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=='''Addressable Conjugation in Bacterial Networks'''==
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<div id="about">
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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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|-
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|}
 
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</div>
 
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<hr class=divider>
 
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{| cellspacing="5"
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Will Bosworth <br>
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|width="200px" class="green3" |
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Kaitlin A. Davis <br>
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<!-- USER HEADER with edit link-->
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Matt Fleming <br>
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<h3><html>
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Bryan Hernandez <br>
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<img src="http://openwetware.org/images/b/b9/Icon_board.png" alt="Resources">
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Daniel Kluesing <br>
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</html>Team</h3>
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Samantha Liang <br>
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<hr/>
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Jennifer Lu <br>
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<!-- END COMMUNITY HEADER-->
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J. Christopher Anderson <br>
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'''Undergrads'''
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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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[[Bryan Hernandez]]<br>
 
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[[Matt Fleming]]<br>
 
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[[Kaitlin A. Davis]]<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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'''Postdocs'''
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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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[[John Dueber]]<br>
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The specific Aims of our project were:
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[[Chris Anderson]]<br>
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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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|width="360px" class="green2" |
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[[Berkeley2006-RiboregulatorsMain | Riboregulators]] <br>
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<!-- TOOLS HEADER with edit link-->
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[[Berkeley2006-ConjugationMain | Conjugation]] <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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<h3><html>
 
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<img src="http://openwetware.org/images/e/e2/Icon_info.png" alt="News" border="0">
 
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</html>Tools</h3>
 
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<hr/>
 
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<!-- END TOOLS HEADER with edit link-->
 
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[[lab calendar]]
 
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'''The Details'''
 
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[[Berk2006-Oligos | Oligonucleotides]]<br>
 
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[[Berk2006-Sequences | Sequences]]<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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Visit our website at:
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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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[http://openwetware.org/wiki/IGEM:UC_Berkeley/2006 Berkeley 2006 iGEM]
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[[IGEM:UC Berkeley/2006/Plasmid Transformation|Plasmid Transformation]]<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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[[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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'''Subgroup Strategies, Overview'''
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*[[Powerpoint presentations, drafts]]
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|}
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Revision as of 02:26, 28 October 2006

berk2006dummypage

200px

Addressable Conjugation in Bacterial Networks

Will Bosworth
Kaitlin A. Davis
Matt Fleming
Bryan Hernandez
Daniel Kluesing
Samantha Liang
Jennifer Lu
J. Christopher Anderson
John E. Dueber
Adam P. Arkin
Jay D. Keasling


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.

The specific Aims of our project were: 

   1) Construct efficient riboregulator lock/key pairs
   2) Control ***conjugation**
   3) Show ***them together***

Riboregulators
Conjugation
NAND
Networks
Promoter Engineering



Visit our website at:

Berkeley 2006 iGEM

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