Team:UQ-Australia/Modeling

From 2011.igem.org

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|At the completion of the experimental work, we should expect a working clock BioBrick, which should exhibit oscillatory behaviour. We wish to characterise how our clock BioBrick oscillates.
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Of interest is the frequency and regularity at which it oscillates and whether multiple cells containing our BioBrick oscillate in time with each other.
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|[[File:UQ-Australia_logo_2011.png|125x125px|link=https://2011.igem.org/Team:UQ-Australia]]
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|The modelling will involve the mathematical characterisation of the kinetics and synchronisation of the oscillation of our bacteria.
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The kinetics involve modelling how fast our bacteria cells will oscillate and the shape of their oscillation pattern.
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The synchronisation is to characterise how quickly nearby cells would couple any synchronise their oscillation.
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|To give a rough idea of how our cells should be oscillating, mathematical models were described from literature. These would ideally be compared with experimental characterisation of the oscillation.
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== <span style="color:#558822">Kinetics</span> ==
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|width="125" |[[File:Synchronisation viewpdf UQ.png|125x125px|link=https://static.igem.org/mediawiki/2011/f/f4/UQ-Auatralia-Modelling.pdf]]
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| A mathematical investigation into the behaviour of a genetic circuit can give predictions into the behaviour the circuit. Each reaction within a genetic circuit can be modelled as a first order kinetic law. Here we analyse the proposed circuit replicating the behaviour of a biological clock for the UQ-Australia iGEM 2011 entry. Open-source software [http://www.celldesigner.org CellDesigner] was used to perform the simulation of the kinetic laws over time. Although it was expected that there would be some oscillation behaviour, our simulations have shown that there would be no oscillations. However, if the physical genetic circuit did display oscillatory behaviour, then literature values taken would then need to be revised for the model.
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[https://static.igem.org/mediawiki/2011/f/f4/UQ-Auatralia-Modelling.pdf '''Modelling of kinetics for circuit''']
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[https://static.igem.org/mediawiki/2011/2/2d/UQ-Australia-circuit.zip '''Download our CellDesigner file to play with our circuit!''']
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[http://www.celldesigner.org/ Here is the CellDesigner webpage]
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== <span style="color:#558822">Synchronisation</span> ==
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|width="125" |[[File:Synchronisation viewpdf UQ.png|125x125px|link=https://static.igem.org/mediawiki/2011/d/d6/PHYS3900-LitReview-Ann-PrettiedUp.pdf]]
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| Many expressions in language rely on the idea of time. Here, we shall take a journey through time, from the idea of clock synchronisation, first shown about 400 years ago by Christiaan Huygens, to the recent observations of this synchronisation phenomenon in nature. Currently, an understanding of this process is currently being carried out at the genetic level. A union of physical modelling with mathematical theory and biological experimentation is leading to a deeper understanding of synchronisation in all disciplines, but particularly in the biological sciences. [https://static.igem.org/mediawiki/2011/d/d6/PHYS3900-LitReview-Ann-PrettiedUp.pdf '''Here'''] we shall explore the physically interesting, but mathematically...just chaotic, area of clocks.
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[https://static.igem.org/mediawiki/2011/d/d6/PHYS3900-LitReview-Ann-PrettiedUp.pdf '''A timely investigation into the behaviour of clocks''']
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== <span style="color:#558822">Microscopy</span> ==
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| Many teams have been using microscopy during their experiments. Although these (thankfully!) may not directly be any of the submitted BioBricks, microscopy has become important in experimental biology. [https://static.igem.org/mediawiki/2011/a/a9/JamBen42013532_FormattedPopSciArticle_forUQ-iGEM.pdf '''Here'''] we shall present an enlightening introduction the microscopy, tangible for old and new iGEMers!
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[https://static.igem.org/mediawiki/2011/4/4f/Fields_report_for_UQ_iGEM.pdf '''Putting the lumen in luminescence''']
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|width="125" |[[File:Microscopy viewpdf UQ.png|125x125px|link=https://static.igem.org/mediawiki/2011/a/a9/JamBen42013532_FormattedPopSciArticle_forUQ-iGEM.pdf]]
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|width="125" |[[File:Microscopy viewpdf UQ.png|125x125px|link=https://static.igem.org/mediawiki/2011/4/4f/Fields_report_for_UQ_iGEM.pdf]]
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| After [https://static.igem.org/mediawiki/2011/a/a9/JamBen42013532_FormattedPopSciArticle_forUQ-iGEM.pdf '''that enlightening introduction'''], [https://static.igem.org/mediawiki/2011/4/4f/Fields_report_for_UQ_iGEM.pdf '''here'''] we shall investigate the behaviour of light within confocal and two-photon microscopy. By taking established theory describing the behaviour of focused light in three dimensions, we show through computer simulation that the resolution achieved in confocal and two-photon microscopy is dependent on the wavelength of light involved. This article would have greater appeal to those not fearful of as few equations.
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[https://static.igem.org/mediawiki/2011/4/4f/Fields_report_for_UQ_iGEM.pdf '''Resolving power in microscopy''']
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For your enjoyment, MATLAB code used in this discussion is included in the appendix of the report.
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At the completion of the experimental work, we should expect a working clock BioBrick, which should exhibit oscillatory behaviour. We wish to characterise how our clock BioBrick oscillates.
+
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Of interest is the frequency and regularity at which it oscillates and whether multiple cells containing our BioBrick oscillate in time with each other.
+
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+
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The modelling will involve the mathematical characterisation of the kinetics and synchronisation of the oscillation of our bacteria.
+
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The kinetics involve modelling how fast our bacteria cells will oscillate and the shape of their oscillation pattern.
+
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The synchronisation is to characterise how quickly nearby cells would couple any synchronise their oscillation.
+
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To give a rough idea of how our cells should be oscillating, mathematical models were described from literature. These would ideally be compared with experimental characterisation of the oscillation.
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== <span style="color:#558822">Kinetics</span> ==
+
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The BioBrick circuit has been represented as a network in a figure yet to be uploaded. For every reaction indicated in imaginary figure, we have assumed a first order reaction rate. The reaction constants have been taken from literature.
+
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From this, we would then have a system of first order linear ordinary differential equations. This should be solvable and thus give us a prediction as to the nature of the oscillatory behaviour of a cell.
+
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To test the appropriateness of this model, we would then experimentally measure the expression of arbitrary protein and see how close it fits.
+
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== <span style="color:#558822">Synchronisation</span> ==
+
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We have our cells, which are oscillating. Experimentally, we would have a dish of many cells, most of which will be oscillating, but not necessarily oscillation in time with each other. Realistically, for most practical purposes, we would require that the cells are oscillating in a manner such that they are synchronised.
 
-
Of interest to us would be how each cell synchronises itself with its neighbour. We could mathematically characterise this synchronisation. To generalise this, we could model this as the behaviour of many oscillators.
 
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So, of particular interest to us would be the behaviour of, at the very simplest step, two oscillators coupling with each other.
+
Although these articles do not directly contribute towards a new BioBrick part (yet!), we hope this investigation settles any curiosities regarding focused light in microscopes and perhaps inspires iGEMers to further consider the inner working of the apparatus on which they can depend quite heavily.
-
Thus we intend to investigate the coupling of two oscillators in a biological context.
+

Latest revision as of 01:26, 6 October 2011




At the completion of the experimental work, we should expect a working clock BioBrick, which should exhibit oscillatory behaviour. We wish to characterise how our clock BioBrick oscillates.

Of interest is the frequency and regularity at which it oscillates and whether multiple cells containing our BioBrick oscillate in time with each other.

UQ-Australia logo 2011.png
The modelling will involve the mathematical characterisation of the kinetics and synchronisation of the oscillation of our bacteria.

The kinetics involve modelling how fast our bacteria cells will oscillate and the shape of their oscillation pattern. The synchronisation is to characterise how quickly nearby cells would couple any synchronise their oscillation.

To give a rough idea of how our cells should be oscillating, mathematical models were described from literature. These would ideally be compared with experimental characterisation of the oscillation.

Kinetics

Synchronisation viewpdf UQ.png A mathematical investigation into the behaviour of a genetic circuit can give predictions into the behaviour the circuit. Each reaction within a genetic circuit can be modelled as a first order kinetic law. Here we analyse the proposed circuit replicating the behaviour of a biological clock for the UQ-Australia iGEM 2011 entry. Open-source software [http://www.celldesigner.org CellDesigner] was used to perform the simulation of the kinetic laws over time. Although it was expected that there would be some oscillation behaviour, our simulations have shown that there would be no oscillations. However, if the physical genetic circuit did display oscillatory behaviour, then literature values taken would then need to be revised for the model.

Modelling of kinetics for circuit

Download our CellDesigner file to play with our circuit!

[http://www.celldesigner.org/ Here is the CellDesigner webpage]

Synchronisation

Synchronisation viewpdf UQ.png Many expressions in language rely on the idea of time. Here, we shall take a journey through time, from the idea of clock synchronisation, first shown about 400 years ago by Christiaan Huygens, to the recent observations of this synchronisation phenomenon in nature. Currently, an understanding of this process is currently being carried out at the genetic level. A union of physical modelling with mathematical theory and biological experimentation is leading to a deeper understanding of synchronisation in all disciplines, but particularly in the biological sciences. Here we shall explore the physically interesting, but mathematically...just chaotic, area of clocks.

A timely investigation into the behaviour of clocks


Microscopy

Many teams have been using microscopy during their experiments. Although these (thankfully!) may not directly be any of the submitted BioBricks, microscopy has become important in experimental biology. Here we shall present an enlightening introduction the microscopy, tangible for old and new iGEMers!

Putting the lumen in luminescence

Microscopy viewpdf UQ.png


Microscopy viewpdf UQ.png After that enlightening introduction, here we shall investigate the behaviour of light within confocal and two-photon microscopy. By taking established theory describing the behaviour of focused light in three dimensions, we show through computer simulation that the resolution achieved in confocal and two-photon microscopy is dependent on the wavelength of light involved. This article would have greater appeal to those not fearful of as few equations.

Resolving power in microscopy

For your enjoyment, MATLAB code used in this discussion is included in the appendix of the report.


Although these articles do not directly contribute towards a new BioBrick part (yet!), we hope this investigation settles any curiosities regarding focused light in microscopes and perhaps inspires iGEMers to further consider the inner working of the apparatus on which they can depend quite heavily.

Retrieved from "http://2011.igem.org/Team:UQ-Australia/Modeling"