Team:Berkeley Wetlab

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<big><font size="5" face="Book Antiqua"> Abstract</font> </big> <br>
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Cell surface display in ''E. coli'' tethers proteins to the outer membrane in order to localize them to the extracellular environment.  While this form of localization has allowed many novel functions to be engineered into ''E. coli'', work within this space relies on a trial and error approach rather than design principles.  We worked to create a foundation of research which would make the rational design of cell surface display systems in ''E. coli''  possible.  We used a combinatorial approach to compare the ability of different display proteins to display different classes of functional proteins.  This required the development and implementation of an automated assembly method able to construct the large number of devices necessary to draw meaningful conclusions about design within this space. 
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<b>[[Assay Protocols | Functional Assays]] * [[Assay Results | Results]] * [[ Recipes| Recipes]] [[ NoteBooks | NoteBooks ]] </b>
 
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== Preliminary project description ==
 
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The University of California Berkeley iGEM team is proposing to expand the design space of synthetic biology by exploring novel applications of cell surface display within Escherichia coli, the gold standard organism for bacterial engineering. The team envisions a bottom-up design scheme in order to tackle this engineering problem in a well organized, modular fashion. In order to overcome the challenges of engineering Escherichia coli cell surface display, a high throughput, automated, combinatorial strategy is employed to control the system.
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<center><font size="5" face="Book Antiqua">Our Team</font></center> <br>
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<font size="5" face="Book Antiqua">Acknowledgements</font> <br>
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We thank our wonderful advisers: Chris Anderson, Terry Johnson, and Lane Weaver for their guidance and support. We also thank our generous sponsors:<br>
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        <p><span id="Intro_Text">The University of California Berkeley iGem team is proposing to expand the design space of synthetic biology by exploring novel applications of cell surface display within Escherichia coli, the gold standard organism for bacterial engineering. The team envisions a bottom-up design scheme in order to tackle this engineering problem in a well organized, modular fashion. In order to overcome the challenges of engineering Escherichia coli cell surface display, a high throughput, automated, combinatorial strategy is employed to control the system.<br><br></span></p>
 
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  <p><span id="Support_Text"><b><i>Support for Berkeley iGEM 2009 was generously provided by
 
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SynBERC and The Camille and Henry Dreyfus Foundation, Inc.</i></b>
 
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<p>&nbsp;</p>
 
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<h3>The System's Components</h3></td>
 
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<td class="tdboxes"><a href="http://parts.mit.edu/igem07/index.php/BerkiGEM2007Present1"><img src="Berkeley_UC_files/Berk-Icon-Oxygen.png" width="121" border="0" height="121"></a></td>
 
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<td class="tddesc"><b><a href="http://parts.mit.edu/igem07/index.php/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></p></td>
 
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<a href="http://parts.mit.edu/igem07/index.php/BerkiGEM2007Present4"><img src="Berkeley_UC_files/Berk-Icon-Chassis.png" width="121" border="0" height="121"></a></td>
 
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<td class="tddesc"><b><a href="http://parts.mit.edu/igem07/index.php/BerkiGEM2007Present4">The Chassis</a></b><p><i>Our bacterial
 
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chassis has been heavily modified to remove its
 
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sepsis-inducing toxicity, immunogenic factors, and ability to grow
 
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within the bloodstream, as well as promote its ability to last
 
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longer in the bloodstream by masking it from the immune
 
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<a href="http://parts.mit.edu/igem07/index.php/BerkiGEM2007Present3"><img src="Berkeley_UC_files/Berk-Icon-Controller.png" width="121" border="0" height="121"></a></td>
 
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<td class="tddesc"><b><a href="http://parts.mit.edu/igem07/index.php/BerkiGEM2007Present3">The Controller</a></b><p><i>The Controller
 
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is an integrated genetic circuit comprised of two plasmids that allows
 
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stable maintenance of the system's various operons on a large single-copy
 
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plasmid in a dormant state.  Upon induction, the copy number of the
 
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operons and their transcription increase 100-fold resulting in a
 
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dramatic increase in protein expression.</i></p></td>
 
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<a href="http://parts.mit.edu/igem07/index.php/BerkiGEM2007Present5"><img src="Berkeley_UC_files/Berk-Icon-Self-Destruct.png" width="121" border="0" height="121"></a></td>
 
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<td class="tddesc"><b><a href="http://parts.mit.edu/igem07/index.php/BerkiGEM2007Present5">Genetic Self-Destruct</a></b><p><i>To
 
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prevent chance of infection or unwanted proliferation after
 
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hemoglobin production, we have engineered a genetic
 
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self-destruct mechanism whereby when induced, the bacterial
 
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cell will express a genetic material-degrading toxin which
 
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kills the cell, but leaves it physically intact.</i></p></td>
 
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<a href="http://parts.mit.edu/igem07/index.php/BerkiGEM2007Present2"><img src="Berkeley_UC_files/Berk-Icon-Freeze-Drying.png" width="121" border="0" height="121"></a></td>
 
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<td class="tddesc"><b><a href="http://parts.mit.edu/igem07/index.php/BerkiGEM2007Present2">Freeze Drying</a></b><p><i>To
 
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enable preservation of our bacteria for prolonged periods,
 
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we are including the ability to produce the compounds
 
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hydroxyectoine and trehalose that will enable our bacteria to
 
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<td class="tdsmallboxes"><a href="http://parts.mit.edu/igem07/index.php/BerkiGEM2007Present6"><img src="Berkeley_UC_files/Berk-Icon-Small-Patents.png" width="83" border="0" height="83"></a></td>
 
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<td class="tddesc" style="padding-bottom: 0px; padding-top: 7px;"><b><a href="http://parts.mit.edu/igem07/index.php/BerkiGEM2007Present6">Human Practices</a></b><p><i>An
 
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examination of the landscape of patents and the patentablilty of
 
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Bactoblood where its parts are in an open source forum and the
 
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challenges associated with current patenting practices for synthetic
 
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<td class="tdsmallboxes"><a href="http://parts.mit.edu/igem07/index.php/Berkeley_Individual_Contributions"><img src="Berkeley_UC_files/Berk-Icon-Small-References.png" width="83" border="0" height="83"></a></td>
 
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<td class="tddesc"><b><a href="http://parts.mit.edu/igem07/index.php/Berkeley_Individual_Contributions">Individual Contributions</a></b><p><i>The specific contributions made by each team member and advisor.</i></p></td>
 
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<td class="tdsmallboxes"><a href="http://parts.mit.edu/igem07/index.php/BerkiGEM2007_Resources"><img src="Berkeley_UC_files/Berk-Icon-Small-Resources.png" width="83" border="0" height="83"></a></td>
 
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<td class="tddesc"><b><a href="http://parts.mit.edu/igem07/index.php/BerkiGEM2007_Notebooks">Team Notebooks</a></b><p><i>The team members' daily logs of our research.</i></p></td>
 
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<h3>Team Members</h3></td>
 
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<a href="http://parts.mit.edu/igem07/index.php/John_Dueber" title="John Dueber">
 
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John Dueber</a> <font face="Arial">•</font>
 
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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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<a href="http://genomics.lbl.gov/" title="http://genomics.lbl.gov/" rel="nofollow">
 
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Adam Arkin</a> <font face="Arial">•</font>
 
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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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Jay Keasling</a><br>
 
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<p><b>Teaching Assistants</b><br>
 
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<a href="http://parts.mit.edu/igem07/index.php/Farnaz_Nowroozi" title="Farnaz Nowroozi">
 
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Farnaz Nowroozi</a> <font face="Arial">•</font>
 
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<a href="http://parts.mit.edu/igem07/index.php/Amin_Hajimorad" title="Amin Hajimorad">
 
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Amin Hajimorad</a> <font face="Arial">•</font>
 
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<a href="http://parts.mit.edu/igem07/index.php/Rickey_Bonds" title="Rickey Bonds">
 
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Rickey Bonds</a><br></p>
 
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<p><b>Support</b><br>
 
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<a href="http://parts.mit.edu/igem07/index.php/Kate%20Spohr" title="Kate Spohr">
 
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Kate Spohr</a> <font face="Arial">•</font>
 
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<a href="http://parts.mit.edu/igem07/index.php/Kevin%20Costa" title="Kevin Costa">
 
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Kevin Costa</a> <font face="Arial">•</font>
 
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<a href="http://parts.mit.edu/igem07/index.php/Gwyneth%20Terry" title="Gwyneth Terry">
 
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Gwyneth Terry</a><br></p>
 
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<p><b>Undergraduate Researchers</b><br>
 
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<a href="http://parts.mit.edu/igem07/index.php/Arthur_Yu" title="Arthur Yu">
 
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Arthur Yu</a> <font face="Arial">•</font>
 
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<a href="http://parts.mit.edu/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="http://parts.mit.edu/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="http://parts.mit.edu/igem07/index.php/Kristin_Doan" title="Kristin Doan">
 
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Kristin Doan</a> <font face="Arial">•</font>
 
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<a href="http://parts.mit.edu/igem07/index.php/Samantha_Liang" title="Samantha Liang">
 
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Samantha Liang</a> <font face="Arial">•</font>
 
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<a href="http://parts.mit.edu/igem07/index.php/Vaibhavi_Umesh" title="Vaibhavi Umesh">
 
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Vaibhavi Umesh</a> <font face="Arial">•</font>
 
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<a href="http://parts.mit.edu/igem07/index.php/Kristin_Fuller" title="Kristin Fuller">
 
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Kristin Fuller</a><br></p>
 
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<p><b>High School Students</b><br>
 
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<a href="http://parts.mit.edu/igem07/index.php/Vincent_Parker" title="Vincent Parker">
 
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Vincent Parker</a> <font face="Arial">•</font>
 
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<a href="http://parts.mit.edu/igem07/index.php/Nhu_Nguyen" title="Nhu Nguyen">
 
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Nhu Nguyen</a> <font face="Arial">•</font>
 
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<a href="http://parts.mit.edu/igem07/index.php/Hannah_Cole" title="Hannah Cole">
 
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Hannah Cole</a></p></td>
 
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Latest revision as of 19:14, 21 October 2009


Display-o-matic2.png

Abstract
Cell surface display in E. coli tethers proteins to the outer membrane in order to localize them to the extracellular environment. While this form of localization has allowed many novel functions to be engineered into E. coli, work within this space relies on a trial and error approach rather than design principles. We worked to create a foundation of research which would make the rational design of cell surface display systems in E. coli possible. We used a combinatorial approach to compare the ability of different display proteins to display different classes of functional proteins. This required the development and implementation of an automated assembly method able to construct the large number of devices necessary to draw meaningful conclusions about design within this space.




Our Team

BerkeleyWetlabTeam.jpg



Acknowledgements
We thank our wonderful advisers: Chris Anderson, Terry Johnson, and Lane Weaver for their guidance and support. We also thank our generous sponsors:


Berkeleyinvitrogen.jpg Berkeleynsf.jpg Berkeleyqbs.jpg Berkeleysynberg.png

Retrieved from "http://2009.igem.org/Team:Berkeley_Wetlab"