Team:UNAM Genomics Mexico/Project

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<center><h1>'''Bacillus booleanus'''</h1></center>  
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<td id="leftcolumn2" align="center"><img src="https://static.igem.org/mediawiki/2012/d/d2/Unamgenomicsnanotubes.jpg" alt="some_text" height="200"/><br /><br /><p>Nanotubes</p></td>
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<td id="contentcolumn2" align="center"><img src="https://static.igem.org/mediawiki/2012/9/96/Unamgenomicsnanotubes1.jpg" alt="some_text" height="200"/><br /><br /><p>The logic</p></td>
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<h1>Project description</h1>
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<td id="rightcolumn2">Random info</td>
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A logic gate is an idealized (or physical) device implementing a Boolean function that performs a logic operation on one or more logic inputs and produces a single logic output. A single logic gate is not a computer, many of them are necessary and they need to communicate with each other to compute stuff. In this way, a complex logic system can be created, like a computer. The architecture of gene regulatory networks is reminiscent of electronic circuits. Modular building blocks that respond in a logical way to one or several inputs are connected to perform a variety of complex tasks. Taking these two main ideas, it could be possible to create a “biological computer”. Bacillus booleanus is a project that wants to link several Boolean operations to make the beginnings of a biological computer. How does everything work? We are working on the creation of different strains of Bacillus subtilis. Each one will be able to perform a single Boolean operation, just like transistors do in an electronic computer. As we mentioned, our bacteria need to communicate to achieve trascendence, but how could this be possible? In 2011 Ben-Yehuda et. al. identified a type of bacterial communication mediated by nanotubes that bridge neighboring cells, providing a network for exchange of cellular molecules within, and between species. By using these nanotubes, our bacteria will be capable to communicate with others, creating complex networks of logic gates. Using this, it could be possible to develop a complex network of operators to regulate, for example, a synthetic metabolic pathway.
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Due to the fact that our construction introduces exogenous transcription factors to the cell, we wanted to make sure that there would be no crosstalk, meaning that they wouldn’t recognize other promoters and create noise in the system. For this purpose, we downloaded weight matrixes for the sequences recognized by our transcription factors from PRODORIC database, and we downloaded the sequences for promoters (-200, +50 parting from the TSS) using retrieve sequence from RSA-tools. We chose Bacillus subtilis strain 168 because our strain is a derivative of this strain (I like the word strain…strain, strain, strain yay!). After that, we used quick matrix-scan in RSA-tools (Regulation Sequence Analysis-tools) to compare the sequences of the promoters to the weight matrixes to see if any of our transcription factors could bind in a troublesome place. We soon found out that this was not the case. Satisfied with our new-found self-confidence, we proceeded undauntedly to explore the more obscure parts of our project as our doubts
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wore away in the computational demonstration that they were, in fact, unworthy of being called truths.
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Here are the boring details of the deed:
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Details summary:
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    <td width="249" valign="top"><p>Tf</p></td>
 
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    <td width="249" valign="top"><p>Sequence</p></td>
 
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    <td width="249" valign="top"><p>Matches</p></td>
 
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    <td width="249" valign="top"><p>AraC belonging to E. coli</p></td>
 
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    <td width="249" valign="top"><p>Bacillus subtilis promoters</p></td>
 
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    <td width="249" valign="top"><p>AraR belonging to B. subtilis</p></td>
 
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    <td width="249" valign="top"><p>Pbad/Pxyl promoter</p></td>
 
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    <td width="249" valign="top"><p>LasR belonging to P. aeruginosa</p></td>
 
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    <td width="249" valign="top"><p>Bacillus subtilis promoters</p></td>
 
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    <td width="249" valign="top"><p>XylR belonging to B. subtilits</p></td>
 
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    <td width="249" valign="top"><p>Pbad promoter</p></td>
 
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    <td width="249" valign="top"><p>0</p></td>
 
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    <td width="249" valign="top"><p>XylR belonging to E. coli</p></td>
 
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    <td width="249" valign="top"><p>Bacillus subtilis promoters</p></td>
 
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    <td width="249" valign="top"><p>0</p></td>
 
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Latest revision as of 22:15, 26 October 2012


UNAM-Genomics_Mexico

Bacillus booleanus


Project description



A logic gate is an idealized (or physical) device implementing a Boolean function that performs a logic operation on one or more logic inputs and produces a single logic output. A single logic gate is not a computer, many of them are necessary and they need to communicate with each other to compute stuff. In this way, a complex logic system can be created, like a computer. The architecture of gene regulatory networks is reminiscent of electronic circuits. Modular building blocks that respond in a logical way to one or several inputs are connected to perform a variety of complex tasks. Taking these two main ideas, it could be possible to create a “biological computer”. Bacillus booleanus is a project that wants to link several Boolean operations to make the beginnings of a biological computer. How does everything work? We are working on the creation of different strains of Bacillus subtilis. Each one will be able to perform a single Boolean operation, just like transistors do in an electronic computer. As we mentioned, our bacteria need to communicate to achieve trascendence, but how could this be possible? In 2011 Ben-Yehuda et. al. identified a type of bacterial communication mediated by nanotubes that bridge neighboring cells, providing a network for exchange of cellular molecules within, and between species. By using these nanotubes, our bacteria will be capable to communicate with others, creating complex networks of logic gates. Using this, it could be possible to develop a complex network of operators to regulate, for example, a synthetic metabolic pathway.

UnamgenomcisLogiv.png