Team:British Columbia/Project

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<!--- The Mission, Experiments --->
<!--- The Mission, Experiments --->
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== 'Overview of the Traffic Light Biosensor: <br> A ''flexible'', ''modular'', and ''transparent'' system for multi-level assessment of variable inputs.' ==
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==Traffic Light Overview==
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Biosensors have a diverse variety of real-world functions, ranging from measuring blood glucose levels in diabetes patients to assessing environmental contamination of trace toxins. The majority of these sensors are highly specific for a single input, and their outputs often require specialized equipment such as surface plasmon resonance chips. Our project aims to create a biosensor that recognizes a specific target and alters its output fluorescence from green, to yellow, to red as a function of concentration up to critical levels (hence, a biological "traffic light").
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Depending on the concentration of a particular substrate in the medium, E. coli will respond accordingly by producing different coloured fluorescence proteins. A diagram would look like this:
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[[Image:E_coli_Traffic_Light_Subprojects.png|center|thumb||400px|The ''E. coli'' Traffic Light Biosensor is composed of three major subparts: variable arabinose-inducible promoters, RNA lock and key system, and reverse antisense promoters for input detection, color activation and traffic light switching respectively.]]
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[[Image:E_coli_Traffic_Light_Subprojects.png|center|thumb||600px|The ''E. coli'' Traffic Light Biosensor is composed of three major subparts: variable arabinose-inducible promoters, RNA lock and key system, and reverse antisense promoters for input detection, color activation and traffic light switching respectively.]]
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Subparts:<br>
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Here is what's happening inside our traffic light:
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1. A variable sensitivity biosensor<br>
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2. A lock-and-key logic gate system
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[[Image:E_coli_Traffic_Light_Step_by_Step.png|thumb|center|850px|Schematic black-box representation of the E. coli Biosensor that detects various concentration inputs and color outputs. The idea is discrete analog outputs based on a user-specified threshold for each range of concentration.]]
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For our ideas to work, we will need:<br>
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1. [https://2009.igem.org/Team:British_Columbia/pBAD A variable sensitivity biosensor]<br>
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2. [https://2009.igem.org/Team:British_Columbia/LockandKey A lock-and-key logic gate system]]<br>
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3. [https://2009.igem.org/Team:British_Columbia/Jammer An antisense "off" switch]
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== Miscellaneous Data ==
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== Tools used and produced ==
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We also produced a couple tools to help out the project:
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To assist our project, we produced a Biobrick digestion engine and Biobrick picture maker to help out the project:
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:[[Media:Biobricks.zip|Biobricks.zip]] - Fasta file containing every biobrick from [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=List Here]
 
:http://www.pkts.ca/bb - Biobrick digestion engine - enter the name of a biobrick plasmid and biobrick insert, and this will show you the product of an EcoRI and PstI digestion/ligation as a FASTA file (suitable for viewing in your favorite program).
:http://www.pkts.ca/bb - Biobrick digestion engine - enter the name of a biobrick plasmid and biobrick insert, and this will show you the product of an EcoRI and PstI digestion/ligation as a FASTA file (suitable for viewing in your favorite program).
:http://www.pkts.ca/brickedit/ - Biobrick picture maker - enter a sequence of letters corresponding to the icons, and the program will produce a concatenated file of the Biobrick.
:http://www.pkts.ca/brickedit/ - Biobrick picture maker - enter a sequence of letters corresponding to the icons, and the program will produce a concatenated file of the Biobrick.
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== Links ==
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Also, we generated a handy Fasta file containing every biobrick from [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=List Here]:
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:[[Media:Biobricks.zip|Biobricks.zip]] - Fasta file containing every biobrick
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We also found the following tools very helpful:
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http://rna.tbi.univie.ac.at/ - a package of prediction tools for RNA structures; we used RNAfold to annotate the key and lock structures
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:http://rna.tbi.univie.ac.at/ - a package of prediction tools for RNA structures; we used RNAfold to annotate the key and lock structures
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http://mobyle.pasteur.fr/cgi-bin/portal.py - a set of web-accessible bioinformatics tools including Mfold, which determines 2D RNA structure and draws it
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:http://mobyle.pasteur.fr/cgi-bin/portal.py - a set of web-accessible bioinformatics tools including Mfold, which determines 2D RNA structure and draws it
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http://frodo.wi.mit.edu/ - Primer3, a primer design program
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:http://frodo.wi.mit.edu/ - Primer3, a primer design program

Latest revision as of 03:08, 22 October 2009

Traffic Light Overview

Depending on the concentration of a particular substrate in the medium, E. coli will respond accordingly by producing different coloured fluorescence proteins. A diagram would look like this:

The E. coli Traffic Light Biosensor is composed of three major subparts: variable arabinose-inducible promoters, RNA lock and key system, and reverse antisense promoters for input detection, color activation and traffic light switching respectively.

Here is what's happening inside our traffic light:

Schematic black-box representation of the E. coli Biosensor that detects various concentration inputs and color outputs. The idea is discrete analog outputs based on a user-specified threshold for each range of concentration.

For our ideas to work, we will need:
1. A variable sensitivity biosensor
2. A lock-and-key logic gate system]
3. An antisense "off" switch






Tools used and produced

To assist our project, we produced a Biobrick digestion engine and Biobrick picture maker to help out the project:

http://www.pkts.ca/bb - Biobrick digestion engine - enter the name of a biobrick plasmid and biobrick insert, and this will show you the product of an EcoRI and PstI digestion/ligation as a FASTA file (suitable for viewing in your favorite program).
http://www.pkts.ca/brickedit/ - Biobrick picture maker - enter a sequence of letters corresponding to the icons, and the program will produce a concatenated file of the Biobrick.

Also, we generated a handy Fasta file containing every biobrick from [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=List Here]:

Biobricks.zip - Fasta file containing every biobrick

We also found the following tools very helpful:

http://rna.tbi.univie.ac.at/ - a package of prediction tools for RNA structures; we used RNAfold to annotate the key and lock structures
http://mobyle.pasteur.fr/cgi-bin/portal.py - a set of web-accessible bioinformatics tools including Mfold, which determines 2D RNA structure and draws it
http://frodo.wi.mit.edu/ - Primer3, a primer design program
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