IGEM:UC Berkeley/2006

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<div id="about">
<div id="about">
{|
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| rowspan=2 | [[Image:Berkeley.jpg|200px]]
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| rowspan=2 | [[Image:Berkeley.jpg|left|200px]]'''Addressable Conjugation in Bacterial Networks'''
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| '''UC Berkeley''' <br>
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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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'''The presentation of our results for the 2006 Jamboree is available at the [http://parts2.mit.edu/wiki/index.php/University_of_California_Berkeley_2006 iGEM Website]'''<br>
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We are researching addressable cell-to-cell communication in e.coli. By manipulating the process of conjugation, our cells may selectively pass plasmids to other cells. Information contained in the transfered plasmids may be regulated at translation by implementing RNA based locks and keys. These key research advances may allow for implmentation of complex systems of NAND logic gates in bacterial cultures.  <br>   
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[[Image:Microsoft_Logo.jpg|right|200 px]]
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[[Image:GettingStarted iconbaby.png]] [[OpenWetWare:Getting started|'''Getting Started on OWW''']]<br>
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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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[[IGEM:UC Berkeley/2006/Procedure Overview (Plasmid DNA to Sequencing)|Procedure Overview (Plasmid DNA to Sequencing)]]<br>
[[IGEM:UC Berkeley/2006/Procedure Overview (Plasmid DNA to Sequencing)|Procedure Overview (Plasmid DNA to Sequencing)]]<br>
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[[IGEM:UC Berkeley/2006/Competent cell production|Competent cell production]]<br>
[[IGEM:UC Berkeley/2006/Plasmid Transformation|Plasmid Transformation]]<br>
[[IGEM:UC Berkeley/2006/Plasmid Transformation|Plasmid Transformation]]<br>
[[IGEM:UC Berkeley/2006/Digestion1|Digestion]]<br>
[[IGEM:UC Berkeley/2006/Digestion1|Digestion]]<br>
[[IGEM:UC Berkeley/2006/Ligation|Ligation]]<br>
[[IGEM:UC Berkeley/2006/Ligation|Ligation]]<br>
[[IGEM:UC Berkeley/2006/Sequencing|Sequencing]]<br>
[[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/OverlapExtensionRxn|Overlap extension of oligos]]<br>
[[IGEM:UC Berkeley/2006/PCRPrep|PCR prep]]<br>
[[IGEM:UC Berkeley/2006/PCRPrep|PCR prep]]<br>
[[IGEM:UC Berkeley/2006/Conjugation|Conjugation]]<br>
[[IGEM:UC Berkeley/2006/Conjugation|Conjugation]]<br>
[[IGEM:UC Berkeley/2006/DNAGelPrep|DNA Gel pouring]]<br>
[[IGEM:UC Berkeley/2006/DNAGelPrep|DNA Gel pouring]]<br>
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[[IGEM:UC Berkeley/2006/Short DNA frag cleanup|Short DNA frag cleanup]]<br>
 
[[IGEM:UC Berkeley/2006/DNA purifications|DNA purifications]]<br>
[[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 (extend kit)]]<br>
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[[IGEM:UC Berkeley/2006/PCR machine program (extend kit)|PCR machine program (Expand kit)]]<br>
[[IGEM:UC Berkeley/2006/Knockouts|Knockouts]]<br>
[[IGEM:UC Berkeley/2006/Knockouts|Knockouts]]<br>
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[[IGEM:UC Berkeley/2006/PCR Cleanup|PCR Cleanup]]
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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'''
'''Subgroup Notebooks'''
[[Berk2006-ConjugationTeam | Conjugation 6/7/06-7/21/06]]<br>
[[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>
[[Berk2006-LocksAndKeysTeam | Locks and Keys]]<br>
[[Berk2006-LocksAndKeysTeam | Locks and Keys]]<br>
[[Berk2006-LogicGatesTeam | Logic Gates]]<br>
[[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>
<br>
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'''Addressable Cell-to-Cell Communication'''
'''Addressable Cell-to-Cell Communication'''
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*[[Image:071906-JCAGroupMeeting.ppt| 071906 JCA Group Meeting]]
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*[[Media:071906-JCAGroupMeeting.ppt| 071906 JCA Group Meeting]]
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*[[Image:060506-Meeting.ppt| 060506 Meeting]]
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*[[Media:060506-Meeting.ppt| 060506 Meeting]]
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*[[Image:Berkeley 2005 Jamboree.ppt| Berkeley 2005 'Jamboree']]
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*[[Media:Berkeley 2005 Jamboree.ppt| Berkeley 2005 'Jamboree']]
*[http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005 2005 Project]
*[http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005 2005 Project]
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*[http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&group=iGEM2006_Berkeley '''2006 Parts List''']
'''Useful Links'''
'''Useful Links'''
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*[http://parts2.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM&group=iGEM_Berkeley 2005 Biobricks]
*[http://parts2.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM&group=iGEM_Berkeley 2005 Biobricks]
*[[Image:iGEM2006Distribution.xls|iGEM2006 Distribution compiled list]]
*[[Image:iGEM2006Distribution.xls|iGEM2006 Distribution compiled list]]
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*[http://parts2.mit.edu/wiki/index.php/University_of_California_Berkeley_2006 | iGEM site]
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'''Subgroup Strategies, Overview'''
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*[[Powerpoint presentations, drafts]]
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|}

Current revision


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.
The presentation of our results for the 2006 Jamboree is available at the iGEM Website

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


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)
Competent cell production
Plasmid Transformation
Digestion
Ligation
Sequencing
Overlap extension of oligos
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

Personal tools