USTC

From 2007.igem.org

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''From left to right''<BR>
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''Back row:'' [[USTC/ZhaoYun|Zhao Yun]], [[USTC/LiuZiqing|Liu Ziqing]], [[USTC/MaXiaoyu|Ma Xiaoyu]]<BR>
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''Front row:'' [[USTC/MaRui|Ma Rui]], [[USTC/SuXiaofeng|Su Xiaofeng]], [[USTC/DingBo|Ding Bo]], [[USTC/ZhanJian|Zhan Jian]]
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<!-- <font color="red">
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There are'''<html><script language="JAVASCRIPT"><!-- update your browser, silly-->
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Today = new Date();
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Jamboree = new Date("November 3, 2007");
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msInADay = 1000 * 60 * 60 * 24;
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display = Math.floor((Jamboree.getTime() - Today.getTime())/msInADay);
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// </script></html>'''days left until the Jamboree!
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=== Our Project:<BR>Extensible Logic Circuit in Bacteria ===
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=== Our Project: Extensible Logic Circuit in Bacteria ===
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Artificial Bio-Logic Circuit is composed of "logic gates" and "wires" like Digital Electronic Circuits. Though we have been enjoying the advantages of ultra-large-scale electronic circuits in modern life, we still cannot implement a somewhat small-scale circuit <i>in vivo</i> with several levels of gates.
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Our project is to provide a new method for building up a fully extensible bio-logic circuit in bacteria. A small fragment of DNA containing cis-acting elements, favored for its small scale and potential to implement complex logic computation <i>in vivo</i>, can be systematically built up and act as a gate. Meanwhile, artificial repressors with highly-specific DNA-recognition regions are able to transmit signals without mutual interference, just as enameled wires. In this way, a circuit can be constructed regardless of the number of logic gates and the layout of the wires.
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Artificial Cell Signaling Network (ACS Network) and Integrated Circuit Network (IC Network) are both signaling networks. Now we are enjoying the advantage of Ultra Large Scale IC (ULSI), but at least today we cannot implement a somewhat large ACS Network in actual experiments.
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A demonstration system has also been assembled to show the practicality of this method. Just like Digital Electronic Circuits in early days, it is simple and ugly. Nevertheless, how will it appear in future?
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Our project is to provide a new viewpoint for building up fully extensible ACS Networks. We are going to produce biologic logic gates such as NAND, NOR, NOT for some biological conveniences. In other words, modern logic IC Networks are built upon these three gates-- NAND, NOR and NOT. Logic gates are only the basic elements of logic IC, on the other hand, the more important factors we think which make IC Network to be easily enlarged are: Reducing the scale of elements; Tuning elements to eliminate interference; Calibrating elements for interconnection. Cis-acting elements may provide smaller scale than trans-acting ones, while the other two factors can be achieved by standardization. We will present the method for standardization and demonstrate an ACS Network made by these biologic logic gates.
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This ACS Network may not be large, but the important factors we implement in it will naturally make it fully extensible. IC has been born for 50 years and how hugely it impacts our modern life! So, what about biologic logic circuit in next 50 years? '''A new world is waiting'''...
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<font color="#AAAAAA">''For detailed description, please click each hyperlink below.''</font>
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[[Image:DSCN1243.png|330px]]
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<font color="#AAAAAA">''From left to right''</font><BR>
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<font color="#AAAAAA">''Back row:''</font> [[USTC/ZhaoYun|Zhao Yun]], [[USTC/LiuZiqing|Liu ZQ]], [[USTC/MaXiaoyu|Ma XY]]<BR>
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<font color="#AAAAAA">''Front row:''</font> [[USTC/MaRui|Ma Rui]], [[USTC/SuXiaofeng|Su XF]], [[USTC/DingBo|Ding Bo]], [[USTC/ZhanJian|Zhan Jian]]
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<BR clear="both">
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{| cellspacing="2px" cellpadding="20" border="0" style="padding: 0px; width: 750px
{| cellspacing="2px" cellpadding="20" border="0" style="padding: 0px; width: 750px
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<h3>Events</h3>
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<h3>Project</h3>
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'''01/08/2007'''
 
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There is a mistake in my preparing X-Gal solution. Please rework your correlative experiments. Sorry!
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[[USTC/Introduction|Introduction]]
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( by Ma Rui )
 
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'''30/07/2007'''
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'''Core Logic Components:'''
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First designed repressors. Good job, Bo and Xiaofeng!
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[[USTC/Logic-Gate_Promoters|Logic-Gate Promoters]]
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'''01/06/2007'''
 
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Primary experiments begin around this day.
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'''Wires without Interference:'''
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[[USTC/Previous|'''Previous''']]
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[[USTC/Repressor_Evolution_on_Plates|Repressor Evolution on Plates]]
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[[USTC/Repressor_Evolution_in_Silico|Repressor Evolution <i>in Silico</i>]]
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<h3>Tasks</h3>
 
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[[USTC/PoPSConvertors|PoPS Convertors]]
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'''Peripheral Devices:'''
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[[USTC/LogicGates|Biologic Logic Gates]]
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[[USTC/Inputs_and_Outputs|Inputs and Outputs]]
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[[USTC/RepressorDesigning|Redesign the Lac Repressor]]
 
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[[USTC/PoPSReporter|Fluorescent Reporters]]
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'''Extensible System:'''
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[[USTC/OverallSystem|Link All Things Together]]
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[[USTC/Demonstration|A Demonstration]]
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<!-- [[USTC/XORGate|A simpler design for an XOR gate]] -->
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[[USTC/Further_More|Further More]]
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<!-- [[USTC/ANDGate|An AND gate]] -->
 
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<!-- [[USTC/BiobricksManual|A BioBricks Manual in Chinese]] -->
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<h3>Members</h3>
<h3>Members</h3>
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<center>
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'''Graduates:'''<BR>
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'''4 Graduates:'''<BR>
[[USTC/ZhanJian|Zhan Jian]]<BR>
[[USTC/ZhanJian|Zhan Jian]]<BR>
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[[USTC/DingBo|Ding Bo]]<BR>
 
[[USTC/MaRui|Ma Rui]]<BR>
[[USTC/MaRui|Ma Rui]]<BR>
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[[USTC/DingBo|Ding Bo]]<BR>
[[USTC/MaXiaoyu|Ma Xiaoyu]]<BR>
[[USTC/MaXiaoyu|Ma Xiaoyu]]<BR>
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'''Undergraduates:'''<BR>
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'''3 Undergraduates:'''<BR>
[[USTC/SuXiaofeng|Su Xiaofeng]]<BR>
[[USTC/SuXiaofeng|Su Xiaofeng]]<BR>
[[USTC/LiuZiqing|Liu Ziqing]]<BR>
[[USTC/LiuZiqing|Liu Ziqing]]<BR>
[[USTC/ZhaoYun|Zhao Yun]]
[[USTC/ZhaoYun|Zhao Yun]]
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'''Faculty Advisors:'''<BR>
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'''3 Faculty Advisors:'''<BR>
Prof. HY Liu<BR>
Prof. HY Liu<BR>
Prof. JR Wu<BR>
Prof. JR Wu<BR>
Prof. ZH Hou
Prof. ZH Hou
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</center>
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|width=240px style="padding: 5px; background-color: #FFFF99" |
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<h3>Snapshot</h3>
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[http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2007&group=USTC '''<font color="#bb0000">247</font> Part Sequences''']
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'''<font color="#bb0000">123</font> Parts Submitted'''
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'''77''' Synthesized Promoters
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'''11''' Novel Artificial Repressors
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'''~ 350''' New Strains
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'''~ 130''' DNA Strands Sequenced
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'''> 5000''' Colonies Screened
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'''~ 400''' Quantitative Assays
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<br>
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<br>
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<br>
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[[USTC/Events|'''Previous Events''']]
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<h3>Resources</h3>
<h3>Resources</h3>
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[[USTC/Protocols|Protocols]]
[[USTC/Protocols|Protocols]]
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[[USTC/PromoterDesign|Promoter Design]]
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[[USTC/Sponsors|Sponsors]]
[[USTC/ServiceProviders|Service Providers]]
[[USTC/ServiceProviders|Service Providers]]
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<h3>Gallery</h3>
<h3>Gallery</h3>
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[http://sg.ustc.edu.cn/mediawiki/index.php/IGEM_USTC_2007:HuangshanPhotos Huangshan Mountain]
[http://sg.ustc.edu.cn/mediawiki/index.php/IGEM_USTC_2007:HuangshanPhotos Huangshan Mountain]
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<h3>Links</h3>
<h3>Links</h3>
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[http://partsregistry.org iGEM standard parts' catalog ]
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[http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2007&group=USTC Parts Made by USTC iGEM 2007]
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[http://www.ustc.edu.cn Univ. of Sci. and Tech. of China ]
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[http://partsregistry.org iGEM Standard Parts' Catalog ]
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[http://groups.google.com/group/iGEMChina iGEM China Group]
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[[IGEM2007 Team List]]
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[http://www.ustc.edu.cn Univ. of Sci. and Tech. of China ]
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Latest revision as of 10:51, 8 March 2011


USTC Logo.png

Today = new Date(); Jamboree = new Date("November 3, 2007"); msInADay = 1000 * 60 * 60 * 24; display = Math.floor((Jamboree.getTime() - Today.getTime())/msInADay); document.write(" " + display +" "); // </script></html>days left until the Jamboree! </font> -->

Our Project:
Extensible Logic Circuit in Bacteria

Artificial Bio-Logic Circuit is composed of "logic gates" and "wires" like Digital Electronic Circuits. Though we have been enjoying the advantages of ultra-large-scale electronic circuits in modern life, we still cannot implement a somewhat small-scale circuit in vivo with several levels of gates.

Our project is to provide a new method for building up a fully extensible bio-logic circuit in bacteria. A small fragment of DNA containing cis-acting elements, favored for its small scale and potential to implement complex logic computation in vivo, can be systematically built up and act as a gate. Meanwhile, artificial repressors with highly-specific DNA-recognition regions are able to transmit signals without mutual interference, just as enameled wires. In this way, a circuit can be constructed regardless of the number of logic gates and the layout of the wires.

A demonstration system has also been assembled to show the practicality of this method. Just like Digital Electronic Circuits in early days, it is simple and ugly. Nevertheless, how will it appear in future?

For detailed description, please click each hyperlink below.

DSCN1243.png

From left to right
Back row: Zhao Yun, Liu ZQ, Ma XY
Front row: Ma Rui, Su XF, Ding Bo, Zhan Jian


Project


Introduction


Core Logic Components:

Logic-Gate Promoters


Wires without Interference:

Repressor Evolution on Plates

Repressor Evolution in Silico


Peripheral Devices:

Inputs and Outputs


Extensible System:

A Demonstration

Further More


Members


4 Graduates:
Zhan Jian
Ma Rui
Ding Bo
Ma Xiaoyu


3 Undergraduates:
Su Xiaofeng
Liu Ziqing
Zhao Yun


3 Faculty Advisors:
Prof. HY Liu
Prof. JR Wu
Prof. ZH Hou

Snapshot


[http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2007&group=USTC 247 Part Sequences]

123 Parts Submitted


77 Synthesized Promoters

11 Novel Artificial Repressors


~ 350 New Strains

~ 130 DNA Strands Sequenced

> 5000 Colonies Screened

~ 400 Quantitative Assays






Previous Events

Resources

Modeling Utilities

Protocols

Sponsors

Service Providers

Gallery

Team Photos

Laboratory

[http://sg.ustc.edu.cn/mediawiki/index.php/IGEM_USTC_2007:USTCPhotos USTC Photos]

[http://sg.ustc.edu.cn/mediawiki/index.php/IGEM_USTC_2007:HuangshanPhotos Huangshan Mountain]

Links

[http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2007&group=USTC Parts Made by USTC iGEM 2007]

[http://partsregistry.org iGEM Standard Parts' Catalog ]

IGEM2007 Team List

[http://www.ustc.edu.cn Univ. of Sci. and Tech. of China ]

Retrieved from "http://2007.igem.org/wiki/index.php/USTC"