Team:Montreal/Project

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==Taming The Repressilator==
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==Experimental==
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[[Image:mcgill_quorum.jpg||thumb|right|300px | Quorum sensing at work in e. coli bacteria]]Building on previous years of research, the McGill University iGEM team intends to construct a set of Biobricks that will maintain synchronous oscillations in a large population of cells. If accomplished, our theorists and experimentalists will cooperate to refine this system using various modifications to further our understanding of biological clocks and their functioning.
-
To create our functional bacteria, we intend to transform a line of MC4100 E. coli cells used by Elowitz with '''two plasmids'''. The first plasmid will contain the '''Repressilator''' (&lambda;cI, TetR and LacI), described in his 2000 paper. The second plasmid will be a triple-ligation of the '''I<sub>14001</sub>''' bio-brick, the '''J<sub>40001</sub>''' bio-brick and the '''Elowitz reporter''' (TetR, YFP).
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<br><br><br><br>
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-
If successful, we intend to observe and experiment with our cells with fluorescence microscopy and spectrophotometry. Using three individual filters, we can microscopically observe the oscillations of individual components by the three fluorescent proteins (ECFP, GFP and RFP) embedded in the system.
+
==Project Objectives==
==Project Objectives==
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===Cloning Plan===
+
===Experimental===
 +
To create our functional bacteria, we intend to transform a line of MC4100 E. coli cells used by Elowitz with '''two plasmids'''. The first plasmid will contain the '''Repressilator''' (&lambda;cI, TetR and LacI), described in his 2000 paper. The second plasmid will be a triple-ligation of the '''I-like''' bio-brick, the '''J<sub>40001</sub>''' bio-brick and the '''Elowitz reporter''' (TetR, YFP).
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'''Plasmid<sub>A</sub>''': &lambda;cI + TetR + LacI (Elowitz Repressilator)
+
If successful, we intend to observe oscillating fluorescence with large amplitudes in microscopy and spectrophotometry experiments. Using three individual filters, we can microscopically observe the oscillations of individual components by the three fluorescent proteins (ECFP, GFP and RFP) embedded in the system.
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* Sent by Dr. Michael Elowitz (Caltech).
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-
'''Plasmid<sub>B</sub>''': I<sub>14001</sub> + J<sub>40001</sub> + TetR/YFP (Elowitz Reporter) + kan<sup>+</sup>
 
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1. Cut J-brick genes out of plasmid with XbaI/SpeI
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===Parts===
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[[Image:osc-rep.jpg||thumb|right|300px]]
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2. Ligate to J-brick genes to I-brick plasmid cut with XbaI (+dephosphorylation)
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*The Repressilator
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[[Image:repressilator.png||left|500px]]
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<br><br><br><br>
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3. Select on amp<sup>+</sup>/kan<sup>+</sup> plates (I-brick plasmid carries resistance for both ampicillin and kanomycin)
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*J40001<br>
 +
[[Image:J40001.png||left|250px]]
 +
<br><br><br><br>
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4. Cut of I and J-brick genes with EcoRI
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*I-like brick: gene synthesized for use with our system. Somewhat similar to BBa_I15004
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5. Ligate genes to Elowitz reporter plasmid cut with EcoRI (3-way ligation)
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<u><b>plac</b> - rbs - <b>luxI</b> - <b>RFP</b> - STOP - <b>J23119</b> - rbs - <b>luxR</b> - STOP</u>
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6. Select on kan<sup>+</sup> LB plates
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<br>
 +
*'''Plasmid A''': &lambda;cI + TetR + LacI (Elowitz Repressilator) <b>Ampicillin Resistant</b>
 +
*'''Plasmid B''': I-like + J<sub>40001</sub> + TetR/YFP (Elowitz Reporter) <b>Kanamycin Resistant</b>
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==Modelling==
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<br><br>
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[[Image:Theoteam1.jpg|right|frame|Theorists: Vincent Quenneville-Bélair and Alexandra Ortan]]
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Using coupled differential equations, we are modeling the repressilator, which is a network of three genes, whose product proteins are repressing each other's growth. This cycle is taking place in each of a colony of cells, who communicate amongst themselves by exchanging an autoinducer molecule. The model attempts to take into account a sparse, heterogeneous distribution of cells with depletion of the autoinducer molecule and leakage.
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===[[Team:Montreal/Modeling|Modeling]]===
 +
 
 +
The modeling effort attempts to simulate a repressilator network using a system of coupled differential equations. The repressilator itself is modelled as a loop of three proteins which inhibit each other's growth. Each cell in the network contains a repressilator, and the cells communicate amongst themselves by exchanging an autoinducer molecule, which feeds back the repressilator loop. The simulation is currently done using Mathematica, along with the xCellerator and NDelayDSolve packages.
 +
 
 +
The model is assuming continuous levels of the different proteins, as well as a continuous spatial distribution of these proteins. It attempts to take into account lab issues such as depletion of the autoinducer molecule and leakage by introducing a time delay in the equations and by considering sparse distributions of cells within the field of view.
 +
 
 +
Once the model is set up, the goal is to explore different cell configurations and observe how the behaviour of the repressilator changes as a result. In particular, we are interested in the concentration of the auto-inducer molecule as a function of time, their period of oscillation, the speed with which the cells synchronise (if they do) or the phase difference between various clusters of cells (if they don't).
 +
<br><br>
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For this purpose, the model is currently being coded up in Mathematica. The simulations, based on that continuous model, are generated using xCellerator and NDelayDSolve for different cell configurations; the results obtained are graphs of the concentration of molecules in the system versus time. That is, our interest lies in the phase difference between clusters of cells. As of now, a low number of cells is being used for testing, but a higher one will be reached later.
 
==Future Applications==  
==Future Applications==  
===Pacemaking Technology===
===Pacemaking Technology===
-
Once of the better known sinusoidal oscillators in the human body are the cells of the sinoatrial node of the heart that establish a regular rhythm of action potentials that propagate throughout the atria and ventricles to generate beats. While current artificial pacemakers focus primarily on re-establishing this rhythm by generating electrical potentials, a biological alternative could prove more effective and less invasive than its mechanical counterpart with further research.
+
[[Image:mcgill_pacemaker.jpg||thumb|left|100px]]Once of the better known sinusoidal oscillators in the human body are the cells of the sinoatrial node of the heart that establish a regular rhythm of action potentials that propagate throughout the atria and ventricles to generate beats. While current artificial pacemakers focus primarily on re-establishing this rhythm by generating electrical potentials, a biological alternative could prove more effective and less invasive than its mechanical counterpart with further research.
 +
<br><br>
 +
 
===Continuous Cultures in Industrial Bio-Reactors===  
===Continuous Cultures in Industrial Bio-Reactors===  
-
A common problem in bio-reactors used by pharmaceutical and biotechnology companies results from difficulties in growing cells in continuous cultures due to various complications in recycling nutrients and draining metabolites. An effectively oscillating system could reduce the reliance on current fed-batch systems by allowing more effective cycles of cell growth and protein expression.
+
[[Image:mcgill_reactor.jpg||thumb|left|100px]]A common problem in bio-reactors used by pharmaceutical and biotechnology companies results from difficulties in growing cells in continuous cultures due to various complications in recycling nutrients and draining metabolites. An effectively oscillating system could reduce the reliance on current fed-batch systems by allowing more effective cycles of cell growth and protein expression.
 +
 
 +
<br><br>
 +
<br><br>
 +
 
===Biological Drug Delivery===
===Biological Drug Delivery===
-
With biological alternatives now being increasingly explored as mechanisms of delivering therapeutics, a functionally oscillating system could prove invaluable to tailoring drug regimes to specific systems. Innumerable biological processes function in rhythmic on/off switches and being able to control the release of certain cellular components to such a schedule may permit more effective treatment.&bull;
+
[[Image:mcgill_drugdel.jpg||thumb|left|100px]]With biological alternatives now being increasingly explored as mechanisms of delivering therapeutics, a functionally oscillating system could prove invaluable to tailoring drug regimes to specific systems. Innumerable biological processes function in rhythmic on/off switches and being able to control the release of certain cellular components to such a schedule may permit more effective treatment.
 +
<br><br><br><br>
 +
 
 +
==Past McGill iGEM Projects==
 +
===2006 & 2007===
 +
The two-gene intercellular oscillatory system ([http://www.utm.utoronto.ca/~mcmillen/ McMillen] [http://www.pnas.org/cgi/reprint/99/2/679.pdf 2002]) examined in past projects developed irregular, triangular-shaped oscillation curves over extended periods of time. In an effort to improve the consistency and regularity of the oscillations, the Repressilator will be used. The system in theory should have better long-term fidelity in oscillation patterns and develop a more natural sinusoidal oscillatory pattern.
 +
<br><br>

Latest revision as of 05:19, 6 August 2008

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Contents

Taming The Repressilator

Quorum sensing at work in e. coli bacteria
Building on previous years of research, the McGill University iGEM team intends to construct a set of Biobricks that will maintain synchronous oscillations in a large population of cells. If accomplished, our theorists and experimentalists will cooperate to refine this system using various modifications to further our understanding of biological clocks and their functioning.





Project Objectives

Experimental

To create our functional bacteria, we intend to transform a line of MC4100 E. coli cells used by Elowitz with two plasmids. The first plasmid will contain the Repressilator (λcI, TetR and LacI), described in his 2000 paper. The second plasmid will be a triple-ligation of the I-like bio-brick, the J40001 bio-brick and the Elowitz reporter (TetR, YFP).

If successful, we intend to observe oscillating fluorescence with large amplitudes in microscopy and spectrophotometry experiments. Using three individual filters, we can microscopically observe the oscillations of individual components by the three fluorescent proteins (ECFP, GFP and RFP) embedded in the system.


Parts

Osc-rep.jpg
  • The Repressilator
Repressilator.png





  • J40001
J40001.png





  • I-like brick: gene synthesized for use with our system. Somewhat similar to BBa_I15004

plac - rbs - luxI - RFP - STOP - J23119 - rbs - luxR - STOP


  • Plasmid A: λcI + TetR + LacI (Elowitz Repressilator) Ampicillin Resistant
  • Plasmid B: I-like + J40001 + TetR/YFP (Elowitz Reporter) Kanamycin Resistant



Modeling

The modeling effort attempts to simulate a repressilator network using a system of coupled differential equations. The repressilator itself is modelled as a loop of three proteins which inhibit each other's growth. Each cell in the network contains a repressilator, and the cells communicate amongst themselves by exchanging an autoinducer molecule, which feeds back the repressilator loop. The simulation is currently done using Mathematica, along with the xCellerator and NDelayDSolve packages.

The model is assuming continuous levels of the different proteins, as well as a continuous spatial distribution of these proteins. It attempts to take into account lab issues such as depletion of the autoinducer molecule and leakage by introducing a time delay in the equations and by considering sparse distributions of cells within the field of view.

Once the model is set up, the goal is to explore different cell configurations and observe how the behaviour of the repressilator changes as a result. In particular, we are interested in the concentration of the auto-inducer molecule as a function of time, their period of oscillation, the speed with which the cells synchronise (if they do) or the phase difference between various clusters of cells (if they don't).


Future Applications

Pacemaking Technology

Mcgill pacemaker.jpg
Once of the better known sinusoidal oscillators in the human body are the cells of the sinoatrial node of the heart that establish a regular rhythm of action potentials that propagate throughout the atria and ventricles to generate beats. While current artificial pacemakers focus primarily on re-establishing this rhythm by generating electrical potentials, a biological alternative could prove more effective and less invasive than its mechanical counterpart with further research.




Continuous Cultures in Industrial Bio-Reactors

Mcgill reactor.jpg
A common problem in bio-reactors used by pharmaceutical and biotechnology companies results from difficulties in growing cells in continuous cultures due to various complications in recycling nutrients and draining metabolites. An effectively oscillating system could reduce the reliance on current fed-batch systems by allowing more effective cycles of cell growth and protein expression.






Biological Drug Delivery

Mcgill drugdel.jpg
With biological alternatives now being increasingly explored as mechanisms of delivering therapeutics, a functionally oscillating system could prove invaluable to tailoring drug regimes to specific systems. Innumerable biological processes function in rhythmic on/off switches and being able to control the release of certain cellular components to such a schedule may permit more effective treatment.





Past McGill iGEM Projects

2006 & 2007

The two-gene intercellular oscillatory system ([http://www.utm.utoronto.ca/~mcmillen/ McMillen] [http://www.pnas.org/cgi/reprint/99/2/679.pdf 2002]) examined in past projects developed irregular, triangular-shaped oscillation curves over extended periods of time. In an effort to improve the consistency and regularity of the oscillations, the Repressilator will be used. The system in theory should have better long-term fidelity in oscillation patterns and develop a more natural sinusoidal oscillatory pattern.