Team:UNAM Genomics Mexico/Project

From 2012.igem.org

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<h2>BACILLUS BOOLEANUS</h2>  
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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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<br /><br />
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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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<br />
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A logic gate is an  idealized  or  physical  device  implementing  a  Boolean  function,  that  is,  it  performs  a  logical  operation  on  one  or  more  logic  inputs  and  produces  a  single  logic  output.  To  build  a  functionally  complete  logic  system,  transistors  can  be  used.  A  single  transistor  is  not  a  computer,  many  of  them  are  necessary  and  they  need  to communicate  with  each  other,  in  this  way  a  complex  logic  system  can  be  created. 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  “molecular  computer”. Bacillus Booleanus  is  a  project  that  wants  create  a  “molecular  computer”.  How  it  works?  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  a  transistor. As  we  mentioned  our  transistors  need  to  communicate,  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  bacterium  will  be  capable  to  communicate  with  others  so  that  create  complex  networks  of  logic  gates.  Using  this  it  could  be  possible  to  develop  a  complex  network  of  "transistors" to create,  for  example,  a  synthetic  metabolic  pathway.
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Details summary:
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<table border="1" cellspacing="0" cellpadding="0">
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  <tr>
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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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  </tr>
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  <tr>
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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>0</p></td>
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  </tr>
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  <tr>
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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>0</p></td>
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  </tr>
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  <tr>
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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>0</p></td>
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  </tr>
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  <tr>
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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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  </tr>
 +
  <tr>
 +
    <td width="249" valign="top"><p>XylR belonging to E. coli</p></td>
 +
    <td width="249" valign="top"><p>Bacillus subtilis promoters</p></td>
 +
    <td width="249" valign="top"><p>0</p></td>
 +
  </tr>
 +
</table>
}}
}}

Revision as of 20:58, 26 September 2012


UNAM-Genomics_Mexico

some_text

Nanotubes

 some_text

The logic

 Random info



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

wore away in the computational demonstration that they were, in fact, unworthy of being called truths.

Here are the boring details of the deed:
Details summary:

Tf

Sequence

Matches

AraC belonging to E. coli

Bacillus subtilis promoters

0

AraR belonging to B. subtilis

Pbad/Pxyl promoter

0

LasR belonging to P. aeruginosa

Bacillus subtilis promoters

0

XylR belonging to B. subtilits

Pbad promoter

0

XylR belonging to E. coli

Bacillus subtilis promoters

0
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