Team:USTC

From 2009.igem.org

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== Welcome to the Wiki of USTC iGEM 2009 Wet Lab Team! ==
== Welcome to the Wiki of USTC iGEM 2009 Wet Lab Team! ==
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'''We sincerely appreciate your visit. From this wiki, you'll step into the mystical world of our explorations in synthetic biology this year!'''
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[[Image:USTC-1.jpg||240px]][[Image:USTC-2.jpg|240px]][[Image:USTC-3.jpg|240px]][[Image:USTC-4.jpg|240px]]
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=== Team USTC ===
=== Team USTC ===
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University of Science and Technology of China ([http://en.ustc.edu.cn/about.php USTC]), located in the beautiful city Hefei in Anhui province, is one of the most famous universities in China. This is the 3rd year for USTC to participate in iGEM. This year we have two teams, the wet lab team USTC and the dry lab team [[Team:USTC_Software|USTC_Software]]. The two teams are readily collaborating with each other to solve interdisciplinary problems.
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The wet lab team consists of 7 undergraduate students, 3 graduate students, 2 PhD student instructors, 2 faculty instructors and 2 faculty advisors. We are from different departments of USTC: Department of Systems Biology, Department of Molecular Biology and Cell Biology, Department of Chemical Physics, Department of Chemistry, and Department of Polymer Science and Engineering. However, we are with the same enthusiasm and confidence to do some things both fundamental and original.
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[[Image:Team_USTC_logo.png|200px|right|thumb|USTC team logo]]
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Our team is consist of members with different backgrounds, saying biology, mathematics, chemistry, computer science and physics, but with the same enthusiasm and confidence to do some thing both fundamental and original. We really appreciate your visit, and from this wiki you'll find records of our meetings and discussions, as well as keep up with our everyday progress.
 
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|[[Image:Team_USTC_logo.png|200px|right|frame|USTC team logo]]
 
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=== Project E.ADEM ===
=== Project E.ADEM ===
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Evolution is more powerful than the God, as Charles Darwin told us 150 years ago. This year, our team is trying to manage the power of evolution, the power of creating everything from molecules to ecosystems, by engineering an '''''E. coli'' Automatic Directed Evolution Machine (E.ADEM)'''.
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Evolution is more powerful than the God, as Charles Darwin told us 150 years ago. This year, our team is trying to manage the power of evolution, the power of creating everything from biomolecules to ecosystems, by engineering an '''''E. coli'' Automatic Directed Evolution Machine (E.ADEM)'''.
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Our goal is to make E.ADEM a universal framework for directed evolution of almost anything: from promoters, regulators, receptors, binding partners, enzymes, aptamers, ribozymes and RBS, to sensors, logic devices, reporters, metabolic pathways, entire genomes, and even solutions of mathematic problems. The versatility of E.ADEM will be accomplished by its modular design and using PoPS as common signal carriers.
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The ultimate goal is to make E.ADEM a universal framework for evolutionary approaches in synthetic biology. Anything we want in synthetic biology can be automatically created, from promoters, RBS, regulators, receptors, binding partners, aptamers, enzymes and ribozymes, to sensors, logic devices, reporters, metabolic pathways, entire genomes, and even solutions of mathematic problems.
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To each evolution object you want it to evolve, a scoring function can be designed to output PoPS as the score of [http://en.wikipedia.org/wiki/Fitness_%28biology%29 fitness], then you can ligate the scoring function into the E.ADEM plasmid, transform ''E. coli'', culture the cells to let them evolve automatically and robustly, and get what you want.
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To each evolution object you want it to evolve, a scoring function can be designed to output PoPS as the [http://en.wikipedia.org/wiki/Fitness_%28biology%29 fitness] score to your demand. After that, you can ligate the scoring function device into the E.ADEM plasmid, transform ''E. coli'', culture the cells and wait for them to evolve automatically and robustly, and get what you want at last.
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E.ADEM is designed by implement [http://en.wikipedia.org/wiki/Evolutionary_algorithms evolutionary algorithm] back into biology. The scoring function is connected to a logic controller module to adjust variation rate and [http://en.wikipedia.org/wiki/Selection_pressure selection pressure]. The logic controller then calls 4 other modules, a quorum sensing device designed to calculate population size and average score, a variation function to change the evolution object by mutation or recombination, a selection function to control the survival or death of the cell, and a reporter module to report the score to the user. The detail of the project will be updated in the [[Team:USTC/Project|project page]].
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E.ADEM is designed by implementing [http://en.wikipedia.org/wiki/Evolutionary_algorithms evolutionary algorithm] back into biology. The output of the scoring function is connected to the core of E.ADEM, a self-adaptive controller that can adjust variation rate and [http://en.wikipedia.org/wiki/Selection_pressure selection pressure], base on the fitness score, the population size and the average fitness score calculated by a quorum sensing device. To carry out individual functions, 3 more modules are also designed: a variation function to change the evolution object by mutation or recombination, a selection function to control the survival or death of the cell, and a reporter module to report the score to the user.  
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|[[Image:Team_USTC.png|right|frame|USTC team picture]]
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We performed comprehensive measurement using constitutive promoter family stimulus signals and modeling of each components. A prototype machine with the self-adaptive controller is built. Modular design and PoPS device boundary standard will ensure the extensibility and universality of the machine.
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Please goto [[Team:USTC/Project|project page]] for more details.
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[[Image:Team_USTC.jpg|300px|center|thumb|USTC team picture]]
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[[Image:Team_USTC_tshirt.jpg|300px|center|thumb|USTC team t-shirt]]
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|align="center"|[[Team:USTC/Team|Team USTC]]
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== Links ==
== Links ==
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*[http://parts.mit.edu/igem07/index.php/USTC USTC 2007 Team Wiki]
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*[https://2007.igem.org/USTC USTC 2007 Team Wiki]
*[https://2008.igem.org/Team:USTC USTC 2008 Team Wiki]
*[https://2008.igem.org/Team:USTC USTC 2008 Team Wiki]
*[[Team:USTC_Software|USTC_Software 2009 Team Wiki]]
*[[Team:USTC_Software|USTC_Software 2009 Team Wiki]]
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*[http://igem.ustc.edu.cn/ External Team Wiki]
*[http://igem.ustc.edu.cn/ External Team Wiki]
*[http://spreadsheets.google.com/pub?key=plR27rERjfUK_lAs01fg5YA Summary of iGEM Teams]
*[http://spreadsheets.google.com/pub?key=plR27rERjfUK_lAs01fg5YA Summary of iGEM Teams]
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*[http://en.ustc.edu.cn/about.php About USTC]
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*[http://www.ustc.edu.cn/zh_CN/ USTC (Chinese)]
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*[http://en.ustc.edu.cn/index.php USTC (English)]
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== Sponsors ==
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'''Our project is supported by the following divisions of USTC:'''
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[[Image:USTC_emblem.png|180px|USTC emblem]]
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*Teaching Affairs Office
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*Graduate School
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*Foreign Affairs Office
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*School of Life Sciences
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== Acknowledgements ==
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'''We would like to thank the following people for their help:'''
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[http://www.duke.edu/~you/ Prof. Lingchong You] and Yu Tanouchi (Duke University) provided us the plasmid containing lacZalpha-ccdB.
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Tony Pharo, Barbara Geissbuhler and Katharine Kramer ([http://www.scarabgenomics.com/ Scarab Genomics, LLC]) helped us in the shipment of their product MDS42 and MDS42recA Blue strains, and in using the strains.
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Prof. Maikun Teng and Prof. Congzhao Zhou (USTC), helped us to get the funding.
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Dr. Huichao Ou (USTC) helped us to design our team logo and t-shirt, and took photographs for us. Lidan Wu (USTC) also helped us to design our team t-shirt.
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People in USTC_Software team helped us in modeling of our systems.
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[[Image:USTC-5.jpg|240px]][[Image:USTC-6.jpg|240px]][[Image:USTC-7.jpg|240px]][[Image:USTC-8.jpg|240px]]

Latest revision as of 07:47, 14 November 2009

USTC
Home Team Project Modeling Parts Standard & Protocol Software Tool Human Practice Notebook

Team:USTC

Contents


Welcome to the Wiki of USTC iGEM 2009 Wet Lab Team!

We sincerely appreciate your visit. From this wiki, you'll step into the mystical world of our explorations in synthetic biology this year!


USTC-1.jpgUSTC-2.jpgUSTC-3.jpgUSTC-4.jpg

Team USTC

University of Science and Technology of China ([http://en.ustc.edu.cn/about.php USTC]), located in the beautiful city Hefei in Anhui province, is one of the most famous universities in China. This is the 3rd year for USTC to participate in iGEM. This year we have two teams, the wet lab team USTC and the dry lab team USTC_Software. The two teams are readily collaborating with each other to solve interdisciplinary problems.

The wet lab team consists of 7 undergraduate students, 3 graduate students, 2 PhD student instructors, 2 faculty instructors and 2 faculty advisors. We are from different departments of USTC: Department of Systems Biology, Department of Molecular Biology and Cell Biology, Department of Chemical Physics, Department of Chemistry, and Department of Polymer Science and Engineering. However, we are with the same enthusiasm and confidence to do some things both fundamental and original.

USTC team logo

Project E.ADEM

Evolution is more powerful than the God, as Charles Darwin told us 150 years ago. This year, our team is trying to manage the power of evolution, the power of creating everything from biomolecules to ecosystems, by engineering an E. coli Automatic Directed Evolution Machine (E.ADEM).

The ultimate goal is to make E.ADEM a universal framework for evolutionary approaches in synthetic biology. Anything we want in synthetic biology can be automatically created, from promoters, RBS, regulators, receptors, binding partners, aptamers, enzymes and ribozymes, to sensors, logic devices, reporters, metabolic pathways, entire genomes, and even solutions of mathematic problems.

To each evolution object you want it to evolve, a scoring function can be designed to output PoPS as the [http://en.wikipedia.org/wiki/Fitness_%28biology%29 fitness] score to your demand. After that, you can ligate the scoring function device into the E.ADEM plasmid, transform E. coli, culture the cells and wait for them to evolve automatically and robustly, and get what you want at last.

E.ADEM is designed by implementing [http://en.wikipedia.org/wiki/Evolutionary_algorithms evolutionary algorithm] back into biology. The output of the scoring function is connected to the core of E.ADEM, a self-adaptive controller that can adjust variation rate and [http://en.wikipedia.org/wiki/Selection_pressure selection pressure], base on the fitness score, the population size and the average fitness score calculated by a quorum sensing device. To carry out individual functions, 3 more modules are also designed: a variation function to change the evolution object by mutation or recombination, a selection function to control the survival or death of the cell, and a reporter module to report the score to the user.

We performed comprehensive measurement using constitutive promoter family stimulus signals and modeling of each components. A prototype machine with the self-adaptive controller is built. Modular design and PoPS device boundary standard will ensure the extensibility and universality of the machine.

Please goto project page for more details.

USTC team picture
USTC team t-shirt


Links

  • USTC 2007 Team Wiki
  • USTC 2008 Team Wiki
  • USTC_Software 2009 Team Wiki
  • [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2009&group=USTC USTC 2009 Parts]
  • [http://biotech.ustc.edu.cn/forum/forumdisplay.php?fid=26 External Team Forum]
  • [http://igem.ustc.edu.cn/ External Team Wiki]
  • [http://spreadsheets.google.com/pub?key=plR27rERjfUK_lAs01fg5YA Summary of iGEM Teams]
  • [http://www.ustc.edu.cn/zh_CN/ USTC (Chinese)]
  • [http://en.ustc.edu.cn/index.php USTC (English)]


Sponsors

Our project is supported by the following divisions of USTC:

USTC emblem

  • Teaching Affairs Office
  • Graduate School
  • Foreign Affairs Office
  • School of Life Sciences

Acknowledgements

We would like to thank the following people for their help:

[http://www.duke.edu/~you/ Prof. Lingchong You] and Yu Tanouchi (Duke University) provided us the plasmid containing lacZalpha-ccdB.

Tony Pharo, Barbara Geissbuhler and Katharine Kramer ([http://www.scarabgenomics.com/ Scarab Genomics, LLC]) helped us in the shipment of their product MDS42 and MDS42recA Blue strains, and in using the strains.

Prof. Maikun Teng and Prof. Congzhao Zhou (USTC), helped us to get the funding.

Dr. Huichao Ou (USTC) helped us to design our team logo and t-shirt, and took photographs for us. Lidan Wu (USTC) also helped us to design our team t-shirt.

People in USTC_Software team helped us in modeling of our systems.


USTC-5.jpgUSTC-6.jpgUSTC-7.jpgUSTC-8.jpg

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