Team:XMU-China/Data

From 2011.igem.org

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=='''How our devices work'''==
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[[Image:XMU_China_111.jpg|left|frame|Figure 1: The synthesis of LuxR protein and the signalling molecule  N-acyl-homoserine lactone (AHL) is induced by adding  Isopropyl β-D-1-thiogalactopyranoside (IPTG). The AHL accumulates in the experimental medium and inside the cells as the cell density increases. At sufficiently high concentrations, it binds and activates the LuxR transcriptional regulator, which in turn induces the expression of a killer gene ''ccdB'' under the control of a promoter lux pR. Sufficiently high levels of the killer protein cause cell death. This circuit programmes a bacterial population to maintain a cell density that is lower than the limits imposed by the environment.]]
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[[Image:XMU_China_112.jpg]]
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<img src="http://partsregistry.org/wiki/images/4/41/XMU_China_block.jpg">
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== '''Data for favorite new parts''' ==
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<a  href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K658003 "  target="_blank">[BBa_K658003] </a></html>--'''a bacteria population-control device with RBS0.6 driven by lacl+pL'''
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The device is designed to build a programmed bacterial death circuit.Based on the device,a series of bacteria population-control devices (BBa_K658001,BBa_K658004,BBa_K658005) are designed using RBSs of different strength in the killer protein producer. Also, we have designed a series of population-control devices(BBa_K658010,BBa_K658011,BBa_K658012) by mutagenesis at positition 3,5and 3/5 of lux pR.
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A comparison in performance of all the population-control devices can be found in the experience page.
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<html>
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<a  href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K658005 "  target="_blank">[BBa_K658005] </a></html>--'''a bacteria population-control device with RBS0.07 driven by lacl+pL'''
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The device is designed to build a programmed bacterial death circuit. The cell growth curve of BL21 and BL21 with the programmed bacterial denth circuit can be found in the [experience] page, which indicates that this device has the ability to maintain cell density of the bacteria population at a relatively low value compared with bacteria without this circuit and extends the stable stage.
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<a  href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K658016 "  target="_blank">[BBa_K658016] </a></html>--'''LuxI->LuxR->lux pR->GFP'''
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This part is designed to test the strength of promoters lux pR(BBa_R0062) and its 3 mutants lux pR-3 (BBa_K658006), lux pR-5(BBa_K658007), lux pR-3/5(BBa_K658008) in our project.Based on the device, a series of devices(BBa_K658017, BBa_658018, BBa_658019)are designed by mutagenesis at positition 3,5and 3/5 of lux pR. A comparison in performance of the devices can be found in the experience page.
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== '''Data for pre-exsiting parts''' ==
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Experience<html>
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<a  href="http://partsregistry.org/Part:BBa_F2622:Experience "  target="_blank">[BBa_F2622] </a></html>--'''3OC6HSL Receiver Device controlled by PLlac 0-1'''
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The expression test is conducted to show thatthe biobrick can be expressed in BL21 in the presence of IPTG.
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Experience<html>
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<a  href="http://partsregistry.org/Part:BBa_K137018:Experience "  target="_blank">[BBa_K137018] </a></html>
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-- '''luxr->GFP'''
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Different concentration of AHL lead to distinct expression levels of the gfp gene.
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== '''Data for improved parts''' ==
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We improved promoter lux pR's strength by site-directed mutagenesis.
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Experience for <html>
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<a  href="http://partsregistry.org/Part:BBa_R0062:Experience "  target="_blank">[BBa_R0062] </a></html>
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Parts involve
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<a  href="http://partsregistry.org/Part:BBa_K658006"  target="_blank">[BBa_K658006] </a></html>--'''position 3 mutated promoter lux pR-3 (luxR & HSL regulated)'''
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<a  href="http://partsregistry.org/Part:BBa_K658007"  target="_blank">[BBa_K658007] </a></html>--'''position 5 mutated promoter lux pR-5 (luxR & HSL regulated)'''
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<a  href="http://partsregistry.org/Part:BBa_K658008"  target="_blank">[BBa_K658008] </a></html>-- --'''position 3&5 mutated promoter lux pR-3/5 (luxR & HSL regulated)'''
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== We’ve also created and characterized the following parts  ==
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=== Population-control devices(iccdB) with RBS of different strength ===
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<a  href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K658001 "  target="_blank">[BBa_K658001] </a></html> --a bacteria population-control device with RBS1.0 driven by lacl+pL
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<a  href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K658004 "  target="_blank">[BBa_K658004] </a></html> --a bacteria population-control device with RBS0.3 driven by lacl+pL
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=== Population-control devices(iccdB) with mutagenesis at positition 3,5and 3/5 of lux pR ===
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<a  href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K658010 "  target="_blank">[BBa_K658010] </a></html> --a bacteria population-control device with lux pR-3 driven by lacl+pL
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<a  href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K658011 "  target="_blank">[BBa_K658011] </a></html> --a bacteria population-control device with lux pR-5 driven by lacl+pL
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<a  href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K658012 "  target="_blank">[BBa_K658012] </a></html> -- a bacteria population-control device with lux pR-3/5 driven by lacl+pL
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=== IR-GFP devices with mutagenesis at positition 3,5and 3/5 of lux pR ===
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<a  href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K658017 "  target="_blank">[BBa_K658017] </a></html> --LuxI->LuxR->lux pR-3->GFP
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== '''Project Name''' ==
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<a  href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K658018 "  target="_blank">[BBa_K658018] </a></html> -- LuxI->LuxR->lux pR-5->GFP
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<a  href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K658019 "  target="_blank">[BBa_K658019] </a></html> -- LuxI->LuxR->lux pR-3/5->GFP
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i-''ccdB'': intelligent Control of Cell Density in Bacteria
 
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== Project Abstract==
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=== 3OC6HSL Sender and Receiver Device with mutagenesis of lux pR ===
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<a  href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K658012 "  target="_blank">[BBa_K658012] </a></html> --3OC6HSL Sender and Receiver Device Driven by PLlac 0-1
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We have developed a series of devices which program a bacteria population to maintain at different cell densities. We have designed and characterized the genetic circuit to establish a bacterial ‘population-control’ device in ''E. coli'' based on the well-known quorum-sensing system from ''Vibrio fischeri'', which autonomously regulates the density of an ''E. coli'' population. The cell density however is influenced by the expression levels of a killer gene (''ccdB'') in our device. As such, we have successfully controlled the expression levels of ''ccdB'' by site-directed mutagenesis of a ''luxR'' promoter (''lux pr'') and error-prone PCR of gene ''luxR'', and finally we have built a database for a series of mutation sites corresponding to different cell densities. An artificial neural network has then been built to model and predict the cell density of an ''E. coli'' population. This work can serve as a foundation for future advances involving fermentation industry and information processing.
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<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K658013 "  target="_blank">[BBa_K658013] </a></html> --3OC6HSL Sender and Receiver Device with lux pR-3 Driven by PLlac 0-1
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<a  href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K658014 "  target="_blank">[BBa_K658014] </a></html> --3OC6HSL Sender and Receiver Device with lux pR-5 Driven by PLlac 0-1
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<a  href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K658015 "  target="_blank">[BBa_K658015] </a></html> --3OC6HSL Sender and Receiver Device with lux pR-3/5 Driven by PLlac 0-1
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=== Backgrounds ===
 
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=== Project Detail===
 
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== Results ==
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=== Others ===
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<a  href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K658020 "  target="_blank">[BBa_K658020] </a></html>--iccdB->GFP

Latest revision as of 02:15, 6 October 2011



Contents

How our devices work

Figure 1: The synthesis of LuxR protein and the signalling molecule N-acyl-homoserine lactone (AHL) is induced by adding Isopropyl β-D-1-thiogalactopyranoside (IPTG). The AHL accumulates in the experimental medium and inside the cells as the cell density increases. At sufficiently high concentrations, it binds and activates the LuxR transcriptional regulator, which in turn induces the expression of a killer gene ccdB under the control of a promoter lux pR. Sufficiently high levels of the killer protein cause cell death. This circuit programmes a bacterial population to maintain a cell density that is lower than the limits imposed by the environment.

XMU China 112.jpg


Data for favorite new parts

[BBa_K658003] --a bacteria population-control device with RBS0.6 driven by lacl+pL

The device is designed to build a programmed bacterial death circuit.Based on the device,a series of bacteria population-control devices (BBa_K658001,BBa_K658004,BBa_K658005) are designed using RBSs of different strength in the killer protein producer. Also, we have designed a series of population-control devices(BBa_K658010,BBa_K658011,BBa_K658012) by mutagenesis at positition 3,5and 3/5 of lux pR.

A comparison in performance of all the population-control devices can be found in the experience page.

[BBa_K658005] --a bacteria population-control device with RBS0.07 driven by lacl+pL

The device is designed to build a programmed bacterial death circuit. The cell growth curve of BL21 and BL21 with the programmed bacterial denth circuit can be found in the [experience] page, which indicates that this device has the ability to maintain cell density of the bacteria population at a relatively low value compared with bacteria without this circuit and extends the stable stage.

[BBa_K658016] --LuxI->LuxR->lux pR->GFP

This part is designed to test the strength of promoters lux pR(BBa_R0062) and its 3 mutants lux pR-3 (BBa_K658006), lux pR-5(BBa_K658007), lux pR-3/5(BBa_K658008) in our project.Based on the device, a series of devices(BBa_K658017, BBa_658018, BBa_658019)are designed by mutagenesis at positition 3,5and 3/5 of lux pR. A comparison in performance of the devices can be found in the experience page.

Data for pre-exsiting parts

Experience [BBa_F2622] --3OC6HSL Receiver Device controlled by PLlac 0-1

The expression test is conducted to show thatthe biobrick can be expressed in BL21 in the presence of IPTG.

Experience [BBa_K137018] -- luxr->GFP

Different concentration of AHL lead to distinct expression levels of the gfp gene.


Data for improved parts

We improved promoter lux pR's strength by site-directed mutagenesis.

Experience for [BBa_R0062] Parts involve

[BBa_K658006] --position 3 mutated promoter lux pR-3 (luxR & HSL regulated)

[BBa_K658007] --position 5 mutated promoter lux pR-5 (luxR & HSL regulated)

[BBa_K658008] -- --position 3&5 mutated promoter lux pR-3/5 (luxR & HSL regulated)


We’ve also created and characterized the following parts

Population-control devices(iccdB) with RBS of different strength

[BBa_K658001] --a bacteria population-control device with RBS1.0 driven by lacl+pL

[BBa_K658004] --a bacteria population-control device with RBS0.3 driven by lacl+pL


Population-control devices(iccdB) with mutagenesis at positition 3,5and 3/5 of lux pR

[BBa_K658010] --a bacteria population-control device with lux pR-3 driven by lacl+pL

[BBa_K658011] --a bacteria population-control device with lux pR-5 driven by lacl+pL

[BBa_K658012] -- a bacteria population-control device with lux pR-3/5 driven by lacl+pL


IR-GFP devices with mutagenesis at positition 3,5and 3/5 of lux pR

[BBa_K658017] --LuxI->LuxR->lux pR-3->GFP

[BBa_K658018] -- LuxI->LuxR->lux pR-5->GFP

[BBa_K658019] -- LuxI->LuxR->lux pR-3/5->GFP


3OC6HSL Sender and Receiver Device with mutagenesis of lux pR

[BBa_K658012] --3OC6HSL Sender and Receiver Device Driven by PLlac 0-1

[BBa_K658013] --3OC6HSL Sender and Receiver Device with lux pR-3 Driven by PLlac 0-1

[BBa_K658014] --3OC6HSL Sender and Receiver Device with lux pR-5 Driven by PLlac 0-1

[BBa_K658015] --3OC6HSL Sender and Receiver Device with lux pR-3/5 Driven by PLlac 0-1


Others

[BBa_K658020] --iccdB->GFP

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