Team:LCG-UNAM-Mexico:CA
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- | =Modeling bacteria behaviour and Bacteriophage infection using Cellular Automata= | + | =Multi-Scale Stochastic Modeling for bacteria behaviour and Bacteriophage infection using Cellular Automata= |
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With this ouput we can see the evolution of the system (see video). | With this ouput we can see the evolution of the system (see video). | ||
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- | The main goal of the Cellular Automata was to assemble the information contained in the Molecular Distributions (particularly the [[Team:LCG-UNAM-Mexico:BSD | BSD]] with a population simulation in order to observe the behaviour of the whole system under different conditions. The [[Team:LCG-UNAM-Mexico | + | The main goal of the Cellular Automata was to assemble the information contained in the Molecular Distributions (particularly the [[Team:LCG-UNAM-Mexico:BSD | BSD]] with a population simulation in order to observe the behaviour of the whole system under different conditions. The [[Team:LCG-UNAM-Mexico/LauraJournal#October | experimental work with T7]] and the CA show the same overall behaviour.<br><br> By changing the initial conditions and parameters on our CA it's possible to simulate a wide range of bacteriophage infection processes. The CA was designed to work along with the molecular simulations in a single Matlab script, but it's alwats possible to use the CA as a stand alone application to simulate infection dynamics. |
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- | [[Image:growth_T3_t7.png|thumb| | + | [[Image:growth_T3_t7.png|thumb|left|300px|alt=Experimental Obtained Growth Curves.|Experiment: T3 and T7 infection on E. Coli; population proportion:19 bacterias/1 phage; Optical Density at 550nm ]] |
- | population proportion:19 bacterias/1 phage; Optical Density at 550nm ]] | + | |
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- | The above video shows the simulation of the T7 infection process in wild type Escherichia Coli. Our Experimental results for the bacterial growth curve | + | The above video shows the simulation of the T7 infection process in wild type Escherichia Coli. Our Experimental results for the bacterial growth curve exhibit the same behaviour. The initial condition for both experiment and simulation is a proportion: 1 phage for each 19 bacteria. As expected the bacteria population losses the fight. About 100 min after infection all bacteria are dead. |
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+ | The image on the left shows our experimental results for T3 and T7 infection on Wild Type E. Coli. The same initial conditions in the experiment were used in the above Automata Simulation.<br><br> | ||
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===Infection With Our system=== | ===Infection With Our system=== | ||
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- | [[Team:LCG-UNAM-Mexico:Molecular model | Molecuar Simulations using the kamikaze system]] showed that our construction works as expected. We performed a sensitivity analysis for the crucial parameter in our kamikaze system: the ribosome deactivation rate by Colicin E3. We observed that over a wide range of values (10^-1 - 10^- | + | [[Team:LCG-UNAM-Mexico:Molecular model | Molecuar Simulations using the kamikaze system]] showed that our construction works as expected. We performed a sensitivity analysis for the crucial parameter in our kamikaze system: the ribosome deactivation rate by Colicin E3. We observed that over a wide range of values (10^-1 - 10^-4) the mean of the BSD was reduced to 0, nevertheless we performed CA simulations for both the zero and non zero mean BS. |
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+ | Cellular Automaton Simulation. Mean of the Burst Size Distribution Sampled: 0.0 | ||
+ | <object width="560" height="340"><param name="movie" value="http://www.youtube.com/v/tmq-KfVWeKE&hl=en&fs=1&"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/tmq-KfVWeKE&hl=en&fs=1&" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="560" height="340"></embed></object> | ||
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+ | The above video shows a simulation in which we used the results obtained from the molecular simulations using the kamikaze system. Burst Size Mean = 0. Bacteria wins the fight. This behaviour is observed for a wide range of values for the rate of ribosome inactivation by Colicin E3 (10e-1 ~ 10e-4). This results suggests that our system indeed works as expected. Experimental results for Colicin E3 kinetics are needed in order to validate and improve our model, sadly we didn’t obtained this results. | ||
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+ | Cellular Automaton Simulation. Mean of the Burst Size Distribution Sampled: 5.8 | ||
+ | <object width="560" height="340"><param name="movie" value="http://www.youtube.com/v/CCZdjdatnOw&hl=en&fs=1&color1=0x006699&color2=0x54abd6"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/CCZdjdatnOw&hl=en&fs=1&color1=0x006699&color2=0x54abd6" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="560" height="340"></embed></object></center> | ||
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+ | Using the value of 5.8 for the burst size we observe that the population, after a brave struggle with phages, sadly dies. This result was expected since the latency period of T7 is smaller than the duplication time of E.Coli and each infected bacterium will produce an average of 6 phages!<br> | ||
+ | Our system work as expected for burst size values less or equal to 1. Sensitivity analysis shows that our system works for a wide range of values for the ribosome inactivation rate but even a small burst size value like 6 will eventually kill the whole population. | ||
==Design== | ==Design== |
Latest revision as of 02:59, 22 October 2009