Assignments made for next meeting.<br />
*Plan-Complete abstract, finalize title and track by Sept. 18.<br />
:1. Cole Peterson - Set up ligation of pRL1383a/BBa_I20260 and test.<br />
:2. Alex Hatch - Submit schedule for availability to Cole, assist Cole with vector construction, write team background and post on the wiki.<br />
:3. Garrett Hinton - Write a general project description for the front page of the wiki (see last years wiki, and other team's wiki's to get an idea of what you should write about and ask Libby, Trent, or Cole if you've any questions.<br />
:4. Tyrell Rupp- Have a draft-version of a flash animation for our project. <br />
:5. Rachel Porter- Have 3 logo ideas ready for the team to choose from.<br />
:6. Jody Jerez/Jeff Karren- Edit/Post protocols on Wiki (you will need to contact other people in lab for help with revisions). Edit these so that they are also not just cut and paste from last years. <br />
<br />
;''September 17''<br />
:Had final discussions on project title and track we intend to compete in. Reviewed the project abstract. Discussed Wiki progress.</div>Ahatchhttp://2009.igem.org/File:USU6.gifFile:USU6.gif2009-09-22T01:35:34Z<p>Ahatch: </p>
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<div></div>Ahatchhttp://2009.igem.org/File:USU5.gifFile:USU5.gif2009-09-22T01:33:53Z<p>Ahatch: uploaded a new version of "Image:USU5.gif"</p>
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<div></div>Ahatchhttp://2009.igem.org/File:USU5.gifFile:USU5.gif2009-09-22T01:14:36Z<p>Ahatch: </p>
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<div></div>Ahatchhttp://2009.igem.org/Team:Utah_State/TeamTeam:Utah State/Team2009-09-22T01:07:36Z<p>Ahatch: </p>
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<div>{|style="font color="#CC3300"; background-color:#212223; cellpadding="3" cellspacing="5" border="2" bordercolor="#cd0000"border-spacing:6px; text-align:center" width="960px"<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State|<font color="#ffffff">Home</font>]]<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State/Team|<font color="#A9A9A9">The Team</font>]]<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State/Project|<font color="#ffffff">The Project</font>]]<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State/Parts|<font color="#ffffff">Parts</font>]]<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State/Notebook|<font color="#ffffff">Notebook</font>]]<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State/Protocols|<font color="#ffffff">Protocols</font>]]<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State/Links|<font color="#ffffff">Links</font>]]<br />
|}<br />
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[[Image:OldMain.jpg|540px|right]]<br />
[[Image:USU1.gif|left|410px]]<br />
{|align="justify"<br />
|You can write a background of your team here. Give us a background of your team, the members, etc. Or tell us more about something of your choosing.<br />
|[[Image:Example_logo.png|200px|right|frame]]<br />
|-<br />
|<br />
''Tell us more about your project. Give us background. Use this is the abstract of your project. Be descriptive but concise (1-2 paragraphs)''<br />
|-<br />
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|align="center"|[[Team:Utah_State | Team Example 2]]<br />
|}<br />
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<br />
== '''Who we are''' ==<br />
{|border = "0"<br />
|-<br />
|rowspan="3"|<br />
<br />
'''FACULTY ADVISORS:'''<br />
*'''Scott Hinton''': Dean of the College of Engineering, USU<br />
*'''Dr. Charles Miller''': Department of Biological and Irrigation Engineering, USU<br />
*'''Dr. Ronald C. Sims''': Department of Biological and Irrigation Engineering, USU<br />
<br />
'''GRADUATE STUDENTS:''' <br />
*'''Brad Henrie''': Department of Biological and Irrigation Engineering, USU <br />
*'''Elisabeth Linton''': Department of Biological and Irrigation Engineering, USU <br />
*'''Trent Mortensen''': Department of Biological and Irrigation Engineering, USU <br />
<br />
'''UNDERGRADUATE STUDENTS:'''<br />
*'''Amanda Feldt''': Department of Biological and Irrigation Engineering, USU<br />
*'''Alex Hatch''': Department of Biological and Irrigation Engineering, USU<br />
*'''Rachel Nicole Porter Jackson''': Department of Biological and Irrigation Engineering, USU <br />
*'''Cole Peterson''': Department of Biological and Irrigation Engineering, USU<br />
<br />
'''HIGH SCHOOL STUDENTS:'''<br />
*'''Sean Bedingfield''': Sky View High School<br />
*'''Garrett Hinton''': Sky View High School<br />
*'''Jody Jerez''': InTech Collegiate High School<br />
*'''Jeff Karren''': InTech Collegiate High School <br />
*'''Hyunjin Kim''': InTech Collegiate High School<br />
*'''Tyrel Rupp''': Sky View High School<br />
|<br />
<gallery><br />
Image:Dean_Hinton.jpg|Dean Scott Hinton<br />
Image:Ron_Sims.jpg|Dr. Ron Sims<br />
Image:Miller1.png|Charles Miller<br />
Image:Brad's_temp_iGEM_picture.JPG|Brad Henrie<br />
Image:LibbieL.jpg|Elisabeth Linton<br />
Image:Trent Mortensen iGEM.jpg|Trent Mortensen<br />
Image:RachelJacksonigem.jpg|Rachel Nicole Porter Jackson<br />
Image:AlexPicture.jpg|Alex Hatch<br />
Image:DSCN3548.JPG|Cole Peterson<br />
Image:SeanBedingfield.jpg|Sean Bedingfield<br />
Image:Jody.JPG|Jody Jerez<br />
Image:Jeff Karren.jpg|Jeff Karren<br />
Image:Jins.JPG|Hyun-Jin Kim</gallery><br />
<br />
|}<br />
<br />
== '''More About Us'''==<br />
<br />
*'''Trent Mortensen''' is a master's student in Biological Engineering. His main research direction is biomedical in nature, studying the antimycobacterial properties of the St. John's Wort herb. He was on the 2008 Utah State iGEM team and is working as a graduate advisor for the 2009 team.<br />
<br />
*'''Elisabeth Linton''' is a Biological Engineering student. Her research is focused on polyhydroxyalkanoates. For the iGEM team, Libbie helped in project determination and planning, as well as literature review and topic research. She also carried out work in the laboratory like restriction enzyme digestions, gel electrophoresis, DNA isolation, and bacterial transformations. She was also responsible for coordinating efforts and organizing the wiki.<br />
<br />
*'''Rachel Nicole Porter Jackson''' is in her third year at Utah State University majoring in Biological Engineering. For the iGEM project, she helped to carry out some of the lab work, work on the logo, and contribute to the wiki. In the lab, she helped isolate and purify DNA, prepare and run electrophoresis gels, and culture cells.<br />
<br />
*'''Matthew Sims''' is a Senior attending Logan High School. This is his first year participating in laboratory research at Utah State University. He plans to go to college next fall and continue his studies in molecular biology and biochemistry. He helped during the summer months to carry out many experiments and obtain and analyze data.<br />
<br />
*'''Garrett Hinton''' is a senior at Sky View High School in Smithfield, Utah. He was heavily involved in the project discussion meetings, as well as the background literature research. Garrett spent many hours working on this project and carried out a substantial portion of the laboratory work.<br />
<br />
*'''Sean Bedingfield''' is a freshman at Utah State University majoring in Biological Engineering/pre-med. He has been involved with some lab work and research into the systems of various bacteria for the project.<br />
<br />
*'''Hyunjin Kim''' is a freshmen at InTech Collegiate High School. He is from Gwangju, South Korea. He has followed his father, who is a visiting professor, to Logan, Utah and got interested at the iGEM project and joined the team. He is now learning many skills in the laboratory by his helpers.<br />
<br />
*'''Jeff Karren''' is a senior at InTech Collegiate High School, and hails from Logan, Utah. As one of several InTech students selected to participate in internships with USU's biological engineering department, he had the opportunity to join the iGEM team at USU. He has specialized mostly in helping with the wiki, but has assisted in some lab work, including using CTAB to isolate DNA plasmids.<br />
<br />
*'''Tyrel Rupp''' is a senior at Sky View High School in Smithfield, Utah. This is his first year involved in iGEM. As well as being an excellent pipetter, he is skilled in many of the laboratory arts such as electrophoresis and DNA transformation.<br />
<br />
*'''Alex Hatch''' is a junior at Utah State University with a major in Biological Engineering and a pre-med emphasis. He's a Utah native. Currently he's working on research dealing with microbial diversity in bioremediation, with a developing interest in synthetic biology.<br />
<br />
== '''Logan and USU''' ==<br />
[[Image:USU_Campus.jpg|right|450px]]<br />
[[Image:USU1.gif|left|508px]]<br />
[[Image:Logo_horizontal.gif]]<br />
<br />
<html><br />
<style type="text/css"><br />
<br />
</style> <br />
<b><a href="http://www.usu.edu/">Utah State University</a></b> is located in Logan, Utah. Logan is about 80 miles north of Salt Lake City, Utah. The city of Logan is located in the heart of Cache Valley near the western slopes of the Bear River Mountains, the northernmost branch of the Wasatch Range. The city has a population of approximately 47,000. Logan was established in 1859 and has a rich heritage and wonderful culture. The city of Logan has been stated to be among the safest cities in America.<br><br />
<br><br />
Utah State University was established in 1888 as the Agricultural College of Utah. Its name was later changed to Utah State Agricultural College and finally became Utah State University (USU) in 1957. As the land-grant university in Utah, USU conducts world-class research in a variety of agricultural and natural resource disciplines, and has several projects in conjunction with the Department of Defense and NASA. Utah State University also conducts extensive aerospace research. The main campus is located in Logan, Utah. Beyond the Logan campus, Utah State's Extension programs extend academic resources and support throughout the entire state of Utah, having extension locations in each of Utah's 29 counties.<br><br />
<br />
<br />
</html><br />
<br />
[[Image:600px-Sant_Blgd.jpg|right|frame|''The Sant Building is home to the new USU synthetic biology laboratory'']]<br />
[[Image:Utah_State.jpg]]<br />
[[Image:USUheader.gif]]</div>Ahatchhttp://2009.igem.org/File:OldMain.jpgFile:OldMain.jpg2009-09-22T01:01:13Z<p>Ahatch: </p>
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<div></div>Ahatchhttp://2009.igem.org/Team:Utah_State/LinksTeam:Utah State/Links2009-09-22T00:12:42Z<p>Ahatch: </p>
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<div>{|style="font color="#CC3300"; background-color:#212223; cellpadding="3" cellspacing="5" border="2" bordercolor="#cd0000"border-spacing:6px; text-align:center" width="960px"<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State|<font color="#ffffff">Home</font>]]<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State/Team|<font color="#ffffff">The Team</font>]]<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State/Project|<font color="#ffffff">The Project</font>]]<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State/Parts|<font color="#ffffff">Parts</font>]]<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State/Notebook|<font color="#ffffff">Notebook</font>]]<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State/Protocols|<font color="#ffffff">Protocols</font>]]<br />
!style="text-align:center; background-color:#212223; border-width:0px; padding:2px;"|[[Team:Utah_State/Links|<font color="#A9A9A9">Links</font>]]<br />
|}<br />
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body {background-image:url("https://static.igem.org/mediawiki/2008/6/63/Bkgnd14.gif");background-repeat:repeat; }</div>Ahatch