Berkeley UC

From 2007.igem.org

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'''The global demand and importance''' for cheap, available, and disease free blood substitutes is undisputed. There are currently no red blood cell substitutes approved for clinical use in the US or the UK, and whole blood is almost always in short supply. Underdeveloped countries that need blood the most simply don’t have the infrastructure to support donation and storage, in addition a sizeable fraction of the population are disease carriers.
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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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We have developed an innovative and cheap red blood cell substitute by modifying the E. coli chassis to make it safer to inject into the human bloodstream, and by adding components for oxygen delivery. A modified lipopolysaccharide should significantly (1000-10000x) reduce sepsis activity in the human bloodstream. A hemoglobin mutated to increase OD50 to match that of natural human blood cells after diphosphoglycerase. Heme and cytochrome B5 and B5 reductase complement the hemoglobin. Additional chaperone proteins such as sodC, HPI-katG, map, and AHSP were added to increase hardiness and prolong the half-life of the E. coli in the bloodstream. We are also investigating myoglobin, and potential freeze-drying to preserve E. coli, with OtsA, OtsB, thpA through D (trihelose - ots) (hydroxyectoine).<br>  
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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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</td>
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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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<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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<p><span id="Support_Text"><b><i>Support for Berkeley iGEM 2007 was generously provided by
 +
SynBERC and The Camille and Henry Dreyfus Foundation, Inc.</i></b>
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</span></p><hr />
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<p>&nbsp;</p>
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<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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<!--<tr>
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<td class="tdheadL">&nbsp;</td>
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<td class="tdheadR"><b>Project Modules</b></td>
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</tr>-->
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<tr>
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<td class="tdheadR" colspan="2">
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<h3>The System's Components</h3></td>
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</tr>
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<tr>
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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>
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<td class="tddesc"><b><a href="https://2007.igem.org/BerkiGEM2007Present1">Oxygen Transport</a></b><p><i>Our system is
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designed to produce Hemoglobin, Heme, and the necessary
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chaperones and detoxifying agents to promote the transport
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of oxygen throughout the bloodstream.&nbsp; We also
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investigated alternates to hemoglobin and other strategies
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for its production.</i></td>
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</tr>
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<tr>
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<td class="tdboxes">
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<a href="https://2007.igem.org/BerkiGEM2007Present4"><img border="0" src="https://static.igem.org/mediawiki/2007/b/ba/Berk-Icon-Chassis.png" width="121" height="121"></a></td>
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<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
 +
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.</i></td>
 +
</tr>
 +
<tr>
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<td class="tdboxes">
 +
<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
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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.</i></td>
 +
</tr>
 +
<tr>
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<td class="tdboxes">
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<a href="https://2007.igem.org/BerkiGEM2007Present5"><img border="0" src="https://static.igem.org/mediawiki/2007/c/c5/Berk-Icon-Self-Destruct.png" width="121" height="121"></a></td>
 +
<td class="tddesc"><b><a href="https://2007.igem.org/BerkiGEM2007Present5">Genetic Self-Destruct</a></b><p><i>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.</i></td>
 +
</tr>
 +
<tr>
 +
<td class="tdboxes">
 +
<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>
 +
<td class="tddesc"><b><a href="https://2007.igem.org/BerkiGEM2007Present2">Freeze Drying</a></b><p><i>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.&nbsp; This will dramatically
 +
increase shelf-life and decrease transport costs.</i></td>
 +
</tr>
 +
</table>
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----
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<p><br /></p>
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<table width="100%" id="table2" border="2" cellpadding="0" style="padding: 0px; width: 100%; color: navyblue; background-color: lightblue;" id="Secondary_Icons_Table">
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<!--<tr>
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<td class="tdheadR" colspan="2">
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<h3>Other Stuff</h3></td>
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</tr>-->
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<tr>
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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>
 +
<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>
 +
</tr>
 +
<tr>
 +
<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>
 +
<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>
 +
</tr>
 +
<tr>
 +
<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>
 +
<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>
 +
</tr>
 +
<tr>
 +
<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>
 +
<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>
 +
</tr>
 +
</table>
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{| cellspacing="2px" cellpadding="5" border="2" style="padding: 0px; width: 780px; color: navyblue; background-color: lightblue;"
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<p><br /></p>
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|-valign="top"
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|width=189.25px style="padding: 10px; background-color: lightblue; border: 2px solid #993300;" |
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<center><h3>Team Members</h3></center>
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<table width="100%" id="table3" border="2" style="padding: 0px; width: 100%; color: navyblue; background-color: #ffffaa;" id="Team_Members_Table">
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<tr>
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----
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<td class="tdheadR" style="background-color: #ffffaa;">
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<h3>Team Members</h3></td>
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</tr>
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'''Advisors'''<br>
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<tr>
-
[[John Dueber]]<br>
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<td class="tddesc"><b>Advisors</b><br />
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[http://www.openwetware.org/wiki/User:JCAnderson Christopher Anderson]<br>
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<a href="/igem07/index.php/John_Dueber" title="John Dueber">
-
[http://genomics.lbl.gov/ Adam Arkin]<br>
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John Dueber</a> <font face="Arial">•</font>
-
[https://keaslinglab.lbl.gov/wiki/index.php/Main_Page Jay Keasling]<br>
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<a href="http://www.openwetware.org/wiki/User:JCAnderson" title="http://www.openwetware.org/wiki/User:JCAnderson" rel="nofollow">
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Christopher Anderson</a> <font face="Arial">•</font>
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'''Teaching Assistants''' <br>
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<a href="http://genomics.lbl.gov/" title="http://genomics.lbl.gov/" rel="nofollow">
-
[[Farnaz Nowroozi]]<br>
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Adam Arkin</a> <font face="Arial">•</font>
-
[[Amin Hajimorad]]<br>
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<a href="https://keaslinglab.lbl.gov/wiki/index.php/Main_Page" title="https://keaslinglab.lbl.gov/wiki/index.php/Main Page" rel="nofollow">
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[[Rickey Bonds]]<br>
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Jay Keasling</a><br />
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<p><b>Teaching Assistants</b><br />
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'''Undergraduate Researchers''' <br>
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<a href="/igem07/index.php/Farnaz_Nowroozi" title="Farnaz Nowroozi">
-
[[Arthur Yu]]<br>
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Farnaz Nowroozi</a> <font face="Arial">•</font>
-
[[Austin Day]]<br>
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<a href="/igem07/index.php/Amin_Hajimorad" title="Amin Hajimorad">
-
[[David Tulga]]<br>
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Amin Hajimorad</a> <font face="Arial">•</font>
-
[[Kristin Doan]]<br>
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<a href="/igem07/index.php/Rickey_Bonds" title="Rickey Bonds">
-
[[Samantha Liang]]<br>
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Rickey Bonds</a><br /></p>
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[[Vaibhavi Umesh]]<br>
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<p><b>Support</b><br />
-
[[Kristin Fuller]]<br>
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<a href="/igem07/index.php/Kate Spohr" title="Kate Spohr">
-
 
+
Kate Spohr</a> <font face="Arial">•</font>
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'''High School Students''' <br>
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<a href="/igem07/index.php/Kevin Costa" title="Kevin Costa">
-
[[Vincent Parker]]<br>
+
Kevin Costa</a> <font face="Arial">•</font>
-
[[Nhu Nguyen]]<br>
+
<a href="/igem07/index.php/Gwyneth Terry" title="Gwyneth Terry">
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[[Hannah Cole]]<br>
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Gwyneth Terry</a><br /></p>
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<p><b>Undergraduate Researchers</b><br />
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|width=189.25px style="padding:10px; background-color: #ffffaa; border: 2px solid #993300;" |
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<a href="/igem07/index.php/Arthur_Yu" title="Arthur Yu">
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Arthur Yu</a> <font face="Arial">•</font>
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<center><h3>Team Resources</h3></center>
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<a href="/igem07/index.php/Austin_Day" title="Austin Day">
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Austin Day</a> <font face="Arial">•</font>
-
----
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<a href="/igem07/index.php/David_Tulga" title="David Tulga">
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David Tulga</a> <font face="Arial">•</font>
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+
<a href="/igem07/index.php/Kristin_Doan" title="Kristin Doan">
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[http://spreadsheets.google.com/ccc?key=pUQEpr4ZqU9TxjeURaNm1Vw Oligo List Spreadsheet]<br>
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Kristin Doan</a> <font face="Arial">•</font>
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[http://spreadsheets.google.com/ccc?key=pUQEpr4ZqU9TerIU8gSvKbQ CloneSaver Spreadsheet]<br>
+
<a href="/igem07/index.php/Samantha_Liang" title="Samantha Liang">
-
[http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2007&group=Berkeley_UC Our BioBrick Parts]<br>
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Samantha Liang</a> <font face="Arial">•</font>
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[[BerkiGEM2007_AllConstructionFiles | All construction files]]<br>
+
<a href="/igem07/index.php/Vaibhavi_Umesh" title="Vaibhavi Umesh">
-
[[BerkiGEM2007_AllSequencingFiles | All sequencing files]]<br>
+
Vaibhavi Umesh</a> <font face="Arial">•</font>
-
 
+
<a href="/igem07/index.php/Kristin_Fuller" title="Kristin Fuller">
-
''If you need an invitation to the spreadsheets, ask Sam.''
+
Kristin Fuller</a><br /></p>
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+
<p><b>High School Students</b><br />
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+
<a href="/igem07/index.php/Vincent_Parker" title="Vincent Parker">
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'''Tools and Guides'''<br>
+
Vincent Parker</a> <font face="Arial">•</font>
-
 
+
<a href="/igem07/index.php/Nhu_Nguyen" title="Nhu Nguyen">
-
[http://www.openwetware.org/wiki/Arking:JCAOligoTutorialHome Biobricks and Cloning Tutorials]<br>
+
Nhu Nguyen</a> <font face="Arial">•</font>
-
[http://pir.georgetown.edu/pirwww/search/pairwise.shtml Pairwise Alignment Online]<br>
+
<a href="/igem07/index.php/Hannah_Cole" title="Hannah Cole">
-
[http://align.genome.jp/ Multiple Sequence Alignment]<br>
+
Hannah Cole</a></p></td>
-
[http://en.wikipedia.org/wiki/Help:Wikitext_examples Wiki Formatting Guide]<br>
+
</tr>
-
 
+
</table>
-
 
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<div id="Footer_Stuff">&nbsp;</div>
-
'''Useful Links'''
+
</html>
-
 
+
-
[http://openwetware.org/wiki/IGEM:UC_Berkeley/2006 UC Berkeley iGEM 2006 OpenWetWare] <br>
+
-
[http://parts2.mit.edu/wiki/index.php/University_of_California_Berkeley_2006 UC Berkeley iGEM 2006 wiki] <br>
+
-
iGEM wikis: [http://parts2.mit.edu/wiki/index.php/Main_Page 2006], [[Main_Page|2007]]<br>
+
-
[http://partsregistry.org/Main_Page Registry of Standard Biological Parts] <br>
+
-
Biobricks Parts Lists: [http://parts2.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM&group=iGEM_Berkeley 2005], [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006&group=Berkeley 2006], [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2007&group=Berkeley_UC 2007]<br>
+
-
[http://openwetware.org/wiki/Arking:JCAOligoTutorialHome Tutorials]
+
-
 
+
-
 
+
-
|width=300.25px style="padding: 10px; background-color: lightblue; border: 2px solid #993300;" |
+
-
 
+
-
<center><h3>Team Notebooks</h3></center>
+
-
 
+
-
----
+
-
 
+
-
 
+
-
[[John Dueber Notebook]]<br>
+
-
[[Christopher Anderson Notebook]]<br>
+
-
[[Farnaz Nowroozi Notebook]]<br>
+
-
[[Amin Hajimorad Notebook]]<br>
+
-
[[Rickey Bonds Notebook]]<br>
+
-
 
+
-
 
+
-
''Keep your wiki notebooks, sequencing/construction logs, and the registry updated!''
+
-
 
+
-
 
+
-
[[Arthur Yu Notebook | Arthur Yu's 1337 Notebook]]<br>
+
-
[[Austin Day Notebook]]<br>
+
-
[[David Tulga Notebook | David Tulga's Notebook]]<br>
+
-
[[Kristin Doan Notebook]]<br>
+
-
[[Samantha Liang Notebook | Samantha's Notebook (June - July 19, 2007]]<br>
+
-
[[Samantha Liang Notebook2 | Samantha's Notebook (July 20, 2007 - present)]]<br>
+
-
[[Vaibhavi Umesh Notebook]]<br>
+
-
[[Kristin Fuller Notebook]]<br>
+
-
 
+
-
 
+
-
[[Vincent Parker Notebook]]<br>
+
-
[[Nhu Nguyen Notebook]]<br>
+
-
[[Hannah Cole Notebook]]<br>
+
-
|}
+

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

Retrieved from "http://2007.igem.org/wiki/index.php/Berkeley_UC"