User:Vincent Rouilly/Hands On BioBrick Activity: Difference between revisions

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'''[[User:Vincent Rouilly|Vincent]] 13:42, 6 June 2007 (EDT)''': feel free to comment on the content of the activity described and its design.  
'''[[User:Vincent Rouilly|Vincent]] 13:42, 6 June 2007 (EDT)''': feel free to comment on the content of the activity described and its design.  
==Context==
==Context==
* Following last year [[IGEM:IMPERIAL/2006 || Imperial College participation to iGEM]], my group is putting together an exhibit for the [http://www.royalsoc.ac.uk/event.asp?id=5388&month=11,2006 Royal Society Summer Science Exhibition 2007].
* Following last year [[IGEM:IMPERIAL/2006 | Imperial College participation to iGEM]], my group is putting together an exhibit for the [[Kitney:Projects/Royal_Society_Summer_Science_Exhibition_2007 | Royal Society Summer Science Exhibition 2007]].
* We feel it is a great opportunity to engage with the Public on the concepts behind Synthetic Biology.
* We feel it is a great opportunity to engage with the Public on the concepts behind Synthetic Biology.
* The exhibit attracts a diverse audience from school kids to science enthusiasts.  
* The exhibit attracts a diverse audience from school kids to science enthusiasts.  
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** motor driving some flagella
** motor driving some flagella
** fan to illustrate secretion
** fan to illustrate secretion
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[[Image:RSSE2007_ImperialCollege_Exhibit_1.JPG|180px]] [[Image:RSSE2007_ImperialCollege_Exhibit_3.JPG|180px]] [[Image:RSSE2007_ImperialCollege_Exhibit_4.JPG|100px]]
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[[Image:RSSE2007_ImperialCollege_HandsOn_Activity_1.JPG|200px]] [[Image:RSSE2007_ImperialCollege_HandsOn_Activity_2.JPG|200px]]
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==Components and Schematics==
==Components and Schematics==
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| [[Image:HandsOnBioBrick_FusionProteinGenerator.png|300px|Activated Promoter Component]]
| [[Image:HandsOnBioBrick_FusionProteinGenerator.png|300px|Activated Promoter Component]]
| [[Image:HandsOnBioBrick_MonocystronicProteinGenerator.png|300px|Repressed Promoter Component]]
| [[Image:HandsOnBioBrick_MonocystronicProteinGenerator.png|300px|Repressed Promoter Component]]
 
|-
|
* the protein expression level is tuned by the potentiometers of the promoter and the RBS
* the protein expression level can be picked up with a fiber optic to drive another promoter or an output modules (flagella motor or secretion fan).
|
* the expression level of both proteins is tuned by the potentiometers of the promoter and the RBS. It is the same for both proteins.
* the protein expression levels can be picked up with a fiber optic to drive another promoter or an output modules (flagella motor or secretion fan).
|
* control over the protein expression levels is tuned by the potentiometer of the promoter, but also, independently controlled by the potentiometers of the RBSs.
* the protein expression levels can be picked up with a fiber optic to drive another promoter or an output modules (flagella motor or secretion fan).
|}
|}


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==Material==
===Biobricks===
*'''constitutive promoter''':
**Duplo brick 2x2
**potentiometer
**connector
**battery
**electronic circuit
*'''activated/repressed promoter''':
**Duplo brick 2x2
**LED sensor: [http://www.maplin.co.uk/Module.aspx?TabID=1&ModuleNo=97354&doy=2m6 sensor1]
**connector [http://www.maplin.co.uk/Module.aspx?TabID=1&ModuleNo=1310&doy=2m6 connector] [http://www.maplin.co.uk/Search.aspx?menuno=12330&MenuName=Test%20Connectors&FromMenu=y&worldid=-2&doy=2m6 others] [http://www.maplin.co.uk/Search.aspx?menuno=12293&MenuName=2.5mm%20Stereo%20Jacks&FromMenu=y&worldid=-2&doy=2m6 others]
**battery
**electronic circuit
*'''ribosome binding site'''
**Duplo brick 2x2
***potentiometer to tune strength of RBS
***battery
**connectors x2
*'''Protein coding region'''
**Duplo brick 4x2
**LED (with different colors): [http://www.maplin.co.uk/family.aspx?menu=1692&MenuName=Optoelectronics&worldid=-2&doy=2m6 LEDs]
**multi level bar graph LED + electronic circuit: [http://www.maplin.co.uk/Search.aspx?menuno=12414&MenuName=Bar%20Graph%20Displays&FromMenu=y&worldid=-2&doy=2m6 bar graph display], [http://www.maplin.co.uk/Search.aspx?criteria=LM3914&source=15&SD=Y bar graph driver]
**connectors x2
*'''Stop codon'''
**Duplo brick 2x2
**Connector x1
===Inputs Sensors===
*'''Temperature''':[http://www.maplin.co.uk/Module.aspx?TabID=1&ModuleNo=97358&doy=2m6 kit]
*'''Touch''': [http://www.maplin.co.uk/Module.aspx?TabID=1&ModuleNo=97357&doy=2m6 kit]
*'''Infra-red''': [http://www.maplin.co.uk/Module.aspx?TabID=1&ModuleNo=97356&doy=2m6 kit]
*'''Humidity''': [http://www.maplin.co.uk/Module.aspx?TabID=1&ModuleNo=97359&doy=2m6 kit]
===Motors===
*motor: [http://www.maplin.co.uk/Module.aspx?TabID=1&ModuleNo=97341&doy=2m6 motors]
*fans: [http://www.maplin.co.uk/Module.aspx?ModuleNo=97338&&source=14&doy=2m6 fans]
===Electronic Circuits===
*[http://www.aaroncake.net/circuits/lightdrk.asp Light/Dark detector]
*[http://www.uoguelph.ca/~antoon/circ/actrelay.htm temperature AOP]
*[http://www.elecfree.com/electronic/light-relay-switch-by-bc547-bc337/ light sensor based on transistors]
*[http://www.elecdesign.com/Articles/Index.cfm?AD=1&ArticleID=1684 optic fibre transmitter]
*[http://www.discovercircuits.com/DJ-Circuits/daj-opt-sensors.htm good stuff]


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Latest revision as of 06:50, 27 February 2008

Vincent 13:42, 6 June 2007 (EDT): feel free to comment on the content of the activity described and its design.

Context

Intentions behind the activity

  • To set the background in terms of Molecular and Celluar Biology:
    • DNA, Central Dogma, Cells and Bacteria
    • Genetic Engineering techniques
  • To touch on Synthetic Biology concepts:
    • BioBricks
    • Modularity
    • Re-usability
  • To give an opportunity to build simple genetic circuits based on opto-electronic components:
    • Protein Generator
    • Inverter, Toggle switch & Repressilator
    • Link circuits with inputs such as: temperature sensor, Infra-red sensor, Touch sensor, Humidity sensor.
    • Link circuits with outputs such as: flagella motor, secretion fan.

Overview

Overview General setting
Hands on BioBrick table Hands on BioBrick IO modules
  • the activity stands on an oval table, decorated as an E.Coli bacteria.
  • on the right side of the table, DNA, gene expression machinery are illustrated.
  • the hands on activity is placed on the left side:
    • a set of available biobricks implemented as Lego bricks filled with some opto-electronic components.
    • a conductive surface
    • a set of fiber optics to link the different genetic circuits.
  • the activity offers a set of possible inputs for the genetic circuits to be built:
    • temperature sensor (to illustrate heat shock response).
    • infra-red sensor - with remote - (to illustrate UV response)
    • touch sensor
    • humidity sensor
  • 2 outputs are also available:
    • motor driving some flagella
    • fan to illustrate secretion

Components and Schematics

Constitutive Promoter Activated Promoter Repressed Promoter
Constitutive Promoter Component Activated Promoter Component Repressed Promoter Component
  • Strength of the promoter is set through the potentiometer
  • A battery is embedded into the lego brick
  • The Lego brick is sealed with a conductive plate to make contact with the table.
  • Activity of the promoter is driven by the amount of light received on the photo-sensor.
  • A battery is embedded into the lego brick
  • The Lego brick is sealed with a conductive plate to make contact with the table.
  • Activity of the promoter is driven by the amount of light received on the photo-sensor.
  • A battery is embedded into the lego brick
  • The Lego brick is sealed with a conductive plate to make contact with the table.
RBS Protein Coding Region Stop Codon
Constitutive Promoter Component Activated Promoter Component Repressed Promoter Component
  • Strength of the RBS is set through the potentiometer
  • a 10-LEDs graph bar is used to indicate the level of expression.
  • a LED is used separately to potentially drive another promoter through a fiber optic.
  • the Resistor-Capacitor is used to add a delay.
  • The stop codon enables the circuit to connect to earth through the table

Basic Gene Expression Circuits

Protein Generator Fusion Protein Generator Monocystronic Protein Generator
Constitutive Promoter Component Activated Promoter Component Repressed Promoter Component
  • the protein expression level is tuned by the potentiometers of the promoter and the RBS
  • the protein expression level can be picked up with a fiber optic to drive another promoter or an output modules (flagella motor or secretion fan).
  • the expression level of both proteins is tuned by the potentiometers of the promoter and the RBS. It is the same for both proteins.
  • the protein expression levels can be picked up with a fiber optic to drive another promoter or an output modules (flagella motor or secretion fan).
  • control over the protein expression levels is tuned by the potentiometer of the promoter, but also, independently controlled by the potentiometers of the RBSs.
  • the protein expression levels can be picked up with a fiber optic to drive another promoter or an output modules (flagella motor or secretion fan).

Elementary Genetic Circuits

Inverter Repressillator
Constitutive Promoter Component Activated Promoter Component


Material

Biobricks

  • constitutive promoter:
    • Duplo brick 2x2
    • potentiometer
    • connector
    • battery
    • electronic circuit
  • ribosome binding site
    • Duplo brick 2x2
      • potentiometer to tune strength of RBS
      • battery
    • connectors x2
  • Stop codon
    • Duplo brick 2x2
    • Connector x1

Inputs Sensors

Motors


Electronic Circuits

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