Berkeley UC

From 2007.igem.org

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<h1>UC Berkeley iGEM 2007</h1>
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<div id="apDiv3"><a href="https://2007.igem.org/Main_Page" title="iGEM 2007" alt="iGEM 2007"><img name="Coverlogo" src="https://static.igem.org/mediawiki/2007/0/0e/Coverlogojpeg.jpg" width="101" height="87" alt="iGEM 2007"></a></div>
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<table cellpadding="0" cellspacing="0" border="0" align="left" width="280" height="220" id="Header_Table" class="table_header" bgcolor="#8A0202"><tr><td id="Header_Table_TD" class="td_table_header" bgcolor="#8A0202">
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<a href="/igem07/index.php/Image:Berkeley_BactobloodHeader.jpg" class="image" title="BactoBlood">
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<script type="text/javascript">
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<img src="/igem07/images/c/cd/Berkeley_BactobloodHeader.jpg" alt="BactoBlood" width="940" height="305" longdesc="BactoBlood Image" /></a><br />
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<p><b>The necessity</b> of inexpensive, available, disease free, and  
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</td>
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universally compatible blood substitutes is undisputed. There are  
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currently no blood substitutes approved for use in the US or the UK,  
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and whole blood is almost always in short supply. Developing  
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<img src="https://static.igem.org/mediawiki/2007/d/da/BerkiGEM2007-Bactoblood_text.jpg" border="0" id="Bactoblood_Header_Text_Img">
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countries have the greatest need for blood transfusions, however
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<p><span id="Intro_Text">The necessity of inexpensive, disease-free, and universally compatible blood substitutes is undisputed. There are currently no blood substitutes approved for use in the US or the UK, and whole blood is almost always in short supply. Developing countries have the greatest need for blood transfusions, yet many lack the necessary donation and storage infrastructure and the required pool of healthy donors. To address this problem, we are developing a cost-effective red blood cell substitute constructed from engineered <i>E. coli</i> bacteria. Our system is designed to safely transport oxygen in the bloodstream without inducing sepsis, and to be stored for prolonged periods in a freeze-dried state.<br /><br /></span></p>
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many lack the necessary donation and storage infrastructure and the  
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<p><span id="Support_Text"><b><i>Support for Berkeley iGEM 2007 was generously provided by  
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required number of healthy donors. To address this problem, we are  
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SynBERC and The Camille and Henry Dreyfus Foundation, Inc.</i></b>
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developing an innovative and cost-effective blood substitute  
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</span></p><hr />
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constructed from <i>E. coli</i> bacteria engineered to include the
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critical capabilities of human erythrocytes. Our bacterial system  
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includes the ability to safely exist in the bloodstream, carry
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oxygen with hemoglobin, and be stored for prolonged periods in a  
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freeze-dried state.<br /><br /></p>
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<p><b><i>Support for Berkeley iGEM 2007 was generously provided by  
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SynBERC and The Camille and Henry Dreyfus Foundation, Inc.</i> </b>
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</p><hr />
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<p>&nbsp;</p>
<p>&nbsp;</p>
<p align="left">
<p align="left">
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<table width="100%" id="table2" border="2" cellpadding="0" style="padding: 0px; width: 100%; color: navyblue; background-color: lightblue;" id="Main_Icons_Table">
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<h3>Project Modules</h3></td>
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<h3>The System's Components</h3></td>
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<td class="tdboxes"><a href="https://2007.igem.org/BerkiGEM2007Present1"><img border="0" src="https://static.igem.org/mediawiki/2007/e/e5/Berk-Icon-Oxygen.png" width="121" height="121"></a></td>
<td class="tdboxes"><a href="https://2007.igem.org/BerkiGEM2007Present1"><img border="0" src="https://static.igem.org/mediawiki/2007/e/e5/Berk-Icon-Oxygen.png" width="121" height="121"></a></td>
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<td class="tddesc"><b><a href="https://2007.igem.org/BerkiGEM2007Present1">Oxygen Carrying</a></b><p><i>Our system is  
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<td class="tddesc"><b><a href="https://2007.igem.org/BerkiGEM2007Present1">Oxygen Transport</a></b><p><i>Our system is  
designed to produce Hemoglobin, Heme, and the necessary  
designed to produce Hemoglobin, Heme, and the necessary  
chaperones and detoxifying agents to promote the transport  
chaperones and detoxifying agents to promote the transport  
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<td class="tddesc"><b><a href="https://2007.igem.org/BerkiGEM2007Present4">The Chassis</a></b><p><i>Our bacterial  
<td class="tddesc"><b><a href="https://2007.igem.org/BerkiGEM2007Present4">The Chassis</a></b><p><i>Our bacterial  
chassis has been heavily modified to remove its  
chassis has been heavily modified to remove its  
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sepsis-inducing toxicity, as well as promote its ability to  
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sepsis-inducing toxicity, immunogenic factors, and ability to grow
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last longer in the bloodstream by masking it from the immune  
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within the bloodstream, as well as promote its ability to last
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system.&nbsp; We performed this by lipopolysaccharide
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longer in the bloodstream by masking it from the immune  
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modifications as well as adding the K-capsule and O-antigen.</i></td>
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system.</i></td>
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<a href="https://2007.igem.org/BerkiGEM2007Present3"><img border="0" src="https://static.igem.org/mediawiki/2007/8/8d/Berk-Icon-Controller.png" width="121" height="121"></a></td>
<a href="https://2007.igem.org/BerkiGEM2007Present3"><img border="0" src="https://static.igem.org/mediawiki/2007/8/8d/Berk-Icon-Controller.png" width="121" height="121"></a></td>
<td class="tddesc"><b><a href="https://2007.igem.org/BerkiGEM2007Present3">The Controller</a></b><p><i>The Controller  
<td class="tddesc"><b><a href="https://2007.igem.org/BerkiGEM2007Present3">The Controller</a></b><p><i>The Controller  
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is an integrated genetic circuit, comprised of two plasmids,
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is an integrated genetic circuit comprised of two plasmids that allows
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that directs the initiation and production of the primary
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stable maintenance of the system's various operons on a large single-copy
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systems proteins through its component operons.&nbsp; It is
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plasmid in a dormant state. Upon induction, the copy number of the
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composed of a pSC101 controller plasmid and an amplifiable
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operons and their transcription increase 100-fold resulting in a
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BAC utilizing the T7 RNAP expression system.</i></td>
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dramatic increase in protein expression.</i></td>
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<a href="https://2007.igem.org/BerkiGEM2007Present2"><img border="0" src="https://static.igem.org/mediawiki/2007/c/ce/Berk-Icon-Freeze-Drying.png" width="121" height="121"></a></td>
<a href="https://2007.igem.org/BerkiGEM2007Present2"><img border="0" src="https://static.igem.org/mediawiki/2007/c/ce/Berk-Icon-Freeze-Drying.png" width="121" height="121"></a></td>
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<td class="tddesc"><b><a href="https://2007.igem.org/BerkiGEM2007Present2">Freeze Drying</a></b><p><i>In order to
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<td class="tddesc"><b><a href="https://2007.igem.org/BerkiGEM2007Present2">Freeze Drying</a></b><p><i>To
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enable preservation of our bacteria for long time periods,  
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enable preservation of our bacteria for prolonged periods,  
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we have included the ability to produce compounds, such as
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we are including the ability to produce the compounds  
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hydroxyectoine, that will enable our bacteria to survive
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hydroxyectoine and trehalose that will enable our bacteria to  
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freeze-drying intact.&nbsp; This will dramatically increase
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survive freeze-drying intact.&nbsp; This will dramatically  
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shelf-life and decrease transport costs.</i></td>
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increase shelf-life and decrease transport costs.</i></td>
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<p><br /></p>
<p><br /></p>
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<h3>Other Stuff</h3></td>
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<td class="tdsmallboxes"><a href="https://2007.igem.org/BerkiGEM2007Present6"><img border="0" src="https://static.igem.org/mediawiki/2007/8/8b/Berk-Icon-Small-Patents.png" width="83" height="83"></a></td>
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<td class="tddesc" style="padding-bottom: 0px; padding-top: 7px;"><b><a href="https://2007.igem.org/BerkiGEM2007Present6">Human Practices</a></b><p><i>An examination of the landscape of patents and the patentablilty of Bactoblood where its parts are in an open source forum and the challenges associated with current patenting practices for synthetic biology.</i></td>
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<td class="tdsmallboxes"><a href="https://2007.igem.org/Berkeley_Individual_Contributions"><img border="0" src="https://static.igem.org/mediawiki/2007/0/06/Berk-Icon-Small-References.png" width="83" height="83"></a></td>
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<td class="tddesc"><b><a href="https://2007.igem.org/Berkeley_Individual_Contributions">Individual Contributions</a></b><p><i>The specific contributions made by each team member and advisor.</i></td>
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<td class="tdsmallboxes"><a href="https://2007.igem.org/BerkiGEM2007_Resources"><img border="0" src="https://static.igem.org/mediawiki/2007/d/da/Berk-Icon-Small-Resources.png" width="83" height="83"></a></td>
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<td class="tddesc"><b><a href="https://2007.igem.org/BerkiGEM2007_Resources">Team Resources</a></b><p><i>Organizational spreadsheets, useful tools and links.</i></td>
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</tr>
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<tr>
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<td class="tdsmallboxes"><a href="https://2007.igem.org/BerkiGEM2007_Notebooks"><img border="0" src="https://static.igem.org/mediawiki/2007/7/77/Berk-Icon-Small-Notebooks.png" width="83" height="83"></a></td>
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<td class="tddesc"><b><a href="https://2007.igem.org/BerkiGEM2007_Notebooks">Team Notebooks</a></b><p><i>The team members' daily logs of our research.</i></td>
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</tr>
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</table>
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<p><br /></p>
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<a href="/igem07/index.php/Rickey_Bonds" title="Rickey Bonds">
<a href="/igem07/index.php/Rickey_Bonds" title="Rickey Bonds">
Rickey Bonds</a><br /></p>
Rickey Bonds</a><br /></p>
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<p><b>Support</b><br />
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<a href="/igem07/index.php/Kate Spohr" title="Kate Spohr">
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Kate Spohr</a> <font face="Arial">•</font>
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<a href="/igem07/index.php/Kevin Costa" title="Kevin Costa">
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Kevin Costa</a> <font face="Arial">•</font>
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<a href="/igem07/index.php/Gwyneth Terry" title="Gwyneth Terry">
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Gwyneth Terry</a><br /></p>
<p><b>Undergraduate Researchers</b><br />
<p><b>Undergraduate Researchers</b><br />
<a href="/igem07/index.php/Arthur_Yu" title="Arthur Yu">
<a href="/igem07/index.php/Arthur_Yu" title="Arthur Yu">
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<h3>Team Resources</h3></div><hr />
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<p><br />
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<a href="/igem07/index.php/BerkiGEM2007Setup" title="BerkiGEM2007Setup">
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Presentation Setup</a></p>
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<p>
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<a href="http://spreadsheets.google.com/ccc?key=pUQEpr4ZqU9TxjeURaNm1Vw" class='external text' title="http://spreadsheets.google.com/ccc?key=pUQEpr4ZqU9TxjeURaNm1Vw" rel="nofollow">
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Oligo List Spreadsheet</a><br />
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<a href="http://spreadsheets.google.com/ccc?key=pUQEpr4ZqU9TerIU8gSvKbQ" class='external text' title="http://spreadsheets.google.com/ccc?key=pUQEpr4ZqU9TerIU8gSvKbQ" rel="nofollow">
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CloneSaver Spreadsheet</a><br />
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<a href="http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2007&amp;group=Berkeley_UC" class='external text' title="http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2007&amp;group=Berkeley UC" rel="nofollow">
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Our BioBrick Parts</a><br />
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<a href="/igem07/index.php/BerkiGEM2007_AllConstructionFiles" title="BerkiGEM2007 AllConstructionFiles">
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All construction files</a><br />
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<a href="/igem07/index.php/BerkiGEM2007_AllSequencingFiles" title="BerkiGEM2007 AllSequencingFiles">
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All sequencing files</a></p>
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<p><br /><b>Tools and Guides</b><br /></p>
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<p>
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<a href="http://www.openwetware.org/wiki/Arking:JCAOligoTutorialHome" class='external text' title="http://www.openwetware.org/wiki/Arking:JCAOligoTutorialHome" rel="nofollow">
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Biobricks and Cloning Tutorials</a><br />
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<a href="http://pir.georgetown.edu/pirwww/search/pairwise.shtml" class='external text' title="http://pir.georgetown.edu/pirwww/search/pairwise.shtml" rel="nofollow">
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Pairwise Alignment Online</a><br />
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<a href="http://align.genome.jp/" class='external text' title="http://align.genome.jp/" rel="nofollow">
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Multiple Sequence Alignment</a><br />
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<a href="http://en.wikipedia.org/wiki/Help:Wikitext_examples" class='external text' title="http://en.wikipedia.org/wiki/Help:Wikitext examples" rel="nofollow">
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Wiki Formatting Guide</a><br /></p>
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<p><br /><b>Useful Links</b> </p>
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<p>
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<a href="http://openwetware.org/wiki/IGEM:UC_Berkeley/2006" class='external text' title="http://openwetware.org/wiki/IGEM:UC Berkeley/2006" rel="nofollow">
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UC Berkeley iGEM 2006 OpenWetWare</a> <br />
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<a href="http://parts2.mit.edu/wiki/index.php/University_of_California_Berkeley_2006" class='external text' title="http://parts2.mit.edu/wiki/index.php/University of California Berkeley 2006" rel="nofollow">
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UC Berkeley iGEM 2006 wiki</a> <br />iGEM wikis:
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<a href="http://parts2.mit.edu/wiki/index.php/Main_Page" class='external text' title="http://parts2.mit.edu/wiki/index.php/Main Page" rel="nofollow">
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2006</a>,
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<a href="/igem07/index.php/Main_Page" title="Main Page">2007</a><br />
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<a href="http://partsregistry.org/Main_Page" class='external text' title="http://partsregistry.org/Main Page" rel="nofollow">
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Registry of Standard Biological Parts</a> <br />Biobricks
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Parts Lists:
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<a href="http://parts2.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM&amp;group=iGEM_Berkeley" class='external text' title="http://parts2.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM&amp;group=iGEM Berkeley" rel="nofollow">
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2005</a>,
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<a href="http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006&amp;group=Berkeley" class='external text' title="http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006&amp;group=Berkeley" rel="nofollow">
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2006</a>,
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<a href="http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2007&amp;group=Berkeley_UC" class='external text' title="http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2007&amp;group=Berkeley UC" rel="nofollow">
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2007</a><br />
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<a href="http://openwetware.org/wiki/Arking:JCAOligoTutorialHome" class='external text' title="http://openwetware.org/wiki/Arking:JCAOligoTutorialHome" rel="nofollow">
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Tutorials</a> <br /> </p></td>
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<h3>Team Notebooks</h3></div><hr />
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<p><br />
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<a href="/igem07/index.php?title=John_Dueber_Notebook&amp;action=edit" class="new" title="John Dueber Notebook">
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John Dueber Notebook</a><br />
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<a href="/igem07/index.php/Christopher_Anderson_Notebook" title="Christopher Anderson Notebook">
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Christopher Anderson Notebook</a><br />
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<a href="/igem07/index.php?title=Farnaz_Nowroozi_Notebook&amp;action=edit" class="new" title="Farnaz Nowroozi Notebook">
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Farnaz Nowroozi Notebook</a><br />
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<a href="/igem07/index.php?title=Amin_Hajimorad_Notebook&amp;action=edit" class="new" title="Amin Hajimorad Notebook">
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Amin Hajimorad Notebook</a><br />
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<a href="/igem07/index.php/Rickey_Bonds_Notebook" title="Rickey Bonds Notebook">
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Rickey Bonds Notebook</a><br /></p>
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<p><br /><i>Keep your wiki notebooks,
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sequencing/construction logs, and the registry updated!</i>
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</p>
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<p><br />
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<a href="/igem07/index.php/Arthur_Yu_Notebook" title="Arthur Yu Notebook">
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Arthur Yu&#39;s 1337 Notebook</a><br />
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<a href="/igem07/index.php/Austin_Day_Notebook" title="Austin Day Notebook">
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Austin Day Notebook</a><br />
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<a href="/igem07/index.php/David_Tulga_Notebook" title="David Tulga Notebook">
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David Tulga&#39;s Notebook</a><br />
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<a href="/igem07/index.php/Kristin_Doan_Notebook" title="Kristin Doan Notebook">
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Kristin Doan Notebook</a><br />
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<a href="/igem07/index.php/Samantha_Liang_Notebook" title="Samantha Liang Notebook">
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Samantha&#39;s Notebook (June - July 19, 2007</a><br />
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<a href="/igem07/index.php/Samantha_Liang_Notebook2" title="Samantha Liang Notebook2">
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Samantha&#39;s Notebook (July 20, 2007 - present)</a><br />
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<a href="/igem07/index.php/Vaibhavi_Umesh_Notebook" title="Vaibhavi Umesh Notebook">
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Vaibhavi Umesh Notebook</a><br />
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<a href="/igem07/index.php/Kristin_Fuller_Notebook" title="Kristin Fuller Notebook">
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Kristin Fuller Notebook</a><br /></p>
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<p><br />
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<a href="/igem07/index.php/Vincent_Parker_Notebook" title="Vincent Parker Notebook">
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Vincent Parker Notebook</a><br />
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-
<a href="/igem07/index.php/Nhu_Nguyen_Notebook" title="Nhu Nguyen Notebook">
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Nhu Nguyen Notebook</a><br />
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<a href="/igem07/index.php/Hannah_Cole_Notebook" title="Hannah Cole Notebook">
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Hannah Cole Notebook</a></p></td>
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Latest revision as of 05:42, 17 July 2008

iGEM 2007

The necessity of inexpensive, disease-free, and universally compatible blood substitutes is undisputed. There are currently no blood substitutes approved for use in the US or the UK, and whole blood is almost always in short supply. Developing countries have the greatest need for blood transfusions, yet many lack the necessary donation and storage infrastructure and the required pool of healthy donors. To address this problem, we are developing a cost-effective red blood cell substitute constructed from engineered E. coli bacteria. Our system is designed to safely transport oxygen in the bloodstream without inducing sepsis, and to be stored for prolonged periods in a freeze-dried state.

Support for Berkeley iGEM 2007 was generously provided by SynBERC and The Camille and Henry Dreyfus Foundation, Inc.

 

The System's Components
Oxygen Transport

Our system is designed to produce Hemoglobin, Heme, and the necessary chaperones and detoxifying agents to promote the transport of oxygen throughout the bloodstream.  We also investigated alternates to hemoglobin and other strategies for its production.
The Chassis

Our bacterial chassis has been heavily modified to remove its sepsis-inducing toxicity, immunogenic factors, and ability to grow within the bloodstream, as well as promote its ability to last longer in the bloodstream by masking it from the immune system.
The Controller

The Controller is an integrated genetic circuit comprised of two plasmids that allows stable maintenance of the system's various operons on a large single-copy plasmid in a dormant state. Upon induction, the copy number of the operons and their transcription increase 100-fold resulting in a dramatic increase in protein expression.
Genetic Self-Destruct

To prevent chance of infection or unwanted proliferation after hemoglobin production, we have engineered a genetic self-destruct mechanism whereby when induced, the bacterial cell will express a genetic material-degrading toxin which kills the cell, but leaves it physically intact.
Freeze Drying

To enable preservation of our bacteria for prolonged periods, we are including the ability to produce the compounds hydroxyectoine and trehalose that will enable our bacteria to survive freeze-drying intact.  This will dramatically increase shelf-life and decrease transport costs.


Human Practices

An examination of the landscape of patents and the patentablilty of Bactoblood where its parts are in an open source forum and the challenges associated with current patenting practices for synthetic biology.
Individual Contributions

The specific contributions made by each team member and advisor.
Team Resources

Organizational spreadsheets, useful tools and links.
Team Notebooks

The team members' daily logs of our research.


Team Members
Advisors
John Dueber • Christopher Anderson • Adam Arkin • Jay Keasling

Teaching Assistants
Farnaz Nowroozi • Amin Hajimorad • Rickey Bonds

Support
Kate Spohr • Kevin Costa • Gwyneth Terry

Undergraduate Researchers
Arthur Yu • Austin Day • David Tulga • Kristin Doan • Samantha Liang • Vaibhavi Umesh • Kristin Fuller

High School Students
Vincent Parker • Nhu Nguyen • Hannah Cole

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