Team:UANL Mty-Mexico/Project/The Code

From 2011.igem.org

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(Created page with "{{:Team:UANL_Mty-Mexico/Templates/Header}} == The Code == The main idea consists of enabling a bacterial community to interpret a simple code. The code will be composed of just...")
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{{:Team:UANL_Mty-Mexico/Templates/Header}}
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<html>
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<head>
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== The Code ==
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<!--
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The main idea consists of enabling a bacterial community to interpret a simple code. The code will be composed of just red and green lights. The genetic circuit on which the interpretation relies is not dependent on the nature of the stimuli though, whether light or chemical the information processing remains the same. We use light because it is an elegant non-invasive input.
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============================================================================================
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*** Acknowledgments ***
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The message sent to bacteria will depend on the pattern of light. The community should be able to interpret five messages and tell it did it right when expressing a reporter gene. As there will only be two lights, five patterns of them will be used. The five fluorescent proteins available in the registry (GFP,YFP,RFP,CFP,BFP) fit perfectly to this purpose. The next figure illustrates the five patterns of light that will result in the five different messages sent, each of them represented by the expression of a fluorescent protein.
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>>>To TU_Delf Team
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[[File:Code-fig1.jpg|thumb|330px|center|'''Figure 1.''' The code. Short pulses of a single light will mean message one, while a long continuous pulse will mean a second message.  That gives us two messages controlled by each light, summing up to four results. The fifth message will be sent with both lights present at the same time.]]
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Thank you so much to TU_Delft iGEM2010 team for providing us with so many examples of html code and how to apply them.
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If you like some of this code please check it out in their wiki: https://2010.igem.org/Team:TU_Delft#page=Modeling/wiki-tips-tricks
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== The Community ==
 
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Constructing the necessary genetic circuitry inside one single cell may be possible but probably much harder to achieve. That being so, we decided to construct the genetic circuit divided in blocks on separate cells that overall interpret the code. We consider this an advantageous approach since compartmentalizing the circuit lowers the construction size and metabolic charge per cell.
 
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There will be three kinds of cells with different genotypes, although initially all share the same E. coli strain. Two of them will have similar interpretation mechanisms, which will allow each one to take a single light as input and decide whether to express the first or the second reporter gene included in its genotype (decision that will depend on the code). The third kind of cell will be the one taking the input from both lights to express the last protein. Until now the community managed to control the expression of five fluorescent proteins, however we said each of them should be controlled independently. This is accomplished with cell to cell communication through quorum sensing. The following figure illustrates the way the cells within the community work together:
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============================================================================================
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[[File:Code-fig2.jpg|thumb|550px|center|'''Figure 2.''' The community. Cells one and two control each the expression of two different fluorescent proteins. Cell three controls the expression of the fifth protein. Independent expression of each of the reporter genes is achieved through quorum sensing. Cells one and two have the capability to send and receive a different QS molecule each (QS1 and QS2 respectively), while cell three is only a receiver. When cell one or two receive an activating message, the production of a QS molecule is activated as well. These molecules will then diffuse through the medium and reach the rest of the cells. The effect of quorum sensing will depend on the receiver. QS2 molecules, when reaching cell one, will unleash the expression of a repressor that will block the production of any of cell’s one reporter genes. QS1 molecules will have the same effect on cell two. On the other hand, cell three will be activated only when both QS molecules are present and therefore cells one and two are off.]]
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    <p>Information processing through living things remains a challenge to science. Genetic logic-gates and switches have been used to this purpose[1]; however, most of this constructions use chemical inputs. Nonetheless, light induction systems have been constructed and characterized in the last few years[2]. Our project aims to enable a bacterial community, constituted by three <i>E. coli</i> strains that communicate through quorum sensing, to overall interpret a simple light based code. We attempt to insert the necessary genes for the light induction into <i>E. coli</i>'s chromosome, in order to create three different light responsive strains.</p><p> Since light induction is becoming increasingly used in synthetic biology, we propose these modified <i>E. coli</i> strains as photochassis that could make useful tools in the field. Furthermore, each strain will contain different plasmids carrying the genetic constructions needed for the interpretation of the code. This mechanism will mainly rely on genetic logic-gates and switches. The use of phage lambda's based biphasic switch[4], which will theoretically allow the independent control of transcription from two different promoters through a single input, is introduced to iGEM.
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<ol><li> Tamsir A, Tabor JJ, Voigt CA. (2010). Robust multicellular computing using genetically encoded NOR gates and chemical 'wires'. <i>Nature</i>. <b>469</b>: 212-215.
 +
<li> Tabor JJ, Levskaya A, Voigt CA. (2010). Multichromatic Control of Gene Expression in <i>Escherichia coli</i>. <i>J. Mol. Biol.</i> <b>405</b>: 315-324.
 +
</li><li> Dodd BI, Perkins AJ, Tsemitsidis D, Egan BJ. (2001) Octamerization of CI repressor is needed for effective repression of PRM and efficient switching from lysogeny.  <i>Gene Dev</i>, <b>15</b>:3013–3022.
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Revision as of 00:11, 14 September 2011

Team: UANL_Mty-Mexico

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Overview

Information processing through living things remains a challenge to science. Genetic logic-gates and switches have been used to this purpose[1]; however, most of this constructions use chemical inputs. Nonetheless, light induction systems have been constructed and characterized in the last few years[2]. Our project aims to enable a bacterial community, constituted by three E. coli strains that communicate through quorum sensing, to overall interpret a simple light based code. We attempt to insert the necessary genes for the light induction into E. coli's chromosome, in order to create three different light responsive strains.

Since light induction is becoming increasingly used in synthetic biology, we propose these modified E. coli strains as photochassis that could make useful tools in the field. Furthermore, each strain will contain different plasmids carrying the genetic constructions needed for the interpretation of the code. This mechanism will mainly rely on genetic logic-gates and switches. The use of phage lambda's based biphasic switch[4], which will theoretically allow the independent control of transcription from two different promoters through a single input, is introduced to iGEM.

References
  1. Tamsir A, Tabor JJ, Voigt CA. (2010). Robust multicellular computing using genetically encoded NOR gates and chemical 'wires'. Nature. 469: 212-215.
  2. Tabor JJ, Levskaya A, Voigt CA. (2010). Multichromatic Control of Gene Expression in Escherichia coli. J. Mol. Biol. 405: 315-324.
  3. Dodd BI, Perkins AJ, Tsemitsidis D, Egan BJ. (2001) Octamerization of CI repressor is needed for effective repression of PRM and efficient switching from lysogeny. Gene Dev, 15:3013–3022.

OurSymbol

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