Team:Groningen/Biofilm model

From 2010.igem.org

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(Biofilm Dynamics)
(Biofilm Dynamics)
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Biofilms are multicellular conglomerates which attach to surfaces. The formation of biofilms is triggered by high cell density and limited resources. The sensing is of these conditions is often mediated by an extracellular signaling compound which increases in concentration and triggers regulating circuitry. This process is called [quorum sensing] and it plays an important role in the dynamics of multicellular systems.  
Biofilms are multicellular conglomerates which attach to surfaces. The formation of biofilms is triggered by high cell density and limited resources. The sensing is of these conditions is often mediated by an extracellular signaling compound which increases in concentration and triggers regulating circuitry. This process is called [quorum sensing] and it plays an important role in the dynamics of multicellular systems.  
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Quorum sensing systems can cause complicated effects including cell differentiation within single species conglomerates. A recent example of this can be seen in the difference of expression in the [TasA protein] which plays a major role in the formation of the biofilm matrix by forming amyloid fibers. Expression of this protein is mediated by competitive inhibitive systems by, amongst others, the [yqxM gene] which linked to the ComXPA quorum sensing system.  
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Quorum sensing systems can cause complicated effects including cell differentiation within single species conglomerates. A recent example of this can be seen in the difference of expression in the [http://subtiwiki.uni-goettingen.de/wiki/index.php/TasA TasA protein] which plays a major role in the formation of the biofilm matrix by forming amyloid fibers. Expression of this protein is mediated by competitive inhibitive systems by, amongst others, the [http://subtiwiki.uni-goettingen.de/wiki/index.php/YqxM yqxM gene](<partinfo>BBa_K305006</<partinfo> which linked to the [http://2010.igem.org/Team:Groningen#/expression_model ComXPA quorum sensing] system.  
However it has been found that not all bacteria respond to the signaling molecules in the same way. It was shown that biofilm formation in ''Bacillus subtilis'' involves paracrine signaling in which most cells produce and secrete the signaling molecule ComX but only a sub population of the cells is triggered to make surfactin. Surfactin serves as paracrine signaling molecule and the cells which are not able to make surfactin, respond to surfactin by making extracellular matrix components for the biofilm.  
However it has been found that not all bacteria respond to the signaling molecules in the same way. It was shown that biofilm formation in ''Bacillus subtilis'' involves paracrine signaling in which most cells produce and secrete the signaling molecule ComX but only a sub population of the cells is triggered to make surfactin. Surfactin serves as paracrine signaling molecule and the cells which are not able to make surfactin, respond to surfactin by making extracellular matrix components for the biofilm.  
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Cellular Automata are discrete computational models. The model consist of a finite grid (of any dimension) in which each of the cells can be in one of a finite set of states. The model behaves discretely in time by evaluating the number of neighbors of each cell and updating its state by some algebraic rule. A popular example of such a model with only two possible states, on and off, and a 2 dimensional grid is Conways Game of life. A possible instantiation of this "game" (it is a zero player game in the sense that it plays itself) is shown below.  
Cellular Automata are discrete computational models. The model consist of a finite grid (of any dimension) in which each of the cells can be in one of a finite set of states. The model behaves discretely in time by evaluating the number of neighbors of each cell and updating its state by some algebraic rule. A popular example of such a model with only two possible states, on and off, and a 2 dimensional grid is Conways Game of life. A possible instantiation of this "game" (it is a zero player game in the sense that it plays itself) is shown below.  
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[[Image:Groningen-wiki-Gospers_glider_gun.gif|frame|none|Conways Game of life(from wikipedia)]]
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[[Image:Groningen-wiki-Gospers_glider_gun.gif|frame|none|[Conways Game of life(from [http://en.wikipedia.org/wiki/Conway_game_of_life wikipedia])]]
Simpler one dimensional models are an important subject of study in theoretical computer science. We modeled unrestricted bacterial growth by Cellular Automata. The model is a 2D grid of 400x400 pixels, the states are on and off indicating the presence of biomass. The grid is initialized randomly with a fixed distribution of "on" states. At every time step the following rule is applied by evaluating each of the cells 8 neighbors, if a cell has 3 or 4 neighbors with the "on" state the cell itself becomes "on" (a growth step, or birth), if a cell has 4, 5, or 6 neighbors which are on the cell is allowed to live and thus remains on. If any cell does not meet these criteria the cell will remain or become off. An animation of this model is shown below.
Simpler one dimensional models are an important subject of study in theoretical computer science. We modeled unrestricted bacterial growth by Cellular Automata. The model is a 2D grid of 400x400 pixels, the states are on and off indicating the presence of biomass. The grid is initialized randomly with a fixed distribution of "on" states. At every time step the following rule is applied by evaluating each of the cells 8 neighbors, if a cell has 3 or 4 neighbors with the "on" state the cell itself becomes "on" (a growth step, or birth), if a cell has 4, 5, or 6 neighbors which are on the cell is allowed to live and thus remains on. If any cell does not meet these criteria the cell will remain or become off. An animation of this model is shown below.

Revision as of 18:07, 26 October 2010

Biofilm Dynamics

Introduction

Biofilms are multicellular conglomerates which attach to surfaces. The formation of biofilms is triggered by high cell density and limited resources. The sensing is of these conditions is often mediated by an extracellular signaling compound which increases in concentration and triggers regulating circuitry. This process is called [quorum sensing] and it plays an important role in the dynamics of multicellular systems.

Quorum sensing systems can cause complicated effects including cell differentiation within single species conglomerates. A recent example of this can be seen in the difference of expression in the TasA protein which plays a major role in the formation of the biofilm matrix by forming amyloid fibers. Expression of this protein is mediated by competitive inhibitive systems by, amongst others, the yqxM gene(No part name specified with partinfo tag.