Berkeley UC

From 2007.igem.org

Revision as of 19:29, 11 October 2007 by Dtulga (Talk | contribs)

Berkeley BactobloodHeader.jpg

The necessity of cheap, available, disease free, and universally usable 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, however many lack the necessary donation and storage infrastructure and the required number of healthy donors. To address this problem, we are developing an innovative and inexpensive blood substitute constructed from E. coli bacteria engineered to include the critical capabilities of human erythrocytes. Our bacterial system includes the ability to safely exist in the bloodstream, carry oxygen with hemoglobin, and 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.


Project Modules

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Berk-Icon-Oxygen.png
Oxygen Carrying

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.

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The Chassis

Our bacterial chassis has been heavily modified to remove its sepsis-inducing toxicity, as well as promote its ability to last longer in the bloodstream by masking it from the immune system. We performed this by lipopolysaccharide modifications as well as adding the K-capsule and O-antigen.

Berk-Icon-Controller.png
The Controller

The Controller is an integrated genetic circuit, comprised of two plasmids, that directs the initiation and production of the primary systems proteins through its component operons. It is composed of a pSC101 controller plasmid and an amplifiable BAC utilizing the T7 RNAP expression system.

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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.

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Freeze Drying

In order to enable preservation of our bacteria for long periods of time, we have included the ability to produce compounds such as hydroxyectoine that will enable our bacteria to survive freeze-drying intact. This will dramatically increase shelf-life and decrease transport costs.



Team Members



Advisors
John Dueber
[http://www.openwetware.org/wiki/User:JCAnderson Christopher Anderson]
[http://genomics.lbl.gov/ Adam Arkin]
Jay Keasling

Teaching Assistants
Farnaz Nowroozi
Amin Hajimorad
Rickey Bonds

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

Team Resources



[http://spreadsheets.google.com/ccc?key=pUQEpr4ZqU9TxjeURaNm1Vw Oligo List Spreadsheet]
[http://spreadsheets.google.com/ccc?key=pUQEpr4ZqU9TerIU8gSvKbQ CloneSaver Spreadsheet]
[http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2007&group=Berkeley_UC Our BioBrick Parts]
All construction files
All sequencing files

If you need an invitation to the spreadsheets, ask Sam.


Tools and Guides

[http://www.openwetware.org/wiki/Arking:JCAOligoTutorialHome Biobricks and Cloning Tutorials]
[http://pir.georgetown.edu/pirwww/search/pairwise.shtml Pairwise Alignment Online]
[http://align.genome.jp/ Multiple Sequence Alignment]
[http://en.wikipedia.org/wiki/Help:Wikitext_examples Wiki Formatting Guide]


Useful Links

[http://openwetware.org/wiki/IGEM:UC_Berkeley/2006 UC Berkeley iGEM 2006 OpenWetWare]
[http://parts2.mit.edu/wiki/index.php/University_of_California_Berkeley_2006 UC Berkeley iGEM 2006 wiki]
iGEM wikis: [http://parts2.mit.edu/wiki/index.php/Main_Page 2006], 2007
[http://partsregistry.org/Main_Page Registry of Standard Biological Parts]
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]
[http://openwetware.org/wiki/Arking:JCAOligoTutorialHome Tutorials]


Team Notebooks



John Dueber Notebook
Christopher Anderson Notebook
Farnaz Nowroozi Notebook
Amin Hajimorad Notebook
Rickey Bonds Notebook


Keep your wiki notebooks, sequencing/construction logs, and the registry updated!


Arthur Yu's 1337 Notebook
Austin Day Notebook
David Tulga's Notebook
Kristin Doan Notebook
Samantha's Notebook (June - July 19, 2007
Samantha's Notebook (July 20, 2007 - present)
Vaibhavi Umesh Notebook
Kristin Fuller Notebook


Vincent Parker Notebook
Nhu Nguyen Notebook
Hannah Cole Notebook
Setup