Berkeley UC

From 2007.igem.org

(Difference between revisions)
m
 
(82 intermediate revisions not shown)
Line 1: Line 1:
-
[[Image:Berkeley_BactobloodHeader.jpg]]
+
<html>
 +
<style>
 +
#apDiv3 {
 +
position:absolute;
 +
left:10px;
 +
top:-108px;
 +
width:101px;
 +
height:87px;
 +
z-index:900;
 +
}
 +
</style>
 +
<link rel="stylesheet" href="http://www.davidtulga.com/iGEM_Berkeley_Stylesheet.css" type="text/css" />
 +
<script type="text/javascript" src="http://www.davidtulga.com/flash.js"></script>
-
I haven't had time to update this section of the wiki. Someone should replace this block of text with something legit when they have downtime. -Sam <br>
+
<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>
-
'''Networks of interacting cells provide the basis for neural learning. We have developed the process of addressable conjugation for communication within a network of E. coli bacteria. Here, bacteria send messages to one another via conjugation of plasmid DNAs, but the message is only meaningful to cells with a matching address sequence. In this way, the Watson Crick base-pairing of addressing sequences replaces the spatial connectivity present in neural systems. To construct this system, we have adapted natural conjugation systems as the communication device. Information contained in the transferred plasmids is only accessable by "unlocking" the message using RNA based 'keys'. The resulting addressable conjugation process is being adapted to construct a network of NAND logic gates in bacterial cultures. Ultimately, this will allow us to develop networks of bacteria capable of trained learning.  <br>'''
+
 +
<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">
 +
<script type="text/javascript">
 +
writeFlash("http://www.davidtulga.com/iGEM_Berkeley_Header_Logo_Only.swf", "iGEM_Berkeley_Header", "270", "220", "4", "");
 +
</script>
 +
</td>
 +
</tr>
 +
</table>
 +
<img src="https://static.igem.org/mediawiki/2007/d/da/BerkiGEM2007-Bactoblood_text.jpg" border="0" id="Bactoblood_Header_Text_Img">
 +
<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>
 +
<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>
 +
</span></p><hr />
 +
<p>&nbsp;</p>
-
----
+
<p align="left">
 +
<table width="100%" id="table2" border="2" cellpadding="0" style="padding: 0px; width: 100%; color: navyblue; background-color: lightblue;" id="Main_Icons_Table">
 +
<!--<tr>
 +
<td class="tdheadL">&nbsp;</td>
 +
<td class="tdheadR"><b>Project Modules</b></td>
 +
</tr>-->
 +
<tr>
 +
<td class="tdheadR" colspan="2">
 +
<h3>The System's Components</h3></td>
 +
</tr>
 +
<tr>
 +
<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="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
 +
chaperones and detoxifying agents to promote the transport
 +
of oxygen throughout the bloodstream.&nbsp; We also
 +
investigated alternates to hemoglobin and other strategies
 +
for its production.</i></td>
 +
</tr>
 +
<tr>
 +
<td class="tdboxes">
 +
<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>
 +
<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>
 +
<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
 +
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>
 +
<td class="tdboxes">
 +
<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>
 +
<p><br /></p>
-
{| cellspacing="2px" cellpadding="5" border="2" style="padding: 0px; width: 780px; color: navyblue; background-color: lightblue;"
+
<table width="100%" id="table2" border="2" cellpadding="0" style="padding: 0px; width: 100%; color: navyblue; background-color: lightblue;" id="Secondary_Icons_Table">
-
|-valign="top"
+
<!--<tr>
-
|width=189.25px style="padding: 10px; background-color: lightblue; border: 2px solid #993300;" |
+
<td class="tdheadR" colspan="2">
 +
<h3>Other Stuff</h3></td>
 +
</tr>-->
 +
<tr>
 +
<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>
-
<center><h3>Team Members</h3></center>
+
<p><br /></p>
-
----
+
<table width="100%" id="table3" border="2" style="padding: 0px; width: 100%; color: navyblue; background-color: #ffffaa;" id="Team_Members_Table">
-
 
+
<tr>
-
 
+
<td class="tdheadR" style="background-color: #ffffaa;">
-
'''Advisors'''<br>
+
<h3>Team Members</h3></td>
-
[[John Dueber]]<br>
+
</tr>
-
[http://www.openwetware.org/wiki/User:JCAnderson Christopher Anderson]<br>
+
<tr>
-
[http://genomics.lbl.gov/ Adam Arkin]<br>
+
<td class="tddesc"><b>Advisors</b><br />
-
[https://keaslinglab.lbl.gov/wiki/index.php/Main_Page Jay Keasling]<br>
+
<a href="/igem07/index.php/John_Dueber" title="John Dueber">
-
 
+
John Dueber</a> <font face="Arial">•</font>
-
'''Teaching Assistants''' <br>
+
<a href="http://www.openwetware.org/wiki/User:JCAnderson" title="http://www.openwetware.org/wiki/User:JCAnderson" rel="nofollow">
-
[[Farnaz Nowroozi]]<br>
+
Christopher Anderson</a> <font face="Arial">•</font>
-
[[Amin Hajimorad]]<br>
+
<a href="http://genomics.lbl.gov/" title="http://genomics.lbl.gov/" rel="nofollow">
-
[[Rickey Bonds]]<br>
+
Adam Arkin</a> <font face="Arial">•</font>
-
 
+
<a href="https://keaslinglab.lbl.gov/wiki/index.php/Main_Page" title="https://keaslinglab.lbl.gov/wiki/index.php/Main Page" rel="nofollow">
-
'''Undergraduate Researchers''' <br>
+
Jay Keasling</a><br />
-
[[Arthur Yu]]<br>
+
<p><b>Teaching Assistants</b><br />
-
[[Austin Day]]<br>
+
<a href="/igem07/index.php/Farnaz_Nowroozi" title="Farnaz Nowroozi">
-
[[David Tulga]]<br>
+
Farnaz Nowroozi</a> <font face="Arial">•</font>
-
[[Kristin Doan]]<br>
+
<a href="/igem07/index.php/Amin_Hajimorad" title="Amin Hajimorad">
-
[[Samantha Liang]]<br>
+
Amin Hajimorad</a> <font face="Arial">•</font>
-
[[Vaibhavi Umesh]]<br>
+
<a href="/igem07/index.php/Rickey_Bonds" title="Rickey Bonds">
-
[[Kristin Fuller]]<br>
+
Rickey Bonds</a><br /></p>
-
 
+
<p><b>Support</b><br />
-
'''High School Students''' <br>
+
<a href="/igem07/index.php/Kate Spohr" title="Kate Spohr">
-
[[Vincent Parker]]<br>
+
Kate Spohr</a> <font face="Arial">•</font>
-
[[Nhu Nguyen]]<br>
+
<a href="/igem07/index.php/Kevin Costa" title="Kevin Costa">
-
[[Hannah Cole]]<br>
+
Kevin Costa</a> <font face="Arial">•</font>
-
 
+
<a href="/igem07/index.php/Gwyneth Terry" title="Gwyneth Terry">
-
|width=189.25px style="padding:10px; background-color: #ffffaa; border: 2px solid #993300;" |
+
Gwyneth Terry</a><br /></p>
-
 
+
<p><b>Undergraduate Researchers</b><br />
-
<center><h3>Team Resources</h3></center>
+
<a href="/igem07/index.php/Arthur_Yu" title="Arthur Yu">
-
 
+
Arthur Yu</a> <font face="Arial">•</font>
-
----
+
<a href="/igem07/index.php/Austin_Day" title="Austin Day">
-
 
+
Austin Day</a> <font face="Arial">•</font>
-
 
+
<a href="/igem07/index.php/David_Tulga" title="David Tulga">
-
[http://spreadsheets.google.com/ccc?key=pUQEpr4ZqU9TxjeURaNm1Vw Oligo List Spreadsheet]<br>
+
David Tulga</a> <font face="Arial">•</font>
-
[http://spreadsheets.google.com/ccc?key=pUQEpr4ZqU9TerIU8gSvKbQ CloneSaver Spreadsheet]<br>
+
<a href="/igem07/index.php/Kristin_Doan" title="Kristin Doan">
-
[http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2007&group=Berkeley_UC Our BioBrick Parts]<br>
+
Kristin Doan</a> <font face="Arial">•</font>
-
[[BerkiGEM2007_AllConstructionFiles | All construction files]]<br>
+
<a href="/igem07/index.php/Samantha_Liang" title="Samantha Liang">
-
[[BerkiGEM2007_AllSequencingFiles | All sequencing files]]<br>
+
Samantha Liang</a> <font face="Arial">•</font>
-
 
+
<a href="/igem07/index.php/Vaibhavi_Umesh" title="Vaibhavi Umesh">
-
''If you need an invitation to the spreadsheets, ask Sam.''
+
Vaibhavi Umesh</a> <font face="Arial">•</font>
-
 
+
<a href="/igem07/index.php/Kristin_Fuller" title="Kristin Fuller">
-
 
+
Kristin Fuller</a><br /></p>
-
'''Tools and Guides'''<br>
+
<p><b>High School Students</b><br />
-
 
+
<a href="/igem07/index.php/Vincent_Parker" title="Vincent Parker">
-
[http://www.openwetware.org/wiki/Arking:JCAOligoTutorialHome Biobricks and Cloning Tutorials]<br>
+
Vincent Parker</a> <font face="Arial">•</font>
-
[http://pir.georgetown.edu/pirwww/search/pairwise.shtml Pairwise Alignment Online]<br>
+
<a href="/igem07/index.php/Nhu_Nguyen" title="Nhu Nguyen">
-
[http://en.wikipedia.org/wiki/Help:Wikitext_examples Wiki Formatting Guide]<br>
+
Nhu Nguyen</a> <font face="Arial">•</font>
-
 
+
<a href="/igem07/index.php/Hannah_Cole" title="Hannah Cole">
-
 
+
Hannah Cole</a></p></td>
-
'''Useful Links'''
+
</tr>
-
 
+
</table>
-
[http://openwetware.org/wiki/IGEM:UC_Berkeley/2006 UC Berkeley iGEM 2006 OpenWetWare] <br>
+
<div id="Footer_Stuff">&nbsp;</div>
-
[http://parts2.mit.edu/wiki/index.php/University_of_California_Berkeley_2006 UC Berkeley iGEM 2006 wiki] <br>
+
</html>
-
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>
+
-
[http://parts2.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM&group=iGEM_Berkeley 2005 Biobricks]<br>
+
-
[http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006&group=Berkeley '''2006 Parts List''']<br>
+
-
 
+
-
|width=189.25px 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]]<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"