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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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{| cellspacing="5"
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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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<hr class=divider>
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Matt Fleming<br>
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<div id="about">
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Kaitlin A. Davis<br>
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{|
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| rowspan=2 | [[Image:Berkeley.jpg|left|200px]]'''Addressable Conjugation in Bacterial Networks'''
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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.  <br>
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[[Image:GettingStarted iconbaby.png]] [[OpenWetWare:Getting started|'''Getting Started on OWW''']]<br>
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{| cellspacing="5"
 
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<!-- USER HEADER with edit link-->
 
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<h3><html>
 
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<img src="http://openwetware.org/images/b/b9/Icon_board.png" alt="Resources">
 
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</html>Team</h3>
 
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<hr/>
 
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<!-- END COMMUNITY HEADER-->
 
'''Undergrads'''
'''Undergrads'''
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[[Bryan Hernandez]]<br>
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Bryan Hernandez<br>
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[[Matt Fleming]]<br>
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Jennifer Lu<br>
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[[Kaitlin A. Davis]]<br>
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Samantha Liang<br>
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[[Jennifer Lu]]<br>
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Daniel Kluesing<br>
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[[Samantha Liang]]<br>
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Will Bosworth<br>
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[[Daniel Kluesing]]<br>
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[[Will Bosworth]]<br>
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'''Postdocs'''
'''Postdocs'''
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[[John Dueber]]<br>
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John E. Dueber<br>
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[[Chris Anderson]]<br>
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J. Christopher Anderson<br>
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'''Faculty Advisors'''
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<!-- TOOLS HEADER with edit link-->
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<h3><html>
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Adam P. Arkin<br>
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<img src="http://openwetware.org/images/e/e2/Icon_info.png" alt="News" border="0">
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Jay D. Keasling<br>
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</html>Tools</h3>
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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:Berkeley2006IgemRocks.jpg | 60px]]'''Develop promoter tools to tune gene expression'''<br>
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</span>
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<!-- END TOOLS HEADER with edit link-->
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To learn more about our system, follow the series of descriptions below:
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[[lab calendar]]
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<span style='font-size:15.0pt'>
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[[Berkeley2006-RiboregulatorsMain | High-performance Riboregulators]] <br>
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'''The Details'''
 
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[[Berk2006-Oligos | Oligonucleotides]]<br>
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<span style='font-size:15.0pt'>
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[[Berk2006-Sequences | Sequences]]<br>
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[[Berkeley2006-ConjugationMain | Harnessing Bacterial Conjugation]] <br>
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[[Berk2006-Constructs | Construction Files]]<br>
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[[Berk2006-StockBoxes | -80 Stocks]]<br>
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[[Berk2006-Sequencing | Sequencing]]<br>
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'''Procedures'''
 
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[[IGEM:UC Berkeley/2006/Procedure Overview (Plasmid DNA to Sequencing)|Procedure Overview (Plasmid DNA to Sequencing)]]<br>
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<span style='font-size:15.0pt'>
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[[IGEM:UC Berkeley/2006/Plasmid Transformation|Plasmid Transformation]]<br>
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[[Berkeley2006-NandMain | NAND Logic in Cellular Networks]]<br>
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[[IGEM:UC Berkeley/2006/Digestion1|Digestion]]<br>
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[[IGEM:UC Berkeley/2006/Ligation|Ligation]]<br>
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[[IGEM:UC Berkeley/2006/Sequencing|Sequencing]]<br>
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[[IGEM:UC Berkeley/2006/Competent cell production|Competent cell production]]<br>
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[[IGEM:UC Berkeley/2006/PCRPrep|PCR prep]]<br>
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[[IGEM:UC Berkeley/2006/Conjugation|Conjugation]]<br>
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[[IGEM:UC Berkeley/2006/DNAGelPrep|DNA Gel pouring]]<br>
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[[IGEM:UC Berkeley/2006/DNA purifications|DNA purifications]]<br>
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[[IGEM:UC Berkeley/2006/PCR machine program (extend kit)|PCR machine program (Expand kit)]]<br>
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[[IGEM:UC Berkeley/2006/Knockouts|Knockouts]]<br>
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[[IGEM:UC Berkeley/2006/Knockouts by Electroporation of pOX38 x pKD46|Knockouts by Electroporation of pOX38 x pKD46]]<br>
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'''Subgroup Notebooks'''
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<span style='font-size:15.0pt'>
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[[Berkeley2006-NetworksMain | Extending to Cellular Networks]] <br>
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[[Berk2006-ConjugationTeam | Conjugation 6/7/06-7/21/06]]<br>
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[[Berk2006-ConjugationTeam2 | Conjugation 7/24/06 - 09/07/06]]<br>
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[[Berk2006-ConjugationTeam3 | Conjugation 09/07/06- present]]<br>
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[[Berk2006-LocksAndKeysTeam | Locks and Keys]]<br>
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[[Berk2006-LogicGatesTeam | Logic Gates]]<br>
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[http://www.openwetware.org/wiki/IGEM:UC_Berkeley/2006/bryans_notebook  Bryan's Lock and Keys]<br>
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[[Berk2006-Samantha's Notebook | Samantha's Notebook]]<br>
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<br>
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|width="200px" class="green3" |
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<!-- USER HEADER with edit link-->
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<h3><html>
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<img src="http://openwetware.org/images/b/b9/Icon_board.png" alt="Resources">
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</html>Project</h3>
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<hr/>
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<!-- END PROJECT HEADER-->
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'''Addressable Cell-to-Cell Communication'''
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*[[Media:071906-JCAGroupMeeting.ppt| 071906 JCA Group Meeting]]
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*[[Media:060506-Meeting.ppt| 060506 Meeting]]
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*[[Media:Berkeley 2005 Jamboree.ppt| Berkeley 2005 'Jamboree']]
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*[http://2006.igem.org/UC_Berkeley_2005 2005 Project]
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*[http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006&group=Berkeley '''2006 Parts List''']
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'''Useful Links'''
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*[[IGEM|iGEM]]
 
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*[http://2006.igem.org/University_of_California_Berkeley_2006 UC Berkeley iGEM wiki]
 
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*[http://2006.igem.org/Main_Page iGEM wiki]
 
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*[http://partsregistry.org/Main_Page Registry of Standard Biological Parts]
 
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*[http://parts2.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM&group=iGEM_Berkeley 2005 Biobricks]
 
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*[[Image:iGEM2006Distribution.xls|iGEM2006 Distribution compiled list]]
 
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<span style='font-size:15.0pt'>
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[[Berkeley2006-PromoterMain | Tuning Constitutive Expression Levels]] <br>
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'''Subgroup Strategies, Overview'''
 
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*[[Powerpoint presentations, drafts]]
 
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Visit our working website at  [http://openwetware.org/wiki/IGEM:UC_Berkeley/2006 Berkeley 2006 iGEM]

Latest revision as of 03:53, 28 October 2006

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
Berkeley2006IgemRocks.jpgDevelop promoter tools to tune gene expression

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

High-performance Riboregulators


Harnessing Bacterial Conjugation


NAND Logic in Cellular Networks


Extending to Cellular Networks


Tuning Constitutive Expression Levels

Visit our working website at [http://openwetware.org/wiki/IGEM:UC_Berkeley/2006 Berkeley 2006 iGEM]

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