Berk2006dummypage

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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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|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>Team</h3>
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<hr/>
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<!-- END COMMUNITY HEADER-->
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'''Undergrads'''
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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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[[John Dueber]]<br>
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[[Chris Anderson]]<br>
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=='''Addressable Conjugation in Bacterial Networks'''==
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|width="360px" class="green2" |
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<!-- TOOLS HEADER with edit link-->
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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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Will Bosworth <br>
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[[lab calendar]]
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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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'''The Details'''
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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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[[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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The specific Aims of our project were:
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'''Procedures'''
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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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[[IGEM:UC Berkeley/2006/Procedure Overview (Plasmid DNA to Sequencing)|Procedure Overview (Plasmid DNA to Sequencing)]]<br>
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[[Berkeley2006-ConjugationMain | Conjugation]] <br>
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[[IGEM:UC Berkeley/2006/Plasmid Transformation|Plasmid Transformation]]<br>
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[[Berkeley2006-NandMain | NAND]]<br>
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[[IGEM:UC Berkeley/2006/Digestion1|Digestion]]<br>
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[[Berkeley2006-NetworksMain | Networks]] <br>
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[[IGEM:UC Berkeley/2006/Ligation|Ligation]]<br>
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[[Berkeley2006-PromoterMain | Promoter Engineering]] <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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Visit our website at:
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|width="200px" class="green3" |
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<!-- USER HEADER with edit link-->
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[http://openwetware.org/wiki/IGEM:UC_Berkeley/2006 Berkeley 2006 iGEM]
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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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|}

Revision as of 02:10, 28 October 2006

200px
Addressable Conjugation in Bacterial Networks

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.
File:GettingStarted iconbaby.png Getting Started on OWW

Resources Team

Undergrads

Bryan Hernandez
Matt Fleming
Kaitlin A. Davis
Jennifer Lu
Samantha Liang
Daniel Kluesing
Will Bosworth

Postdocs

John Dueber
Chris Anderson

News Tools

lab calendar

The Details

Oligonucleotides
Sequences
Construction Files
-80 Stocks
Sequencing

Procedures

Procedure Overview (Plasmid DNA to Sequencing)
Plasmid Transformation
Digestion
Ligation
Sequencing
Competent cell production
PCR prep
Conjugation
DNA Gel pouring
DNA purifications
PCR machine program (Expand kit)
Knockouts
Knockouts by Electroporation of pOX38 x pKD46


Subgroup Notebooks

Conjugation 6/7/06-7/21/06
Conjugation 7/24/06 - 09/07/06
Conjugation 09/07/06- present
Locks and Keys
Logic Gates
Bryan's Lock and Keys
Samantha's Notebook

Resources Project

Addressable Cell-to-Cell Communication

Useful Links


Subgroup Strategies, Overview

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