University of California Berkeley 2006

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[[Image:Berkeley.jpg|left|200px]]
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[[Image:Berkeley200BestPartPic.jpg|650px]]<br>
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==Awarded:==
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'''1st place for Best Part'''<br>
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<br>
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'''3rd place for Best Measurement and Part Characterization'''<br>
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<br>
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=='''Addressable Conjugation in Bacterial Networks'''==
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==Special Thanks:==
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[[Image:Microsoft_Logo.jpg|right|200 px]]
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''The Berkeley iGEM team very gratefully acknowledges the generous support of Microsoft, which helped make our team members' participation possible.''<br>
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<h1>Addressable Conjugation in Bacterial Networks</h1>
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[[Image:Berkeley2006School.jpg|left|200px]]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>
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{|
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|width="180px"  style="background: moccasin; border: 1px solid rgb(153, 153, 153)"|
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<span style='font-size:12.0pt'>Our Team</span>
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<hr/>
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'''High School'''
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Will Bosworth <br>
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Matt Fleming<br>
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Kaitlin A. Davis <br>
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Kaitlin A. Davis<br>
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Matt Fleming <br>
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Bryan Hernandez <br>
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Daniel Kluesing <br>
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Samantha Liang <br>
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Jennifer Lu <br>
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J. Christopher Anderson <br>
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John E. Dueber <br>
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Adam P. Arkin <br>
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Jay D. Keasling <br>
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'''Undergrads'''
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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.
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Bryan Hernandez<br>
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Jennifer Lu<br>
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Samantha Liang<br>
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Daniel Kluesing<br>
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Will Bosworth<br>
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The specific Aims of our project were:
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'''Postdocs'''
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    1) Construct efficient riboregulator lock/key pairs
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    2) Control ***conjugation**
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    3) Show ***them together***
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[[Berkeley2006-RiboregulatorsMain | Riboregulators]] <br>
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John E. Dueber<br>
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[[Berkeley2006-ConjugationMain | Conjugation]] <br>
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J. Christopher Anderson<br>
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[[Berkeley2006-NandMain | NAND]]<br>
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[[Berkeley2006-NetworksMain | Networks]] <br>
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[[Berkeley2006-PromoterMain | Promoter Engineering]] <br>
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'''Faculty Advisors'''
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Adam P. Arkin<br>
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Jay D. Keasling<br>
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|width="20px"|
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|width="600px"|
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<span style='font-size:12.0pt'>
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'''The specific goals of our project were to:'''<br>
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<span style='font-size:12.0pt'>
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[[Image:Berkeley2006IgemRocks.jpg | 60px]]'''Construct high-performance riboregulator pairs'''<br>
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[[Image:Berkeley2006IgemRocks.jpg | 60px]]'''Harness the process of bacterial conjugation'''<br>
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[[Image:Berkeley2006IgemRocks.jpg | 60px]]'''Demonstrate transmission of a coded message'''<br>
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[[Image:Berkeley2006IgemStillRocks.jpg | 60px]]'''Construct a bacterial learning network'''<br>
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</span>
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<hr/>
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To learn more about our system, follow the series of descriptions below:
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Visit our website at:
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<span style='font-size:15.0pt'>
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[[Berkeley2006-RiboregulatorsMain | High-performance Riboregulators]] <br>
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[http://openwetware.org/wiki/IGEM:UC_Berkeley/2006 Berkeley 2006 iGEM]
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<span style='font-size:15.0pt'>
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[[Berkeley2006-ConjugationMain | Harnessing Bacterial Conjugation]] <br>
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<span style='font-size:15.0pt'>
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[[Berkeley2006-PromoterMain | Controlling Message Sending and Receiving]] <br>
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<span style='font-size:15.0pt'>
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[[Berkeley2006-PlasmidPartsMain | New Biobrick-Compatible Plasmids]] <br>
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<span style='font-size:15.0pt'>
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[[Berkeley2006-NandMain | Logic Computation in Bacterial Networks]]<br>
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<span style='font-size:15.0pt'>
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[[Berkeley2006-NetworksMain | Trained Learning in a Bacterial Network]] <br>
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|}
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----
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To view our notebooks and protocols, visit our working website at  [http://openwetware.org/wiki/IGEM:UC_Berkeley/2006 Berkeley 2006 iGEM]<br>
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See our parts list at [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006&group=Berkeley Registry 2006 Berkeley iGEM]<br>
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Download our [[Media:Berk2006iGEM.ppt | Powerpoint presentation ]]<br>

Latest revision as of 15:05, 15 April 2007

Berkeley200BestPartPic.jpg

Awarded:

1st place for Best Part

3rd place for Best Measurement and Part Characterization

Special Thanks:

Microsoft Logo.jpg

The Berkeley iGEM team very gratefully acknowledges the generous support of Microsoft, which helped make our team members' participation possible.

Addressable Conjugation in Bacterial Networks

Berkeley2006School.jpg
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.

Our Team

High School

Matt Fleming
Kaitlin A. Davis

Undergrads

Bryan Hernandez
Jennifer Lu
Samantha Liang
Daniel Kluesing
Will Bosworth

Postdocs

John E. Dueber
J. Christopher Anderson

Faculty Advisors

Adam P. Arkin
Jay D. Keasling

The specific goals of our project were to:

Berkeley2006IgemRocks.jpgConstruct high-performance riboregulator pairs
Berkeley2006IgemRocks.jpgHarness the process of bacterial conjugation
Berkeley2006IgemRocks.jpgDemonstrate transmission of a coded message
Berkeley2006IgemStillRocks.jpgConstruct a bacterial learning network

To learn more about our system, follow the series of descriptions below:

High-performance Riboregulators


Harnessing Bacterial Conjugation


Controlling Message Sending and Receiving


New Biobrick-Compatible Plasmids


Logic Computation in Bacterial Networks


Trained Learning in a Bacterial Network


To view our notebooks and protocols, visit our working website at [http://openwetware.org/wiki/IGEM:UC_Berkeley/2006 Berkeley 2006 iGEM]
See our parts list at [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006&group=Berkeley Registry 2006 Berkeley iGEM]
Download our Powerpoint presentation

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