USTC

From 2007.igem.org

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=== Our Project:<BR>Extensible Logic Circuit in Bacteria ===
=== Our Project:<BR>Extensible Logic Circuit in Bacteria ===
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Logic Artificial Biological Circuit (ABC) and logic Integrated Circuit (IC) are both composed by "components" and "wires". Though we have been enjoying the advantages of Ultra Large Scale IC (ULSI), we still cannot implement in real experiments a somewhat large-scaled logic ABC with several levels of logic gates in it.
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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 logic ABC. For some biological convenience, we are going to produce such biological logic gates as NAND, NOR, NOT which are exactly the basis for modern logic IC. More importantly, several factors  influence the scale of ABC and IC, such as, the size and power of the components, the interference between wires, and standardization of intercommunication. Cis-acting components in ABC may present a smaller scale and power request than trans-acting ones, while the other two factors can be improved by novelly-designed and calibrated wires. We are also going to demonstrate an ABC made by these biological logic gates and wires.
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Such an ABC may not be large, but the important factors we implement in it will naturally make it fully extensible. IC has existed for 50 years, and now how huge its impact is on our modern lives! Then what about the biological logic circuits in the next 50 years? A new world is waiting...
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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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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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<font color="#AAAAAA">''For detailed description, please click each hyperlink below.''</font>
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[[Image:DSCN1243.png|330px]]
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''From left to right''<BR>
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<font color="#AAAAAA">''From left to right''</font><BR>
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''Back row:'' [[USTC/ZhaoYun|Zhao Yun]], [[USTC/LiuZiqing|Liu ZQ]], [[USTC/MaXiaoyu|Ma XY]]<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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''Front row:'' [[USTC/MaRui|Ma Rui]], [[USTC/SuXiaofeng|Su XF]], [[USTC/DingBo|Ding Bo]], [[USTC/ZhanJian|Zhan Jian]]
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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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<a href="http://www3.clustrmaps.com/counter/maps.php?url=https://2007.igem.org/USTC" id="clustrMapsLink"><img src="http://www3.clustrmaps.com/counter/index2.php?url=https://2007.igem.org/USTC" style="border:0px;" alt="Locations of visitors to this page" title="Locations of visitors to this page" id="clustrMapsImg" />
 
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<h3>Events</h3>
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<h3>Project</h3>
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'''25/08/2007'''<br>
 
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The fluorescent reporter (GFP-aav) in double-reporters system does not work. This fact was confirmed by Ma Rui using several times of fluorescence assays. New version is under construction for next step of NAND gate, and these days Ma Rui have to use classical ONPG method to determine data for designing NOR gate.
 
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'''22/08/2007'''<br>
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[[USTC/Introduction|Introduction]]
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Most members of the co-repression promoter family show that they can be repressed by either designed repressor. This result shows that NOR and NOT gates have been got, but no one is suitable for NAND gate. We are considering to modify our scheme to search NAND gate. 
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[[USTC/Previous|'''Previous''']]
 
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'''Core Logic Components:'''
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<h3>Tasks</h3>
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[[USTC/Logic-Gate_Promoters|Logic-Gate Promoters]]
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<center>
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'''Wires without Interference:'''
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[[USTC/Project Description|Project Description]]
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[[USTC/Repressor_Evolution_on_Plates|Repressor Evolution on Plates]]
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[[USTC/PoPSConverters|PoPS Converters]]
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[[USTC/Repressor_Evolution_in_Silico|Repressor Evolution <i>in Silico</i>]]
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[[USTC/LogicGates|Biological Logic Gates]]
 
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[[USTC/PromoterDesigning|Promoter Designing]]
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'''Peripheral Devices:'''
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[[USTC/RepressorDesigning|Lac Repressor Redesigning]]
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[[USTC/Inputs_and_Outputs|Inputs and Outputs]]
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[[USTC/PoPSReporter|Fluorescent Reporters]]
 
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[[USTC/OverallSystem|All Things Linking Together]]
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'''Extensible System:'''
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</center>
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[[USTC/Demonstration|A Demonstration]]
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[[USTC/Further_More|Further More]]
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<h3>Members</h3>
<h3>Members</h3>
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<center>
<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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<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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[[USTC/Events|'''Previous Events''']]
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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>

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 ]

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