Team:LCG-UNAM-Mexico:KZM
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<br>For the purpose of this project we are particularly concerned in the abundance of phage T7 (burst size) at the end of the cycle (720 seconds) in each infection event. | <br>For the purpose of this project we are particularly concerned in the abundance of phage T7 (burst size) at the end of the cycle (720 seconds) in each infection event. | ||
<br>Ensembles of runs of WTM and KZM will provide us with data to build Burst Size Distributions for each model. | <br>Ensembles of runs of WTM and KZM will provide us with data to build Burst Size Distributions for each model. | ||
- | '''A Kamikaze BSD is next utilized by the population models to recreate the impact of our synthetic circuit in the infection at population level.''' | + | '''A Kamikaze BSD is next utilized by the population models to recreate the impact of our synthetic circuit in the infection at population level.'''<br><br> |
+ | ''See also [[Team:LCG-UNAM-Mexico:WTM |WTM]], [[Team:LCG-UNAM-Mexico:BSD |BSD]], [[Team:LCG-UNAM-Mexico:Population |Population Model]], [[Team:LCG-UNAM-Mexico:CA |Cellular Automata]].'' | ||
<br> | <br> | ||
__TOC__ | __TOC__ | ||
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* <h2>Insertion and translocation of T7 DNA at different times</h2> | * <h2>Insertion and translocation of T7 DNA at different times</h2> | ||
Entry of T7 DNA into the host cell occurs in several distinct stages. | Entry of T7 DNA into the host cell occurs in several distinct stages. | ||
- | <br>Phage's DNA is arranged in three classes of genes depending on their positions, it is translocated into the cell between 6 to 10 minutes after attachment, so this order and timing drives the phage's development. This phenomenon of DNA translocation is modeled here taking into account reported insertion speeds [ | + | <br>Phage's DNA is arranged in three classes of genes depending on their positions, it is translocated into the cell between 6 to 10 minutes after attachment, so this order and timing drives the phage's development. This phenomenon of DNA translocation is modeled here taking into account reported insertion speeds by Drew Endy et al. 1996 [1] and F. Buchholtz et al. 1987 [2]. |
* <h2>Transcription of different T7 DNA segments into polycistronic mRNAs</h2> | * <h2>Transcription of different T7 DNA segments into polycistronic mRNAs</h2> | ||
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* <h2>Degradation of phage mRNAs</h2> | * <h2>Degradation of phage mRNAs</h2> | ||
- | We assume the same degradation rate for all T7 polycistronic mRNAs. Until now impact of this phenomenon had not been studied. It has been found that phage messengers are stabler than Bacterial mRNAs | + | We assume the same degradation rate for all T7 polycistronic mRNAs. Until now impact of this phenomenon had not been studied. It has been found by Yoshihiko Yamada et al. 1976 [3] that phage messengers are stabler than Bacterial mRNAs . |
* <h2>Translation of phage mRNAs into proteins</h2> | * <h2>Translation of phage mRNAs into proteins</h2> | ||
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* <h2>Procapsid Assembly</h2> | * <h2>Procapsid Assembly</h2> | ||
- | This phenomenon is simulated in almost the same way as Drew Endy et al. 1996 using mass action kinetics. | + | This phenomenon is simulated in almost the same way as Drew Endy et al. 1996[1] using mass action kinetics. |
* <h2>DNA packaging and final assembly</h2> | * <h2>DNA packaging and final assembly</h2> | ||
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* <h2>Simulation, performance and BSD construction</h2> | * <h2>Simulation, performance and BSD construction</h2> | ||
- | + | <br>The next video has been recorded from a single simulation of KZM, molecular species monitoring in time is one of the fundamental objectives of this mode. | |
- | + | <br><br>In order to accurately simulate the infection at population scale we study the amount of phages an infected bacteria will produce at the end of the lytic cycle of T7, burst size. Furthermore we construct burst size distributions of KZM (BSD) and [[Team:LCG-UNAM-Mexico:WTM |WTM]] so we can compare the performance of our synthetic kamikaze system vs wild-type behavior. | |
- | + | <br>The following video plots the abundance of ABproteins a main procapsid component of viral coat and assembled T7 phages, it is noteworthy to see the impact of the toxin in the amount of viral proteins and in the final number of assembled particles of T7, burst sizes are significantly lower than the wild-type burst sizes, for more details go to [[Team:LCG-UNAM-Mexico:BSD |BSD]]. | |
<br><br> | <br><br> | ||
<html> | <html> | ||
<body> | <body> | ||
<center> | <center> | ||
- | <object width="480" height="295"><param name="movie" value="http://www.youtube.com/v/ | + | <object width="480" height="295"><param name="movie" value="http://www.youtube.com/v/28HEKUNwWio&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/28HEKUNwWio&hl=en&fs=1&color1=0x006699&color2=0x54abd6" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="480" height="295"></embed></object></center> |
- | + | <br><br><br> | |
- | + | Ribosome decay can be monitored in the next video. | |
- | + | The action and abundance of the toxin bring about an overall translation decay in the cell, as a consequence of this viral protein production is reduced, this in turn provokes an unfavorable amount of phages at the end of the cycle. | |
+ | We also plot the amount of ribosome-inactivating colicinE3 in purple, GFP in green and LuxI (A quorum sensing protein) in red. | ||
+ | <br><br><center> | ||
<object width="480" height="295"><param name="movie" value="http://www.youtube.com/v/FJTy8xFFMQI&hl=en&fs=1&color1=0x3a3a3a&color2=0x999999"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/FJTy8xFFMQI&hl=en&fs=1&color1=0x3a3a3a&color2=0x999999" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="480" height="295"></embed></object> | <object width="480" height="295"><param name="movie" value="http://www.youtube.com/v/FJTy8xFFMQI&hl=en&fs=1&color1=0x3a3a3a&color2=0x999999"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/FJTy8xFFMQI&hl=en&fs=1&color1=0x3a3a3a&color2=0x999999" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="480" height="295"></embed></object> | ||
</center> | </center> | ||
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</html> | </html> | ||
<h2>References</h2> | <h2>References</h2> | ||
+ | <br>[1] Drew Endy, Deyu Kong, John Yin. 1996. '''Intracellular Kinetics of a Growing Virus: A Genetically Structured Simulation for Bacteriophage T7''' | ||
+ | <br>[2] F. Buchholtz and F.W. Schneider. 1987. '''Computer simulation of T3/T7 phage infection using lag times''' | ||
+ | <br>[3] Yoshihiko Yamada, Patricia A. Whitaker and Dai Nakada. 1975. '''Chemical Stability of Bacteriophage T7 Early mRNA''' | ||
|} | |} | ||
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Latest revision as of 01:03, 22 October 2009