Team:Edinburgh/Modelling/Signalling

From 2010.igem.org

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  <li><a href="http://2010.igem.org/Team:Edinburgh/Notebook" class="dir">lab notes&nbsp;&nbsp;&nbsp;</a>
  <li><a href="http://2010.igem.org/Team:Edinburgh/Notebook" class="dir">lab notes&nbsp;&nbsp;&nbsp;</a>
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   <li><a href="http://2010.igem.org/Team:Edinburgh/Notebook">collaboration</a></li>
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   <li><a href="http://2010.igem.org/Team:Edinburgh/Notebook/Collaboration">collaboration</a></li>
   <li><a href="http://2010.igem.org/Team:Edinburgh/Notebook/BRIDGE">BRIDGE</a></li>
   <li><a href="http://2010.igem.org/Team:Edinburgh/Notebook/BRIDGE">BRIDGE</a></li>
   <li><a href="http://2010.igem.org/Team:Edinburgh/Notebook/Red_light_producer">red light</a></li>
   <li><a href="http://2010.igem.org/Team:Edinburgh/Notebook/Red_light_producer">red light</a></li>
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<p>During the <a href="http://2010.igem.org/Team:Edinburgh/Modelling/Bacterial">intracellular modelling of bacterial BRIDGEs</a>, it became apparent that perturbations alone would not suffice to demonstrate the interactions of light based communication between bacteria. What was needed was modelling of entire colonies of bacteria. The goals of this modelling would be to demonstrate <i>in-silico</i> the light based communication between bacteria that we are trying to develop, and to establish whether light based communication is feasible given the few <i>in-vitro</i> measurements we are able to make.</p>
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<p>During the <a href="http://2010.igem.org/Team:Edinburgh/Modelling/Bacterial">intracellular modelling of bacterial BRIDGEs</a>, it became <b>apparent</b> that perturbations alone would not suffice to <b>demonstrate</b> the <b>interactions</b> of light-based communication between bacteria. What was needed was modelling of entire colonies of bacteria. The <b>goals</b> of this modelling would be to <b>demonstrate</b> <i>in-silico</i> the light-based communication between bacteria that we were trying to <b>develop</b>, and to <b>establish</b> whether light-based communication was <b>feasible</b> given the few <i>in-vitro</i> measurements we were able to make.</p>
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<p>The ideal is to be able to simulate a colony in an initial random state spontaneously synchronising. Realistically, however, this is a very difficult problem. The computational complexity of simply replicating the intracellular model for lots of individual cells and simulating them all together is prohibitive (especially given the hardware we have available). Also, there are a lot of unknowns that will have to be dealt with:</p>
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<p>The <b>ideal</b> would be to be able to <b>simulate</b> the spontaneous synchronisation of a colony in a random initial state. <b>Realistically</b>, however, this would be a very difficult problem. The computational <b>complexity</b> of simply replicating the intracellular model for lots of individual cells and simulating them all together was <b>prohibitive</b> (especially given the hardware we had available). Also, there were a lot of <b>unknowns</b> that would have to be <b>dealt</b> with:</p>
<ul>
<ul>
  <li>How is the light output from one bacterium converted into signal input by a neighbouring bacterium?</li>
  <li>How is the light output from one bacterium converted into signal input by a neighbouring bacterium?</li>
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<p>The proposed plan is to simplify the intracellular model. The aim would be to produce a model which produces the three light outputs and reacts to varying levels of three light inputs in exactly the same way as the current, full intracellular model. This is a non-trivial task: first, 'exact' is difficult to define with stochastic modelling - no two
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<p>The <b>proposed</b> plan was to simplify the intracellular model. The <b>aim</b> would be to produce a model which <b>replicated</b> the three light outputs and <b>reacted</b> to varying levels of three light inputs in exactly the same way as the full <a href="http://2010.igem.org/Team:Edinburgh/Modelling/Bacterial">intracellular model</a>. This was a <b>non-trivial</b> task: first, 'exact' is difficult to <b>define</b> with stochastic modelling - no two simulation runs will be the same. The simplest <b>approach</b> would be to run the simulation repeatedly and <b>compute</b> both the mean and standard deviation for the observables (light output), for each of a number of test profiles (light input). Then we would <b>develop</b> a simplified model which matched the output for each of these profiles. Again, 'matching' would need to be <b>defined</b> as some means of scoring.</p>
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simulation runs will be the same. The simplest approach would be to run the simulation repeatedly and compute both the mean and standard deviation for the observables (light output), for each of a number of test profiles (light input). Then we somehow develop a simplified model which matches output for each of these profiles. Again, 'matching' needs to be defined as some means of scoring.</p>
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<p>The development of this model will be automated, since there is not the time available to redevelop the simplified model every time the full intracellular model is refined with new experimental data. Either mathematical analysis or evolutionary model development through genetic algorithms can thus be used to accomplish this; both are difficult tasks, but genetic algorithms may be within our capabilities.</p>
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<p>The <b>development</b> of this model would be automated, since there was not the time available to redevelop the simplified intercellular model every time the full <a href="http://2010.igem.org/Team:Edinburgh/Modelling/Bacterial">intracellular model</a> was <b>refined</b> with new experimental data. It was thought that either mathematical <b>analysis</b> or evolutionary model <b>development</b> through genetic algorithms could thus be used to <b>accomplish</b> this; both would <b>entail</b> difficult tasks, but it was thought that genetic algorithms would be within our <b>capabilities</b>.</p>
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<p>With a simplified intracellular model, we can think about intercellular communication. There are two elements here; how we represent the interaction of neighbouring cells over time, and how we transform the light output of one cell into the light input of its neighbours (and itself), taking into account attenuation, multiple conflicting signals, etc.</p>
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<p>With the development of a simplified intracellular model, we would be able to think about intercellular <b>communication</b>. This would involve two elements; how to <b>represent</b> the interaction of neighbouring cells over time, and how to <b>transform</b> the light output of one cell into the light input of its neighbours (and itself), taking into account attenuation, multiple conflicting signals, and other factors.</p>
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<p>Our proposed solution is to create a simulation based on both stochastic modelling and cellular automata. For the initial implementation we will make the simplifying assumptions that the cells are non-motile, and regularly packed into a two-dimensional hexagonal mesh. Each cell will receive input from its six nearest neighbours (and itself).</p>
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<p>Our proposed <b>solution</b> was to create a simulation based on both stochastic modelling and cellular automata. For the initial <b>implementation</b> we would make the simplifying <b>assumptions</b> that the cells were non-motile and regularly packed into a two-dimensional hexagonal mesh. Each cell would <b>receive</b> input from its six nearest neighbours (and itself).</p>
<center><br><br><p><img src="http://2010.igem.org/wiki/images/d/d4/Ed10-Inter1.jpg"></p><br>
<center><br><br><p><img src="http://2010.igem.org/wiki/images/d/d4/Ed10-Inter1.jpg"></p><br>
<p><b>Figure 1:</b> The two-dimensional hexagonal mesh that forms the underlying structure of our proposed intercellular model.</p><br><br></center>
<p><b>Figure 1:</b> The two-dimensional hexagonal mesh that forms the underlying structure of our proposed intercellular model.</p><br><br></center>
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<p>The stochastic model will hold a representation of a colony laid out in the above hexagonal mesh. Each cell will have an individual representation of the simplified intra-cellular model. The model will be run stochastically with each cell effectively operating independently. After every time interval delta-t has elapsed, the values of each of the three light inputs in a cell is calculated based on the observed light output at that timepoint of the cell itself and its 6 closest
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<p>The stochastic model would hold a <b>representation</b> of a colony laid out in the above hexagonal mesh. Each cell would have an individual representation of the simplified intracellular model. The model would be run stochastically with each cell effectively operating <b>independently</b>. After the elapsing of every time interval delta-t, the values of each of the three light inputs in a cell would be calculated based on the observed light output at that timepoint of the cell itself and its six closest neighbours:</p>
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neighbours:</p>
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<p>The functions f<sub>red</sub>, f<sub>green</sub>, and f<sub>blue</sub> have yet to be defined, but will hopefully be based on experimental data.</p>
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<p>The functions f<sub>red</sub>, f<sub>green</sub>, and f<sub>blue</sub> have yet to be <b>defined</b>, but would hopefully be based on experimental data.</p>
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<p>After updating the input value of all cells in the mesh, stochastic simulation is resumed. The cycle then repeats after every delta-t time units. This should give us a basis for the simulation of bacterial colony synchronisation.</p><br>
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<p>After updating the input value of all cells in the mesh, the stochastic simulation would be resumed. The cycle would then repeat after every delta-t time units. This would thus give us a basis for the simulation of bacterial colony synchronisation.</p><br>
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Revision as of 13:44, 7 October 2010







Overview: Modelling intercellular bacterial BRIDGEs


During the intracellular modelling of bacterial BRIDGEs, it became apparent that perturbations alone would not suffice to demonstrate the interactions of light-based communication between bacteria. What was needed was modelling of entire colonies of bacteria. The goals of this modelling would be to demonstrate in-silico the light-based communication between bacteria that we were trying to develop, and to establish whether light-based communication was feasible given the few in-vitro measurements we were able to make.

The ideal would be to be able to simulate the spontaneous synchronisation of a colony in a random initial state. Realistically, however, this would be a very difficult problem. The computational complexity of simply replicating the intracellular model for lots of individual cells and simulating them all together was prohibitive (especially given the hardware we had available). Also, there were a lot of unknowns that would have to be dealt with:

  • How is the light output from one bacterium converted into signal input by a neighbouring bacterium?
  • What is the distribution of the light sensing molecules in the receiving bacterium?
  • How is the light attenuated by distance between the bacteria?
  • How is the light attenuated by passing through two cell membranes?
  • Will motility of the bacteria be an important factor?
  • How much light from other bacteria will be required to not be swamped by the light output of the receiving bacterium itself?
  • How will a bacterium cope with multiple conflicting signals from neighbouring bacteria?
  • Will the light emission within a single bacterium be homogeneous, or will there be multiple different outputs from different regions within the bacterium?


The Model


The proposed plan was to simplify the intracellular model. The aim would be to produce a model which replicated the three light outputs and reacted to varying levels of three light inputs in exactly the same way as the full intracellular model. This was a non-trivial task: first, 'exact' is difficult to define with stochastic modelling - no two simulation runs will be the same. The simplest approach would be to run the simulation repeatedly and compute both the mean and standard deviation for the observables (light output), for each of a number of test profiles (light input). Then we would develop a simplified model which matched the output for each of these profiles. Again, 'matching' would need to be defined as some means of scoring.

The development of this model would be automated, since there was not the time available to redevelop the simplified intercellular model every time the full intracellular model was refined with new experimental data. It was thought that either mathematical analysis or evolutionary model development through genetic algorithms could thus be used to accomplish this; both would entail difficult tasks, but it was thought that genetic algorithms would be within our capabilities.

With the development of a simplified intracellular model, we would be able to think about intercellular communication. This would involve two elements; how to represent the interaction of neighbouring cells over time, and how to transform the light output of one cell into the light input of its neighbours (and itself), taking into account attenuation, multiple conflicting signals, and other factors.

Our proposed solution was to create a simulation based on both stochastic modelling and cellular automata. For the initial implementation we would make the simplifying assumptions that the cells were non-motile and regularly packed into a two-dimensional hexagonal mesh. Each cell would receive input from its six nearest neighbours (and itself).




Figure 1: The two-dimensional hexagonal mesh that forms the underlying structure of our proposed intercellular model.



The stochastic model would hold a representation of a colony laid out in the above hexagonal mesh. Each cell would have an individual representation of the simplified intracellular model. The model would be run stochastically with each cell effectively operating independently. After the elapsing of every time interval delta-t, the values of each of the three light inputs in a cell would be calculated based on the observed light output at that timepoint of the cell itself and its six closest neighbours:


inputred = fred(outputcell; (outputneighbour - i : i = 1::6))
inputgreen = fgreen(outputcell; (outputneighbour - i : i = 1::6))
inputblue = fblue(outputcell; (outputneighbour - i : i = 1::6))

The functions fred, fgreen, and fblue have yet to be defined, but would hopefully be based on experimental data.

After updating the input value of all cells in the mesh, the stochastic simulation would be resumed. The cycle would then repeat after every delta-t time units. This would thus give us a basis for the simulation of bacterial colony synchronisation.





Results


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