Team:Tsinghua

From 2008.igem.org

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'''Internationally Genetically Engineered Machine Competition'''
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<div style="background-color:#d2fcd9; color:#d2fcd9">
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<!--- The Mission, Experiments --->
 
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{| style="color:#0c6;background-color:#9E0393;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"
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{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="100%" align="center"
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!align="center"|[[Team:Tsinghua|Home]]
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!align="center"|[[Team:Tsinghua|HOME]]
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!align="center"|[[Team:Tsinghua/Team|The Team]]
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!align="center"|[[Team:Tsinghua/Team|Team]]
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!align="center"|[[Team:Tsinghua/Project|The Project]]
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!align="center"|[[Team:Tsinghua/Project|Project 1]]
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!align="center"|[[Team:Tsinghua/Parts|Parts Submitted to the Registry]]
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!align="center"|[[Team:Tsinghua/Project2|Project 2]]
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!align="center"|[[Team:Tsinghua/Parts|Parts]]
!align="center"|[[Team:Tsinghua/Modelling|Modelling]]
!align="center"|[[Team:Tsinghua/Modelling|Modelling]]
!align="center"|[[Team:Tsinghua/Notebook|Notebook]]
!align="center"|[[Team:Tsinghua/Notebook|Notebook]]
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!align="center"|[[Team:Tsinghua/Doodle|Doodle Board]]
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<br>
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[[Image:554.jpg|center|]]
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<br>
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[[石川]]
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=Our ideas=
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[[Image:Girls' Day 4.jpg]] 
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Dynamics
 
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  GF taq is recommended in our PCR reactions. 2008.June.25
 
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  The first plasmid is successfully constrcuted. 2008.Jul.20
 
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  The gene we need is at synthesis in Geneart.  2008.Jul.24
 
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  The standard vector pSB1A3 lost in the transformation. 2008.Jul.28
 
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  Then it finally succeeds.  2008.Jul.31
 
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  Template of one of the receptors are still in vacancy.
 
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  New edition of project interpretation are in process.
 
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{|align="justify"
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====Poor Driver In a Strange Car====
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The car is strange because it can only run forward or tumble. The probability of the two states is controlled through a handle in it. Even worth, there are no windows on this car but a barometer showing local altitude. How should the driver do to reach the top of the hill and stay at there?
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...
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If you think about the design of bacterial chemotaxis pathway, you will find that this pathway just plays the role of the driver in the story above. Interestingly, we find E. coli chemotaxis pathway realizes this delicate dicision-making process through the interactions amount handful molecules. Our project will show how we learn the design principles from native pathway to complete our device.
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== Our Team ==
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|<html><object width="425" height="350"> <param name="movie"value="http://www.youtube.com/v/EfY4RTA93ME"</center> </param> <embed src="http://www.youtube.com/v/EfY4RTA93ME" type="application/x-shockwave-flash" width="425" height="350"></embed></object></html>
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=Introduction of Tsinghua University=
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<background-color:#ACF8AE; color:#ACF8AE">
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|Tsinghua University was established in 1911, originally under the name “Tsinghua Xuetang”. The school was renamed "Tsinghua School" in 1912. The university section was founded in 1925. The name “National Tsinghua University” was adopted in 1928.[[gallery|click here to see more pictures]]
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== Campus==
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The educational philosophy of Tsinghua is to "train students with integrity." Among over 120,000 students who have graduated from Tsinghua since its founding are many outstanding scholars, eminent entrepreneurs and great statesmen remembered and respected by their fellow Chinese citizens.
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[[Image:Library2.jpg]]   
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[[Image:Medicine.jpg]]
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With the motto of “Self-Discipline and Social Commitment” and the spirit of “Actions Speak Louder than Words”, Tsinghua University is dedicated to the well-being of Chinese society and to world development.
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[[Image:West Stadium2.jpg]]
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|[[image:thu_1.jpg|right]]
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|}
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[[Image:Soul of Tsinghua.jpg]]
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=News=
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  Jamboree is coming in  8 days!
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  Tsinghua team, Beijing_Normal team, USTC team will lodge together during the Jamboree.
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  last edit by [[User:Ylzouyilong|Ylzouyilong]] Oct 29.2008
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[[Image:Astro.jpg]]
 
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==    == Team Roster == ==
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= Communication =
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[[ Communication and Interaction ]]
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Guoqiang Chen Professor chengq@mail.tsinghua.edu.cn
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= Acknowledgement =
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Shao Li Professor shaoli@tsinghua.edu.cn
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[[Image:Tsinghua.gif]][[Image:Biobricks.png]][[Image:SB4.0.gif]][[Image:invitrogen.jpg]][[Image:mathwork.jpg]][[Image:geneart.gif]][[Image:DSM3.GIF]]
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Zhirong Sun Professor sunzhr@mail.tsinghua.edu.cn
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{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="100%" align="center"
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!align="center"|[[Team:Tsinghua|HOME]]
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Syna Gao Ph.D         synagao@gmail.com
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!align="center"|[[Team:Tsinghua/Team|Team]]
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Tao  Ma Ph.D         mat07@mails.thu.edu.cn
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!align="center"|[[Team:Tsinghua/Project|Project 1]]
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Yanchao Han Ph.D         haytcb@gmail.com
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!align="center"|[[Team:Tsinghua/Project2|Project 2]]
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Feng Liu Undergraduate liufeng04@mails.tsinghua.edu.cn
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!align="center"|[[Team:Tsinghua/Parts|Parts]]
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!align="center"|[[Team:Tsinghua/Modelling|Modelling]]
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Junjie Luo Undergraduate jjluo54@163.com
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!align="center"|[[Team:Tsinghua/Notebook|Notebook]]
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Yaxuan Yang Undergraduate yangyx04@mails.tsinghua.edu.cn
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!align="center"|[[Team:Tsinghua/Doodle|Doodle Board]]
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Jun Wang Undergraduate wj-cn@163.com
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Chao Wang Undergraduate wangchao05@mails.tsinghua.edu.cn
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Qi  Liu Undergraduate q-liu05@mails.tsinghua.edu.cn
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Shiqing Wang Undergraduate wangsq05@mails.thu.edu.cn
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Tong  Si Undergraduate sit05@mails.thu.edu.cn
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Shan Lin Undergraduate coolls03@163.com
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Yilong Zou Undergraduate ylzouyilong@yahoo.cn
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Ziying Liu Undergraduate liuzy05@mails.tsinghua.edu.cn
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Xing Rong Undergraduate rongx05@mails.thu.edu.cn
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Yicheng Long Undergraduate longyc05@mails.tsinghua.edu.cn
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Luying Jia Undergraduate jialy05@mails.tsinghua.edu.cn
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Yuemeng Wang Undergraduate wym05@mails.tsinghua.edu.cn
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Junya Peng Undergraduate junya.peng@gmail.com
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Xiaoxi Yuan Undergraduate tangbf1983@gmail.com
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Chong Wang Undergraduate wangchongxn@yahoo.com.cn
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Feng  Tian Undergraduate tianf06@mails.tsinghua.edu.cn
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Yuanfan  Yang Undergraduate yangyf06@mails.tsinghua.edu.cn
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Liang Zheng Undergraduate 1000zhengliang@sina.com
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Yongqiang Gou Undergraduate gouyongqiang007@163.com
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He  Yang Undergraduate yanghemary@gmail.com
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Zi  Wang Undergraduate fiona99988@yahoo.com.cn
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Gechong  Ruan    Undergraduate  rgc06@mails.tsinghua.edu.cn
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Bing  Xing      Undergraduate  binxing1987@gmail.com
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== == Team Members == ==
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          Yaxuan Yang [[Image:Yaxuan Yang.jpg]]   Chao Wang  [[Image:Chao Wang.jpg]]   Qi Liu[[Image:Qi Liu2.jpg]]     
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Shiqing Wang[[Image:Shiqing Wang2.jpg]] Yilong Zou[[Image:Yilong Zou.jpg]]     Yicheng Long [[Image:Yicheng Long.jpg]]
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  Luying Jia[[Image:Luying Jia2.jpg]]   Yuemeng Wang[[Image:Yuemeng Wang2.jpg]] Feng Tian [[Image:Feng Tian.jpg]] 
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Yuanfan Yang[[Image:Yuanfan Yang2.jpg]]  He Yang  [[Image:He Yang2.jpg]]  Zi Wang[[Image:Zi Wang3.jpg]]   
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  Gechong Ruan[[Image:Gechong Ruan2.jpg]]    Bin Xing[[Image:Bin Xing.jpg]]
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== == Our Schedule == ==
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  Time                       Events
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Dec. 15, 2007               Team of Tsinghua University Founded
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Dec. 31, 2007               Brain Storm(1)
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Jan-Feb, 2008               Backgroud Investigation
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Feb.25, 2008               Brain Storm(2)
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Mar., 2008               Experimental procedure design;
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                              Modeling in silico Started 
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Apr.1,2008               Wet Lab work started
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Apr.-Aug.,2008               Wet Lab Work
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May.1, 2008               Team Registry
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May.25, 2008               Students’ Association of Synthetic Biology(SASB) Founded
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June.21, 2008               “Teach the teacher “workshop, in Kyoto, Japan
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Sept.-Oct., 2008       Inspection and Revision   
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Oct.20,2008               Summary, Presentation Preparation
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Nov.8-9,2008               Jamboree In MIT
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== Project ==
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== == Abstract == ==
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  This year we are trying to work at the motility of bacteria. E.coli senses some chemicals and moves toward
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or stays still, this behavior is called chemotaxis. Any modification of the pathway from the sensor to
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the        motile apparatus will cause into different chemotactic effcts.   
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  Moreover，most of the biosensors today are designed for a specific target signal, and they can not
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substitute  each other in most cases. By structural analysis we find that most receptors for the same type
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of    ligands exhibits great similarity, both in sequence information and characteristics. Our project
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is        designed toward an "Interchangeable Biosensor". The strategy is almost trial and error, to find
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an    appropriate pathway between chemical molecules and corresponding reactions. Signals other than
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chemicals  are much harder to manipulate, and to integrate together the signals seems even more
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challenging,we    are trying to isolate the elements and standardise them.
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== == Background == ==
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Motile bacteria can respond to chemical gradients in their environment. Such directed movement in response to special chemicals is defined as chemotaxis. If organisms detect substances beneficial for surviving, positive chemotaxis occurs and cells will move in the direction of increasing concentration. In contrast, negative chemotaxis occurs when motile bacteria move away from a repellant. Both kinds of responses adjust the behaviors of organisms to the environment, thus improve their ability of surviving.
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One typical chemotactic behavior is the response of Escherichia coli toward certain nutritions, which plays a key role in seeking food. Researchers have investigated thoroughly into the molecular mechanism of it.
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Motility in prokaryotes is accomplished by flagellum, a complex structure moving the cell by rotation, much like the propeller in a motor boat. In E.coli, counterclockwise rotation moves the cell in a direction called a run, while clockwise rotation results in tumbling of the cell.
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The direction of rotation is controlled by phosphorylation of CheY, a signaling protein in the chemotaxis pathway of E.coli. Low level of phosphorylation results in counterclockwise rotation of flagella and makes the cell move forward. In contrast, phosphorylated CheY favors tumbling.
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The level of protein phosphorylation is regulated by certain attractant or repellent, which can bind specific receptors on the cell surface. Signals are then passed through a series of intracellular biochemical reactions, in which phosphorylation of CheY is controlled. In this way bacteria accomplish chemotactic behavior.
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Escherichia coli is a common kind of engineer bacteria, which is convenient for genetic manipulation. It is likely that we make use of the chemotactic pathway in E.coli, making them detect and move toward a special chemical substance, maybe a certain kind of pollutant. If the genetic engineering strain also has the ability of degrading aimed chemicals, efficiency of pollution treatment can be hopefully improved a lot. However, the natural ligands concerning chemotaxis in E.coli are limited in several kinds of nutrition, such as carbohydrate and amino acids. Strains that can detecting more kinds of organic substances and even heavy metal ions is planed to be got through the reconstruction of chemotaxis system.
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== == Design == ==
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== == Predicted Result == ==
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== == Related literature == ==
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== Modeling ==
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== Laboratory Work ==
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== == Scheme == ==
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== == Lab Log == ==
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==  ==  Protocols == ==
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== == == Molecular cloning == == ==
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  1  PCR
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  1.1 Gold Faster Taq system:
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    Reagent           Concentration/Activity 50ul 100ul
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    GF taq buffer        10x                         5      10
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    GF taq                                 0.5   0.5
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    dNTPmix             10mM each                 1   2
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    Primer 1             10uM                 1   2
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    Primer 2             10um                 1   2
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    Template DNA       changeable                 0.5   1
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    MgCl2             0.2M                 0.5   1
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    ddH2O                 ---                 40.5 81
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  1.2 The program under Gold faster taq system
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    Progress     Program I                 Program 2
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    Predenaturing    95℃        2-5 min         95℃  2-5 min
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    Denaturing     95℃        10-20sec         95℃  10-20sec
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    Annealing     (Tm-5) ℃  2-5 sec         68℃  10-15sec/1kb
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    Extension     72℃        10-15sec/1kb
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                  25-30cycle               25-30cycle
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    Last extension   1-2min or skipped       1-2min or skipped
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    2 Restriction cut:
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            Reagent         Concentration/Activity Volume(50ul system)
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            Restriction cut buffer 10x           5ul
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            Enzyme 1                 --           2.5ul
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            Enzyme 2                 --           2.5ul
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  Incubate at 37℃, 1.5 hrs or longer
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  (Enzymes from Takara Co., Ltd)
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      3  Ligation:
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              Reagent     Volume(10ul system)
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              Solution I 5ul
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              DNA fragment 3.5ul
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              Vector         1.5ul
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    Incubate at 16-18℃,1hr or longer
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    (Ligation kit from Takara)
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== == == Bacteria behavior == == ==
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== Devices and Parts ==
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== == Parts == ==
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== == == Protein Coding == == ==
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== == == Regulatory == == ==
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== == == Vectors == == ==
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== == == Others == == ==
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== == Devices == ==
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== Communication ==
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== == Meet up == ==
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    2007.Dec.1          With Peking University team leaders.
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    2007.Dec.15        With all the students from different academies.
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    2008. Feb          With candidate instructors in Our Department.
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    2008. March        With Faculties from Professor Lee's lab.
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    2008. April        With Drew Endy in Peking University.
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    2008. April        With Peking University.
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    2008. June.21-22    On Teachers' Workshop, with most Asia teams.
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    2008. July.17      With Beijing Normal University Team
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    2008.July.25        With Invitrogen.Co. Ltd.
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== == Phone == ==
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== == E-mails == ==
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  2008. July          With ETH_Zurich by E-mail
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== Doodle Board ==
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            [[Image:Friends.jpg]]
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The organism grew on the plate was not bacteria,but fungi.  2008.July .23 
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{| style="color:#0c6;background-color:#9E0393;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"
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!align="center"|[[Team:Example|Home]]
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!align="center"|[[Team:Example/Team|The Team]]
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!align="center"|[[Team:Example/Project|The Project]]
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!align="center"|[[Team:Example/Parts|Parts Submitted to the Registry]]
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!align="center"|[[Team:Example/Modelling|Modelling]]
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!align="center"|[[Team:Example/e-Notebook|e-Notebook]]
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<!--- The Mission, Experiments --->
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[[image:06.jpeg|center|]]
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== Headline text ==
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    Contact us: sasbthu@yahoo.cn
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Latest revision as of 04:44, 30 October 2008


HOME Team Project 1 Project 2 Parts Modelling Notebook Doodle Board


554.jpg


Contents

Our ideas

Poor Driver In a Strange Car

The car is strange because it can only run forward or tumble. The probability of the two states is controlled through a handle in it. Even worth, there are no windows on this car but a barometer showing local altitude. How should the driver do to reach the top of the hill and stay at there? ... If you think about the design of bacterial chemotaxis pathway, you will find that this pathway just plays the role of the driver in the story above. Interestingly, we find E. coli chemotaxis pathway realizes this delicate dicision-making process through the interactions amount handful molecules. Our project will show how we learn the design principles from native pathway to complete our device.

Introduction of Tsinghua University

<background-color:#ACF8AE; color:#ACF8AE">

Tsinghua University was established in 1911, originally under the name “Tsinghua Xuetang”. The school was renamed "Tsinghua School" in 1912. The university section was founded in 1925. The name “National Tsinghua University” was adopted in 1928.click here to see more pictures

The educational philosophy of Tsinghua is to "train students with integrity." Among over 120,000 students who have graduated from Tsinghua since its founding are many outstanding scholars, eminent entrepreneurs and great statesmen remembered and respected by their fellow Chinese citizens.

With the motto of “Self-Discipline and Social Commitment” and the spirit of “Actions Speak Louder than Words”, Tsinghua University is dedicated to the well-being of Chinese society and to world development.

Thu 1.jpg

News

 Jamboree is coming in  8 days!
 Tsinghua team, Beijing_Normal team, USTC team will lodge together during the Jamboree.
  last edit by Ylzouyilong Oct 29.2008


Communication

Communication and Interaction

Acknowledgement

Tsinghua.gifBiobricks.pngSB4.0.gifInvitrogen.jpgMathwork.jpgGeneart.gifDSM3.GIF

HOME Team Project 1 Project 2 Parts Modelling Notebook Doodle Board
06.jpeg
== Headline text ==
Retrieved from "http://2008.igem.org/Team:Tsinghua"