http://2012.igem.org/wiki/index.php?title=Special:Contributions&feed=atom&limit=250&target=Helengood&year=&month=2012.igem.org - User contributions [en]2024-03-28T17:56:53ZFrom 2012.igem.orgMediaWiki 1.16.0http://2012.igem.org/Team:Tianjin/NotebookTeam:Tianjin/Notebook2013-05-09T05:16:28Z<p>Helengood: /* Sept. 18th, 2012 */</p>
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<div>{{:Team:Tianjin/frame/notebook}}<br />
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<p class="menu_head">Notebook Contents</p><br />
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<a href="https://2012.igem.org/Team:Tianjin/Notebook/Modeling">Modeling Notebook</a><br />
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<a href="https://2012.igem.org/Team:Tianjin/Notebook/HumanPractice">Human Practice Notebook</a><br />
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<p class="menu_head">July, 2012</p><br />
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<center><span style="font-size:46px;font-family:Cambria;margin-top:10px;line-height:80%">Notes of Experiments</span></center><br />
==July 6th, 2012==<br />
#We discuss our all of the possible projects, and finally choose one. And then allocate works to specific member.<br />
#Do some pre-experiment and make some reagants.<br />
##Liquid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl <br />
##Solid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl<br />
###20g agar<br />
#Cleaned up the lab and laboratory instruments<br />
<br />
==July 8th, 2012==<br />
#Solutions for extracting plasmid.<br />
##50mM Glucose / 25mM Tris-Cl / 10mM EDTA,pH=8.0<br />
##0.2N NaOH / 1% SDS<br />
##3M KOAc / 2M HOAc<br />
#Experiment technologies training, such as making gel, gel electrophoresis.<br />
[[File:TJU2012-Note-gel-1.png|center|350px|gel 1]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-2.png|center|350px|gel 2]]<br />
<br />
==July 11th, 2012==<br />
#Designed primers and sent orders.<br />
#Optimized the project and allocated work.<br />
#Experiment technologies and knowledge training<br />
##PCR principle and operation<br />
##Gel Extraction<br />
[[File:TJU2012-Note-gel-3.png|center|350px|gel 3]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-4.png|center|350px|gel 4]]<br />
<br />
==July 13th, 2012==<br />
1. Received the oligo and began to mutate 16S rrnB operator.<br />
[[File:TJU2012-Note-gen-1.png|center|350px|Gene1]]<br />
2. Mutated RBS of RFP and checked through gel electrophoresis.<br />
[[File:TJU2012-Note-gen-2.png|center|250px|Gene2]]<br />
[[File:TJU2012-Note-gel-5.png|thumb|center|250px|~1800bp, constant with anticipation]]<br />
<br />
==July 14th, 2012==<br />
#Transform two plasmids of we got yestday together into E.coli.[[File:TJU2012-Note-gen-3.png|center|500px|Gene 3]]<br />
#PCR verification of colonies on the LB plates.<br />
#Inculcated the right colonies in Liquid LB.<br />
<br />
==July 15th, 2012==<br />
#Extract plasmid of cells inculcated after one day.<br />
#Enzyme test of the extracted plasmid.[[File:TJU2012-Note-gel-6.png|center|200px|Gel 6]]<br />
#Inclucated the right cells in Liquid LB and added Ala partly.<br />
<br />
==July 20th, 2012==<br />
Analyse the results.<br />
[[File:TJU2012-Note-form-1.png|center|500px|Form 1]]<br />
[[File:TJU2012-Note-fig-2.png|center|300px|Fig 2]]<br />
<br />
==July 24th, 2012==<br />
#Linked the GRP gene and O-RBS RFP gene. Gel extract the previous product again, and ligate using T4 with the following gradient.[[File:TJU2012-Note-form-2.png|center|500px|form 2]]<br />
#In the same method to construct three other systems.<br />
[[File:TJU2012-Mode-cal-fig-2.png|center|500px|fig 3]]<br />
[[File:TJU2012-Mode-cal-fig-3.png|center|500px|fig 4]]<br />
[[File:TJU2012-Mode-cal-fig-4.png|center|500px|fig 5]]<br />
<br />
==July 30th, 2012==<br />
#Learned Fluorescence spectrophotometer.<br />
#measure the strength of GFP and RFP.<br />
[[File:TJU2012-Note-form-3.png|center|500px|form 3]]<br />
<br />
==Aug. 2nd, 2012==<br />
#mutated the RBS of the Amp resistance gene.[[File:TJU2012-Note-gen-4.png|center|250px|Gene 4]]<br />
#linked genes and transformed them into E. coli.<br />
<br />
==Aug. 4th, 2012==<br />
Results of plates<br />
[[File:TJU2012-Note-fig-3.png|center|300px|fig 3]]<br />
[[File:TJU2012-Note-form-4.png|center|500px|form 4]]<br />
<br />
==Aug. 8th, 2012==<br />
Began to construct the five parts needed in Assembler in Yeast. Part 1 and part 2.<br />
<br />
==Aug. 11th, 2012==<br />
Verified part 1 and 2. Synthesized the two small parts and linked through overlap PCR. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-4.png|center|600px|fig 4]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-5.png|center|500px|fig 5]]<br />
<br />
==Aug. 12th, 2012==<br />
Began to build part 3, 4 and 5. Synthesized the two small parts and linked through overlap PCR.<br />
<br />
==Aug. 14th, 2012==<br />
Verify part 3, 4 and 5. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-6.png|center|500px|fig 6]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-7.png|center|500px|fig 7]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-8.png|center|500px|fig 8]]<br />
<br />
==Aug. 18th, 2012==<br />
Transformed all the five parts into Yeast for Assembler in Yeast.<br />
<br />
==Aug. 20th, 2012==<br />
#Results of the transformation.[[File:TJU2012-Note-fig-9.png|center|300px|fig 9]]<br />
#Extract plasmids from the Yeast.<br />
<br />
==Aug. 22nd, 2012==<br />
#Transformed the plasmid from the Yeast into cells.[[File:TJU2012-Note-fig-10.png|thumb|center|300px|There are purple spots on the plates]]<br />
#Extracted plasmid and checked through gel electrophoresis.[[File:TJU2012-Note-gel-7.png|center|300px|gel 7]]<br />
#Some other results of Assembler in Yeast.<br />
[[File:TJU2012-Note-fig-11.png|center|300px|fig 11]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-12.png|center|300px|fig 12]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-13.png|center|300px|fig 13]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-14.png|center|300px|fig 14]]<br />
<br />
==Aug. 25th, 2012==<br />
#Began to build biobricks.[[File:Tianjin_BB2.PNG|center|500px|BB 2]]<br />
#Began to search articles on phages.<br />
<br />
==Sept. 1st, 2012==<br />
Went to Peking University for exchanges.<br />
[[File:TJU2012-Note-fig-15.png|center|500px|fig 15]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-16.png|center|500px|fig 16]]<br />
<br />
==Sept. 2nd, 2012==<br />
#Found out phi X174 and firstly proposed our ideas.<br />
#The second sections of our biobricks.<br />
[[File:Tianjin_BB1.PNG|center|500px|BB 1]]<br />
<br />
==Sept. 5th, 2012==<br />
#Some experiments on phages.<br />
#Optimized our biobricks.<br />
#Designed primers needed for mutating Phi X174 and send orders.<br />
<br />
==Sept. 11th, 2012==<br />
#Began to mutate gene G and E.<br />
#Optimized our biobricks.<br />
<br />
==Sept. 18th, 2012==<br />
Began to sort out our materials for wiki and upload the website.<br />
[[File:new1.jpg|center|500px|fig 17]]<br />
our team in Hongkong <br />
<br />
<br />
[[File:new2.jpg|center|500px|fig 18]]<br />
our gold award<br />
<br />
<br />
[[File:new3.jpg|center|500px|fig 19]]<br />
presentation in MIT<br />
<br />
<br />
{{:Team:Tianjin/footer}}</div>Helengoodhttp://2012.igem.org/Team:Tianjin/TeamTeam:Tianjin/Team2013-05-09T05:14:40Z<p>Helengood: </p>
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<body><br />
<div class="container"><br />
<ul class="tabs"><br />
<li class="active"><a href="#tab1">The Whole Team</a></li><br />
<li><a href="#tab16">Advisor</a></li><br />
<li><a href="#tab2" id="">Bin Jia</a></li><br />
<li><a href="#tab3">Qinfeng Wu </a></li><br />
<li><a href="#tab17"> Jiaquan Liu </a></li><br />
<li><a href="#tab4">Shu Gong</a></li><br />
<li><a href="#tab5">Dongchang Qin</a></li><br />
<li><a href="#tab6">Jinlai Zhang</a></li><br />
<li><a href="#tab7">Xiaonan Cheng</a></li><br />
<li><a href="#tab8">Andi Wangzhou</a></li><br />
<li><a href="#tab9">Yapeng Su</a></li><br />
<li><a href="#tab10">Yufei Wei</a></li><br />
<li><a href="#tab11">Yifeng Shao</a></li><br />
<li><a href="#tab12">Lingli Ni</a></li><br />
<li><a href="#tab13">Hengqian Ren</a></li><br />
<li><a href="#tab14">Linlin Song</a></li><br />
<li><a href="#tab15">Yang Li</a></li><br />
<br />
</ul><br />
<div class="tab_container"><br />
<div id="tab1" class="tab_content" style="display: block;"><br />
<img src="https://static.igem.org/mediawiki/2012/1/17/TJU2012-GROUP_DSC0499.JPG"><br />
<b>Proudly present: Tianjin 2012 iGEM Team!</b><br><br>From left to right:<br> Back Row: Yang LI, Shu GONG, Linlin SONG, Lingli NI, Andi WANGZHOU, Bingzhi LI, Bin JIA, Qinfeng WU<br><br />
Front Row: Yufei WEI, Jinlai ZHANG, Hengqian REN, Yingjin YUAN, Dongchang QIN, Yapeng SU, Yifeng SHAO, Xiaonan CHENG<br />
</div><br />
<div id="tab16" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/4/45/TJU2012-Team-Yuan.png"><br />
<b>Prof. Yingjin YUAN</b><br><br><br />
Professor Yingjin Yuan is the founder of iGEM Asia platform. He and MIT worked together, and successfully promoted the iGEM in Asia. He is also one of fist introducers of synthetic biology to China. He has been enthusiastically supporting since iGEM in Tianjin University since year one. <br />
</div><br />
<div id="tab2" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/7/7a/TJU2012-Team-Jia.png"><br />
<div class="teamimgtext"><b>Name: </b>Bin JIA<br><br><b>Major:</b> Bioengineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Graduate Student<br><br><b>Home:</b> Qinshui, Shanxi</div><br />
</div><br />
<div id="tab3" class="tab_content" style="display: none;"><img src="https://static.igem.org/mediawiki/2012/a/ac/Jja.png" style="width:600px;"><br />
<div class="teamimgtext"><b>Name:</b> Qinfeng WU;<br><br> <b>Major:</b> Chemical Engineering;<br><br> <b>School:</b> Chemical Engineering;<br><br> <b>Year:</b> Fourth Year Student;<br><br> <b>Home:</b> Chongqing.</div><br />
</div><br />
<div id="tab17" class="tab_content" style="display: none;"><img src="https://static.igem.org/mediawiki/2012/3/32/Jjb.jpg" style="width:600px;"><br />
<div class="teamimgtext"><b>Name:</b> Jiaquan LIU;<br><br> <b>Major:</b> Applied Chemistry;<br><br> <b>School:</b> Chemical Engineering;<br><br> <b>Year:</b> Third Year Student;<br><br> <b>Home:</b> Shenyang, Liaoning.<br><br></div><br />
</div><br />
<br />
<br />
<br />
<div id="tab4" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/8/85/TJU2012-Team-Gong.png"><br />
<div class="teamimgtext"><b>Name: </b>Shu GONG<br><br><b>Major:</b> Pharmaceutical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Third Year Student<br><br><b>Home:</b> Deyang, Sichuan</div><br />
</div><br />
<div id="tab5" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/2/2e/TJU2012-Team-Qin.png"><br />
<div class="teamimgtext"><b>Name: </b>Dongchang QIN<br><br><b>Major:</b> Bioengineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Fourth Year Student<br><br><b>Home:</b> Xinxiang, Henan</div><br />
</div><br />
<div id="tab6" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/6/6b/TJU2012-Team-Zhang.png"><br />
<div class="teamimgtext"><b>Name: </b>Jinlai ZHANG<br><br><b>Major:</b> Bioengineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Fourth Year Student<br><br><b>Home:</b> Tianjin</div><br />
</div><br />
<div id="tab7" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/0/02/TJU2012-Team-Cheng.png"><br />
<div class="teamimgtext"><b>Name: </b>Xiaonan CHENG<br><br><b>Major:</b> Chemical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Fourth Year Student<br><br><b>Home:</b> Yantai, Shandong</div><br />
</div><br />
<div id="tab8" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/2/2a/TJU2012-Team-WZ.png"><br />
<div class="teamimgtext"><b>Name: </b>Andi WANGZHOU<br><br><b>Major:</b> Bioengineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Fourth Year Student<br><br><b>Home:</b> Beijing</div><br />
</div><br />
<div id="tab9" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/9/9d/TJU2012-Team-Su.png"><br />
<div class="teamimgtext"><b>Name: </b>Yapeng SU<br><br><b>Major:</b> Chemical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Fourth Year Student<br><br><b>Home:</b> Xingtai, Hebei</div><br />
</div><br />
<div id="tab10" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/3/3a/TJU2012-Team-Wei.png"><br />
<div class="teamimgtext"><b>Name: </b>Yufei WEI<br><br><b>Major:</b> Chemical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Third Year Student<br><br><b>Home:</b> Handan, Hebei</div><br />
</div><br />
<div id="tab11" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/a/aa/TJU2012-Team-Shao.png"><br />
<div class="teamimgtext"><b>Name: </b>Yifeng SHAO<br><br><b>Major:</b> Chemical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Third Year Student<br><br><b>Home:</b> Lanzhou, Gansu</div><br />
</div><br />
<div id="tab12" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/7/7d/TJU2012-Team-Ni.png"><br />
<div class="teamimgtext"><b>Name: </b>Lingli NI<br><br><b>Major:</b> Chemical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Third Year Student<br><br><b>Home:</b> Fuzhou, Fujian</div><br />
</div><br />
<div id="tab13" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/9/93/TJU2012-Team-Ren.png"><br />
<div class="teamimgtext"><b>Name: </b>Hengqian REN<br><br><b>Major:</b> Chemical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Fourth Year Student<br><br><b>Home:</b> Tianjin</div><br />
</div><br />
<div id="tab14" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/b/b0/TJU2012-Team-Song.png"><br />
<div class="teamimgtext"><b>Name: </b>Linlin SONG<br><br><b>Major:</b> Pharmaceutical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Third Year Student<br><br><b>Home:</b> Handan, Hebei</div><br />
</div><br />
<div id="tab15" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/4/48/TJU2012-Team-Li.png"><br />
<div class="teamimgtext"><b>Name: </b>Yang LI<br><br><b>Major:</b> Pharmaceutical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Third Year Student<br><br><b>Home:</b> Jinzhou, Liaoning</div><br />
</div><br />
<br />
</div><br />
</div><br />
</body><br />
</html><br />
{{:Team:Tianjin/nowrapfooter}}</div>Helengoodhttp://2012.igem.org/Team:Tianjin/TeamTeam:Tianjin/Team2013-05-09T05:12:57Z<p>Helengood: </p>
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</head><br />
<body><br />
<div class="container"><br />
<ul class="tabs"><br />
<li class="active"><a href="#tab1">The Whole Team</a></li><br />
<li><a href="#tab16">Advisor</a></li><br />
<li><a href="#tab2" id="">Bin Jia</a></li><br />
<li><a href="#tab3">Qinfeng Wu </a></li><br />
<li><a href="#tab17"> Jiaquan Liu </a></li><br />
<li><a href="#tab4">Shu Gong</a></li><br />
<li><a href="#tab5">Dongchang Qin</a></li><br />
<li><a href="#tab6">Jinlai Zhang</a></li><br />
<li><a href="#tab7">Xiaonan Cheng</a></li><br />
<li><a href="#tab8">Andi Wangzhou</a></li><br />
<li><a href="#tab9">Yapeng Su</a></li><br />
<li><a href="#tab10">Yufei Wei</a></li><br />
<li><a href="#tab11">Yifeng Shao</a></li><br />
<li><a href="#tab12">Lingli Ni</a></li><br />
<li><a href="#tab13">Hengqian Ren</a></li><br />
<li><a href="#tab14">Linlin Song</a></li><br />
<li><a href="#tab15">Yang Li</a></li><br />
<br />
</ul><br />
<div class="tab_container"><br />
<div id="tab1" class="tab_content" style="display: block;"><br />
<img src="https://static.igem.org/mediawiki/2012/1/17/TJU2012-GROUP_DSC0499.JPG"><br />
<b>Proudly present: Tianjin 2012 iGEM Team!</b><br><br>From left to right:<br> Back Row: Yang LI, Shu GONG, Linlin SONG, Lingli NI, Andi WANGZHOU, Bingzhi LI, Bin JIA, Qinfeng WU<br><br />
Front Row: Yufei WEI, Jinlai ZHANG, Hengqian REN, Yingjin YUAN, Dongchang QIN, Yapeng SU, Yifeng SHAO, Xiaonan CHENG<br />
</div><br />
<div id="tab16" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/4/45/TJU2012-Team-Yuan.png"><br />
<b>Prof. Yingjin YUAN</b><br><br><br />
Professor Yingjin Yuan is the founder of iGEM Asia platform. He and MIT worked together, and successfully promoted the iGEM in Asia. He is also one of fist introducers of synthetic biology to China. He has been enthusiastically supporting since iGEM in Tianjin University since year one. <br />
</div><br />
<div id="tab2" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/7/7a/TJU2012-Team-Jia.png"><br />
<div class="teamimgtext"><b>Name: </b>Bin JIA<br><br><b>Major:</b> Bioengineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Graduate Student<br><br><b>Home:</b> Qinshui, Shanxi</div><br />
</div><br />
<div id="tab3" class="tab_content" style="display: none;"><img src="https://static.igem.org/mediawiki/2012/b/b4/TJU2012-Team-LW.png" style="width:600px;"><br />
<div class="teamimgtext"><b>Name:</b> Qinfeng WU;<br><br> <b>Major:</b> Chemical Engineering;<br><br> <b>School:</b> Chemical Engineering;<br><br> <b>Year:</b> Fourth Year Student;<br><br> <b>Home:</b> Chongqing.</div><br />
</div><br />
<div id="tab17" class="tab_content" style="display: none;"><img src="https://static.igem.org/mediawiki/2012/b/b4/TJU2012-Team-LW.png" style="width:600px;"><br />
<div style="teamimgtext"><b>Name:</b> Jiaquan LIU;<br><br> <b>Major:</b> Applied Chemistry;<br><br> <b>School:</b> Chemical Engineering;<br><br> <b>Year:</b> Third Year Student;<br><br> <b>Home:</b> Shenyang, Liaoning.<br><br></div><br />
</div><br />
<br />
<br />
<br />
<div id="tab4" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/8/85/TJU2012-Team-Gong.png"><br />
<div class="teamimgtext"><b>Name: </b>Shu GONG<br><br><b>Major:</b> Pharmaceutical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Third Year Student<br><br><b>Home:</b> Deyang, Sichuan</div><br />
</div><br />
<div id="tab5" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/2/2e/TJU2012-Team-Qin.png"><br />
<div class="teamimgtext"><b>Name: </b>Dongchang QIN<br><br><b>Major:</b> Bioengineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Fourth Year Student<br><br><b>Home:</b> Xinxiang, Henan</div><br />
</div><br />
<div id="tab6" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/6/6b/TJU2012-Team-Zhang.png"><br />
<div class="teamimgtext"><b>Name: </b>Jinlai ZHANG<br><br><b>Major:</b> Bioengineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Fourth Year Student<br><br><b>Home:</b> Tianjin</div><br />
</div><br />
<div id="tab7" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/0/02/TJU2012-Team-Cheng.png"><br />
<div class="teamimgtext"><b>Name: </b>Xiaonan CHENG<br><br><b>Major:</b> Chemical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Fourth Year Student<br><br><b>Home:</b> Yantai, Shandong</div><br />
</div><br />
<div id="tab8" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/2/2a/TJU2012-Team-WZ.png"><br />
<div class="teamimgtext"><b>Name: </b>Andi WANGZHOU<br><br><b>Major:</b> Bioengineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Fourth Year Student<br><br><b>Home:</b> Beijing</div><br />
</div><br />
<div id="tab9" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/9/9d/TJU2012-Team-Su.png"><br />
<div class="teamimgtext"><b>Name: </b>Yapeng SU<br><br><b>Major:</b> Chemical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Fourth Year Student<br><br><b>Home:</b> Xingtai, Hebei</div><br />
</div><br />
<div id="tab10" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/3/3a/TJU2012-Team-Wei.png"><br />
<div class="teamimgtext"><b>Name: </b>Yufei WEI<br><br><b>Major:</b> Chemical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Third Year Student<br><br><b>Home:</b> Handan, Hebei</div><br />
</div><br />
<div id="tab11" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/a/aa/TJU2012-Team-Shao.png"><br />
<div class="teamimgtext"><b>Name: </b>Yifeng SHAO<br><br><b>Major:</b> Chemical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Third Year Student<br><br><b>Home:</b> Lanzhou, Gansu</div><br />
</div><br />
<div id="tab12" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/7/7d/TJU2012-Team-Ni.png"><br />
<div class="teamimgtext"><b>Name: </b>Lingli NI<br><br><b>Major:</b> Chemical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Third Year Student<br><br><b>Home:</b> Fuzhou, Fujian</div><br />
</div><br />
<div id="tab13" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/9/93/TJU2012-Team-Ren.png"><br />
<div class="teamimgtext"><b>Name: </b>Hengqian REN<br><br><b>Major:</b> Chemical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Fourth Year Student<br><br><b>Home:</b> Tianjin</div><br />
</div><br />
<div id="tab14" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/b/b0/TJU2012-Team-Song.png"><br />
<div class="teamimgtext"><b>Name: </b>Linlin SONG<br><br><b>Major:</b> Pharmaceutical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Third Year Student<br><br><b>Home:</b> Handan, Hebei</div><br />
</div><br />
<div id="tab15" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/4/48/TJU2012-Team-Li.png"><br />
<div class="teamimgtext"><b>Name: </b>Yang LI<br><br><b>Major:</b> Pharmaceutical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Third Year Student<br><br><b>Home:</b> Jinzhou, Liaoning</div><br />
</div><br />
<br />
</div><br />
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</body><br />
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{{:Team:Tianjin/nowrapfooter}}</div>Helengoodhttp://2012.igem.org/Team:Tianjin/TeamTeam:Tianjin/Team2013-05-09T05:11:48Z<p>Helengood: </p>
<hr />
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<li class="active"><a href="#tab1">The Whole Team</a></li><br />
<li><a href="#tab16">Advisor</a></li><br />
<li><a href="#tab2" id="">Bin Jia</a></li><br />
<li><a href="#tab3">Qinfeng Wu </a></li><br />
<li><a href="#tab17"> Jiaquan Liu </a></li><br />
<li><a href="#tab4">Shu Gong</a></li><br />
<li><a href="#tab5">Dongchang Qin</a></li><br />
<li><a href="#tab6">Jinlai Zhang</a></li><br />
<li><a href="#tab7">Xiaonan Cheng</a></li><br />
<li><a href="#tab8">Andi Wangzhou</a></li><br />
<li><a href="#tab9">Yapeng Su</a></li><br />
<li><a href="#tab10">Yufei Wei</a></li><br />
<li><a href="#tab11">Yifeng Shao</a></li><br />
<li><a href="#tab12">Lingli Ni</a></li><br />
<li><a href="#tab13">Hengqian Ren</a></li><br />
<li><a href="#tab14">Linlin Song</a></li><br />
<li><a href="#tab15">Yang Li</a></li><br />
<br />
</ul><br />
<div class="tab_container"><br />
<div id="tab1" class="tab_content" style="display: block;"><br />
<img src="https://static.igem.org/mediawiki/2012/1/17/TJU2012-GROUP_DSC0499.JPG"><br />
<b>Proudly present: Tianjin 2012 iGEM Team!</b><br><br>From left to right:<br> Back Row: Yang LI, Shu GONG, Linlin SONG, Lingli NI, Andi WANGZHOU, Bingzhi LI, Bin JIA, Qinfeng WU<br><br />
Front Row: Yufei WEI, Jinlai ZHANG, Hengqian REN, Yingjin YUAN, Dongchang QIN, Yapeng SU, Yifeng SHAO, Xiaonan CHENG<br />
</div><br />
<div id="tab16" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/4/45/TJU2012-Team-Yuan.png"><br />
<b>Prof. Yingjin YUAN</b><br><br><br />
Professor Yingjin Yuan is the founder of iGEM Asia platform. He and MIT worked together, and successfully promoted the iGEM in Asia. He is also one of fist introducers of synthetic biology to China. He has been enthusiastically supporting since iGEM in Tianjin University since year one. <br />
</div><br />
<div id="tab2" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/7/7a/TJU2012-Team-Jia.png"><br />
<div class="teamimgtext"><b>Name: </b>Bin JIA<br><br><b>Major:</b> Bioengineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Graduate Student<br><br><b>Home:</b> Qinshui, Shanxi</div><br />
</div><br />
<div id="tab3" class="tab_content" style="display: none;"><img src="https://static.igem.org/mediawiki/2012/b/b4/TJU2012-Team-LW.png" style="width:600px;"><br />
<div class="teamimgtext"><b>Name:</b> Qinfeng WU;<br><br> <b>Major:</b> Chemical Engineering;<br><br> <b>School:</b> Chemical Engineering;<br><br> <b>Year:</b> Fourth Year Student;<br><br> <b>Home:</b> Chongqing.</div><br />
</div><br />
<div id="tab17" class="tab_content" style="display: none;"><img src="https://static.igem.org/mediawiki/2012/b/b4/TJU2012-Team-LW.png" style="width:600px;"><br />
<div style="float:left;margin-left:20px;"><b>Name:</b> Qinfeng WU;<br><br> <b>Major:</b> Chemical Engineering;<br><br> <b>School:</b> Chemical Engineering;<br><br> <b>Year:</b> Fourth Year Student;<br><br> <b>Home:</b> Chongqing.</div><br />
<div style="float:right;margin-right:20px;"><b>Name:</b> Jiaquan LIU;<br><br> <b>Major:</b> Applied Chemistry;<br><br> <b>School:</b> Chemical Engineering;<br><br> <b>Year:</b> Third Year Student;<br><br> <b>Home:</b> Shenyang, Liaoning.<br><br></div><br />
</div><br />
<br />
<br />
<br />
<div id="tab4" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/8/85/TJU2012-Team-Gong.png"><br />
<div class="teamimgtext"><b>Name: </b>Shu GONG<br><br><b>Major:</b> Pharmaceutical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Third Year Student<br><br><b>Home:</b> Deyang, Sichuan</div><br />
</div><br />
<div id="tab5" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/2/2e/TJU2012-Team-Qin.png"><br />
<div class="teamimgtext"><b>Name: </b>Dongchang QIN<br><br><b>Major:</b> Bioengineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Fourth Year Student<br><br><b>Home:</b> Xinxiang, Henan</div><br />
</div><br />
<div id="tab6" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/6/6b/TJU2012-Team-Zhang.png"><br />
<div class="teamimgtext"><b>Name: </b>Jinlai ZHANG<br><br><b>Major:</b> Bioengineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Fourth Year Student<br><br><b>Home:</b> Tianjin</div><br />
</div><br />
<div id="tab7" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/0/02/TJU2012-Team-Cheng.png"><br />
<div class="teamimgtext"><b>Name: </b>Xiaonan CHENG<br><br><b>Major:</b> Chemical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Fourth Year Student<br><br><b>Home:</b> Yantai, Shandong</div><br />
</div><br />
<div id="tab8" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/2/2a/TJU2012-Team-WZ.png"><br />
<div class="teamimgtext"><b>Name: </b>Andi WANGZHOU<br><br><b>Major:</b> Bioengineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Fourth Year Student<br><br><b>Home:</b> Beijing</div><br />
</div><br />
<div id="tab9" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/9/9d/TJU2012-Team-Su.png"><br />
<div class="teamimgtext"><b>Name: </b>Yapeng SU<br><br><b>Major:</b> Chemical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Fourth Year Student<br><br><b>Home:</b> Xingtai, Hebei</div><br />
</div><br />
<div id="tab10" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/3/3a/TJU2012-Team-Wei.png"><br />
<div class="teamimgtext"><b>Name: </b>Yufei WEI<br><br><b>Major:</b> Chemical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Third Year Student<br><br><b>Home:</b> Handan, Hebei</div><br />
</div><br />
<div id="tab11" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/a/aa/TJU2012-Team-Shao.png"><br />
<div class="teamimgtext"><b>Name: </b>Yifeng SHAO<br><br><b>Major:</b> Chemical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Third Year Student<br><br><b>Home:</b> Lanzhou, Gansu</div><br />
</div><br />
<div id="tab12" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/7/7d/TJU2012-Team-Ni.png"><br />
<div class="teamimgtext"><b>Name: </b>Lingli NI<br><br><b>Major:</b> Chemical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Third Year Student<br><br><b>Home:</b> Fuzhou, Fujian</div><br />
</div><br />
<div id="tab13" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/9/93/TJU2012-Team-Ren.png"><br />
<div class="teamimgtext"><b>Name: </b>Hengqian REN<br><br><b>Major:</b> Chemical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Fourth Year Student<br><br><b>Home:</b> Tianjin</div><br />
</div><br />
<div id="tab14" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/b/b0/TJU2012-Team-Song.png"><br />
<div class="teamimgtext"><b>Name: </b>Linlin SONG<br><br><b>Major:</b> Pharmaceutical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Third Year Student<br><br><b>Home:</b> Handan, Hebei</div><br />
</div><br />
<div id="tab15" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/4/48/TJU2012-Team-Li.png"><br />
<div class="teamimgtext"><b>Name: </b>Yang LI<br><br><b>Major:</b> Pharmaceutical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Third Year Student<br><br><b>Home:</b> Jinzhou, Liaoning</div><br />
</div><br />
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{{:Team:Tianjin/nowrapfooter}}</div>Helengoodhttp://2012.igem.org/Team:Tianjin/TeamTeam:Tianjin/Team2013-05-09T05:10:24Z<p>Helengood: </p>
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<body><br />
<div class="container"><br />
<ul class="tabs"><br />
<li class="active"><a href="#tab1">The Whole Team</a></li><br />
<li><a href="#tab16">Advisor</a></li><br />
<li><a href="#tab2" id="">Bin Jia</a></li><br />
<li><a href="#tab3">Qinfeng Wu </a></li><br />
<li><a href="#tab17"> Jiaquan Liu </a></li><br />
<li><a href="#tab4">Shu Gong</a></li><br />
<li><a href="#tab5">Dongchang Qin</a></li><br />
<li><a href="#tab6">Jinlai Zhang</a></li><br />
<li><a href="#tab7">Xiaonan Cheng</a></li><br />
<li><a href="#tab8">Andi Wangzhou</a></li><br />
<li><a href="#tab9">Yapeng Su</a></li><br />
<li><a href="#tab10">Yufei Wei</a></li><br />
<li><a href="#tab11">Yifeng Shao</a></li><br />
<li><a href="#tab12">Lingli Ni</a></li><br />
<li><a href="#tab13">Hengqian Ren</a></li><br />
<li><a href="#tab14">Linlin Song</a></li><br />
<li><a href="#tab15">Yang Li</a></li><br />
<br />
</ul><br />
<div class="tab_container"><br />
<div id="tab1" class="tab_content" style="display: block;"><br />
<img src="https://static.igem.org/mediawiki/2012/1/17/TJU2012-GROUP_DSC0499.JPG"><br />
<b>Proudly present: Tianjin 2012 iGEM Team!</b><br><br>From left to right:<br> Back Row: Yang LI, Shu GONG, Linlin SONG, Lingli NI, Andi WANGZHOU, Bingzhi LI, Bin JIA, Qinfeng WU<br><br />
Front Row: Yufei WEI, Jinlai ZHANG, Hengqian REN, Yingjin YUAN, Dongchang QIN, Yapeng SU, Yifeng SHAO, Xiaonan CHENG<br />
</div><br />
<div id="tab16" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/4/45/TJU2012-Team-Yuan.png"><br />
<b>Prof. Yingjin YUAN</b><br><br><br />
Professor Yingjin Yuan is the founder of iGEM Asia platform. He and MIT worked together, and successfully promoted the iGEM in Asia. He is also one of fist introducers of synthetic biology to China. He has been enthusiastically supporting since iGEM in Tianjin University since year one. <br />
</div><br />
<div id="tab2" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/7/7a/TJU2012-Team-Jia.png"><br />
<div class="teamimgtext"><b>Name: </b>Bin JIA<br><br><b>Major:</b> Bioengineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Graduate Student<br><br><b>Home:</b> Qinshui, Shanxi</div><br />
</div><br />
<div id="tab3" class="tab_content" style="display: none;"><img src="https://static.igem.org/mediawiki/2012/b/b4/TJU2012-Team-LW.png" style="width:600px;"><br />
<div style="float:left;margin-left:20px;"><b>Name:</b> Qinfeng WU;<br><br> <b>Major:</b> Chemical Engineering;<br><br> <b>School:</b> Chemical Engineering;<br><br> <b>Year:</b> Fourth Year Student;<br><br> <b>Home:</b> Chongqing.</div><br />
</div><br />
<div id="tab17" class="tab_content" style="display: none;"><img src="https://static.igem.org/mediawiki/2012/b/b4/TJU2012-Team-LW.png" style="width:600px;"><br />
<div style="float:left;margin-left:20px;"><b>Name:</b> Qinfeng WU;<br><br> <b>Major:</b> Chemical Engineering;<br><br> <b>School:</b> Chemical Engineering;<br><br> <b>Year:</b> Fourth Year Student;<br><br> <b>Home:</b> Chongqing.</div><br />
<div style="float:right;margin-right:20px;"><b>Name:</b> Jiaquan LIU;<br><br> <b>Major:</b> Applied Chemistry;<br><br> <b>School:</b> Chemical Engineering;<br><br> <b>Year:</b> Third Year Student;<br><br> <b>Home:</b> Shenyang, Liaoning.<br><br></div><br />
</div><br />
<br />
<br />
<br />
<div id="tab4" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/8/85/TJU2012-Team-Gong.png"><br />
<div class="teamimgtext"><b>Name: </b>Shu GONG<br><br><b>Major:</b> Pharmaceutical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Third Year Student<br><br><b>Home:</b> Deyang, Sichuan</div><br />
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<div id="tab5" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/2/2e/TJU2012-Team-Qin.png"><br />
<div class="teamimgtext"><b>Name: </b>Dongchang QIN<br><br><b>Major:</b> Bioengineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Fourth Year Student<br><br><b>Home:</b> Xinxiang, Henan</div><br />
</div><br />
<div id="tab6" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/6/6b/TJU2012-Team-Zhang.png"><br />
<div class="teamimgtext"><b>Name: </b>Jinlai ZHANG<br><br><b>Major:</b> Bioengineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Fourth Year Student<br><br><b>Home:</b> Tianjin</div><br />
</div><br />
<div id="tab7" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/0/02/TJU2012-Team-Cheng.png"><br />
<div class="teamimgtext"><b>Name: </b>Xiaonan CHENG<br><br><b>Major:</b> Chemical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Fourth Year Student<br><br><b>Home:</b> Yantai, Shandong</div><br />
</div><br />
<div id="tab8" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/2/2a/TJU2012-Team-WZ.png"><br />
<div class="teamimgtext"><b>Name: </b>Andi WANGZHOU<br><br><b>Major:</b> Bioengineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Fourth Year Student<br><br><b>Home:</b> Beijing</div><br />
</div><br />
<div id="tab9" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/9/9d/TJU2012-Team-Su.png"><br />
<div class="teamimgtext"><b>Name: </b>Yapeng SU<br><br><b>Major:</b> Chemical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Fourth Year Student<br><br><b>Home:</b> Xingtai, Hebei</div><br />
</div><br />
<div id="tab10" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/3/3a/TJU2012-Team-Wei.png"><br />
<div class="teamimgtext"><b>Name: </b>Yufei WEI<br><br><b>Major:</b> Chemical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Third Year Student<br><br><b>Home:</b> Handan, Hebei</div><br />
</div><br />
<div id="tab11" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/a/aa/TJU2012-Team-Shao.png"><br />
<div class="teamimgtext"><b>Name: </b>Yifeng SHAO<br><br><b>Major:</b> Chemical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Third Year Student<br><br><b>Home:</b> Lanzhou, Gansu</div><br />
</div><br />
<div id="tab12" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/7/7d/TJU2012-Team-Ni.png"><br />
<div class="teamimgtext"><b>Name: </b>Lingli NI<br><br><b>Major:</b> Chemical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Third Year Student<br><br><b>Home:</b> Fuzhou, Fujian</div><br />
</div><br />
<div id="tab13" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/9/93/TJU2012-Team-Ren.png"><br />
<div class="teamimgtext"><b>Name: </b>Hengqian REN<br><br><b>Major:</b> Chemical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Fourth Year Student<br><br><b>Home:</b> Tianjin</div><br />
</div><br />
<div id="tab14" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/b/b0/TJU2012-Team-Song.png"><br />
<div class="teamimgtext"><b>Name: </b>Linlin SONG<br><br><b>Major:</b> Pharmaceutical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Third Year Student<br><br><b>Home:</b> Handan, Hebei</div><br />
</div><br />
<div id="tab15" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/4/48/TJU2012-Team-Li.png"><br />
<div class="teamimgtext"><b>Name: </b>Yang LI<br><br><b>Major:</b> Pharmaceutical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Third Year Student<br><br><b>Home:</b> Jinzhou, Liaoning</div><br />
</div><br />
<br />
</div><br />
</div><br />
</body><br />
</html><br />
{{:Team:Tianjin/nowrapfooter}}</div>Helengoodhttp://2012.igem.org/Team:Tianjin/TeamTeam:Tianjin/Team2013-05-09T05:06:43Z<p>Helengood: </p>
<hr />
<div>{{:Team:Tianjin/frame/team}}<br />
<html xmlns="http://www.w3.org/1999/xhtml"><br />
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<script type="text/javascript" src="http://www.xker.com/js/img/jquery1.3.2.js"></script><br />
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</head><br />
<body><br />
<div class="container"><br />
<ul class="tabs"><br />
<li class="active"><a href="#tab1">The Whole Team</a></li><br />
<li><a href="#tab16">Advisor</a></li><br />
<li><a href="#tab2" id="">Bin Jia</a></li><br />
<li><a href="#tab3">Qinfeng Wu </a></li><br />
<li><a href="#tab17"> Jiaquan Liu </a></li><br />
<li><a href="#tab4">Shu Gong</a></li><br />
<li><a href="#tab5">Dongchang Qin</a></li><br />
<li><a href="#tab6">Jinlai Zhang</a></li><br />
<li><a href="#tab7">Xiaonan Cheng</a></li><br />
<li><a href="#tab8">Andi Wangzhou</a></li><br />
<li><a href="#tab9">Yapeng Su</a></li><br />
<li><a href="#tab10">Yufei Wei</a></li><br />
<li><a href="#tab11">Yifeng Shao</a></li><br />
<li><a href="#tab12">Lingli Ni</a></li><br />
<li><a href="#tab13">Hengqian Ren</a></li><br />
<li><a href="#tab14">Linlin Song</a></li><br />
<li><a href="#tab15">Yang Li</a></li><br />
<br />
</ul><br />
<div class="tab_container"><br />
<div id="tab1" class="tab_content" style="display: block;"><br />
<img src="https://static.igem.org/mediawiki/2012/1/17/TJU2012-GROUP_DSC0499.JPG"><br />
<b>Proudly present: Tianjin 2012 iGEM Team!</b><br><br>From left to right:<br> Back Row: Yang LI, Shu GONG, Linlin SONG, Lingli NI, Andi WANGZHOU, Bingzhi LI, Bin JIA, Qinfeng WU<br><br />
Front Row: Yufei WEI, Jinlai ZHANG, Hengqian REN, Yingjin YUAN, Dongchang QIN, Yapeng SU, Yifeng SHAO, Xiaonan CHENG<br />
</div><br />
<div id="tab16" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/4/45/TJU2012-Team-Yuan.png"><br />
<b>Prof. Yingjin YUAN</b><br><br><br />
Professor Yingjin Yuan is the founder of iGEM Asia platform. He and MIT worked together, and successfully promoted the iGEM in Asia. He is also one of fist introducers of synthetic biology to China. He has been enthusiastically supporting since iGEM in Tianjin University since year one. <br />
</div><br />
<div id="tab2" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/7/7a/TJU2012-Team-Jia.png"><br />
<div class="teamimgtext"><b>Name: </b>Bin JIA<br><br><b>Major:</b> Bioengineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Graduate Student<br><br><b>Home:</b> Qinshui, Shanxi</div><br />
</div><br />
<div id="tab3" class="tab_content" style="display: none;"><img src="https://static.igem.org/mediawiki/2012/b/b4/TJU2012-Team-LW.png" style="width:600px;"><br />
<div style="float:left;margin-left:20px;"><b>Name:</b> Qinfeng WU;<br><br> <b>Major:</b> Chemical Engineering;<br><br> <b>School:</b> Chemical Engineering;<br><br> <b>Year:</b> Fourth Year Student;<br><br> <b>Home:</b> Chongqing.</div><br />
<div style="float:right;margin-right:20px;"><b>Name:</b> Jiaquan LIU;<br><br> <b>Major:</b> Applied Chemistry;<br><br> <b>School:</b> Chemical Engineering;<br><br> <b>Year:</b> Third Year Student;<br><br> <b>Home:</b> Shenyang, Liaoning.<br><br></div><br />
</div><br />
<div id="tab4" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/8/85/TJU2012-Team-Gong.png"><br />
<div class="teamimgtext"><b>Name: </b>Shu GONG<br><br><b>Major:</b> Pharmaceutical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Third Year Student<br><br><b>Home:</b> Deyang, Sichuan</div><br />
</div><br />
<div id="tab5" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/2/2e/TJU2012-Team-Qin.png"><br />
<div class="teamimgtext"><b>Name: </b>Dongchang QIN<br><br><b>Major:</b> Bioengineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Fourth Year Student<br><br><b>Home:</b> Xinxiang, Henan</div><br />
</div><br />
<div id="tab6" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/6/6b/TJU2012-Team-Zhang.png"><br />
<div class="teamimgtext"><b>Name: </b>Jinlai ZHANG<br><br><b>Major:</b> Bioengineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Fourth Year Student<br><br><b>Home:</b> Tianjin</div><br />
</div><br />
<div id="tab7" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/0/02/TJU2012-Team-Cheng.png"><br />
<div class="teamimgtext"><b>Name: </b>Xiaonan CHENG<br><br><b>Major:</b> Chemical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Fourth Year Student<br><br><b>Home:</b> Yantai, Shandong</div><br />
</div><br />
<div id="tab8" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/2/2a/TJU2012-Team-WZ.png"><br />
<div class="teamimgtext"><b>Name: </b>Andi WANGZHOU<br><br><b>Major:</b> Bioengineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Fourth Year Student<br><br><b>Home:</b> Beijing</div><br />
</div><br />
<div id="tab9" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/9/9d/TJU2012-Team-Su.png"><br />
<div class="teamimgtext"><b>Name: </b>Yapeng SU<br><br><b>Major:</b> Chemical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Fourth Year Student<br><br><b>Home:</b> Xingtai, Hebei</div><br />
</div><br />
<div id="tab10" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/3/3a/TJU2012-Team-Wei.png"><br />
<div class="teamimgtext"><b>Name: </b>Yufei WEI<br><br><b>Major:</b> Chemical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Third Year Student<br><br><b>Home:</b> Handan, Hebei</div><br />
</div><br />
<div id="tab11" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/a/aa/TJU2012-Team-Shao.png"><br />
<div class="teamimgtext"><b>Name: </b>Yifeng SHAO<br><br><b>Major:</b> Chemical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Third Year Student<br><br><b>Home:</b> Lanzhou, Gansu</div><br />
</div><br />
<div id="tab12" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/7/7d/TJU2012-Team-Ni.png"><br />
<div class="teamimgtext"><b>Name: </b>Lingli NI<br><br><b>Major:</b> Chemical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Third Year Student<br><br><b>Home:</b> Fuzhou, Fujian</div><br />
</div><br />
<div id="tab13" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/9/93/TJU2012-Team-Ren.png"><br />
<div class="teamimgtext"><b>Name: </b>Hengqian REN<br><br><b>Major:</b> Chemical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Fourth Year Student<br><br><b>Home:</b> Tianjin</div><br />
</div><br />
<div id="tab14" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/b/b0/TJU2012-Team-Song.png"><br />
<div class="teamimgtext"><b>Name: </b>Linlin SONG<br><br><b>Major:</b> Pharmaceutical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Third Year Student<br><br><b>Home:</b> Handan, Hebei</div><br />
</div><br />
<div id="tab15" class="tab_content" style="display: none;"><br />
<img src="https://static.igem.org/mediawiki/2012/4/48/TJU2012-Team-Li.png"><br />
<div class="teamimgtext"><b>Name: </b>Yang LI<br><br><b>Major:</b> Pharmaceutical Engineering<br><br><b>School:</b> Chemical Engineering<br><br><b>Year:</b> Third Year Student<br><br><b>Home:</b> Jinzhou, Liaoning</div><br />
</div><br />
<br />
</div><br />
</div><br />
</body><br />
</html><br />
{{:Team:Tianjin/nowrapfooter}}</div>Helengoodhttp://2012.igem.org/File:Jjb.jpgFile:Jjb.jpg2013-05-09T05:01:20Z<p>Helengood: </p>
<hr />
<div></div>Helengoodhttp://2012.igem.org/File:Jja.pngFile:Jja.png2013-05-09T04:58:23Z<p>Helengood: </p>
<hr />
<div></div>Helengoodhttp://2012.igem.org/Team:Tianjin/NotebookTeam:Tianjin/Notebook2013-05-09T04:57:27Z<p>Helengood: /* Sept. 18th, 2012 */</p>
<hr />
<div>{{:Team:Tianjin/frame/notebook}}<br />
__NOTOC__<br />
<html><br />
<style type="text/css"><br />
#secondpane {color:#fff;<br />
width: 190px;<br />
margin-left:5px;<br />
}<br />
.menu_list {<br />
position:fixed;top:20px;}<br />
.menu_head {<br />
padding: 5px 10px;<br />
cursor: pointer;<br />
position: relative;<br />
border:1px solid #fff;<br />
margin:1px;<br />
font-weight:bold;<br />
background: #0096db;<br />
color:#fff<br />
}<br />
.menu_head:hover <br />
{ <br />
cursor: pointer;<br />
color: #fff; <br />
background: #003764; <br />
text-decoration: none; <br />
background-position: 0 0; <br />
} <br />
.menu_body {<br />
display:none;<br />
}<br />
.menu_children {<br />
background: #aaa;<br />
cursor: pointer;<br />
padding: 5px 10px;<br />
font-size:12px;<br />
border-top: 1px solid #fff; <br />
border-bottom: 1px solid #fff; <br />
border-left: 1px solid #fff; <br />
border-right: 1px solid #fff; <br />
}<br />
.menu_body a{<br />
display:block;<br />
color:#fff;<br />
padding-left:10px;<br />
font-weight:bold;<br />
text-decoration:none;<br />
}<br />
.menu_children:hover{<br />
cursor: pointer;<br />
color: #fff;<br />
text-decoration:none;<br />
background:#777777;<br />
}<br />
.Calender {<br />
width:190px;<br />
height:161px;<br />
}<br />
.Calender a{<br />
text-align:center;<br />
padding-left:0;}<br />
.Calender-non {<br />
height:23px;<br />
width:23px;<br />
background:#aaa;<br />
float:left;<br />
margin:2px;<br />
text-align:center;<br />
}<br />
.Calender-com {<br />
height:23px;<br />
width:23px;<br />
background:#8dc7e9;<br />
float:left;<br />
margin:2px;<br />
text-align:center;<br />
}<br />
.Calender-click {<br />
height:23px;<br />
width:23px;<br />
background:#0096db;<br />
float:left;<br />
margin:2px;<br />
text-align:center;<br />
}<br />
.Calender-click:hover {<br />
background:#777777;<br />
<br />
</style><br />
<div style="float:left;"><br />
<div id="secondpane"> <!--Code for menu starts here--><br />
<p class="menu_head">Notebook Contents</p><br />
<div class="menu_body"><br />
<div class="menu_children"><br />
<a href="https://2012.igem.org/Team:Tianjin/Notebook/Modeling">Modeling Notebook</a><br />
</div><br />
<div class="menu_children"><br />
<a href="https://2012.igem.org/Team:Tianjin/Notebook/HumanPractice">Human Practice Notebook</a><br />
</div><br />
</div><br />
<p class="menu_head">July, 2012</p><br />
<div class="menu_body"><br />
<div class="Calender"><br />
<div class="Calender-non">Sun<br />
</div> <br />
<div class="Calender-non">Mon<br />
</div> <br />
<div class="Calender-non">Tue<br />
</div> <br />
<div class="Calender-non">Wed<br />
</div><br />
<div class="Calender-non">Thu<br />
</div> <br />
<div class="Calender-non">Fri<br />
</div> <br />
<div class="Calender-non">Sat<br />
</div> <br />
<div class="Calender-com">1<br />
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</div><br />
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</div><br />
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</div><br />
<div class="Calender-click"><a href="#July_6th.2C_2012">6</a><br />
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</div><br />
<div class="Calender-click"><a href="#July_8th.2C_2012">8</a><br />
</div><br />
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</div><br />
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</div><br />
<div class="Calender-click"><a href="#July_11th.2C_2012">11</a><br />
</div><br />
<div class="Calender-com">12<br />
</div><br />
<div class="Calender-click"><a href="#July_13th.2C_2012">13</a><br />
</div><br />
<div class="Calender-click"><a href="#July_14th.2C_2012">14</a><br />
</div><br />
<div class="Calender-click"><a href="#July_15th.2C_2012">15</a><br />
</div><br />
<div class="Calender-com">16<br />
</div><br />
<div class="Calender-com">17<br />
</div><br />
<div class="Calender-com">18<br />
</div><br />
<div class="Calender-com">19<br />
</div><br />
<div class="Calender-click"><a href="#July_20th.2C_2012">20</a><br />
</div><br />
<div class="Calender-com">21<br />
</div><br />
<div class="Calender-com">22<br />
</div><br />
<div class="Calender-com">23<br />
</div><br />
<div class="Calender-click"><a href="#July_24th.2C_2012">24</a><br />
</div><br />
<div class="Calender-com">25<br />
</div><br />
<div class="Calender-com">26<br />
</div><br />
<div class="Calender-com">27<br />
</div><br />
<div class="Calender-com">28<br />
</div><br />
<div class="Calender-com">29<br />
</div><br />
<div class="Calender-click"><a href="#July_30th.2C_2012">30</a><br />
</div><br />
<div class="Calender-com">31<br />
</div><br />
<div class="Calender-com"><br />
</div><br />
<div class="Calender-com"><br />
</div><br />
<div class="Calender-com"><br />
</div><br />
<div class="Calender-com"><br />
</div> <br />
</div><br />
</div><br />
<p class="menu_head">August, 2012</p><br />
<div class="menu_body"><br />
<div class="Calender"><br />
<div class="Calender-non">Sun<br />
</div> <br />
<div class="Calender-non">Mon<br />
</div> <br />
<div class="Calender-non">Tue<br />
</div> <br />
<div class="Calender-non">Wed<br />
</div><br />
<div class="Calender-non">Thu<br />
</div> <br />
<div class="Calender-non">Fri<br />
</div> <br />
<div class="Calender-non">Sat<br />
</div> <br />
<div class="Calender-com"><br />
</div><br />
<div class="Calender-com"><br />
</div><br />
<div class="Calender-com"><br />
</div><br />
<div class="Calender-com">1<br />
</div><br />
<div class="Calender-click"><a href="#Aug._2nd.2C_2012">2</a><br />
</div><br />
<div class="Calender-com">3<br />
</div><br />
<div class="Calender-click"><a href="#Aug._4th.2C_2012">4</a><br />
</div><br />
<div class="Calender-com">5<br />
</div><br />
<div class="Calender-com">6<br />
</div><br />
<div class="Calender-com">7<br />
</div><br />
<div class="Calender-click"><a href="#Aug._8th.2C_2012">8</a><br />
</div><br />
<div class="Calender-com">9<br />
</div><br />
<div class="Calender-com">10<br />
</div><br />
<div class="Calender-click"><a href="#Aug._11th.2C_2012">11</a><br />
</div><br />
<div class="Calender-click"><a href="#Aug._12th.2C_2012">12</a><br />
</div><br />
<div class="Calender-com">13<br />
</div><br />
<div class="Calender-click"><a href="#Aug._14th.2C_2012">14</a><br />
</div><br />
<div class="Calender-com">15<br />
</div><br />
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</div><br />
<div class="Calender-com">17<br />
</div><br />
<div class="Calender-click"><a href="#Aug._18th.2C_2012">18</a><br />
</div><br />
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</div><br />
<div class="Calender-click"><a href="#Aug._20th.2C_2012">20</a><br />
</div><br />
<div class="Calender-com">21<br />
</div><br />
<div class="Calender-click"><a href="#Aug._22nd.2C_2012">22</a><br />
</div><br />
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</div><br />
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</div><br />
<div class="Calender-click"><a href="#Aug._25th.2C_2012">25</a><br />
</div><br />
<div class="Calender-com">26<br />
</div><br />
<div class="Calender-com">27<br />
</div><br />
<div class="Calender-com">28<br />
</div><br />
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</div><br />
<div class="Calender-com">30<br />
</div><br />
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<center><span style="font-size:46px;font-family:Cambria;margin-top:10px;line-height:80%">Notes of Experiments</span></center><br />
==July 6th, 2012==<br />
#We discuss our all of the possible projects, and finally choose one. And then allocate works to specific member.<br />
#Do some pre-experiment and make some reagants.<br />
##Liquid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl <br />
##Solid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl<br />
###20g agar<br />
#Cleaned up the lab and laboratory instruments<br />
<br />
==July 8th, 2012==<br />
#Solutions for extracting plasmid.<br />
##50mM Glucose / 25mM Tris-Cl / 10mM EDTA,pH=8.0<br />
##0.2N NaOH / 1% SDS<br />
##3M KOAc / 2M HOAc<br />
#Experiment technologies training, such as making gel, gel electrophoresis.<br />
[[File:TJU2012-Note-gel-1.png|center|350px|gel 1]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-2.png|center|350px|gel 2]]<br />
<br />
==July 11th, 2012==<br />
#Designed primers and sent orders.<br />
#Optimized the project and allocated work.<br />
#Experiment technologies and knowledge training<br />
##PCR principle and operation<br />
##Gel Extraction<br />
[[File:TJU2012-Note-gel-3.png|center|350px|gel 3]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-4.png|center|350px|gel 4]]<br />
<br />
==July 13th, 2012==<br />
1. Received the oligo and began to mutate 16S rrnB operator.<br />
[[File:TJU2012-Note-gen-1.png|center|350px|Gene1]]<br />
2. Mutated RBS of RFP and checked through gel electrophoresis.<br />
[[File:TJU2012-Note-gen-2.png|center|250px|Gene2]]<br />
[[File:TJU2012-Note-gel-5.png|thumb|center|250px|~1800bp, constant with anticipation]]<br />
<br />
==July 14th, 2012==<br />
#Transform two plasmids of we got yestday together into E.coli.[[File:TJU2012-Note-gen-3.png|center|500px|Gene 3]]<br />
#PCR verification of colonies on the LB plates.<br />
#Inculcated the right colonies in Liquid LB.<br />
<br />
==July 15th, 2012==<br />
#Extract plasmid of cells inculcated after one day.<br />
#Enzyme test of the extracted plasmid.[[File:TJU2012-Note-gel-6.png|center|200px|Gel 6]]<br />
#Inclucated the right cells in Liquid LB and added Ala partly.<br />
<br />
==July 20th, 2012==<br />
Analyse the results.<br />
[[File:TJU2012-Note-form-1.png|center|500px|Form 1]]<br />
[[File:TJU2012-Note-fig-2.png|center|300px|Fig 2]]<br />
<br />
==July 24th, 2012==<br />
#Linked the GRP gene and O-RBS RFP gene. Gel extract the previous product again, and ligate using T4 with the following gradient.[[File:TJU2012-Note-form-2.png|center|500px|form 2]]<br />
#In the same method to construct three other systems.<br />
[[File:TJU2012-Mode-cal-fig-2.png|center|500px|fig 3]]<br />
[[File:TJU2012-Mode-cal-fig-3.png|center|500px|fig 4]]<br />
[[File:TJU2012-Mode-cal-fig-4.png|center|500px|fig 5]]<br />
<br />
==July 30th, 2012==<br />
#Learned Fluorescence spectrophotometer.<br />
#measure the strength of GFP and RFP.<br />
[[File:TJU2012-Note-form-3.png|center|500px|form 3]]<br />
<br />
==Aug. 2nd, 2012==<br />
#mutated the RBS of the Amp resistance gene.[[File:TJU2012-Note-gen-4.png|center|250px|Gene 4]]<br />
#linked genes and transformed them into E. coli.<br />
<br />
==Aug. 4th, 2012==<br />
Results of plates<br />
[[File:TJU2012-Note-fig-3.png|center|300px|fig 3]]<br />
[[File:TJU2012-Note-form-4.png|center|500px|form 4]]<br />
<br />
==Aug. 8th, 2012==<br />
Began to construct the five parts needed in Assembler in Yeast. Part 1 and part 2.<br />
<br />
==Aug. 11th, 2012==<br />
Verified part 1 and 2. Synthesized the two small parts and linked through overlap PCR. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-4.png|center|600px|fig 4]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-5.png|center|500px|fig 5]]<br />
<br />
==Aug. 12th, 2012==<br />
Began to build part 3, 4 and 5. Synthesized the two small parts and linked through overlap PCR.<br />
<br />
==Aug. 14th, 2012==<br />
Verify part 3, 4 and 5. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-6.png|center|500px|fig 6]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-7.png|center|500px|fig 7]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-8.png|center|500px|fig 8]]<br />
<br />
==Aug. 18th, 2012==<br />
Transformed all the five parts into Yeast for Assembler in Yeast.<br />
<br />
==Aug. 20th, 2012==<br />
#Results of the transformation.[[File:TJU2012-Note-fig-9.png|center|300px|fig 9]]<br />
#Extract plasmids from the Yeast.<br />
<br />
==Aug. 22nd, 2012==<br />
#Transformed the plasmid from the Yeast into cells.[[File:TJU2012-Note-fig-10.png|thumb|center|300px|There are purple spots on the plates]]<br />
#Extracted plasmid and checked through gel electrophoresis.[[File:TJU2012-Note-gel-7.png|center|300px|gel 7]]<br />
#Some other results of Assembler in Yeast.<br />
[[File:TJU2012-Note-fig-11.png|center|300px|fig 11]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-12.png|center|300px|fig 12]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-13.png|center|300px|fig 13]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-14.png|center|300px|fig 14]]<br />
<br />
==Aug. 25th, 2012==<br />
#Began to build biobricks.[[File:Tianjin_BB2.PNG|center|500px|BB 2]]<br />
#Began to search articles on phages.<br />
<br />
==Sept. 1st, 2012==<br />
Went to Peking University for exchanges.<br />
[[File:TJU2012-Note-fig-15.png|center|500px|fig 15]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-16.png|center|500px|fig 16]]<br />
<br />
==Sept. 2nd, 2012==<br />
#Found out phi X174 and firstly proposed our ideas.<br />
#The second sections of our biobricks.<br />
[[File:Tianjin_BB1.PNG|center|500px|BB 1]]<br />
<br />
==Sept. 5th, 2012==<br />
#Some experiments on phages.<br />
#Optimized our biobricks.<br />
#Designed primers needed for mutating Phi X174 and send orders.<br />
<br />
==Sept. 11th, 2012==<br />
#Began to mutate gene G and E.<br />
#Optimized our biobricks.<br />
<br />
==Sept. 18th, 2012==<br />
Began to sort out our materials for wiki and upload the website.<br />
[[File:new1.jpg|center|500px|fig 17]]<br />
our team in Hongkong <br />
<br />
<br />
[[File:new2.jpg|center|500px|fig 18]]<br />
our gold award<br />
<br />
<br />
[[File:new3.jpg|center|500px|fig 19]]<br />
presentation in MIT<br />
<br />
[[File:jja.png|center|500px|fig 20]]<br />
<br />
[[File:jjb.jpg|center|500px|fig 21]]<br />
<br />
{{:Team:Tianjin/footer}}</div>Helengoodhttp://2012.igem.org/Team:Tianjin/NotebookTeam:Tianjin/Notebook2013-05-08T07:36:33Z<p>Helengood: /* Sept. 18th, 2012 */</p>
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<p class="menu_head">Notebook Contents</p><br />
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<a href="https://2012.igem.org/Team:Tianjin/Notebook/Modeling">Modeling Notebook</a><br />
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<a href="https://2012.igem.org/Team:Tianjin/Notebook/HumanPractice">Human Practice Notebook</a><br />
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<p class="menu_head">July, 2012</p><br />
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<center><span style="font-size:46px;font-family:Cambria;margin-top:10px;line-height:80%">Notes of Experiments</span></center><br />
==July 6th, 2012==<br />
#We discuss our all of the possible projects, and finally choose one. And then allocate works to specific member.<br />
#Do some pre-experiment and make some reagants.<br />
##Liquid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl <br />
##Solid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl<br />
###20g agar<br />
#Cleaned up the lab and laboratory instruments<br />
<br />
==July 8th, 2012==<br />
#Solutions for extracting plasmid.<br />
##50mM Glucose / 25mM Tris-Cl / 10mM EDTA,pH=8.0<br />
##0.2N NaOH / 1% SDS<br />
##3M KOAc / 2M HOAc<br />
#Experiment technologies training, such as making gel, gel electrophoresis.<br />
[[File:TJU2012-Note-gel-1.png|center|350px|gel 1]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-2.png|center|350px|gel 2]]<br />
<br />
==July 11th, 2012==<br />
#Designed primers and sent orders.<br />
#Optimized the project and allocated work.<br />
#Experiment technologies and knowledge training<br />
##PCR principle and operation<br />
##Gel Extraction<br />
[[File:TJU2012-Note-gel-3.png|center|350px|gel 3]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-4.png|center|350px|gel 4]]<br />
<br />
==July 13th, 2012==<br />
1. Received the oligo and began to mutate 16S rrnB operator.<br />
[[File:TJU2012-Note-gen-1.png|center|350px|Gene1]]<br />
2. Mutated RBS of RFP and checked through gel electrophoresis.<br />
[[File:TJU2012-Note-gen-2.png|center|250px|Gene2]]<br />
[[File:TJU2012-Note-gel-5.png|thumb|center|250px|~1800bp, constant with anticipation]]<br />
<br />
==July 14th, 2012==<br />
#Transform two plasmids of we got yestday together into E.coli.[[File:TJU2012-Note-gen-3.png|center|500px|Gene 3]]<br />
#PCR verification of colonies on the LB plates.<br />
#Inculcated the right colonies in Liquid LB.<br />
<br />
==July 15th, 2012==<br />
#Extract plasmid of cells inculcated after one day.<br />
#Enzyme test of the extracted plasmid.[[File:TJU2012-Note-gel-6.png|center|200px|Gel 6]]<br />
#Inclucated the right cells in Liquid LB and added Ala partly.<br />
<br />
==July 20th, 2012==<br />
Analyse the results.<br />
[[File:TJU2012-Note-form-1.png|center|500px|Form 1]]<br />
[[File:TJU2012-Note-fig-2.png|center|300px|Fig 2]]<br />
<br />
==July 24th, 2012==<br />
#Linked the GRP gene and O-RBS RFP gene. Gel extract the previous product again, and ligate using T4 with the following gradient.[[File:TJU2012-Note-form-2.png|center|500px|form 2]]<br />
#In the same method to construct three other systems.<br />
[[File:TJU2012-Mode-cal-fig-2.png|center|500px|fig 3]]<br />
[[File:TJU2012-Mode-cal-fig-3.png|center|500px|fig 4]]<br />
[[File:TJU2012-Mode-cal-fig-4.png|center|500px|fig 5]]<br />
<br />
==July 30th, 2012==<br />
#Learned Fluorescence spectrophotometer.<br />
#measure the strength of GFP and RFP.<br />
[[File:TJU2012-Note-form-3.png|center|500px|form 3]]<br />
<br />
==Aug. 2nd, 2012==<br />
#mutated the RBS of the Amp resistance gene.[[File:TJU2012-Note-gen-4.png|center|250px|Gene 4]]<br />
#linked genes and transformed them into E. coli.<br />
<br />
==Aug. 4th, 2012==<br />
Results of plates<br />
[[File:TJU2012-Note-fig-3.png|center|300px|fig 3]]<br />
[[File:TJU2012-Note-form-4.png|center|500px|form 4]]<br />
<br />
==Aug. 8th, 2012==<br />
Began to construct the five parts needed in Assembler in Yeast. Part 1 and part 2.<br />
<br />
==Aug. 11th, 2012==<br />
Verified part 1 and 2. Synthesized the two small parts and linked through overlap PCR. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-4.png|center|600px|fig 4]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-5.png|center|500px|fig 5]]<br />
<br />
==Aug. 12th, 2012==<br />
Began to build part 3, 4 and 5. Synthesized the two small parts and linked through overlap PCR.<br />
<br />
==Aug. 14th, 2012==<br />
Verify part 3, 4 and 5. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-6.png|center|500px|fig 6]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-7.png|center|500px|fig 7]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-8.png|center|500px|fig 8]]<br />
<br />
==Aug. 18th, 2012==<br />
Transformed all the five parts into Yeast for Assembler in Yeast.<br />
<br />
==Aug. 20th, 2012==<br />
#Results of the transformation.[[File:TJU2012-Note-fig-9.png|center|300px|fig 9]]<br />
#Extract plasmids from the Yeast.<br />
<br />
==Aug. 22nd, 2012==<br />
#Transformed the plasmid from the Yeast into cells.[[File:TJU2012-Note-fig-10.png|thumb|center|300px|There are purple spots on the plates]]<br />
#Extracted plasmid and checked through gel electrophoresis.[[File:TJU2012-Note-gel-7.png|center|300px|gel 7]]<br />
#Some other results of Assembler in Yeast.<br />
[[File:TJU2012-Note-fig-11.png|center|300px|fig 11]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-12.png|center|300px|fig 12]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-13.png|center|300px|fig 13]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-14.png|center|300px|fig 14]]<br />
<br />
==Aug. 25th, 2012==<br />
#Began to build biobricks.[[File:Tianjin_BB2.PNG|center|500px|BB 2]]<br />
#Began to search articles on phages.<br />
<br />
==Sept. 1st, 2012==<br />
Went to Peking University for exchanges.<br />
[[File:TJU2012-Note-fig-15.png|center|500px|fig 15]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-16.png|center|500px|fig 16]]<br />
<br />
==Sept. 2nd, 2012==<br />
#Found out phi X174 and firstly proposed our ideas.<br />
#The second sections of our biobricks.<br />
[[File:Tianjin_BB1.PNG|center|500px|BB 1]]<br />
<br />
==Sept. 5th, 2012==<br />
#Some experiments on phages.<br />
#Optimized our biobricks.<br />
#Designed primers needed for mutating Phi X174 and send orders.<br />
<br />
==Sept. 11th, 2012==<br />
#Began to mutate gene G and E.<br />
#Optimized our biobricks.<br />
<br />
==Sept. 18th, 2012==<br />
Began to sort out our materials for wiki and upload the website.<br />
[[File:new1.jpg|center|500px|fig 17]]<br />
our team in Hongkong <br />
<br />
<br />
[[File:new2.jpg|center|500px|fig 18]]<br />
our gold award<br />
<br />
<br />
[[File:new3.jpg|center|500px|fig 19]]<br />
presentation in MIT<br />
<br />
{{:Team:Tianjin/footer}}</div>Helengoodhttp://2012.igem.org/Team:Tianjin/NotebookTeam:Tianjin/Notebook2013-05-08T07:04:16Z<p>Helengood: /* Sept. 18th, 2012 */</p>
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<p class="menu_head">Notebook Contents</p><br />
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<a href="https://2012.igem.org/Team:Tianjin/Notebook/Modeling">Modeling Notebook</a><br />
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<a href="https://2012.igem.org/Team:Tianjin/Notebook/HumanPractice">Human Practice Notebook</a><br />
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<p class="menu_head">July, 2012</p><br />
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<center><span style="font-size:46px;font-family:Cambria;margin-top:10px;line-height:80%">Notes of Experiments</span></center><br />
==July 6th, 2012==<br />
#We discuss our all of the possible projects, and finally choose one. And then allocate works to specific member.<br />
#Do some pre-experiment and make some reagants.<br />
##Liquid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl <br />
##Solid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl<br />
###20g agar<br />
#Cleaned up the lab and laboratory instruments<br />
<br />
==July 8th, 2012==<br />
#Solutions for extracting plasmid.<br />
##50mM Glucose / 25mM Tris-Cl / 10mM EDTA,pH=8.0<br />
##0.2N NaOH / 1% SDS<br />
##3M KOAc / 2M HOAc<br />
#Experiment technologies training, such as making gel, gel electrophoresis.<br />
[[File:TJU2012-Note-gel-1.png|center|350px|gel 1]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-2.png|center|350px|gel 2]]<br />
<br />
==July 11th, 2012==<br />
#Designed primers and sent orders.<br />
#Optimized the project and allocated work.<br />
#Experiment technologies and knowledge training<br />
##PCR principle and operation<br />
##Gel Extraction<br />
[[File:TJU2012-Note-gel-3.png|center|350px|gel 3]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-4.png|center|350px|gel 4]]<br />
<br />
==July 13th, 2012==<br />
1. Received the oligo and began to mutate 16S rrnB operator.<br />
[[File:TJU2012-Note-gen-1.png|center|350px|Gene1]]<br />
2. Mutated RBS of RFP and checked through gel electrophoresis.<br />
[[File:TJU2012-Note-gen-2.png|center|250px|Gene2]]<br />
[[File:TJU2012-Note-gel-5.png|thumb|center|250px|~1800bp, constant with anticipation]]<br />
<br />
==July 14th, 2012==<br />
#Transform two plasmids of we got yestday together into E.coli.[[File:TJU2012-Note-gen-3.png|center|500px|Gene 3]]<br />
#PCR verification of colonies on the LB plates.<br />
#Inculcated the right colonies in Liquid LB.<br />
<br />
==July 15th, 2012==<br />
#Extract plasmid of cells inculcated after one day.<br />
#Enzyme test of the extracted plasmid.[[File:TJU2012-Note-gel-6.png|center|200px|Gel 6]]<br />
#Inclucated the right cells in Liquid LB and added Ala partly.<br />
<br />
==July 20th, 2012==<br />
Analyse the results.<br />
[[File:TJU2012-Note-form-1.png|center|500px|Form 1]]<br />
[[File:TJU2012-Note-fig-2.png|center|300px|Fig 2]]<br />
<br />
==July 24th, 2012==<br />
#Linked the GRP gene and O-RBS RFP gene. Gel extract the previous product again, and ligate using T4 with the following gradient.[[File:TJU2012-Note-form-2.png|center|500px|form 2]]<br />
#In the same method to construct three other systems.<br />
[[File:TJU2012-Mode-cal-fig-2.png|center|500px|fig 3]]<br />
[[File:TJU2012-Mode-cal-fig-3.png|center|500px|fig 4]]<br />
[[File:TJU2012-Mode-cal-fig-4.png|center|500px|fig 5]]<br />
<br />
==July 30th, 2012==<br />
#Learned Fluorescence spectrophotometer.<br />
#measure the strength of GFP and RFP.<br />
[[File:TJU2012-Note-form-3.png|center|500px|form 3]]<br />
<br />
==Aug. 2nd, 2012==<br />
#mutated the RBS of the Amp resistance gene.[[File:TJU2012-Note-gen-4.png|center|250px|Gene 4]]<br />
#linked genes and transformed them into E. coli.<br />
<br />
==Aug. 4th, 2012==<br />
Results of plates<br />
[[File:TJU2012-Note-fig-3.png|center|300px|fig 3]]<br />
[[File:TJU2012-Note-form-4.png|center|500px|form 4]]<br />
<br />
==Aug. 8th, 2012==<br />
Began to construct the five parts needed in Assembler in Yeast. Part 1 and part 2.<br />
<br />
==Aug. 11th, 2012==<br />
Verified part 1 and 2. Synthesized the two small parts and linked through overlap PCR. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-4.png|center|600px|fig 4]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-5.png|center|500px|fig 5]]<br />
<br />
==Aug. 12th, 2012==<br />
Began to build part 3, 4 and 5. Synthesized the two small parts and linked through overlap PCR.<br />
<br />
==Aug. 14th, 2012==<br />
Verify part 3, 4 and 5. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-6.png|center|500px|fig 6]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-7.png|center|500px|fig 7]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-8.png|center|500px|fig 8]]<br />
<br />
==Aug. 18th, 2012==<br />
Transformed all the five parts into Yeast for Assembler in Yeast.<br />
<br />
==Aug. 20th, 2012==<br />
#Results of the transformation.[[File:TJU2012-Note-fig-9.png|center|300px|fig 9]]<br />
#Extract plasmids from the Yeast.<br />
<br />
==Aug. 22nd, 2012==<br />
#Transformed the plasmid from the Yeast into cells.[[File:TJU2012-Note-fig-10.png|thumb|center|300px|There are purple spots on the plates]]<br />
#Extracted plasmid and checked through gel electrophoresis.[[File:TJU2012-Note-gel-7.png|center|300px|gel 7]]<br />
#Some other results of Assembler in Yeast.<br />
[[File:TJU2012-Note-fig-11.png|center|300px|fig 11]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-12.png|center|300px|fig 12]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-13.png|center|300px|fig 13]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-14.png|center|300px|fig 14]]<br />
<br />
==Aug. 25th, 2012==<br />
#Began to build biobricks.[[File:Tianjin_BB2.PNG|center|500px|BB 2]]<br />
#Began to search articles on phages.<br />
<br />
==Sept. 1st, 2012==<br />
Went to Peking University for exchanges.<br />
[[File:TJU2012-Note-fig-15.png|center|500px|fig 15]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-16.png|center|500px|fig 16]]<br />
<br />
==Sept. 2nd, 2012==<br />
#Found out phi X174 and firstly proposed our ideas.<br />
#The second sections of our biobricks.<br />
[[File:Tianjin_BB1.PNG|center|500px|BB 1]]<br />
<br />
==Sept. 5th, 2012==<br />
#Some experiments on phages.<br />
#Optimized our biobricks.<br />
#Designed primers needed for mutating Phi X174 and send orders.<br />
<br />
==Sept. 11th, 2012==<br />
#Began to mutate gene G and E.<br />
#Optimized our biobricks.<br />
<br />
==Sept. 18th, 2012==<br />
Began to sort out our materials for wiki and upload the website.<br />
[[File:new1.jpg|center|500px|fig 17]]<br />
<br />
<br />
[[File:new2.jpg|center|500px|fig 18]]<br />
<br />
<br />
[[File:new3.jpg|center|500px|fig 19]]<br />
<br />
{{:Team:Tianjin/footer}}</div>Helengoodhttp://2012.igem.org/Team:Tianjin/NotebookTeam:Tianjin/Notebook2013-05-08T07:01:11Z<p>Helengood: /* Sept. 18th, 2012 */</p>
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<p class="menu_head">Notebook Contents</p><br />
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<a href="https://2012.igem.org/Team:Tianjin/Notebook/Modeling">Modeling Notebook</a><br />
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<a href="https://2012.igem.org/Team:Tianjin/Notebook/HumanPractice">Human Practice Notebook</a><br />
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<p class="menu_head">July, 2012</p><br />
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<center><span style="font-size:46px;font-family:Cambria;margin-top:10px;line-height:80%">Notes of Experiments</span></center><br />
==July 6th, 2012==<br />
#We discuss our all of the possible projects, and finally choose one. And then allocate works to specific member.<br />
#Do some pre-experiment and make some reagants.<br />
##Liquid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl <br />
##Solid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl<br />
###20g agar<br />
#Cleaned up the lab and laboratory instruments<br />
<br />
==July 8th, 2012==<br />
#Solutions for extracting plasmid.<br />
##50mM Glucose / 25mM Tris-Cl / 10mM EDTA,pH=8.0<br />
##0.2N NaOH / 1% SDS<br />
##3M KOAc / 2M HOAc<br />
#Experiment technologies training, such as making gel, gel electrophoresis.<br />
[[File:TJU2012-Note-gel-1.png|center|350px|gel 1]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-2.png|center|350px|gel 2]]<br />
<br />
==July 11th, 2012==<br />
#Designed primers and sent orders.<br />
#Optimized the project and allocated work.<br />
#Experiment technologies and knowledge training<br />
##PCR principle and operation<br />
##Gel Extraction<br />
[[File:TJU2012-Note-gel-3.png|center|350px|gel 3]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-4.png|center|350px|gel 4]]<br />
<br />
==July 13th, 2012==<br />
1. Received the oligo and began to mutate 16S rrnB operator.<br />
[[File:TJU2012-Note-gen-1.png|center|350px|Gene1]]<br />
2. Mutated RBS of RFP and checked through gel electrophoresis.<br />
[[File:TJU2012-Note-gen-2.png|center|250px|Gene2]]<br />
[[File:TJU2012-Note-gel-5.png|thumb|center|250px|~1800bp, constant with anticipation]]<br />
<br />
==July 14th, 2012==<br />
#Transform two plasmids of we got yestday together into E.coli.[[File:TJU2012-Note-gen-3.png|center|500px|Gene 3]]<br />
#PCR verification of colonies on the LB plates.<br />
#Inculcated the right colonies in Liquid LB.<br />
<br />
==July 15th, 2012==<br />
#Extract plasmid of cells inculcated after one day.<br />
#Enzyme test of the extracted plasmid.[[File:TJU2012-Note-gel-6.png|center|200px|Gel 6]]<br />
#Inclucated the right cells in Liquid LB and added Ala partly.<br />
<br />
==July 20th, 2012==<br />
Analyse the results.<br />
[[File:TJU2012-Note-form-1.png|center|500px|Form 1]]<br />
[[File:TJU2012-Note-fig-2.png|center|300px|Fig 2]]<br />
<br />
==July 24th, 2012==<br />
#Linked the GRP gene and O-RBS RFP gene. Gel extract the previous product again, and ligate using T4 with the following gradient.[[File:TJU2012-Note-form-2.png|center|500px|form 2]]<br />
#In the same method to construct three other systems.<br />
[[File:TJU2012-Mode-cal-fig-2.png|center|500px|fig 3]]<br />
[[File:TJU2012-Mode-cal-fig-3.png|center|500px|fig 4]]<br />
[[File:TJU2012-Mode-cal-fig-4.png|center|500px|fig 5]]<br />
<br />
==July 30th, 2012==<br />
#Learned Fluorescence spectrophotometer.<br />
#measure the strength of GFP and RFP.<br />
[[File:TJU2012-Note-form-3.png|center|500px|form 3]]<br />
<br />
==Aug. 2nd, 2012==<br />
#mutated the RBS of the Amp resistance gene.[[File:TJU2012-Note-gen-4.png|center|250px|Gene 4]]<br />
#linked genes and transformed them into E. coli.<br />
<br />
==Aug. 4th, 2012==<br />
Results of plates<br />
[[File:TJU2012-Note-fig-3.png|center|300px|fig 3]]<br />
[[File:TJU2012-Note-form-4.png|center|500px|form 4]]<br />
<br />
==Aug. 8th, 2012==<br />
Began to construct the five parts needed in Assembler in Yeast. Part 1 and part 2.<br />
<br />
==Aug. 11th, 2012==<br />
Verified part 1 and 2. Synthesized the two small parts and linked through overlap PCR. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-4.png|center|600px|fig 4]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-5.png|center|500px|fig 5]]<br />
<br />
==Aug. 12th, 2012==<br />
Began to build part 3, 4 and 5. Synthesized the two small parts and linked through overlap PCR.<br />
<br />
==Aug. 14th, 2012==<br />
Verify part 3, 4 and 5. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-6.png|center|500px|fig 6]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-7.png|center|500px|fig 7]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-8.png|center|500px|fig 8]]<br />
<br />
==Aug. 18th, 2012==<br />
Transformed all the five parts into Yeast for Assembler in Yeast.<br />
<br />
==Aug. 20th, 2012==<br />
#Results of the transformation.[[File:TJU2012-Note-fig-9.png|center|300px|fig 9]]<br />
#Extract plasmids from the Yeast.<br />
<br />
==Aug. 22nd, 2012==<br />
#Transformed the plasmid from the Yeast into cells.[[File:TJU2012-Note-fig-10.png|thumb|center|300px|There are purple spots on the plates]]<br />
#Extracted plasmid and checked through gel electrophoresis.[[File:TJU2012-Note-gel-7.png|center|300px|gel 7]]<br />
#Some other results of Assembler in Yeast.<br />
[[File:TJU2012-Note-fig-11.png|center|300px|fig 11]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-12.png|center|300px|fig 12]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-13.png|center|300px|fig 13]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-14.png|center|300px|fig 14]]<br />
<br />
==Aug. 25th, 2012==<br />
#Began to build biobricks.[[File:Tianjin_BB2.PNG|center|500px|BB 2]]<br />
#Began to search articles on phages.<br />
<br />
==Sept. 1st, 2012==<br />
Went to Peking University for exchanges.<br />
[[File:TJU2012-Note-fig-15.png|center|500px|fig 15]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-16.png|center|500px|fig 16]]<br />
<br />
==Sept. 2nd, 2012==<br />
#Found out phi X174 and firstly proposed our ideas.<br />
#The second sections of our biobricks.<br />
[[File:Tianjin_BB1.PNG|center|500px|BB 1]]<br />
<br />
==Sept. 5th, 2012==<br />
#Some experiments on phages.<br />
#Optimized our biobricks.<br />
#Designed primers needed for mutating Phi X174 and send orders.<br />
<br />
==Sept. 11th, 2012==<br />
#Began to mutate gene G and E.<br />
#Optimized our biobricks.<br />
<br />
==Sept. 18th, 2012==<br />
Began to sort out our materials for wiki and upload the website.<br />
[[File:new1.jpg|center|500px|fig 17]]<br />
[[File:new2.jpg|center|500px|fig 18]]<br />
[[File:new3.jpg|center|500px|fig 19]]<br />
<br />
{{:Team:Tianjin/footer}}</div>Helengoodhttp://2012.igem.org/File:New3.jpgFile:New3.jpg2013-05-08T06:53:27Z<p>Helengood: </p>
<hr />
<div></div>Helengoodhttp://2012.igem.org/File:New2.jpgFile:New2.jpg2013-05-08T06:52:15Z<p>Helengood: </p>
<hr />
<div></div>Helengoodhttp://2012.igem.org/File:New1.jpgFile:New1.jpg2013-05-08T06:51:23Z<p>Helengood: </p>
<hr />
<div></div>Helengoodhttp://2012.igem.org/Team:Tianjin/NotebookTeam:Tianjin/Notebook2013-05-08T06:50:12Z<p>Helengood: /* Sept. 18th, 2012 */</p>
<hr />
<div>{{:Team:Tianjin/frame/notebook}}<br />
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<p class="menu_head">Notebook Contents</p><br />
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<a href="https://2012.igem.org/Team:Tianjin/Notebook/Modeling">Modeling Notebook</a><br />
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<a href="https://2012.igem.org/Team:Tianjin/Notebook/HumanPractice">Human Practice Notebook</a><br />
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<p class="menu_head">July, 2012</p><br />
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<center><span style="font-size:46px;font-family:Cambria;margin-top:10px;line-height:80%">Notes of Experiments</span></center><br />
==July 6th, 2012==<br />
#We discuss our all of the possible projects, and finally choose one. And then allocate works to specific member.<br />
#Do some pre-experiment and make some reagants.<br />
##Liquid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl <br />
##Solid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl<br />
###20g agar<br />
#Cleaned up the lab and laboratory instruments<br />
<br />
==July 8th, 2012==<br />
#Solutions for extracting plasmid.<br />
##50mM Glucose / 25mM Tris-Cl / 10mM EDTA,pH=8.0<br />
##0.2N NaOH / 1% SDS<br />
##3M KOAc / 2M HOAc<br />
#Experiment technologies training, such as making gel, gel electrophoresis.<br />
[[File:TJU2012-Note-gel-1.png|center|350px|gel 1]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-2.png|center|350px|gel 2]]<br />
<br />
==July 11th, 2012==<br />
#Designed primers and sent orders.<br />
#Optimized the project and allocated work.<br />
#Experiment technologies and knowledge training<br />
##PCR principle and operation<br />
##Gel Extraction<br />
[[File:TJU2012-Note-gel-3.png|center|350px|gel 3]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-4.png|center|350px|gel 4]]<br />
<br />
==July 13th, 2012==<br />
1. Received the oligo and began to mutate 16S rrnB operator.<br />
[[File:TJU2012-Note-gen-1.png|center|350px|Gene1]]<br />
2. Mutated RBS of RFP and checked through gel electrophoresis.<br />
[[File:TJU2012-Note-gen-2.png|center|250px|Gene2]]<br />
[[File:TJU2012-Note-gel-5.png|thumb|center|250px|~1800bp, constant with anticipation]]<br />
<br />
==July 14th, 2012==<br />
#Transform two plasmids of we got yestday together into E.coli.[[File:TJU2012-Note-gen-3.png|center|500px|Gene 3]]<br />
#PCR verification of colonies on the LB plates.<br />
#Inculcated the right colonies in Liquid LB.<br />
<br />
==July 15th, 2012==<br />
#Extract plasmid of cells inculcated after one day.<br />
#Enzyme test of the extracted plasmid.[[File:TJU2012-Note-gel-6.png|center|200px|Gel 6]]<br />
#Inclucated the right cells in Liquid LB and added Ala partly.<br />
<br />
==July 20th, 2012==<br />
Analyse the results.<br />
[[File:TJU2012-Note-form-1.png|center|500px|Form 1]]<br />
[[File:TJU2012-Note-fig-2.png|center|300px|Fig 2]]<br />
<br />
==July 24th, 2012==<br />
#Linked the GRP gene and O-RBS RFP gene. Gel extract the previous product again, and ligate using T4 with the following gradient.[[File:TJU2012-Note-form-2.png|center|500px|form 2]]<br />
#In the same method to construct three other systems.<br />
[[File:TJU2012-Mode-cal-fig-2.png|center|500px|fig 3]]<br />
[[File:TJU2012-Mode-cal-fig-3.png|center|500px|fig 4]]<br />
[[File:TJU2012-Mode-cal-fig-4.png|center|500px|fig 5]]<br />
<br />
==July 30th, 2012==<br />
#Learned Fluorescence spectrophotometer.<br />
#measure the strength of GFP and RFP.<br />
[[File:TJU2012-Note-form-3.png|center|500px|form 3]]<br />
<br />
==Aug. 2nd, 2012==<br />
#mutated the RBS of the Amp resistance gene.[[File:TJU2012-Note-gen-4.png|center|250px|Gene 4]]<br />
#linked genes and transformed them into E. coli.<br />
<br />
==Aug. 4th, 2012==<br />
Results of plates<br />
[[File:TJU2012-Note-fig-3.png|center|300px|fig 3]]<br />
[[File:TJU2012-Note-form-4.png|center|500px|form 4]]<br />
<br />
==Aug. 8th, 2012==<br />
Began to construct the five parts needed in Assembler in Yeast. Part 1 and part 2.<br />
<br />
==Aug. 11th, 2012==<br />
Verified part 1 and 2. Synthesized the two small parts and linked through overlap PCR. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-4.png|center|600px|fig 4]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-5.png|center|500px|fig 5]]<br />
<br />
==Aug. 12th, 2012==<br />
Began to build part 3, 4 and 5. Synthesized the two small parts and linked through overlap PCR.<br />
<br />
==Aug. 14th, 2012==<br />
Verify part 3, 4 and 5. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-6.png|center|500px|fig 6]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-7.png|center|500px|fig 7]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-8.png|center|500px|fig 8]]<br />
<br />
==Aug. 18th, 2012==<br />
Transformed all the five parts into Yeast for Assembler in Yeast.<br />
<br />
==Aug. 20th, 2012==<br />
#Results of the transformation.[[File:TJU2012-Note-fig-9.png|center|300px|fig 9]]<br />
#Extract plasmids from the Yeast.<br />
<br />
==Aug. 22nd, 2012==<br />
#Transformed the plasmid from the Yeast into cells.[[File:TJU2012-Note-fig-10.png|thumb|center|300px|There are purple spots on the plates]]<br />
#Extracted plasmid and checked through gel electrophoresis.[[File:TJU2012-Note-gel-7.png|center|300px|gel 7]]<br />
#Some other results of Assembler in Yeast.<br />
[[File:TJU2012-Note-fig-11.png|center|300px|fig 11]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-12.png|center|300px|fig 12]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-13.png|center|300px|fig 13]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-14.png|center|300px|fig 14]]<br />
<br />
==Aug. 25th, 2012==<br />
#Began to build biobricks.[[File:Tianjin_BB2.PNG|center|500px|BB 2]]<br />
#Began to search articles on phages.<br />
<br />
==Sept. 1st, 2012==<br />
Went to Peking University for exchanges.<br />
[[File:TJU2012-Note-fig-15.png|center|500px|fig 15]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-16.png|center|500px|fig 16]]<br />
<br />
==Sept. 2nd, 2012==<br />
#Found out phi X174 and firstly proposed our ideas.<br />
#The second sections of our biobricks.<br />
[[File:Tianjin_BB1.PNG|center|500px|BB 1]]<br />
<br />
==Sept. 5th, 2012==<br />
#Some experiments on phages.<br />
#Optimized our biobricks.<br />
#Designed primers needed for mutating Phi X174 and send orders.<br />
<br />
==Sept. 11th, 2012==<br />
#Began to mutate gene G and E.<br />
#Optimized our biobricks.<br />
<br />
==Sept. 18th, 2012==<br />
Began to sort out our materials for wiki and upload the website.<br />
[[File:new1.jpg|center|500px|fig 15]]<br />
[[File:new2.jpg|center|500px|fig 16]]<br />
[[File:new3.jpg|center|500px|fig 17]]<br />
<br />
{{:Team:Tianjin/footer}}</div>Helengoodhttp://2012.igem.org/Team:Tianjin/AttributionsTeam:Tianjin/Attributions2013-05-08T03:25:59Z<p>Helengood: /* Team Members */</p>
<hr />
<div>{{:Team:Tianjin/frame/attributions}}<br />
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<div style="float:left;"><br />
<div id="secondpane"> <!--Code for menu starts here--><br />
<p class="menu_head">Attribution</p><br />
<div class="menu_body"><br />
<div class="menu_children"><br />
<a href="#Team_Members">Team Members</a><br />
</div><br />
<br />
</div><br />
<p class="menu_head">Contributions</p><br />
<div class="menu_body"><br />
<div class="menu_children"><br />
<a href="#Special_Thanks_to">Special Thanks to</a><br />
</div><br />
<div class="menu_children"><br />
<a href="#Thanks_to">Thanks to</a><br />
</div><br />
<br />
</div><br />
<p class="menu_head">Links to</p><br />
<div class="menu_body"><br />
<div class="menu_children"><br />
<a href="https://2012.igem.org/Team:Tianjin/Team">Team</a><br />
</div><br />
<br />
</div><br />
</div> <!--Code for menu ends here--><br />
</div><br />
</html><br />
<div id="text-content"><br />
<br />
<br />
<br />
<br><center><span style="font-size:46px;font-family:Cambria;margin-top:10px">Attributions</span></center><br />
<br><br />
=Team Members=<br />
[[Team:Tianjin/Team|'''Bin Jia''']], team leader, project design, experiment operation;<br />
<br />
[[Team:Tianjin/Team|'''Jiaquan Liu''']], project design,experiment operation, wiki construction and composition, presentation;<br />
<br />
[[Team:Tianjin/Team|'''Qinfeng Wu''']], project design, wiki construction, experiment operation, presentation;<br />
<br />
[[Team:Tianjin/Team|'''Jinlai Zhang''']], project design, experiment operation, human practice;<br />
<br />
[[Team:Tianjin/Team|'''Dongchang Qin''']], project design, experiment operation;<br />
<br />
[[Team:Tianjin/Team|'''Lingli Ni''']], human practice, experiment operation;<br />
<br />
[[Team:Tianjin/Team|'''Yifeng Shao''']], human practice, modeling;<br />
<br />
[[Team:Tianjin/Team|'''Yapeng Su''']], modeling, project design, human practice;<br />
<br />
[[Team:Tianjin/Team|'''Yufei Wei''']], modeling, project design, human practice;<br />
<br />
[[Team:Tianjin/Team|'''Xiaonan Cheng''']], wiki design and construction, movie filming and editing, human practice;<br />
<br />
[[Team:Tianjin/Team|'''Andi Wangzhou''']], project design, wiki & poster design and construction, experiment assistance;<br />
<br />
[[Team:Tianjin/Team|'''Hengqian Ren''']], project design, experiment assistance;<br />
<br />
[[Team:Tianjin/Team|'''Yang Li''']], experiment assistance;<br />
<br />
[[Team:Tianjin/Team|'''Linlin Song''']], experiment assistance;<br />
<br />
[[Team:Tianjin/Team|'''Shu Gong''']], experiment assistance.<br />
<br />
<br />
<br><center><span style="font-size:46px;font-family:Cambria;margin-top:10px">Contributions</span></center><br />
<br><br />
<br />
=Special Thanks to=<br />
[[file:TJU2012-Team-Yuan.png|thumb|290px|left|'''Professor Yingjin Yuan''', who offered all the necessary advice and resources including laboratories, funding, and graduate student suggestion in the whole iGEM project.]] [[file:TJU2012-Libingzhi.png|thumb|290px|none|'''Dr. Binzhi Li''', who offered us assistance in details during the project.]]<br />
<br />
<br />
<br />
<br />
'''The Key Laboratory of Systems Biongineering''', which provided us with all equipment and platform that are indispensable to our success.<br />
<br />
'''Tianjin University International Cooperation Office''', for their support in the competition.<br />
<br />
'''Tianjin University Jiankun Foundation,''' for generously paying for our travel expenses.<br />
<br />
=Thanks to=<br />
'''SAST of NKU''', '''SAST of TJU''', '''SAST of School of Life Science (NKU)''', '''Biology Club of Nankai Middle School''', for supporting us in the Visit Activity.<br />
<br />
'''Tianluo Chen,''' who has done a lot for Human Pracitce's paperwork.<br />
<br />
'''Zehua Xia,''' who has helped us to hold the Visit Activity as the chairman of SAST of TJU.<br />
<br />
'''Mengfei Liu,''' who has devoted to the analysis of the modeling,<br />
<br />
'''Stanley Wang,''' for your spectacular performances<br />
<br />
'''Yiyang Cheng,''' for your one of a kind vocal performance.<br />
<br />
'''Weiming Huang,''' for shooting those gorgeous pictures of our team<br />
<br />
<br />
{{:Team:Tianjin/footer}}</div>Helengoodhttp://2012.igem.org/Team:Tianjin/AttributionsTeam:Tianjin/Attributions2013-05-08T03:25:09Z<p>Helengood: /* Team Members */</p>
<hr />
<div>{{:Team:Tianjin/frame/attributions}}<br />
<html><br />
<style type="text/css"><br />
#secondpane {color:#fff;<br />
width: 190px;<br />
margin-left:5px;<br />
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<br />
</style><br />
<div style="float:left;"><br />
<div id="secondpane"> <!--Code for menu starts here--><br />
<p class="menu_head">Attribution</p><br />
<div class="menu_body"><br />
<div class="menu_children"><br />
<a href="#Team_Members">Team Members</a><br />
</div><br />
<br />
</div><br />
<p class="menu_head">Contributions</p><br />
<div class="menu_body"><br />
<div class="menu_children"><br />
<a href="#Special_Thanks_to">Special Thanks to</a><br />
</div><br />
<div class="menu_children"><br />
<a href="#Thanks_to">Thanks to</a><br />
</div><br />
<br />
</div><br />
<p class="menu_head">Links to</p><br />
<div class="menu_body"><br />
<div class="menu_children"><br />
<a href="https://2012.igem.org/Team:Tianjin/Team">Team</a><br />
</div><br />
<br />
</div><br />
</div> <!--Code for menu ends here--><br />
</div><br />
</html><br />
<div id="text-content"><br />
<br />
<br />
<br />
<br><center><span style="font-size:46px;font-family:Cambria;margin-top:10px">Attributions</span></center><br />
<br><br />
=Team Members=<br />
[[Team:Tianjin/Team|'''Bin Jia''']], team leader, project design, experiment operation;<br />
<br />
[[Team:Tianjin/Team|'''Jiaquan Liu''']], project design,experiment operation, wiki construction and composition, presentation;<br />
<br />
[[Team:Tianjin/Team|'''Qinfeng Wu''']], project design, wiki construction, experiment operation, presentation;<br />
<br />
[[Team:Tianjin/Team|'''Jinlai Zhang''']], project design, experiment operation, human practice;<br />
<br />
[[Team:Tianjin/Team|'''Dongchang Qin''']], project design, wiki construction, experiment operation;project design, experiment operation;<br />
[[Team:Tianjin/Team|'''Lingli Ni''']], human practice, experiment operation;<br />
<br />
[[Team:Tianjin/Team|'''Yifeng Shao''']], human practice, modeling;<br />
<br />
[[Team:Tianjin/Team|'''Yapeng Su''']], modeling, project design, human practice;<br />
<br />
[[Team:Tianjin/Team|'''Yufei Wei''']], modeling, project design, human practice;<br />
<br />
[[Team:Tianjin/Team|'''Xiaonan Cheng''']], wiki design and construction, movie filming and editing, human practice;<br />
<br />
[[Team:Tianjin/Team|'''Andi Wangzhou''']], project design, wiki & poster design and construction, experiment assistance;<br />
<br />
[[Team:Tianjin/Team|'''Hengqian Ren''']], project design, experiment assistance;<br />
<br />
[[Team:Tianjin/Team|'''Yang Li''']], experiment assistance;<br />
<br />
[[Team:Tianjin/Team|'''Linlin Song''']], experiment assistance;<br />
<br />
[[Team:Tianjin/Team|'''Shu Gong''']], experiment assistance.<br />
<br />
<br />
<br><center><span style="font-size:46px;font-family:Cambria;margin-top:10px">Contributions</span></center><br />
<br><br />
<br />
=Special Thanks to=<br />
[[file:TJU2012-Team-Yuan.png|thumb|290px|left|'''Professor Yingjin Yuan''', who offered all the necessary advice and resources including laboratories, funding, and graduate student suggestion in the whole iGEM project.]] [[file:TJU2012-Libingzhi.png|thumb|290px|none|'''Dr. Binzhi Li''', who offered us assistance in details during the project.]]<br />
<br />
<br />
<br />
<br />
'''The Key Laboratory of Systems Biongineering''', which provided us with all equipment and platform that are indispensable to our success.<br />
<br />
'''Tianjin University International Cooperation Office''', for their support in the competition.<br />
<br />
'''Tianjin University Jiankun Foundation,''' for generously paying for our travel expenses.<br />
<br />
=Thanks to=<br />
'''SAST of NKU''', '''SAST of TJU''', '''SAST of School of Life Science (NKU)''', '''Biology Club of Nankai Middle School''', for supporting us in the Visit Activity.<br />
<br />
'''Tianluo Chen,''' who has done a lot for Human Pracitce's paperwork.<br />
<br />
'''Zehua Xia,''' who has helped us to hold the Visit Activity as the chairman of SAST of TJU.<br />
<br />
'''Mengfei Liu,''' who has devoted to the analysis of the modeling,<br />
<br />
'''Stanley Wang,''' for your spectacular performances<br />
<br />
'''Yiyang Cheng,''' for your one of a kind vocal performance.<br />
<br />
'''Weiming Huang,''' for shooting those gorgeous pictures of our team<br />
<br />
<br />
{{:Team:Tianjin/footer}}</div>Helengoodhttp://2012.igem.org/File:Example11.jpgFile:Example11.jpg2013-05-07T05:31:20Z<p>Helengood: uploaded a new version of &quot;File:Example11.jpg&quot;</p>
<hr />
<div></div>Helengoodhttp://2012.igem.org/Team:Tianjin/NotebookTeam:Tianjin/Notebook2013-05-07T05:29:21Z<p>Helengood: /* Sept. 18th, 2012 */</p>
<hr />
<div>{{:Team:Tianjin/frame/notebook}}<br />
__NOTOC__<br />
<html><br />
<style type="text/css"><br />
#secondpane {color:#fff;<br />
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.Calender {<br />
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height:161px;<br />
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.Calender a{<br />
text-align:center;<br />
padding-left:0;}<br />
.Calender-non {<br />
height:23px;<br />
width:23px;<br />
background:#aaa;<br />
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height:23px;<br />
width:23px;<br />
background:#8dc7e9;<br />
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margin:2px;<br />
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.Calender-click {<br />
height:23px;<br />
width:23px;<br />
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}<br />
.Calender-click:hover {<br />
background:#777777;<br />
<br />
</style><br />
<div style="float:left;"><br />
<div id="secondpane"> <!--Code for menu starts here--><br />
<p class="menu_head">Notebook Contents</p><br />
<div class="menu_body"><br />
<div class="menu_children"><br />
<a href="https://2012.igem.org/Team:Tianjin/Notebook/Modeling">Modeling Notebook</a><br />
</div><br />
<div class="menu_children"><br />
<a href="https://2012.igem.org/Team:Tianjin/Notebook/HumanPractice">Human Practice Notebook</a><br />
</div><br />
</div><br />
<p class="menu_head">July, 2012</p><br />
<div class="menu_body"><br />
<div class="Calender"><br />
<div class="Calender-non">Sun<br />
</div> <br />
<div class="Calender-non">Mon<br />
</div> <br />
<div class="Calender-non">Tue<br />
</div> <br />
<div class="Calender-non">Wed<br />
</div><br />
<div class="Calender-non">Thu<br />
</div> <br />
<div class="Calender-non">Fri<br />
</div> <br />
<div class="Calender-non">Sat<br />
</div> <br />
<div class="Calender-com">1<br />
</div><br />
<div class="Calender-com">2<br />
</div><br />
<div class="Calender-com">3<br />
</div><br />
<div class="Calender-com">4<br />
</div><br />
<div class="Calender-com">5<br />
</div><br />
<div class="Calender-click"><a href="#July_6th.2C_2012">6</a><br />
</div><br />
<div class="Calender-com">7<br />
</div><br />
<div class="Calender-click"><a href="#July_8th.2C_2012">8</a><br />
</div><br />
<div class="Calender-com">9<br />
</div><br />
<div class="Calender-com">10<br />
</div><br />
<div class="Calender-click"><a href="#July_11th.2C_2012">11</a><br />
</div><br />
<div class="Calender-com">12<br />
</div><br />
<div class="Calender-click"><a href="#July_13th.2C_2012">13</a><br />
</div><br />
<div class="Calender-click"><a href="#July_14th.2C_2012">14</a><br />
</div><br />
<div class="Calender-click"><a href="#July_15th.2C_2012">15</a><br />
</div><br />
<div class="Calender-com">16<br />
</div><br />
<div class="Calender-com">17<br />
</div><br />
<div class="Calender-com">18<br />
</div><br />
<div class="Calender-com">19<br />
</div><br />
<div class="Calender-click"><a href="#July_20th.2C_2012">20</a><br />
</div><br />
<div class="Calender-com">21<br />
</div><br />
<div class="Calender-com">22<br />
</div><br />
<div class="Calender-com">23<br />
</div><br />
<div class="Calender-click"><a href="#July_24th.2C_2012">24</a><br />
</div><br />
<div class="Calender-com">25<br />
</div><br />
<div class="Calender-com">26<br />
</div><br />
<div class="Calender-com">27<br />
</div><br />
<div class="Calender-com">28<br />
</div><br />
<div class="Calender-com">29<br />
</div><br />
<div class="Calender-click"><a href="#July_30th.2C_2012">30</a><br />
</div><br />
<div class="Calender-com">31<br />
</div><br />
<div class="Calender-com"><br />
</div><br />
<div class="Calender-com"><br />
</div><br />
<div class="Calender-com"><br />
</div><br />
<div class="Calender-com"><br />
</div> <br />
</div><br />
</div><br />
<p class="menu_head">August, 2012</p><br />
<div class="menu_body"><br />
<div class="Calender"><br />
<div class="Calender-non">Sun<br />
</div> <br />
<div class="Calender-non">Mon<br />
</div> <br />
<div class="Calender-non">Tue<br />
</div> <br />
<div class="Calender-non">Wed<br />
</div><br />
<div class="Calender-non">Thu<br />
</div> <br />
<div class="Calender-non">Fri<br />
</div> <br />
<div class="Calender-non">Sat<br />
</div> <br />
<div class="Calender-com"><br />
</div><br />
<div class="Calender-com"><br />
</div><br />
<div class="Calender-com"><br />
</div><br />
<div class="Calender-com">1<br />
</div><br />
<div class="Calender-click"><a href="#Aug._2nd.2C_2012">2</a><br />
</div><br />
<div class="Calender-com">3<br />
</div><br />
<div class="Calender-click"><a href="#Aug._4th.2C_2012">4</a><br />
</div><br />
<div class="Calender-com">5<br />
</div><br />
<div class="Calender-com">6<br />
</div><br />
<div class="Calender-com">7<br />
</div><br />
<div class="Calender-click"><a href="#Aug._8th.2C_2012">8</a><br />
</div><br />
<div class="Calender-com">9<br />
</div><br />
<div class="Calender-com">10<br />
</div><br />
<div class="Calender-click"><a href="#Aug._11th.2C_2012">11</a><br />
</div><br />
<div class="Calender-click"><a href="#Aug._12th.2C_2012">12</a><br />
</div><br />
<div class="Calender-com">13<br />
</div><br />
<div class="Calender-click"><a href="#Aug._14th.2C_2012">14</a><br />
</div><br />
<div class="Calender-com">15<br />
</div><br />
<div class="Calender-com">16<br />
</div><br />
<div class="Calender-com">17<br />
</div><br />
<div class="Calender-click"><a href="#Aug._18th.2C_2012">18</a><br />
</div><br />
<div class="Calender-com">19<br />
</div><br />
<div class="Calender-click"><a href="#Aug._20th.2C_2012">20</a><br />
</div><br />
<div class="Calender-com">21<br />
</div><br />
<div class="Calender-click"><a href="#Aug._22nd.2C_2012">22</a><br />
</div><br />
<div class="Calender-com">23<br />
</div><br />
<div class="Calender-com">24<br />
</div><br />
<div class="Calender-click"><a href="#Aug._25th.2C_2012">25</a><br />
</div><br />
<div class="Calender-com">26<br />
</div><br />
<div class="Calender-com">27<br />
</div><br />
<div class="Calender-com">28<br />
</div><br />
<div class="Calender-com">29<br />
</div><br />
<div class="Calender-com">30<br />
</div><br />
<div class="Calender-com">31<br />
</div><br />
<div class="Calender-com"><br />
</div> <br />
</div> <br />
</div><br />
<p class="menu_head">September, 2012</p><br />
<div class="menu_body"><br />
<div class="Calender" style="height:187px;"><br />
<div class="Calender-non">Sun<br />
</div> <br />
<div class="Calender-non">Mon<br />
</div> <br />
<div class="Calender-non">Tue<br />
</div> <br />
<div class="Calender-non">Wed<br />
</div><br />
<div class="Calender-non">Thu<br />
</div> <br />
<div class="Calender-non">Fri<br />
</div> <br />
<div class="Calender-non">Sat<br />
</div> <br />
<div class="Calender-com"><br />
</div><br />
<div class="Calender-com"><br />
</div><br />
<div class="Calender-com"><br />
</div><br />
<div class="Calender-com"><br />
</div><br />
<div class="Calender-com"><br />
</div><br />
<div class="Calender-com"><br />
</div><br />
<div class="Calender-click"><a href="#Sept._1st.2C_2012">1</a><br />
</div><br />
<div class="Calender-click"><a href="#Sept._2nd.2C_2012">2</a><br />
</div><br />
<div class="Calender-com">3<br />
</div><br />
<div class="Calender-com">4<br />
</div><br />
<div class="Calender-click"><a href="#Sept._5th.2C_2012">5</a><br />
</div><br />
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<center><span style="font-size:46px;font-family:Cambria;margin-top:10px;line-height:80%">Notes of Experiments</span></center><br />
==July 6th, 2012==<br />
#We discuss our all of the possible projects, and finally choose one. And then allocate works to specific member.<br />
#Do some pre-experiment and make some reagants.<br />
##Liquid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl <br />
##Solid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl<br />
###20g agar<br />
#Cleaned up the lab and laboratory instruments<br />
<br />
==July 8th, 2012==<br />
#Solutions for extracting plasmid.<br />
##50mM Glucose / 25mM Tris-Cl / 10mM EDTA,pH=8.0<br />
##0.2N NaOH / 1% SDS<br />
##3M KOAc / 2M HOAc<br />
#Experiment technologies training, such as making gel, gel electrophoresis.<br />
[[File:TJU2012-Note-gel-1.png|center|350px|gel 1]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-2.png|center|350px|gel 2]]<br />
<br />
==July 11th, 2012==<br />
#Designed primers and sent orders.<br />
#Optimized the project and allocated work.<br />
#Experiment technologies and knowledge training<br />
##PCR principle and operation<br />
##Gel Extraction<br />
[[File:TJU2012-Note-gel-3.png|center|350px|gel 3]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-4.png|center|350px|gel 4]]<br />
<br />
==July 13th, 2012==<br />
1. Received the oligo and began to mutate 16S rrnB operator.<br />
[[File:TJU2012-Note-gen-1.png|center|350px|Gene1]]<br />
2. Mutated RBS of RFP and checked through gel electrophoresis.<br />
[[File:TJU2012-Note-gen-2.png|center|250px|Gene2]]<br />
[[File:TJU2012-Note-gel-5.png|thumb|center|250px|~1800bp, constant with anticipation]]<br />
<br />
==July 14th, 2012==<br />
#Transform two plasmids of we got yestday together into E.coli.[[File:TJU2012-Note-gen-3.png|center|500px|Gene 3]]<br />
#PCR verification of colonies on the LB plates.<br />
#Inculcated the right colonies in Liquid LB.<br />
<br />
==July 15th, 2012==<br />
#Extract plasmid of cells inculcated after one day.<br />
#Enzyme test of the extracted plasmid.[[File:TJU2012-Note-gel-6.png|center|200px|Gel 6]]<br />
#Inclucated the right cells in Liquid LB and added Ala partly.<br />
<br />
==July 20th, 2012==<br />
Analyse the results.<br />
[[File:TJU2012-Note-form-1.png|center|500px|Form 1]]<br />
[[File:TJU2012-Note-fig-2.png|center|300px|Fig 2]]<br />
<br />
==July 24th, 2012==<br />
#Linked the GRP gene and O-RBS RFP gene. Gel extract the previous product again, and ligate using T4 with the following gradient.[[File:TJU2012-Note-form-2.png|center|500px|form 2]]<br />
#In the same method to construct three other systems.<br />
[[File:TJU2012-Mode-cal-fig-2.png|center|500px|fig 3]]<br />
[[File:TJU2012-Mode-cal-fig-3.png|center|500px|fig 4]]<br />
[[File:TJU2012-Mode-cal-fig-4.png|center|500px|fig 5]]<br />
<br />
==July 30th, 2012==<br />
#Learned Fluorescence spectrophotometer.<br />
#measure the strength of GFP and RFP.<br />
[[File:TJU2012-Note-form-3.png|center|500px|form 3]]<br />
<br />
==Aug. 2nd, 2012==<br />
#mutated the RBS of the Amp resistance gene.[[File:TJU2012-Note-gen-4.png|center|250px|Gene 4]]<br />
#linked genes and transformed them into E. coli.<br />
<br />
==Aug. 4th, 2012==<br />
Results of plates<br />
[[File:TJU2012-Note-fig-3.png|center|300px|fig 3]]<br />
[[File:TJU2012-Note-form-4.png|center|500px|form 4]]<br />
<br />
==Aug. 8th, 2012==<br />
Began to construct the five parts needed in Assembler in Yeast. Part 1 and part 2.<br />
<br />
==Aug. 11th, 2012==<br />
Verified part 1 and 2. Synthesized the two small parts and linked through overlap PCR. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-4.png|center|600px|fig 4]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-5.png|center|500px|fig 5]]<br />
<br />
==Aug. 12th, 2012==<br />
Began to build part 3, 4 and 5. Synthesized the two small parts and linked through overlap PCR.<br />
<br />
==Aug. 14th, 2012==<br />
Verify part 3, 4 and 5. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-6.png|center|500px|fig 6]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-7.png|center|500px|fig 7]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-8.png|center|500px|fig 8]]<br />
<br />
==Aug. 18th, 2012==<br />
Transformed all the five parts into Yeast for Assembler in Yeast.<br />
<br />
==Aug. 20th, 2012==<br />
#Results of the transformation.[[File:TJU2012-Note-fig-9.png|center|300px|fig 9]]<br />
#Extract plasmids from the Yeast.<br />
<br />
==Aug. 22nd, 2012==<br />
#Transformed the plasmid from the Yeast into cells.[[File:TJU2012-Note-fig-10.png|thumb|center|300px|There are purple spots on the plates]]<br />
#Extracted plasmid and checked through gel electrophoresis.[[File:TJU2012-Note-gel-7.png|center|300px|gel 7]]<br />
#Some other results of Assembler in Yeast.<br />
[[File:TJU2012-Note-fig-11.png|center|300px|fig 11]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-12.png|center|300px|fig 12]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-13.png|center|300px|fig 13]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-14.png|center|300px|fig 14]]<br />
<br />
==Aug. 25th, 2012==<br />
#Began to build biobricks.[[File:Tianjin_BB2.PNG|center|500px|BB 2]]<br />
#Began to search articles on phages.<br />
<br />
==Sept. 1st, 2012==<br />
Went to Peking University for exchanges.<br />
[[File:TJU2012-Note-fig-15.png|center|500px|fig 15]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-16.png|center|500px|fig 16]]<br />
<br />
==Sept. 2nd, 2012==<br />
#Found out phi X174 and firstly proposed our ideas.<br />
#The second sections of our biobricks.<br />
[[File:Tianjin_BB1.PNG|center|500px|BB 1]]<br />
<br />
==Sept. 5th, 2012==<br />
#Some experiments on phages.<br />
#Optimized our biobricks.<br />
#Designed primers needed for mutating Phi X174 and send orders.<br />
<br />
==Sept. 11th, 2012==<br />
#Began to mutate gene G and E.<br />
#Optimized our biobricks.<br />
<br />
==Sept. 18th, 2012==<br />
Began to sort out our materials for wiki and upload the website.<br />
[[File:Example11.jpg|center|500px|fig 15]]<br />
<br />
{{:Team:Tianjin/footer}}</div>Helengoodhttp://2012.igem.org/File:Example11.jpgFile:Example11.jpg2013-05-07T05:26:43Z<p>Helengood: uploaded a new version of &quot;File:Example11.jpg&quot;</p>
<hr />
<div></div>Helengoodhttp://2012.igem.org/File:Example11.jpgFile:Example11.jpg2013-05-07T05:21:39Z<p>Helengood: </p>
<hr />
<div></div>Helengoodhttp://2012.igem.org/Team:Tianjin/NotebookTeam:Tianjin/Notebook2013-05-07T05:19:57Z<p>Helengood: /* Sept. 18th, 2012 */</p>
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<p class="menu_head">Notebook Contents</p><br />
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<a href="https://2012.igem.org/Team:Tianjin/Notebook/Modeling">Modeling Notebook</a><br />
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<a href="https://2012.igem.org/Team:Tianjin/Notebook/HumanPractice">Human Practice Notebook</a><br />
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<p class="menu_head">July, 2012</p><br />
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<div id="text-content"><br />
<center><span style="font-size:46px;font-family:Cambria;margin-top:10px;line-height:80%">Notes of Experiments</span></center><br />
==July 6th, 2012==<br />
#We discuss our all of the possible projects, and finally choose one. And then allocate works to specific member.<br />
#Do some pre-experiment and make some reagants.<br />
##Liquid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl <br />
##Solid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl<br />
###20g agar<br />
#Cleaned up the lab and laboratory instruments<br />
<br />
==July 8th, 2012==<br />
#Solutions for extracting plasmid.<br />
##50mM Glucose / 25mM Tris-Cl / 10mM EDTA,pH=8.0<br />
##0.2N NaOH / 1% SDS<br />
##3M KOAc / 2M HOAc<br />
#Experiment technologies training, such as making gel, gel electrophoresis.<br />
[[File:TJU2012-Note-gel-1.png|center|350px|gel 1]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-2.png|center|350px|gel 2]]<br />
<br />
==July 11th, 2012==<br />
#Designed primers and sent orders.<br />
#Optimized the project and allocated work.<br />
#Experiment technologies and knowledge training<br />
##PCR principle and operation<br />
##Gel Extraction<br />
[[File:TJU2012-Note-gel-3.png|center|350px|gel 3]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-4.png|center|350px|gel 4]]<br />
<br />
==July 13th, 2012==<br />
1. Received the oligo and began to mutate 16S rrnB operator.<br />
[[File:TJU2012-Note-gen-1.png|center|350px|Gene1]]<br />
2. Mutated RBS of RFP and checked through gel electrophoresis.<br />
[[File:TJU2012-Note-gen-2.png|center|250px|Gene2]]<br />
[[File:TJU2012-Note-gel-5.png|thumb|center|250px|~1800bp, constant with anticipation]]<br />
<br />
==July 14th, 2012==<br />
#Transform two plasmids of we got yestday together into E.coli.[[File:TJU2012-Note-gen-3.png|center|500px|Gene 3]]<br />
#PCR verification of colonies on the LB plates.<br />
#Inculcated the right colonies in Liquid LB.<br />
<br />
==July 15th, 2012==<br />
#Extract plasmid of cells inculcated after one day.<br />
#Enzyme test of the extracted plasmid.[[File:TJU2012-Note-gel-6.png|center|200px|Gel 6]]<br />
#Inclucated the right cells in Liquid LB and added Ala partly.<br />
<br />
==July 20th, 2012==<br />
Analyse the results.<br />
[[File:TJU2012-Note-form-1.png|center|500px|Form 1]]<br />
[[File:TJU2012-Note-fig-2.png|center|300px|Fig 2]]<br />
<br />
==July 24th, 2012==<br />
#Linked the GRP gene and O-RBS RFP gene. Gel extract the previous product again, and ligate using T4 with the following gradient.[[File:TJU2012-Note-form-2.png|center|500px|form 2]]<br />
#In the same method to construct three other systems.<br />
[[File:TJU2012-Mode-cal-fig-2.png|center|500px|fig 3]]<br />
[[File:TJU2012-Mode-cal-fig-3.png|center|500px|fig 4]]<br />
[[File:TJU2012-Mode-cal-fig-4.png|center|500px|fig 5]]<br />
<br />
==July 30th, 2012==<br />
#Learned Fluorescence spectrophotometer.<br />
#measure the strength of GFP and RFP.<br />
[[File:TJU2012-Note-form-3.png|center|500px|form 3]]<br />
<br />
==Aug. 2nd, 2012==<br />
#mutated the RBS of the Amp resistance gene.[[File:TJU2012-Note-gen-4.png|center|250px|Gene 4]]<br />
#linked genes and transformed them into E. coli.<br />
<br />
==Aug. 4th, 2012==<br />
Results of plates<br />
[[File:TJU2012-Note-fig-3.png|center|300px|fig 3]]<br />
[[File:TJU2012-Note-form-4.png|center|500px|form 4]]<br />
<br />
==Aug. 8th, 2012==<br />
Began to construct the five parts needed in Assembler in Yeast. Part 1 and part 2.<br />
<br />
==Aug. 11th, 2012==<br />
Verified part 1 and 2. Synthesized the two small parts and linked through overlap PCR. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-4.png|center|600px|fig 4]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-5.png|center|500px|fig 5]]<br />
<br />
==Aug. 12th, 2012==<br />
Began to build part 3, 4 and 5. Synthesized the two small parts and linked through overlap PCR.<br />
<br />
==Aug. 14th, 2012==<br />
Verify part 3, 4 and 5. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-6.png|center|500px|fig 6]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-7.png|center|500px|fig 7]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-8.png|center|500px|fig 8]]<br />
<br />
==Aug. 18th, 2012==<br />
Transformed all the five parts into Yeast for Assembler in Yeast.<br />
<br />
==Aug. 20th, 2012==<br />
#Results of the transformation.[[File:TJU2012-Note-fig-9.png|center|300px|fig 9]]<br />
#Extract plasmids from the Yeast.<br />
<br />
==Aug. 22nd, 2012==<br />
#Transformed the plasmid from the Yeast into cells.[[File:TJU2012-Note-fig-10.png|thumb|center|300px|There are purple spots on the plates]]<br />
#Extracted plasmid and checked through gel electrophoresis.[[File:TJU2012-Note-gel-7.png|center|300px|gel 7]]<br />
#Some other results of Assembler in Yeast.<br />
[[File:TJU2012-Note-fig-11.png|center|300px|fig 11]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-12.png|center|300px|fig 12]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-13.png|center|300px|fig 13]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-14.png|center|300px|fig 14]]<br />
<br />
==Aug. 25th, 2012==<br />
#Began to build biobricks.[[File:Tianjin_BB2.PNG|center|500px|BB 2]]<br />
#Began to search articles on phages.<br />
<br />
==Sept. 1st, 2012==<br />
Went to Peking University for exchanges.<br />
[[File:TJU2012-Note-fig-15.png|center|500px|fig 15]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-16.png|center|500px|fig 16]]<br />
<br />
==Sept. 2nd, 2012==<br />
#Found out phi X174 and firstly proposed our ideas.<br />
#The second sections of our biobricks.<br />
[[File:Tianjin_BB1.PNG|center|500px|BB 1]]<br />
<br />
==Sept. 5th, 2012==<br />
#Some experiments on phages.<br />
#Optimized our biobricks.<br />
#Designed primers needed for mutating Phi X174 and send orders.<br />
<br />
==Sept. 11th, 2012==<br />
#Began to mutate gene G and E.<br />
#Optimized our biobricks.<br />
<br />
==Sept. 18th, 2012==<br />
Began to sort out our materials for wiki and upload the website.<br />
[[File:Example11.jpg]]<br />
<br />
{{:Team:Tianjin/footer}}</div>Helengoodhttp://2012.igem.org/Team:Tianjin/NotebookTeam:Tianjin/Notebook2013-05-07T05:19:36Z<p>Helengood: /* Sept. 18th, 2012 */</p>
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<p class="menu_head">Notebook Contents</p><br />
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<a href="https://2012.igem.org/Team:Tianjin/Notebook/Modeling">Modeling Notebook</a><br />
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<a href="https://2012.igem.org/Team:Tianjin/Notebook/HumanPractice">Human Practice Notebook</a><br />
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<p class="menu_head">July, 2012</p><br />
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<center><span style="font-size:46px;font-family:Cambria;margin-top:10px;line-height:80%">Notes of Experiments</span></center><br />
==July 6th, 2012==<br />
#We discuss our all of the possible projects, and finally choose one. And then allocate works to specific member.<br />
#Do some pre-experiment and make some reagants.<br />
##Liquid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl <br />
##Solid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl<br />
###20g agar<br />
#Cleaned up the lab and laboratory instruments<br />
<br />
==July 8th, 2012==<br />
#Solutions for extracting plasmid.<br />
##50mM Glucose / 25mM Tris-Cl / 10mM EDTA,pH=8.0<br />
##0.2N NaOH / 1% SDS<br />
##3M KOAc / 2M HOAc<br />
#Experiment technologies training, such as making gel, gel electrophoresis.<br />
[[File:TJU2012-Note-gel-1.png|center|350px|gel 1]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-2.png|center|350px|gel 2]]<br />
<br />
==July 11th, 2012==<br />
#Designed primers and sent orders.<br />
#Optimized the project and allocated work.<br />
#Experiment technologies and knowledge training<br />
##PCR principle and operation<br />
##Gel Extraction<br />
[[File:TJU2012-Note-gel-3.png|center|350px|gel 3]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-4.png|center|350px|gel 4]]<br />
<br />
==July 13th, 2012==<br />
1. Received the oligo and began to mutate 16S rrnB operator.<br />
[[File:TJU2012-Note-gen-1.png|center|350px|Gene1]]<br />
2. Mutated RBS of RFP and checked through gel electrophoresis.<br />
[[File:TJU2012-Note-gen-2.png|center|250px|Gene2]]<br />
[[File:TJU2012-Note-gel-5.png|thumb|center|250px|~1800bp, constant with anticipation]]<br />
<br />
==July 14th, 2012==<br />
#Transform two plasmids of we got yestday together into E.coli.[[File:TJU2012-Note-gen-3.png|center|500px|Gene 3]]<br />
#PCR verification of colonies on the LB plates.<br />
#Inculcated the right colonies in Liquid LB.<br />
<br />
==July 15th, 2012==<br />
#Extract plasmid of cells inculcated after one day.<br />
#Enzyme test of the extracted plasmid.[[File:TJU2012-Note-gel-6.png|center|200px|Gel 6]]<br />
#Inclucated the right cells in Liquid LB and added Ala partly.<br />
<br />
==July 20th, 2012==<br />
Analyse the results.<br />
[[File:TJU2012-Note-form-1.png|center|500px|Form 1]]<br />
[[File:TJU2012-Note-fig-2.png|center|300px|Fig 2]]<br />
<br />
==July 24th, 2012==<br />
#Linked the GRP gene and O-RBS RFP gene. Gel extract the previous product again, and ligate using T4 with the following gradient.[[File:TJU2012-Note-form-2.png|center|500px|form 2]]<br />
#In the same method to construct three other systems.<br />
[[File:TJU2012-Mode-cal-fig-2.png|center|500px|fig 3]]<br />
[[File:TJU2012-Mode-cal-fig-3.png|center|500px|fig 4]]<br />
[[File:TJU2012-Mode-cal-fig-4.png|center|500px|fig 5]]<br />
<br />
==July 30th, 2012==<br />
#Learned Fluorescence spectrophotometer.<br />
#measure the strength of GFP and RFP.<br />
[[File:TJU2012-Note-form-3.png|center|500px|form 3]]<br />
<br />
==Aug. 2nd, 2012==<br />
#mutated the RBS of the Amp resistance gene.[[File:TJU2012-Note-gen-4.png|center|250px|Gene 4]]<br />
#linked genes and transformed them into E. coli.<br />
<br />
==Aug. 4th, 2012==<br />
Results of plates<br />
[[File:TJU2012-Note-fig-3.png|center|300px|fig 3]]<br />
[[File:TJU2012-Note-form-4.png|center|500px|form 4]]<br />
<br />
==Aug. 8th, 2012==<br />
Began to construct the five parts needed in Assembler in Yeast. Part 1 and part 2.<br />
<br />
==Aug. 11th, 2012==<br />
Verified part 1 and 2. Synthesized the two small parts and linked through overlap PCR. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-4.png|center|600px|fig 4]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-5.png|center|500px|fig 5]]<br />
<br />
==Aug. 12th, 2012==<br />
Began to build part 3, 4 and 5. Synthesized the two small parts and linked through overlap PCR.<br />
<br />
==Aug. 14th, 2012==<br />
Verify part 3, 4 and 5. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-6.png|center|500px|fig 6]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-7.png|center|500px|fig 7]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-8.png|center|500px|fig 8]]<br />
<br />
==Aug. 18th, 2012==<br />
Transformed all the five parts into Yeast for Assembler in Yeast.<br />
<br />
==Aug. 20th, 2012==<br />
#Results of the transformation.[[File:TJU2012-Note-fig-9.png|center|300px|fig 9]]<br />
#Extract plasmids from the Yeast.<br />
<br />
==Aug. 22nd, 2012==<br />
#Transformed the plasmid from the Yeast into cells.[[File:TJU2012-Note-fig-10.png|thumb|center|300px|There are purple spots on the plates]]<br />
#Extracted plasmid and checked through gel electrophoresis.[[File:TJU2012-Note-gel-7.png|center|300px|gel 7]]<br />
#Some other results of Assembler in Yeast.<br />
[[File:TJU2012-Note-fig-11.png|center|300px|fig 11]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-12.png|center|300px|fig 12]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-13.png|center|300px|fig 13]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-14.png|center|300px|fig 14]]<br />
<br />
==Aug. 25th, 2012==<br />
#Began to build biobricks.[[File:Tianjin_BB2.PNG|center|500px|BB 2]]<br />
#Began to search articles on phages.<br />
<br />
==Sept. 1st, 2012==<br />
Went to Peking University for exchanges.<br />
[[File:TJU2012-Note-fig-15.png|center|500px|fig 15]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-16.png|center|500px|fig 16]]<br />
<br />
==Sept. 2nd, 2012==<br />
#Found out phi X174 and firstly proposed our ideas.<br />
#The second sections of our biobricks.<br />
[[File:Tianjin_BB1.PNG|center|500px|BB 1]]<br />
<br />
==Sept. 5th, 2012==<br />
#Some experiments on phages.<br />
#Optimized our biobricks.<br />
#Designed primers needed for mutating Phi X174 and send orders.<br />
<br />
==Sept. 11th, 2012==<br />
#Began to mutate gene G and E.<br />
#Optimized our biobricks.<br />
<br />
==Sept. 18th, 2012==<br />
Began to sort out our materials for wiki and upload the website.<br />
[[File:Example1.jpg]]<br />
<br />
{{:Team:Tianjin/footer}}</div>Helengoodhttp://2012.igem.org/Team:Tianjin/NotebookTeam:Tianjin/Notebook2013-05-07T05:17:23Z<p>Helengood: /* Sept. 18th, 2012 */</p>
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<p class="menu_head">Notebook Contents</p><br />
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<a href="https://2012.igem.org/Team:Tianjin/Notebook/Modeling">Modeling Notebook</a><br />
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<a href="https://2012.igem.org/Team:Tianjin/Notebook/HumanPractice">Human Practice Notebook</a><br />
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<p class="menu_head">July, 2012</p><br />
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<center><span style="font-size:46px;font-family:Cambria;margin-top:10px;line-height:80%">Notes of Experiments</span></center><br />
==July 6th, 2012==<br />
#We discuss our all of the possible projects, and finally choose one. And then allocate works to specific member.<br />
#Do some pre-experiment and make some reagants.<br />
##Liquid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl <br />
##Solid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl<br />
###20g agar<br />
#Cleaned up the lab and laboratory instruments<br />
<br />
==July 8th, 2012==<br />
#Solutions for extracting plasmid.<br />
##50mM Glucose / 25mM Tris-Cl / 10mM EDTA,pH=8.0<br />
##0.2N NaOH / 1% SDS<br />
##3M KOAc / 2M HOAc<br />
#Experiment technologies training, such as making gel, gel electrophoresis.<br />
[[File:TJU2012-Note-gel-1.png|center|350px|gel 1]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-2.png|center|350px|gel 2]]<br />
<br />
==July 11th, 2012==<br />
#Designed primers and sent orders.<br />
#Optimized the project and allocated work.<br />
#Experiment technologies and knowledge training<br />
##PCR principle and operation<br />
##Gel Extraction<br />
[[File:TJU2012-Note-gel-3.png|center|350px|gel 3]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-4.png|center|350px|gel 4]]<br />
<br />
==July 13th, 2012==<br />
1. Received the oligo and began to mutate 16S rrnB operator.<br />
[[File:TJU2012-Note-gen-1.png|center|350px|Gene1]]<br />
2. Mutated RBS of RFP and checked through gel electrophoresis.<br />
[[File:TJU2012-Note-gen-2.png|center|250px|Gene2]]<br />
[[File:TJU2012-Note-gel-5.png|thumb|center|250px|~1800bp, constant with anticipation]]<br />
<br />
==July 14th, 2012==<br />
#Transform two plasmids of we got yestday together into E.coli.[[File:TJU2012-Note-gen-3.png|center|500px|Gene 3]]<br />
#PCR verification of colonies on the LB plates.<br />
#Inculcated the right colonies in Liquid LB.<br />
<br />
==July 15th, 2012==<br />
#Extract plasmid of cells inculcated after one day.<br />
#Enzyme test of the extracted plasmid.[[File:TJU2012-Note-gel-6.png|center|200px|Gel 6]]<br />
#Inclucated the right cells in Liquid LB and added Ala partly.<br />
<br />
==July 20th, 2012==<br />
Analyse the results.<br />
[[File:TJU2012-Note-form-1.png|center|500px|Form 1]]<br />
[[File:TJU2012-Note-fig-2.png|center|300px|Fig 2]]<br />
<br />
==July 24th, 2012==<br />
#Linked the GRP gene and O-RBS RFP gene. Gel extract the previous product again, and ligate using T4 with the following gradient.[[File:TJU2012-Note-form-2.png|center|500px|form 2]]<br />
#In the same method to construct three other systems.<br />
[[File:TJU2012-Mode-cal-fig-2.png|center|500px|fig 3]]<br />
[[File:TJU2012-Mode-cal-fig-3.png|center|500px|fig 4]]<br />
[[File:TJU2012-Mode-cal-fig-4.png|center|500px|fig 5]]<br />
<br />
==July 30th, 2012==<br />
#Learned Fluorescence spectrophotometer.<br />
#measure the strength of GFP and RFP.<br />
[[File:TJU2012-Note-form-3.png|center|500px|form 3]]<br />
<br />
==Aug. 2nd, 2012==<br />
#mutated the RBS of the Amp resistance gene.[[File:TJU2012-Note-gen-4.png|center|250px|Gene 4]]<br />
#linked genes and transformed them into E. coli.<br />
<br />
==Aug. 4th, 2012==<br />
Results of plates<br />
[[File:TJU2012-Note-fig-3.png|center|300px|fig 3]]<br />
[[File:TJU2012-Note-form-4.png|center|500px|form 4]]<br />
<br />
==Aug. 8th, 2012==<br />
Began to construct the five parts needed in Assembler in Yeast. Part 1 and part 2.<br />
<br />
==Aug. 11th, 2012==<br />
Verified part 1 and 2. Synthesized the two small parts and linked through overlap PCR. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-4.png|center|600px|fig 4]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-5.png|center|500px|fig 5]]<br />
<br />
==Aug. 12th, 2012==<br />
Began to build part 3, 4 and 5. Synthesized the two small parts and linked through overlap PCR.<br />
<br />
==Aug. 14th, 2012==<br />
Verify part 3, 4 and 5. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-6.png|center|500px|fig 6]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-7.png|center|500px|fig 7]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-8.png|center|500px|fig 8]]<br />
<br />
==Aug. 18th, 2012==<br />
Transformed all the five parts into Yeast for Assembler in Yeast.<br />
<br />
==Aug. 20th, 2012==<br />
#Results of the transformation.[[File:TJU2012-Note-fig-9.png|center|300px|fig 9]]<br />
#Extract plasmids from the Yeast.<br />
<br />
==Aug. 22nd, 2012==<br />
#Transformed the plasmid from the Yeast into cells.[[File:TJU2012-Note-fig-10.png|thumb|center|300px|There are purple spots on the plates]]<br />
#Extracted plasmid and checked through gel electrophoresis.[[File:TJU2012-Note-gel-7.png|center|300px|gel 7]]<br />
#Some other results of Assembler in Yeast.<br />
[[File:TJU2012-Note-fig-11.png|center|300px|fig 11]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-12.png|center|300px|fig 12]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-13.png|center|300px|fig 13]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-14.png|center|300px|fig 14]]<br />
<br />
==Aug. 25th, 2012==<br />
#Began to build biobricks.[[File:Tianjin_BB2.PNG|center|500px|BB 2]]<br />
#Began to search articles on phages.<br />
<br />
==Sept. 1st, 2012==<br />
Went to Peking University for exchanges.<br />
[[File:TJU2012-Note-fig-15.png|center|500px|fig 15]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-16.png|center|500px|fig 16]]<br />
<br />
==Sept. 2nd, 2012==<br />
#Found out phi X174 and firstly proposed our ideas.<br />
#The second sections of our biobricks.<br />
[[File:Tianjin_BB1.PNG|center|500px|BB 1]]<br />
<br />
==Sept. 5th, 2012==<br />
#Some experiments on phages.<br />
#Optimized our biobricks.<br />
#Designed primers needed for mutating Phi X174 and send orders.<br />
<br />
==Sept. 11th, 2012==<br />
#Began to mutate gene G and E.<br />
#Optimized our biobricks.<br />
<br />
==Sept. 18th, 2012==<br />
Began to sort out our materials for wiki and upload the website.<br />
[[File:20130507033702!Example.jpg]]<br />
<br />
{{:Team:Tianjin/footer}}</div>Helengoodhttp://2012.igem.org/Team:Tianjin/NotebookTeam:Tianjin/Notebook2013-05-07T04:01:36Z<p>Helengood: /* Sept. 18th, 2012 */</p>
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<div>{{:Team:Tianjin/frame/notebook}}<br />
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<p class="menu_head">Notebook Contents</p><br />
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<a href="https://2012.igem.org/Team:Tianjin/Notebook/Modeling">Modeling Notebook</a><br />
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<a href="https://2012.igem.org/Team:Tianjin/Notebook/HumanPractice">Human Practice Notebook</a><br />
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<p class="menu_head">July, 2012</p><br />
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<center><span style="font-size:46px;font-family:Cambria;margin-top:10px;line-height:80%">Notes of Experiments</span></center><br />
==July 6th, 2012==<br />
#We discuss our all of the possible projects, and finally choose one. And then allocate works to specific member.<br />
#Do some pre-experiment and make some reagants.<br />
##Liquid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl <br />
##Solid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl<br />
###20g agar<br />
#Cleaned up the lab and laboratory instruments<br />
<br />
==July 8th, 2012==<br />
#Solutions for extracting plasmid.<br />
##50mM Glucose / 25mM Tris-Cl / 10mM EDTA,pH=8.0<br />
##0.2N NaOH / 1% SDS<br />
##3M KOAc / 2M HOAc<br />
#Experiment technologies training, such as making gel, gel electrophoresis.<br />
[[File:TJU2012-Note-gel-1.png|center|350px|gel 1]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-2.png|center|350px|gel 2]]<br />
<br />
==July 11th, 2012==<br />
#Designed primers and sent orders.<br />
#Optimized the project and allocated work.<br />
#Experiment technologies and knowledge training<br />
##PCR principle and operation<br />
##Gel Extraction<br />
[[File:TJU2012-Note-gel-3.png|center|350px|gel 3]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-4.png|center|350px|gel 4]]<br />
<br />
==July 13th, 2012==<br />
1. Received the oligo and began to mutate 16S rrnB operator.<br />
[[File:TJU2012-Note-gen-1.png|center|350px|Gene1]]<br />
2. Mutated RBS of RFP and checked through gel electrophoresis.<br />
[[File:TJU2012-Note-gen-2.png|center|250px|Gene2]]<br />
[[File:TJU2012-Note-gel-5.png|thumb|center|250px|~1800bp, constant with anticipation]]<br />
<br />
==July 14th, 2012==<br />
#Transform two plasmids of we got yestday together into E.coli.[[File:TJU2012-Note-gen-3.png|center|500px|Gene 3]]<br />
#PCR verification of colonies on the LB plates.<br />
#Inculcated the right colonies in Liquid LB.<br />
<br />
==July 15th, 2012==<br />
#Extract plasmid of cells inculcated after one day.<br />
#Enzyme test of the extracted plasmid.[[File:TJU2012-Note-gel-6.png|center|200px|Gel 6]]<br />
#Inclucated the right cells in Liquid LB and added Ala partly.<br />
<br />
==July 20th, 2012==<br />
Analyse the results.<br />
[[File:TJU2012-Note-form-1.png|center|500px|Form 1]]<br />
[[File:TJU2012-Note-fig-2.png|center|300px|Fig 2]]<br />
<br />
==July 24th, 2012==<br />
#Linked the GRP gene and O-RBS RFP gene. Gel extract the previous product again, and ligate using T4 with the following gradient.[[File:TJU2012-Note-form-2.png|center|500px|form 2]]<br />
#In the same method to construct three other systems.<br />
[[File:TJU2012-Mode-cal-fig-2.png|center|500px|fig 3]]<br />
[[File:TJU2012-Mode-cal-fig-3.png|center|500px|fig 4]]<br />
[[File:TJU2012-Mode-cal-fig-4.png|center|500px|fig 5]]<br />
<br />
==July 30th, 2012==<br />
#Learned Fluorescence spectrophotometer.<br />
#measure the strength of GFP and RFP.<br />
[[File:TJU2012-Note-form-3.png|center|500px|form 3]]<br />
<br />
==Aug. 2nd, 2012==<br />
#mutated the RBS of the Amp resistance gene.[[File:TJU2012-Note-gen-4.png|center|250px|Gene 4]]<br />
#linked genes and transformed them into E. coli.<br />
<br />
==Aug. 4th, 2012==<br />
Results of plates<br />
[[File:TJU2012-Note-fig-3.png|center|300px|fig 3]]<br />
[[File:TJU2012-Note-form-4.png|center|500px|form 4]]<br />
<br />
==Aug. 8th, 2012==<br />
Began to construct the five parts needed in Assembler in Yeast. Part 1 and part 2.<br />
<br />
==Aug. 11th, 2012==<br />
Verified part 1 and 2. Synthesized the two small parts and linked through overlap PCR. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-4.png|center|600px|fig 4]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-5.png|center|500px|fig 5]]<br />
<br />
==Aug. 12th, 2012==<br />
Began to build part 3, 4 and 5. Synthesized the two small parts and linked through overlap PCR.<br />
<br />
==Aug. 14th, 2012==<br />
Verify part 3, 4 and 5. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-6.png|center|500px|fig 6]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-7.png|center|500px|fig 7]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-8.png|center|500px|fig 8]]<br />
<br />
==Aug. 18th, 2012==<br />
Transformed all the five parts into Yeast for Assembler in Yeast.<br />
<br />
==Aug. 20th, 2012==<br />
#Results of the transformation.[[File:TJU2012-Note-fig-9.png|center|300px|fig 9]]<br />
#Extract plasmids from the Yeast.<br />
<br />
==Aug. 22nd, 2012==<br />
#Transformed the plasmid from the Yeast into cells.[[File:TJU2012-Note-fig-10.png|thumb|center|300px|There are purple spots on the plates]]<br />
#Extracted plasmid and checked through gel electrophoresis.[[File:TJU2012-Note-gel-7.png|center|300px|gel 7]]<br />
#Some other results of Assembler in Yeast.<br />
[[File:TJU2012-Note-fig-11.png|center|300px|fig 11]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-12.png|center|300px|fig 12]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-13.png|center|300px|fig 13]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-14.png|center|300px|fig 14]]<br />
<br />
==Aug. 25th, 2012==<br />
#Began to build biobricks.[[File:Tianjin_BB2.PNG|center|500px|BB 2]]<br />
#Began to search articles on phages.<br />
<br />
==Sept. 1st, 2012==<br />
Went to Peking University for exchanges.<br />
[[File:TJU2012-Note-fig-15.png|center|500px|fig 15]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-16.png|center|500px|fig 16]]<br />
<br />
==Sept. 2nd, 2012==<br />
#Found out phi X174 and firstly proposed our ideas.<br />
#The second sections of our biobricks.<br />
[[File:Tianjin_BB1.PNG|center|500px|BB 1]]<br />
<br />
==Sept. 5th, 2012==<br />
#Some experiments on phages.<br />
#Optimized our biobricks.<br />
#Designed primers needed for mutating Phi X174 and send orders.<br />
<br />
==Sept. 11th, 2012==<br />
#Began to mutate gene G and E.<br />
#Optimized our biobricks.<br />
<br />
==Sept. 18th, 2012==<br />
Began to sort out our materials for wiki and upload the website.<br />
<br />
<br />
{{:Team:Tianjin/footer}}</div>Helengoodhttp://2012.igem.org/Team:Tianjin/NotebookTeam:Tianjin/Notebook2013-05-07T03:52:19Z<p>Helengood: /* Sept. 18th, 2012 */</p>
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<p class="menu_head">Notebook Contents</p><br />
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<a href="https://2012.igem.org/Team:Tianjin/Notebook/Modeling">Modeling Notebook</a><br />
</div><br />
<div class="menu_children"><br />
<a href="https://2012.igem.org/Team:Tianjin/Notebook/HumanPractice">Human Practice Notebook</a><br />
</div><br />
</div><br />
<p class="menu_head">July, 2012</p><br />
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<center><span style="font-size:46px;font-family:Cambria;margin-top:10px;line-height:80%">Notes of Experiments</span></center><br />
==July 6th, 2012==<br />
#We discuss our all of the possible projects, and finally choose one. And then allocate works to specific member.<br />
#Do some pre-experiment and make some reagants.<br />
##Liquid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl <br />
##Solid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl<br />
###20g agar<br />
#Cleaned up the lab and laboratory instruments<br />
<br />
==July 8th, 2012==<br />
#Solutions for extracting plasmid.<br />
##50mM Glucose / 25mM Tris-Cl / 10mM EDTA,pH=8.0<br />
##0.2N NaOH / 1% SDS<br />
##3M KOAc / 2M HOAc<br />
#Experiment technologies training, such as making gel, gel electrophoresis.<br />
[[File:TJU2012-Note-gel-1.png|center|350px|gel 1]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-2.png|center|350px|gel 2]]<br />
<br />
==July 11th, 2012==<br />
#Designed primers and sent orders.<br />
#Optimized the project and allocated work.<br />
#Experiment technologies and knowledge training<br />
##PCR principle and operation<br />
##Gel Extraction<br />
[[File:TJU2012-Note-gel-3.png|center|350px|gel 3]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-4.png|center|350px|gel 4]]<br />
<br />
==July 13th, 2012==<br />
1. Received the oligo and began to mutate 16S rrnB operator.<br />
[[File:TJU2012-Note-gen-1.png|center|350px|Gene1]]<br />
2. Mutated RBS of RFP and checked through gel electrophoresis.<br />
[[File:TJU2012-Note-gen-2.png|center|250px|Gene2]]<br />
[[File:TJU2012-Note-gel-5.png|thumb|center|250px|~1800bp, constant with anticipation]]<br />
<br />
==July 14th, 2012==<br />
#Transform two plasmids of we got yestday together into E.coli.[[File:TJU2012-Note-gen-3.png|center|500px|Gene 3]]<br />
#PCR verification of colonies on the LB plates.<br />
#Inculcated the right colonies in Liquid LB.<br />
<br />
==July 15th, 2012==<br />
#Extract plasmid of cells inculcated after one day.<br />
#Enzyme test of the extracted plasmid.[[File:TJU2012-Note-gel-6.png|center|200px|Gel 6]]<br />
#Inclucated the right cells in Liquid LB and added Ala partly.<br />
<br />
==July 20th, 2012==<br />
Analyse the results.<br />
[[File:TJU2012-Note-form-1.png|center|500px|Form 1]]<br />
[[File:TJU2012-Note-fig-2.png|center|300px|Fig 2]]<br />
<br />
==July 24th, 2012==<br />
#Linked the GRP gene and O-RBS RFP gene. Gel extract the previous product again, and ligate using T4 with the following gradient.[[File:TJU2012-Note-form-2.png|center|500px|form 2]]<br />
#In the same method to construct three other systems.<br />
[[File:TJU2012-Mode-cal-fig-2.png|center|500px|fig 3]]<br />
[[File:TJU2012-Mode-cal-fig-3.png|center|500px|fig 4]]<br />
[[File:TJU2012-Mode-cal-fig-4.png|center|500px|fig 5]]<br />
<br />
==July 30th, 2012==<br />
#Learned Fluorescence spectrophotometer.<br />
#measure the strength of GFP and RFP.<br />
[[File:TJU2012-Note-form-3.png|center|500px|form 3]]<br />
<br />
==Aug. 2nd, 2012==<br />
#mutated the RBS of the Amp resistance gene.[[File:TJU2012-Note-gen-4.png|center|250px|Gene 4]]<br />
#linked genes and transformed them into E. coli.<br />
<br />
==Aug. 4th, 2012==<br />
Results of plates<br />
[[File:TJU2012-Note-fig-3.png|center|300px|fig 3]]<br />
[[File:TJU2012-Note-form-4.png|center|500px|form 4]]<br />
<br />
==Aug. 8th, 2012==<br />
Began to construct the five parts needed in Assembler in Yeast. Part 1 and part 2.<br />
<br />
==Aug. 11th, 2012==<br />
Verified part 1 and 2. Synthesized the two small parts and linked through overlap PCR. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-4.png|center|600px|fig 4]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-5.png|center|500px|fig 5]]<br />
<br />
==Aug. 12th, 2012==<br />
Began to build part 3, 4 and 5. Synthesized the two small parts and linked through overlap PCR.<br />
<br />
==Aug. 14th, 2012==<br />
Verify part 3, 4 and 5. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-6.png|center|500px|fig 6]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-7.png|center|500px|fig 7]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-8.png|center|500px|fig 8]]<br />
<br />
==Aug. 18th, 2012==<br />
Transformed all the five parts into Yeast for Assembler in Yeast.<br />
<br />
==Aug. 20th, 2012==<br />
#Results of the transformation.[[File:TJU2012-Note-fig-9.png|center|300px|fig 9]]<br />
#Extract plasmids from the Yeast.<br />
<br />
==Aug. 22nd, 2012==<br />
#Transformed the plasmid from the Yeast into cells.[[File:TJU2012-Note-fig-10.png|thumb|center|300px|There are purple spots on the plates]]<br />
#Extracted plasmid and checked through gel electrophoresis.[[File:TJU2012-Note-gel-7.png|center|300px|gel 7]]<br />
#Some other results of Assembler in Yeast.<br />
[[File:TJU2012-Note-fig-11.png|center|300px|fig 11]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-12.png|center|300px|fig 12]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-13.png|center|300px|fig 13]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-14.png|center|300px|fig 14]]<br />
<br />
==Aug. 25th, 2012==<br />
#Began to build biobricks.[[File:Tianjin_BB2.PNG|center|500px|BB 2]]<br />
#Began to search articles on phages.<br />
<br />
==Sept. 1st, 2012==<br />
Went to Peking University for exchanges.<br />
[[File:TJU2012-Note-fig-15.png|center|500px|fig 15]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-16.png|center|500px|fig 16]]<br />
<br />
==Sept. 2nd, 2012==<br />
#Found out phi X174 and firstly proposed our ideas.<br />
#The second sections of our biobricks.<br />
[[File:Tianjin_BB1.PNG|center|500px|BB 1]]<br />
<br />
==Sept. 5th, 2012==<br />
#Some experiments on phages.<br />
#Optimized our biobricks.<br />
#Designed primers needed for mutating Phi X174 and send orders.<br />
<br />
==Sept. 11th, 2012==<br />
#Began to mutate gene G and E.<br />
#Optimized our biobricks.<br />
<br />
==Sept. 18th, 2012==<br />
Began to sort out our materials for wiki and upload the website.<br />
[[File:20130507034257!Example.jpg]]<br />
<br />
{{:Team:Tianjin/footer}}</div>Helengoodhttp://2012.igem.org/Team:Tianjin/NotebookTeam:Tianjin/Notebook2013-05-07T03:44:33Z<p>Helengood: /* Sept. 18th, 2012 */</p>
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<a href="https://2012.igem.org/Team:Tianjin/Notebook/Modeling">Modeling Notebook</a><br />
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<a href="https://2012.igem.org/Team:Tianjin/Notebook/HumanPractice">Human Practice Notebook</a><br />
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<p class="menu_head">July, 2012</p><br />
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<center><span style="font-size:46px;font-family:Cambria;margin-top:10px;line-height:80%">Notes of Experiments</span></center><br />
==July 6th, 2012==<br />
#We discuss our all of the possible projects, and finally choose one. And then allocate works to specific member.<br />
#Do some pre-experiment and make some reagants.<br />
##Liquid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl <br />
##Solid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl<br />
###20g agar<br />
#Cleaned up the lab and laboratory instruments<br />
<br />
==July 8th, 2012==<br />
#Solutions for extracting plasmid.<br />
##50mM Glucose / 25mM Tris-Cl / 10mM EDTA,pH=8.0<br />
##0.2N NaOH / 1% SDS<br />
##3M KOAc / 2M HOAc<br />
#Experiment technologies training, such as making gel, gel electrophoresis.<br />
[[File:TJU2012-Note-gel-1.png|center|350px|gel 1]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-2.png|center|350px|gel 2]]<br />
<br />
==July 11th, 2012==<br />
#Designed primers and sent orders.<br />
#Optimized the project and allocated work.<br />
#Experiment technologies and knowledge training<br />
##PCR principle and operation<br />
##Gel Extraction<br />
[[File:TJU2012-Note-gel-3.png|center|350px|gel 3]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-4.png|center|350px|gel 4]]<br />
<br />
==July 13th, 2012==<br />
1. Received the oligo and began to mutate 16S rrnB operator.<br />
[[File:TJU2012-Note-gen-1.png|center|350px|Gene1]]<br />
2. Mutated RBS of RFP and checked through gel electrophoresis.<br />
[[File:TJU2012-Note-gen-2.png|center|250px|Gene2]]<br />
[[File:TJU2012-Note-gel-5.png|thumb|center|250px|~1800bp, constant with anticipation]]<br />
<br />
==July 14th, 2012==<br />
#Transform two plasmids of we got yestday together into E.coli.[[File:TJU2012-Note-gen-3.png|center|500px|Gene 3]]<br />
#PCR verification of colonies on the LB plates.<br />
#Inculcated the right colonies in Liquid LB.<br />
<br />
==July 15th, 2012==<br />
#Extract plasmid of cells inculcated after one day.<br />
#Enzyme test of the extracted plasmid.[[File:TJU2012-Note-gel-6.png|center|200px|Gel 6]]<br />
#Inclucated the right cells in Liquid LB and added Ala partly.<br />
<br />
==July 20th, 2012==<br />
Analyse the results.<br />
[[File:TJU2012-Note-form-1.png|center|500px|Form 1]]<br />
[[File:TJU2012-Note-fig-2.png|center|300px|Fig 2]]<br />
<br />
==July 24th, 2012==<br />
#Linked the GRP gene and O-RBS RFP gene. Gel extract the previous product again, and ligate using T4 with the following gradient.[[File:TJU2012-Note-form-2.png|center|500px|form 2]]<br />
#In the same method to construct three other systems.<br />
[[File:TJU2012-Mode-cal-fig-2.png|center|500px|fig 3]]<br />
[[File:TJU2012-Mode-cal-fig-3.png|center|500px|fig 4]]<br />
[[File:TJU2012-Mode-cal-fig-4.png|center|500px|fig 5]]<br />
<br />
==July 30th, 2012==<br />
#Learned Fluorescence spectrophotometer.<br />
#measure the strength of GFP and RFP.<br />
[[File:TJU2012-Note-form-3.png|center|500px|form 3]]<br />
<br />
==Aug. 2nd, 2012==<br />
#mutated the RBS of the Amp resistance gene.[[File:TJU2012-Note-gen-4.png|center|250px|Gene 4]]<br />
#linked genes and transformed them into E. coli.<br />
<br />
==Aug. 4th, 2012==<br />
Results of plates<br />
[[File:TJU2012-Note-fig-3.png|center|300px|fig 3]]<br />
[[File:TJU2012-Note-form-4.png|center|500px|form 4]]<br />
<br />
==Aug. 8th, 2012==<br />
Began to construct the five parts needed in Assembler in Yeast. Part 1 and part 2.<br />
<br />
==Aug. 11th, 2012==<br />
Verified part 1 and 2. Synthesized the two small parts and linked through overlap PCR. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-4.png|center|600px|fig 4]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-5.png|center|500px|fig 5]]<br />
<br />
==Aug. 12th, 2012==<br />
Began to build part 3, 4 and 5. Synthesized the two small parts and linked through overlap PCR.<br />
<br />
==Aug. 14th, 2012==<br />
Verify part 3, 4 and 5. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-6.png|center|500px|fig 6]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-7.png|center|500px|fig 7]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-8.png|center|500px|fig 8]]<br />
<br />
==Aug. 18th, 2012==<br />
Transformed all the five parts into Yeast for Assembler in Yeast.<br />
<br />
==Aug. 20th, 2012==<br />
#Results of the transformation.[[File:TJU2012-Note-fig-9.png|center|300px|fig 9]]<br />
#Extract plasmids from the Yeast.<br />
<br />
==Aug. 22nd, 2012==<br />
#Transformed the plasmid from the Yeast into cells.[[File:TJU2012-Note-fig-10.png|thumb|center|300px|There are purple spots on the plates]]<br />
#Extracted plasmid and checked through gel electrophoresis.[[File:TJU2012-Note-gel-7.png|center|300px|gel 7]]<br />
#Some other results of Assembler in Yeast.<br />
[[File:TJU2012-Note-fig-11.png|center|300px|fig 11]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-12.png|center|300px|fig 12]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-13.png|center|300px|fig 13]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-14.png|center|300px|fig 14]]<br />
<br />
==Aug. 25th, 2012==<br />
#Began to build biobricks.[[File:Tianjin_BB2.PNG|center|500px|BB 2]]<br />
#Began to search articles on phages.<br />
<br />
==Sept. 1st, 2012==<br />
Went to Peking University for exchanges.<br />
[[File:TJU2012-Note-fig-15.png|center|500px|fig 15]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-16.png|center|500px|fig 16]]<br />
<br />
==Sept. 2nd, 2012==<br />
#Found out phi X174 and firstly proposed our ideas.<br />
#The second sections of our biobricks.<br />
[[File:Tianjin_BB1.PNG|center|500px|BB 1]]<br />
<br />
==Sept. 5th, 2012==<br />
#Some experiments on phages.<br />
#Optimized our biobricks.<br />
#Designed primers needed for mutating Phi X174 and send orders.<br />
<br />
==Sept. 11th, 2012==<br />
#Began to mutate gene G and E.<br />
#Optimized our biobricks.<br />
<br />
==Sept. 18th, 2012==<br />
Began to sort out our materials for wiki and upload the website.<br />
[[File:Example.jpg]]<br />
<br />
{{:Team:Tianjin/footer}}</div>Helengoodhttp://2012.igem.org/Team:Tianjin/NotebookTeam:Tianjin/Notebook2013-05-07T03:43:51Z<p>Helengood: /* Sept. 18th, 2012 */</p>
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<p class="menu_head">Notebook Contents</p><br />
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<a href="https://2012.igem.org/Team:Tianjin/Notebook/Modeling">Modeling Notebook</a><br />
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<a href="https://2012.igem.org/Team:Tianjin/Notebook/HumanPractice">Human Practice Notebook</a><br />
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<p class="menu_head">July, 2012</p><br />
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<center><span style="font-size:46px;font-family:Cambria;margin-top:10px;line-height:80%">Notes of Experiments</span></center><br />
==July 6th, 2012==<br />
#We discuss our all of the possible projects, and finally choose one. And then allocate works to specific member.<br />
#Do some pre-experiment and make some reagants.<br />
##Liquid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl <br />
##Solid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl<br />
###20g agar<br />
#Cleaned up the lab and laboratory instruments<br />
<br />
==July 8th, 2012==<br />
#Solutions for extracting plasmid.<br />
##50mM Glucose / 25mM Tris-Cl / 10mM EDTA,pH=8.0<br />
##0.2N NaOH / 1% SDS<br />
##3M KOAc / 2M HOAc<br />
#Experiment technologies training, such as making gel, gel electrophoresis.<br />
[[File:TJU2012-Note-gel-1.png|center|350px|gel 1]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-2.png|center|350px|gel 2]]<br />
<br />
==July 11th, 2012==<br />
#Designed primers and sent orders.<br />
#Optimized the project and allocated work.<br />
#Experiment technologies and knowledge training<br />
##PCR principle and operation<br />
##Gel Extraction<br />
[[File:TJU2012-Note-gel-3.png|center|350px|gel 3]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-4.png|center|350px|gel 4]]<br />
<br />
==July 13th, 2012==<br />
1. Received the oligo and began to mutate 16S rrnB operator.<br />
[[File:TJU2012-Note-gen-1.png|center|350px|Gene1]]<br />
2. Mutated RBS of RFP and checked through gel electrophoresis.<br />
[[File:TJU2012-Note-gen-2.png|center|250px|Gene2]]<br />
[[File:TJU2012-Note-gel-5.png|thumb|center|250px|~1800bp, constant with anticipation]]<br />
<br />
==July 14th, 2012==<br />
#Transform two plasmids of we got yestday together into E.coli.[[File:TJU2012-Note-gen-3.png|center|500px|Gene 3]]<br />
#PCR verification of colonies on the LB plates.<br />
#Inculcated the right colonies in Liquid LB.<br />
<br />
==July 15th, 2012==<br />
#Extract plasmid of cells inculcated after one day.<br />
#Enzyme test of the extracted plasmid.[[File:TJU2012-Note-gel-6.png|center|200px|Gel 6]]<br />
#Inclucated the right cells in Liquid LB and added Ala partly.<br />
<br />
==July 20th, 2012==<br />
Analyse the results.<br />
[[File:TJU2012-Note-form-1.png|center|500px|Form 1]]<br />
[[File:TJU2012-Note-fig-2.png|center|300px|Fig 2]]<br />
<br />
==July 24th, 2012==<br />
#Linked the GRP gene and O-RBS RFP gene. Gel extract the previous product again, and ligate using T4 with the following gradient.[[File:TJU2012-Note-form-2.png|center|500px|form 2]]<br />
#In the same method to construct three other systems.<br />
[[File:TJU2012-Mode-cal-fig-2.png|center|500px|fig 3]]<br />
[[File:TJU2012-Mode-cal-fig-3.png|center|500px|fig 4]]<br />
[[File:TJU2012-Mode-cal-fig-4.png|center|500px|fig 5]]<br />
<br />
==July 30th, 2012==<br />
#Learned Fluorescence spectrophotometer.<br />
#measure the strength of GFP and RFP.<br />
[[File:TJU2012-Note-form-3.png|center|500px|form 3]]<br />
<br />
==Aug. 2nd, 2012==<br />
#mutated the RBS of the Amp resistance gene.[[File:TJU2012-Note-gen-4.png|center|250px|Gene 4]]<br />
#linked genes and transformed them into E. coli.<br />
<br />
==Aug. 4th, 2012==<br />
Results of plates<br />
[[File:TJU2012-Note-fig-3.png|center|300px|fig 3]]<br />
[[File:TJU2012-Note-form-4.png|center|500px|form 4]]<br />
<br />
==Aug. 8th, 2012==<br />
Began to construct the five parts needed in Assembler in Yeast. Part 1 and part 2.<br />
<br />
==Aug. 11th, 2012==<br />
Verified part 1 and 2. Synthesized the two small parts and linked through overlap PCR. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-4.png|center|600px|fig 4]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-5.png|center|500px|fig 5]]<br />
<br />
==Aug. 12th, 2012==<br />
Began to build part 3, 4 and 5. Synthesized the two small parts and linked through overlap PCR.<br />
<br />
==Aug. 14th, 2012==<br />
Verify part 3, 4 and 5. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-6.png|center|500px|fig 6]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-7.png|center|500px|fig 7]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-8.png|center|500px|fig 8]]<br />
<br />
==Aug. 18th, 2012==<br />
Transformed all the five parts into Yeast for Assembler in Yeast.<br />
<br />
==Aug. 20th, 2012==<br />
#Results of the transformation.[[File:TJU2012-Note-fig-9.png|center|300px|fig 9]]<br />
#Extract plasmids from the Yeast.<br />
<br />
==Aug. 22nd, 2012==<br />
#Transformed the plasmid from the Yeast into cells.[[File:TJU2012-Note-fig-10.png|thumb|center|300px|There are purple spots on the plates]]<br />
#Extracted plasmid and checked through gel electrophoresis.[[File:TJU2012-Note-gel-7.png|center|300px|gel 7]]<br />
#Some other results of Assembler in Yeast.<br />
[[File:TJU2012-Note-fig-11.png|center|300px|fig 11]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-12.png|center|300px|fig 12]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-13.png|center|300px|fig 13]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-14.png|center|300px|fig 14]]<br />
<br />
==Aug. 25th, 2012==<br />
#Began to build biobricks.[[File:Tianjin_BB2.PNG|center|500px|BB 2]]<br />
#Began to search articles on phages.<br />
<br />
==Sept. 1st, 2012==<br />
Went to Peking University for exchanges.<br />
[[File:TJU2012-Note-fig-15.png|center|500px|fig 15]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-16.png|center|500px|fig 16]]<br />
<br />
==Sept. 2nd, 2012==<br />
#Found out phi X174 and firstly proposed our ideas.<br />
#The second sections of our biobricks.<br />
[[File:Tianjin_BB1.PNG|center|500px|BB 1]]<br />
<br />
==Sept. 5th, 2012==<br />
#Some experiments on phages.<br />
#Optimized our biobricks.<br />
#Designed primers needed for mutating Phi X174 and send orders.<br />
<br />
==Sept. 11th, 2012==<br />
#Began to mutate gene G and E.<br />
#Optimized our biobricks.<br />
<br />
==Sept. 18th, 2012==<br />
Began to sort out our materials for wiki and upload the website.<br />
<br />
{{:Team:Tianjin/footer}}</div>Helengoodhttp://2012.igem.org/File:Example.jpgFile:Example.jpg2013-05-07T03:42:57Z<p>Helengood: uploaded a new version of &quot;File:Example.jpg&quot;: Reverted to version as of 03:33, 7 May 2013</p>
<hr />
<div></div>Helengoodhttp://2012.igem.org/Team:Tianjin/NotebookTeam:Tianjin/Notebook2013-05-07T03:42:34Z<p>Helengood: /* Sept. 18th, 2012 */</p>
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<p class="menu_head">Notebook Contents</p><br />
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<a href="https://2012.igem.org/Team:Tianjin/Notebook/Modeling">Modeling Notebook</a><br />
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<a href="https://2012.igem.org/Team:Tianjin/Notebook/HumanPractice">Human Practice Notebook</a><br />
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<p class="menu_head">July, 2012</p><br />
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<center><span style="font-size:46px;font-family:Cambria;margin-top:10px;line-height:80%">Notes of Experiments</span></center><br />
==July 6th, 2012==<br />
#We discuss our all of the possible projects, and finally choose one. And then allocate works to specific member.<br />
#Do some pre-experiment and make some reagants.<br />
##Liquid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl <br />
##Solid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl<br />
###20g agar<br />
#Cleaned up the lab and laboratory instruments<br />
<br />
==July 8th, 2012==<br />
#Solutions for extracting plasmid.<br />
##50mM Glucose / 25mM Tris-Cl / 10mM EDTA,pH=8.0<br />
##0.2N NaOH / 1% SDS<br />
##3M KOAc / 2M HOAc<br />
#Experiment technologies training, such as making gel, gel electrophoresis.<br />
[[File:TJU2012-Note-gel-1.png|center|350px|gel 1]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-2.png|center|350px|gel 2]]<br />
<br />
==July 11th, 2012==<br />
#Designed primers and sent orders.<br />
#Optimized the project and allocated work.<br />
#Experiment technologies and knowledge training<br />
##PCR principle and operation<br />
##Gel Extraction<br />
[[File:TJU2012-Note-gel-3.png|center|350px|gel 3]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-4.png|center|350px|gel 4]]<br />
<br />
==July 13th, 2012==<br />
1. Received the oligo and began to mutate 16S rrnB operator.<br />
[[File:TJU2012-Note-gen-1.png|center|350px|Gene1]]<br />
2. Mutated RBS of RFP and checked through gel electrophoresis.<br />
[[File:TJU2012-Note-gen-2.png|center|250px|Gene2]]<br />
[[File:TJU2012-Note-gel-5.png|thumb|center|250px|~1800bp, constant with anticipation]]<br />
<br />
==July 14th, 2012==<br />
#Transform two plasmids of we got yestday together into E.coli.[[File:TJU2012-Note-gen-3.png|center|500px|Gene 3]]<br />
#PCR verification of colonies on the LB plates.<br />
#Inculcated the right colonies in Liquid LB.<br />
<br />
==July 15th, 2012==<br />
#Extract plasmid of cells inculcated after one day.<br />
#Enzyme test of the extracted plasmid.[[File:TJU2012-Note-gel-6.png|center|200px|Gel 6]]<br />
#Inclucated the right cells in Liquid LB and added Ala partly.<br />
<br />
==July 20th, 2012==<br />
Analyse the results.<br />
[[File:TJU2012-Note-form-1.png|center|500px|Form 1]]<br />
[[File:TJU2012-Note-fig-2.png|center|300px|Fig 2]]<br />
<br />
==July 24th, 2012==<br />
#Linked the GRP gene and O-RBS RFP gene. Gel extract the previous product again, and ligate using T4 with the following gradient.[[File:TJU2012-Note-form-2.png|center|500px|form 2]]<br />
#In the same method to construct three other systems.<br />
[[File:TJU2012-Mode-cal-fig-2.png|center|500px|fig 3]]<br />
[[File:TJU2012-Mode-cal-fig-3.png|center|500px|fig 4]]<br />
[[File:TJU2012-Mode-cal-fig-4.png|center|500px|fig 5]]<br />
<br />
==July 30th, 2012==<br />
#Learned Fluorescence spectrophotometer.<br />
#measure the strength of GFP and RFP.<br />
[[File:TJU2012-Note-form-3.png|center|500px|form 3]]<br />
<br />
==Aug. 2nd, 2012==<br />
#mutated the RBS of the Amp resistance gene.[[File:TJU2012-Note-gen-4.png|center|250px|Gene 4]]<br />
#linked genes and transformed them into E. coli.<br />
<br />
==Aug. 4th, 2012==<br />
Results of plates<br />
[[File:TJU2012-Note-fig-3.png|center|300px|fig 3]]<br />
[[File:TJU2012-Note-form-4.png|center|500px|form 4]]<br />
<br />
==Aug. 8th, 2012==<br />
Began to construct the five parts needed in Assembler in Yeast. Part 1 and part 2.<br />
<br />
==Aug. 11th, 2012==<br />
Verified part 1 and 2. Synthesized the two small parts and linked through overlap PCR. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-4.png|center|600px|fig 4]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-5.png|center|500px|fig 5]]<br />
<br />
==Aug. 12th, 2012==<br />
Began to build part 3, 4 and 5. Synthesized the two small parts and linked through overlap PCR.<br />
<br />
==Aug. 14th, 2012==<br />
Verify part 3, 4 and 5. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-6.png|center|500px|fig 6]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-7.png|center|500px|fig 7]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-8.png|center|500px|fig 8]]<br />
<br />
==Aug. 18th, 2012==<br />
Transformed all the five parts into Yeast for Assembler in Yeast.<br />
<br />
==Aug. 20th, 2012==<br />
#Results of the transformation.[[File:TJU2012-Note-fig-9.png|center|300px|fig 9]]<br />
#Extract plasmids from the Yeast.<br />
<br />
==Aug. 22nd, 2012==<br />
#Transformed the plasmid from the Yeast into cells.[[File:TJU2012-Note-fig-10.png|thumb|center|300px|There are purple spots on the plates]]<br />
#Extracted plasmid and checked through gel electrophoresis.[[File:TJU2012-Note-gel-7.png|center|300px|gel 7]]<br />
#Some other results of Assembler in Yeast.<br />
[[File:TJU2012-Note-fig-11.png|center|300px|fig 11]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-12.png|center|300px|fig 12]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-13.png|center|300px|fig 13]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-14.png|center|300px|fig 14]]<br />
<br />
==Aug. 25th, 2012==<br />
#Began to build biobricks.[[File:Tianjin_BB2.PNG|center|500px|BB 2]]<br />
#Began to search articles on phages.<br />
<br />
==Sept. 1st, 2012==<br />
Went to Peking University for exchanges.<br />
[[File:TJU2012-Note-fig-15.png|center|500px|fig 15]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-16.png|center|500px|fig 16]]<br />
<br />
==Sept. 2nd, 2012==<br />
#Found out phi X174 and firstly proposed our ideas.<br />
#The second sections of our biobricks.<br />
[[File:Tianjin_BB1.PNG|center|500px|BB 1]]<br />
<br />
==Sept. 5th, 2012==<br />
#Some experiments on phages.<br />
#Optimized our biobricks.<br />
#Designed primers needed for mutating Phi X174 and send orders.<br />
<br />
==Sept. 11th, 2012==<br />
#Began to mutate gene G and E.<br />
#Optimized our biobricks.<br />
<br />
==Sept. 18th, 2012==<br />
Began to sort out our materials for wiki and upload the website.<br />
<br />
{{:Team:Tianjin/footer}}<br />
[[File:Example.jpg]]</div>Helengoodhttp://2012.igem.org/Team:Tianjin/NotebookTeam:Tianjin/Notebook2013-05-07T03:40:25Z<p>Helengood: /* Sept. 18th, 2012 */</p>
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<p class="menu_head">Notebook Contents</p><br />
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<a href="https://2012.igem.org/Team:Tianjin/Notebook/Modeling">Modeling Notebook</a><br />
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<a href="https://2012.igem.org/Team:Tianjin/Notebook/HumanPractice">Human Practice Notebook</a><br />
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<p class="menu_head">July, 2012</p><br />
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<div id="text-content"><br />
<center><span style="font-size:46px;font-family:Cambria;margin-top:10px;line-height:80%">Notes of Experiments</span></center><br />
==July 6th, 2012==<br />
#We discuss our all of the possible projects, and finally choose one. And then allocate works to specific member.<br />
#Do some pre-experiment and make some reagants.<br />
##Liquid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl <br />
##Solid LB <br />
###10g tryptone <br />
###5g yeast extract <br />
###10g NaCl<br />
###20g agar<br />
#Cleaned up the lab and laboratory instruments<br />
<br />
==July 8th, 2012==<br />
#Solutions for extracting plasmid.<br />
##50mM Glucose / 25mM Tris-Cl / 10mM EDTA,pH=8.0<br />
##0.2N NaOH / 1% SDS<br />
##3M KOAc / 2M HOAc<br />
#Experiment technologies training, such as making gel, gel electrophoresis.<br />
[[File:TJU2012-Note-gel-1.png|center|350px|gel 1]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-2.png|center|350px|gel 2]]<br />
<br />
==July 11th, 2012==<br />
#Designed primers and sent orders.<br />
#Optimized the project and allocated work.<br />
#Experiment technologies and knowledge training<br />
##PCR principle and operation<br />
##Gel Extraction<br />
[[File:TJU2012-Note-gel-3.png|center|350px|gel 3]]<br />
<br />
<br />
[[File:TJU2012-Note-gel-4.png|center|350px|gel 4]]<br />
<br />
==July 13th, 2012==<br />
1. Received the oligo and began to mutate 16S rrnB operator.<br />
[[File:TJU2012-Note-gen-1.png|center|350px|Gene1]]<br />
2. Mutated RBS of RFP and checked through gel electrophoresis.<br />
[[File:TJU2012-Note-gen-2.png|center|250px|Gene2]]<br />
[[File:TJU2012-Note-gel-5.png|thumb|center|250px|~1800bp, constant with anticipation]]<br />
<br />
==July 14th, 2012==<br />
#Transform two plasmids of we got yestday together into E.coli.[[File:TJU2012-Note-gen-3.png|center|500px|Gene 3]]<br />
#PCR verification of colonies on the LB plates.<br />
#Inculcated the right colonies in Liquid LB.<br />
<br />
==July 15th, 2012==<br />
#Extract plasmid of cells inculcated after one day.<br />
#Enzyme test of the extracted plasmid.[[File:TJU2012-Note-gel-6.png|center|200px|Gel 6]]<br />
#Inclucated the right cells in Liquid LB and added Ala partly.<br />
<br />
==July 20th, 2012==<br />
Analyse the results.<br />
[[File:TJU2012-Note-form-1.png|center|500px|Form 1]]<br />
[[File:TJU2012-Note-fig-2.png|center|300px|Fig 2]]<br />
<br />
==July 24th, 2012==<br />
#Linked the GRP gene and O-RBS RFP gene. Gel extract the previous product again, and ligate using T4 with the following gradient.[[File:TJU2012-Note-form-2.png|center|500px|form 2]]<br />
#In the same method to construct three other systems.<br />
[[File:TJU2012-Mode-cal-fig-2.png|center|500px|fig 3]]<br />
[[File:TJU2012-Mode-cal-fig-3.png|center|500px|fig 4]]<br />
[[File:TJU2012-Mode-cal-fig-4.png|center|500px|fig 5]]<br />
<br />
==July 30th, 2012==<br />
#Learned Fluorescence spectrophotometer.<br />
#measure the strength of GFP and RFP.<br />
[[File:TJU2012-Note-form-3.png|center|500px|form 3]]<br />
<br />
==Aug. 2nd, 2012==<br />
#mutated the RBS of the Amp resistance gene.[[File:TJU2012-Note-gen-4.png|center|250px|Gene 4]]<br />
#linked genes and transformed them into E. coli.<br />
<br />
==Aug. 4th, 2012==<br />
Results of plates<br />
[[File:TJU2012-Note-fig-3.png|center|300px|fig 3]]<br />
[[File:TJU2012-Note-form-4.png|center|500px|form 4]]<br />
<br />
==Aug. 8th, 2012==<br />
Began to construct the five parts needed in Assembler in Yeast. Part 1 and part 2.<br />
<br />
==Aug. 11th, 2012==<br />
Verified part 1 and 2. Synthesized the two small parts and linked through overlap PCR. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-4.png|center|600px|fig 4]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-5.png|center|500px|fig 5]]<br />
<br />
==Aug. 12th, 2012==<br />
Began to build part 3, 4 and 5. Synthesized the two small parts and linked through overlap PCR.<br />
<br />
==Aug. 14th, 2012==<br />
Verify part 3, 4 and 5. Verified through ligase digestion and then gel electrophoresis.<br />
[[File:TJU2012-Note-fig-6.png|center|500px|fig 6]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-7.png|center|500px|fig 7]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-8.png|center|500px|fig 8]]<br />
<br />
==Aug. 18th, 2012==<br />
Transformed all the five parts into Yeast for Assembler in Yeast.<br />
<br />
==Aug. 20th, 2012==<br />
#Results of the transformation.[[File:TJU2012-Note-fig-9.png|center|300px|fig 9]]<br />
#Extract plasmids from the Yeast.<br />
<br />
==Aug. 22nd, 2012==<br />
#Transformed the plasmid from the Yeast into cells.[[File:TJU2012-Note-fig-10.png|thumb|center|300px|There are purple spots on the plates]]<br />
#Extracted plasmid and checked through gel electrophoresis.[[File:TJU2012-Note-gel-7.png|center|300px|gel 7]]<br />
#Some other results of Assembler in Yeast.<br />
[[File:TJU2012-Note-fig-11.png|center|300px|fig 11]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-12.png|center|300px|fig 12]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-13.png|center|300px|fig 13]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-14.png|center|300px|fig 14]]<br />
<br />
==Aug. 25th, 2012==<br />
#Began to build biobricks.[[File:Tianjin_BB2.PNG|center|500px|BB 2]]<br />
#Began to search articles on phages.<br />
<br />
==Sept. 1st, 2012==<br />
Went to Peking University for exchanges.<br />
[[File:TJU2012-Note-fig-15.png|center|500px|fig 15]]<br />
<br />
<br />
[[File:TJU2012-Note-fig-16.png|center|500px|fig 16]]<br />
<br />
==Sept. 2nd, 2012==<br />
#Found out phi X174 and firstly proposed our ideas.<br />
#The second sections of our biobricks.<br />
[[File:Tianjin_BB1.PNG|center|500px|BB 1]]<br />
<br />
==Sept. 5th, 2012==<br />
#Some experiments on phages.<br />
#Optimized our biobricks.<br />
#Designed primers needed for mutating Phi X174 and send orders.<br />
<br />
==Sept. 11th, 2012==<br />
#Began to mutate gene G and E.<br />
#Optimized our biobricks.<br />
<br />
==Sept. 18th, 2012==<br />
Began to sort out our materials for wiki and upload the website.<br />
<br />
{{:Team:Tianjin/footer}}<br />
[[File:TJU2012-Note-fig-20.jpg|center|500px|fig 20]]</div>Helengoodhttp://2012.igem.org/File:Example.jpgFile:Example.jpg2013-05-07T03:37:02Z<p>Helengood: uploaded a new version of &quot;File:Example.jpg&quot;: Reverted to version as of 03:31, 7 May 2013</p>
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<div></div>Helengoodhttp://2012.igem.org/File:Example.jpgFile:Example.jpg2013-05-07T03:33:33Z<p>Helengood: uploaded a new version of &quot;File:Example.jpg&quot;: Reverted to version as of 03:30, 7 May 2013</p>
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<div></div>Helengoodhttp://2012.igem.org/File:Example.jpgFile:Example.jpg2013-05-07T03:31:57Z<p>Helengood: uploaded a new version of &quot;File:Example.jpg&quot;</p>
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<div></div>Helengoodhttp://2012.igem.org/File:Example.jpgFile:Example.jpg2013-05-07T03:30:34Z<p>Helengood: uploaded a new version of &quot;File:Example.jpg&quot;</p>
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<div></div>Helengoodhttp://2012.igem.org/Team:Tianjin/AttributionsTeam:Tianjin/Attributions2013-05-05T07:43:16Z<p>Helengood: /* Team Members */</p>
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<br><center><span style="font-size:46px;font-family:Cambria;margin-top:10px">Attributions</span></center><br />
<br><br />
=Team Members=<br />
[[Team:Tianjin/Team|'''Bin Jia''']], team leader, project design, experiment operation;<br />
<br />
[[Team:Tianjin/Team|'''Jinlai Zhang''']], project design, experiment operation, human practice;<br />
<br />
[[Team:Tianjin/Team|'''Dongchang Qin''']], project design, experiment operation;<br />
<br />
[[Team:Tianjin/Team|'''Jiaquan Liu''']], project design, wiki construction and composition, experiment operation;<br />
<br />
[[Team:Tianjin/Team|'''Qinfeng Wu''']], project design, wiki construction, experiment operation;<br />
<br />
[[Team:Tianjin/Team|'''Lingli Ni''']], human practice, experiment operation;<br />
<br />
[[Team:Tianjin/Team|'''Yifeng Shao''']], human practice, modeling;<br />
<br />
[[Team:Tianjin/Team|'''Yapeng Su''']], modeling, project design, human practice;<br />
<br />
[[Team:Tianjin/Team|'''Yufei Wei''']], modeling, project design, human practice;<br />
<br />
[[Team:Tianjin/Team|'''Xiaonan Cheng''']], wiki design and construction, movie filming and editing, human practice;<br />
<br />
[[Team:Tianjin/Team|'''Andi Wangzhou''']], project design, wiki & poster design and construction, experiment assistance;<br />
<br />
[[Team:Tianjin/Team|'''Hengqian Ren''']], project design, experiment assistance;<br />
<br />
[[Team:Tianjin/Team|'''Yang Li''']], experiment assistance;<br />
<br />
[[Team:Tianjin/Team|'''Linlin Song''']], experiment assistance;<br />
<br />
[[Team:Tianjin/Team|'''Shu Gong''']], experiment assistance.<br />
<br />
<br />
<br><center><span style="font-size:46px;font-family:Cambria;margin-top:10px">Contributions</span></center><br />
<br><br />
<br />
=Special Thanks to=<br />
[[file:TJU2012-Team-Yuan.png|thumb|290px|left|'''Professor Yingjin Yuan''', who offered all the necessary advice and resources including laboratories, funding, and graduate student suggestion in the whole iGEM project.]] [[file:TJU2012-Libingzhi.png|thumb|290px|none|'''Dr. Binzhi Li''', who offered us assistance in details during the project.]]<br />
<br />
<br />
<br />
<br />
'''The Key Laboratory of Systems Biongineering''', which provided us with all equipment and platform that are indispensable to our success.<br />
<br />
'''Tianjin University International Cooperation Office''', for their support in the competition.<br />
<br />
'''Tianjin University Jiankun Foundation,''' for generously paying for our travel expenses.<br />
<br />
=Thanks to=<br />
'''SAST of NKU''', '''SAST of TJU''', '''SAST of School of Life Science (NKU)''', '''Biology Club of Nankai Middle School''', for supporting us in the Visit Activity.<br />
<br />
'''Tianluo Chen,''' who has done a lot for Human Pracitce's paperwork.<br />
<br />
'''Zehua Xia,''' who has helped us to hold the Visit Activity as the chairman of SAST of TJU.<br />
<br />
'''Mengfei Liu,''' who has devoted to the analysis of the modeling,<br />
<br />
'''Stanley Wang,''' for your spectacular performances<br />
<br />
'''Yiyang Cheng,''' for your one of a kind vocal performance.<br />
<br />
'''Weiming Huang,''' for shooting those gorgeous pictures of our team<br />
<br />
<br />
{{:Team:Tianjin/footer}}</div>Helengoodhttp://2012.igem.org/Team:Tianjin/Project/GeneTeam:Tianjin/Project/Gene2012-10-27T03:50:06Z<p>Helengood: /* Constructing the Orthogonal Phages */</p>
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__NOTOC__<br />
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<a href="https://2012.igem.org/Team:Tianjin/Project">Project Home</a><br />
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<a href="https://2012.igem.org/Team:Tianjin/Project/OrthogonalSystem">Orthogonal System</a><br />
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<a href="https://2012.igem.org/Team:Tianjin/Project/Regulation">Logic Metabolism Regulation</a><br />
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<a href="https://2012.igem.org/Team:Tianjin/Data">BioBrick</a><br />
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<a href="https://2012.igem.org/Team:Tianjin/Project/Technology">Technology</a><br />
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<p class="menu_head">In this page</p><br />
<div class="menu_body"><br />
<div class="menu_children"><br />
<a href="#Background">Background</a><br />
</div><br />
<div class="menu_children"><br />
<a href="#Principles">Principles</a><br />
</div><br />
<div class="menu_children"><br />
<a href="#Plan_of_φx174">Plan of φx174</a><br />
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<a href="#Prospect">Prospect</a><br />
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<br />
<center><span style="font-size:46px;font-family:Cambria;margin-top:10px;line-height:80%">Future Work</span></center><br />
<br><br />
<br />
=Abstract of Future Work=<br />
[[file:Tianjin_SynBio_Museum.jpg|thumb|250px|right|'''Figure 1.''' Poster of SynBio Museum (by TJU iGEM Team 2012)]]<br />
===Genetic Pollution===<br />
Genetic pollution is the term of genetics in which the genetic information is transferred into the organisms where it is not needed or where this information never existed before. This flow of genetic information is usually undesired and cannot be controlled. The flow of genetic information usually takes place between the genetically modified organisms into the organisms which are not genetically modified.<br />
<br />
Genetic pollution occurs when domesticated or genetically engineered species interbreed with their wild cousins, thus polluting the wild species gene pool. It is seen as negative because it affects the wild population's evolved capability to survive, as well as spreading genes that are not found in nature.<br />
<br />
One of the main issues of genetic pollution lies in the fact that man has tampered with the genetic structure of these species and has created a situation that would not be found naturally. Some people find no issue with genetic pollution however, stating that it is the natural course of events. One thing is certain, genetic pollution irrevocably alters a species, for better or worse.<br />
<br />
Genetic pollution doesn't exist in theories or novels anymore. It is happening in our world. For example, "gold rice" event in China where genetically engineered rice with β-carotene was fed to children for research recently attracted people's large attention. The serious situation calls for new way to prevent genetic pollution. For more information, go to our [[Team:Tianjin/HumanPractice|Human Practice]] page.<br />
<br />
===Genetic Encryption===<br />
[[file:TJU2012-Proj-SE-fig-1.png|thumb|200px|left|'''Figure 2.''' Genetic Encryption (from TJU iGEM Team 2012)]]In the information time, data encryption have always been a vital part of commerce, informatics and Internets. It has become a major research and investment field.<br />
<br />
After the establishment of DNA double helix model, scientists have always been trying to store data through gene. Just as other forms of information flows, if we want to communicate through gene, we have to encrypt and decipher. Many scientists developed some other methods to encrypt in gene. For example, some researchers thought of encrypting through specific inducer. Only adding this inducer, the cell could transcript the gene and express the stored information. Here we offer one new method to encrypt through orthogonal system, and it works well.<br />
<br />
===Pollution Prevention===<br />
[[file:TJU2012-Proj-SE-fig-2.png|thumb|200px|right|'''Figure 3.''' Logo of TJU iGEM Team 2012 (from TJU iGEM Team 2012)]]Biologists across the globe have proposed various solutions to conquer genetic pollution, such as kill-switch. These approaches have their advantages in one way or another, but certain defects too. In this year's project, we come up with a distinctive thinking. We want to construct a new system of orthogonal transcription-translation network, i.e. O-Key. Any genes in O-Key cannot be expressed in normal environment, and then decomposed. In this way, the O-Key can prevent the horizontal gene transfer. In our project this year, we propose several methods to construct orthogonal creature, the phages, such as T7, and φX174. What is more, we have begun to execute the plan of creating the orthogonal φX174. Although this is just a beginning, the future of orthogonal organism and O-Key is sure to be promising.<br />
<br />
=Principles of Future Work=<br />
===Preventing Genetic Pollution and Genetic Encryption===<br />
In order to express a certain gene in an orthogonal transcription-translation system, we need both the o-ribosome and o-mRNA to form the O-Key. We are able to rationally design the SD sequence of an mRNA, to make it inscrutable to canonical ribosome. In the meantime, a plasmid manufacturing orthogonal ribosome can be transformed into the cell to help express the o-mRNA: just like a key opens a lock. This mechanism is highly effective in controlling protein expression. <br />
<br />
What if we want to limit the expression of certain protein? What if we need to accurately regulate the expression under certain circumstances? The O-Key offers us a great choice. We can put an o-RBS to any gene that codes for hazardous protein. By controlling the existence of the O-Key, we can precisely control the expression of this protein. In this way, the synthesis of dangerous proteins can be strictly restricted and controlled by O-Key, thus preventing genetic pollution. The O-Key serves as a safe to contain <br />
<br />
To take one step further O-Key can be applied into biological product. Say we are a pharmaceutical company, and we have a brand new bacterium that can produce an antibiotics. We want to lease bacterium to some companies, but we don't want them to resell it or spread it out. In order to protect our intellectual property, we can use a new encryption technology using the O-Key. <br />
<br />
The RBS of the mRNA of some essential protein that sustains cells' life are switched to O-Lock, and we embedded the gene that manufacture O-Key in the cells to decipher the O-Luck. However, the gene for O-Lock needs special inducer. Thus, our company needs to constantly provide the inducer when the contract is valid. The inducer will result in O-Key. Together with the O-Lock, they serve as the O-Key System to produce the essential protein that sustains cells' life. When the contract expires, we'll stop providing the inducer, and the bacteria will stop manufacturing the antibiotics. <br />
<br />
As demonstrated previously, we can use the O-Key System to restrict genetic pollution, and construct an encryption system that protects intellectual property.<br />
<br />
===Constructing the Orthogonal Phages===<br />
If we could apply the O-Key System to one particular regulation. Why couldn't we apply it to the entire organism? At first, we wanted to build a fully orthogonal cells. But minimal genome for a cell is more than 300, which is obviously beyond our abilities. Therefore, we chose phages as the creature we work on. The reason why we choose phages are mainly based on its simple replication process and relatively small genome.<br />
<br />
However, different phages have different genome, so we should adopt different methods. For the phages with large genome(more than 20kb), we could divide the whole genome into several little parts, mutate the genome one by one and then assembly with "Yest Assembler". For the phages with small genome, we could mutate the gene directly or firstly divide the genome into small parts and then assembly in Gibson assembly method. As the mutation methods are all site-specific mutations, we just take φX174 as an example. <br />
<br />
We will mutate the genome one by one. Once we mutate one gene, we will transform the mutated phage DNA into orthogonal and normal cells to check whether the phage could still replicate, which is revealed by phage plaques. For the overlap gene in the phage DNA, if mutated RBS does affect other genes, we will put this gene before gene A and close the original gene by changing its start codon.<br />
<br />
For the limited time, we just plan to construct fully orthogonal φX174. Why we choose φx174 are based on following facts.<br />
# The first creature that was sequenced whole genome;<br />
# The second artificially synthesized viral;<br />
# We have knew clearly about it(if searching in goggle scholar, articles>300);<br />
# The replication process is simple and clear.<br />
# The genome is small, containing only 11 gene.<br />
# φX174 will not affect the common ''E. coli''.<br />
<br />
===Plan of φx174===<br />
[[file:TJU2012-Proj-SE-fig-5.png|thumb|371px|center|'''Figure 6.''' φX174 assemble process (from TJU iGEM Team 2012)]]<br />
This picture shows one repeated part of our future work to construct a fully orthogonal creature-----O-Phix 174. We tried to mutate the gene’s RBS to O-RBS, and then separately transform into both the N-E.coli and O-E.coli. If the mutation is ok, there will be plaques on the LB flat with O-E.coli, while no plaques on the other flat with N-E.coli. One by one, we could finally mutate all gene’s RBS and the get our targeted fully orthogonal creature.<br />
As for the limited time, we just do some preliminary experiments and design the primers needed for latter work.<br />
<br />
=Modeling on Future Work=<br />
To describe the process of genetic pollution, we have established a model inspired by the popular economical Bass model combined with the biological special conditions, for example the change number of bacteria under ideal and real condition, the spatial diffusion of exogenous gene. This model can predict the time when the critical concentration of bacteria is reached at a specific condition. For more details, see our [[Team:Tianjin/Modeling|Model Part]].<br />
[[file:TJU2012-Mode-HGT-fig-7.png|thumb|500px|center|'''Figure 7.''' Prediction of genetic pollution (from TJU iGEM Team 2012)]]<br />
<br />
=Conclusion of Future Work=<br />
Some people say that 21 century is the bio-century. With the full development of biology, genetic pollution will be a topic that could not be avoided in future. Some method on preventing genetic pollution will receive more and more attention. Our O-Key System, for its robustness,universality,is simple and effective. In the near future, the O-Key System will play a vital role in genetic pollution prevention. What is more, the O-Key System also works well in genetic encryption. Today, we are facing a world, full of information. Of all the parts of statistics flow, data encryption is an essential fragment. Orthogonal encryption system provide a good method to mask information. To our pleasure, we have been contacting with some related companies for application and received some good results. We have confidence that such a system will achieve a good success. <br />
<br />
Finally, we all think building orthogonal creature is a perfect idea. Since we could put orthogonal system in one regulation, why don't we apply it to the whole cell. Just as J C Venter. Other scientists all focused on assembly of a small gene, but he assembled the whole genome of bacterium ''Mycoplasma mycoides''. When we use the orthogonal phages, they could not affect normal cells. Phage pollution is usually common condition in laboratory and need several weeks to disinfect. Orthogonal cells have great advantages in real practice, such as more easily adjusted,never polluting normal cells. We believe that in the future, more orthogonal creatures will be built, and then construct an indispensable system, separate from existing translation and transcription system. Such a system, for its advantages, is more suitable for application in industry and research, blocking the possibility of genetic pollution. However, admittedly, building up such a huge system still require a lots of time and source, we have faith such day will finally come, when real orthogonal system is set up.<br />
<br />
=References=<br />
#Lon M. Chubiz and Christopher V. Rao(2008). Computational design of orthogonal ribosomes, vol.36 no.12<br />
#Wenlin An and Jason W. Chinl(2009). Synthesis of orthogonal transcriptiontranslation networks, vol.106 no.21<br />
#Howard M Salis, Ethan A Mirsky & Christopher A Voigt(2009).Automated design of synthetic ribosome binding sites to control protein expression, doi:10.1038/nbt.1568<br />
#George H.McArthur IV and Stephen S. Fong, Toward Engineering Synthetic Microbial Metabolism<br />
#WANG Haisheng,ZHANG Xiaoxia, et al., Recent research progress of bacterial violacein <br />
#Carotenoid Crystal Formation in Arabidopsis and Carrot Roots Caused by Increased Phytoene Synthase Protein Levels<br />
#Guoyin Kai, Pan Liao, Tong Zhang, Wei Zhou, Jing Wang, Hui Xu, Yuanyun Liu, and Lin Zhang. Characterization,Expression Profiling, and Functional Identification of a Gene Encoding Geranylgeranyl Diphosphate Synthase from Salvia miltiorrhiza<br />
<br />
<br />
{{:Team:Tianjin/footer}}</div>Helengoodhttp://2012.igem.org/Team:Tianjin/Project/GeneTeam:Tianjin/Project/Gene2012-10-27T03:43:47Z<p>Helengood: /* Genetic Pollution */</p>
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<center><span style="font-size:46px;font-family:Cambria;margin-top:10px;line-height:80%">Future Work</span></center><br />
<br><br />
<br />
=Abstract of Future Work=<br />
[[file:Tianjin_SynBio_Museum.jpg|thumb|250px|right|'''Figure 1.''' Poster of SynBio Museum (by TJU iGEM Team 2012)]]<br />
===Genetic Pollution===<br />
Genetic pollution is the term of genetics in which the genetic information is transferred into the organisms where it is not needed or where this information never existed before. This flow of genetic information is usually undesired and cannot be controlled. The flow of genetic information usually takes place between the genetically modified organisms into the organisms which are not genetically modified.<br />
<br />
Genetic pollution occurs when domesticated or genetically engineered species interbreed with their wild cousins, thus polluting the wild species gene pool. It is seen as negative because it affects the wild population's evolved capability to survive, as well as spreading genes that are not found in nature.<br />
<br />
One of the main issues of genetic pollution lies in the fact that man has tampered with the genetic structure of these species and has created a situation that would not be found naturally. Some people find no issue with genetic pollution however, stating that it is the natural course of events. One thing is certain, genetic pollution irrevocably alters a species, for better or worse.<br />
<br />
Genetic pollution doesn't exist in theories or novels anymore. It is happening in our world. For example, "gold rice" event in China where genetically engineered rice with β-carotene was fed to children for research recently attracted people's large attention. The serious situation calls for new way to prevent genetic pollution. For more information, go to our [[Team:Tianjin/HumanPractice|Human Practice]] page.<br />
<br />
===Genetic Encryption===<br />
[[file:TJU2012-Proj-SE-fig-1.png|thumb|200px|left|'''Figure 2.''' Genetic Encryption (from TJU iGEM Team 2012)]]In the information time, data encryption have always been a vital part of commerce, informatics and Internets. It has become a major research and investment field.<br />
<br />
After the establishment of DNA double helix model, scientists have always been trying to store data through gene. Just as other forms of information flows, if we want to communicate through gene, we have to encrypt and decipher. Many scientists developed some other methods to encrypt in gene. For example, some researchers thought of encrypting through specific inducer. Only adding this inducer, the cell could transcript the gene and express the stored information. Here we offer one new method to encrypt through orthogonal system, and it works well.<br />
<br />
===Pollution Prevention===<br />
[[file:TJU2012-Proj-SE-fig-2.png|thumb|200px|right|'''Figure 3.''' Logo of TJU iGEM Team 2012 (from TJU iGEM Team 2012)]]Biologists across the globe have proposed various solutions to conquer genetic pollution, such as kill-switch. These approaches have their advantages in one way or another, but certain defects too. In this year's project, we come up with a distinctive thinking. We want to construct a new system of orthogonal transcription-translation network, i.e. O-Key. Any genes in O-Key cannot be expressed in normal environment, and then decomposed. In this way, the O-Key can prevent the horizontal gene transfer. In our project this year, we propose several methods to construct orthogonal creature, the phages, such as T7, and φX174. What is more, we have begun to execute the plan of creating the orthogonal φX174. Although this is just a beginning, the future of orthogonal organism and O-Key is sure to be promising.<br />
<br />
=Principles of Future Work=<br />
===Preventing Genetic Pollution and Genetic Encryption===<br />
In order to express a certain gene in an orthogonal transcription-translation system, we need both the o-ribosome and o-mRNA to form the O-Key. We are able to rationally design the SD sequence of an mRNA, to make it inscrutable to canonical ribosome. In the meantime, a plasmid manufacturing orthogonal ribosome can be transformed into the cell to help express the o-mRNA: just like a key opens a lock. This mechanism is highly effective in controlling protein expression. <br />
<br />
What if we want to limit the expression of certain protein? What if we need to accurately regulate the expression under certain circumstances? The O-Key offers us a great choice. We can put an o-RBS to any gene that codes for hazardous protein. By controlling the existence of the O-Key, we can precisely control the expression of this protein. In this way, the synthesis of dangerous proteins can be strictly restricted and controlled by O-Key, thus preventing genetic pollution. The O-Key serves as a safe to contain <br />
<br />
To take one step further O-Key can be applied into biological product. Say we are a pharmaceutical company, and we have a brand new bacterium that can produce an antibiotics. We want to lease bacterium to some companies, but we don't want them to resell it or spread it out. In order to protect our intellectual property, we can use a new encryption technology using the O-Key. <br />
<br />
The RBS of the mRNA of some essential protein that sustains cells' life are switched to O-Lock, and we embedded the gene that manufacture O-Key in the cells to decipher the O-Luck. However, the gene for O-Lock needs special inducer. Thus, our company needs to constantly provide the inducer when the contract is valid. The inducer will result in O-Key. Together with the O-Lock, they serve as the O-Key System to produce the essential protein that sustains cells' life. When the contract expires, we'll stop providing the inducer, and the bacteria will stop manufacturing the antibiotics. <br />
<br />
As demonstrated previously, we can use the O-Key System to restrict genetic pollution, and construct an encryption system that protects intellectual property.<br />
<br />
===Constructing the Orthogonal Phages===<br />
If we could apply the O-Key System to one particular regulation. Why can't we apply it to the entire organism? At first, we wanted to build a fully orthogonal cells. But minimal genome for a cell is more than 300, which is obviously beyond our abilities. Therefore, we chose phages as the creature we work on. The reason why we choose phages are mainly based on its simple replication process and relatively small genome.<br />
<br />
However, different phages have different genome, so we should adopt different methods. For the phages with large genome(more than 20kb), we could divide the whole genome into several little parts, mutate the genome one by one and then assembly with "Yest Assembler". For the phages with small genome, we could mutate the gene directly or firstly divide the genome into small parts and then assembly in Gibson assembly method. As the mutation methods are all site-specific mutations, we just take φX174 as an example. <br />
<br />
We will mutate the genome one by one. Once we mutate one gene, we will transform the mutated phage DNA into orthogonal and normal cells to check whether the phage could still replicate, which is revealed by phage plaques. For the overlap gene in the phage DNA, if mutated RBS does affect other genes, we will put this gene before gene A and close the original gene by changing its start codon.<br />
<br />
For the limited time, we just plan to construct fully orthogonal φX174. Why we choose φx174 are based on following facts.<br />
# The first creature that was sequenced whole genome;<br />
# The second artificially synthesized viral;<br />
# We have knew clearly about it(if searching in goggle scholar, articles>300);<br />
# The replication process is simple and clear.<br />
# The genome is small, containing only 11 gene.<br />
# φX174 will not affect the common ''E. coli''.<br />
<br />
===Plan of φx174===<br />
[[file:TJU2012-Proj-SE-fig-5.png|thumb|371px|center|'''Figure 6.''' φX174 assemble process (from TJU iGEM Team 2012)]]<br />
This picture shows one repeated part of our future work to construct a fully orthogonal creature-----O-Phix 174. We tried to mutate the gene’s RBS to O-RBS, and then separately transform into both the N-E.coli and O-E.coli. If the mutation is ok, there will be plaques on the LB flat with O-E.coli, while no plaques on the other flat with N-E.coli. One by one, we could finally mutate all gene’s RBS and the get our targeted fully orthogonal creature.<br />
As for the limited time, we just do some preliminary experiments and design the primers needed for latter work.<br />
<br />
=Modeling on Future Work=<br />
To describe the process of genetic pollution, we have established a model inspired by the popular economical Bass model combined with the biological special conditions, for example the change number of bacteria under ideal and real condition, the spatial diffusion of exogenous gene. This model can predict the time when the critical concentration of bacteria is reached at a specific condition. For more details, see our [[Team:Tianjin/Modeling|Model Part]].<br />
[[file:TJU2012-Mode-HGT-fig-7.png|thumb|500px|center|'''Figure 7.''' Prediction of genetic pollution (from TJU iGEM Team 2012)]]<br />
<br />
=Conclusion of Future Work=<br />
Some people say that 21 century is the bio-century. With the full development of biology, genetic pollution will be a topic that could not be avoided in future. Some method on preventing genetic pollution will receive more and more attention. Our O-Key System, for its robustness,universality,is simple and effective. In the near future, the O-Key System will play a vital role in genetic pollution prevention. What is more, the O-Key System also works well in genetic encryption. Today, we are facing a world, full of information. Of all the parts of statistics flow, data encryption is an essential fragment. Orthogonal encryption system provide a good method to mask information. To our pleasure, we have been contacting with some related companies for application and received some good results. We have confidence that such a system will achieve a good success. <br />
<br />
Finally, we all think building orthogonal creature is a perfect idea. Since we could put orthogonal system in one regulation, why don't we apply it to the whole cell. Just as J C Venter. Other scientists all focused on assembly of a small gene, but he assembled the whole genome of bacterium ''Mycoplasma mycoides''. When we use the orthogonal phages, they could not affect normal cells. Phage pollution is usually common condition in laboratory and need several weeks to disinfect. Orthogonal cells have great advantages in real practice, such as more easily adjusted,never polluting normal cells. We believe that in the future, more orthogonal creatures will be built, and then construct an indispensable system, separate from existing translation and transcription system. Such a system, for its advantages, is more suitable for application in industry and research, blocking the possibility of genetic pollution. However, admittedly, building up such a huge system still require a lots of time and source, we have faith such day will finally come, when real orthogonal system is set up.<br />
<br />
=References=<br />
#Lon M. Chubiz and Christopher V. Rao(2008). Computational design of orthogonal ribosomes, vol.36 no.12<br />
#Wenlin An and Jason W. Chinl(2009). Synthesis of orthogonal transcriptiontranslation networks, vol.106 no.21<br />
#Howard M Salis, Ethan A Mirsky & Christopher A Voigt(2009).Automated design of synthetic ribosome binding sites to control protein expression, doi:10.1038/nbt.1568<br />
#George H.McArthur IV and Stephen S. Fong, Toward Engineering Synthetic Microbial Metabolism<br />
#WANG Haisheng,ZHANG Xiaoxia, et al., Recent research progress of bacterial violacein <br />
#Carotenoid Crystal Formation in Arabidopsis and Carrot Roots Caused by Increased Phytoene Synthase Protein Levels<br />
#Guoyin Kai, Pan Liao, Tong Zhang, Wei Zhou, Jing Wang, Hui Xu, Yuanyun Liu, and Lin Zhang. Characterization,Expression Profiling, and Functional Identification of a Gene Encoding Geranylgeranyl Diphosphate Synthase from Salvia miltiorrhiza<br />
<br />
<br />
{{:Team:Tianjin/footer}}</div>Helengoodhttp://2012.igem.org/File:TJU2012-Mode-hp-fig-1.pngFile:TJU2012-Mode-hp-fig-1.png2012-10-27T02:49:56Z<p>Helengood: uploaded a new version of &quot;File:TJU2012-Mode-hp-fig-1.png&quot;</p>
<hr />
<div></div>Helengoodhttp://2012.igem.org/Team:Tianjin/Project/TechnologyTeam:Tianjin/Project/Technology2012-10-27T01:18:04Z<p>Helengood: /* MAGE */</p>
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<center><span style="font-size:46px;font-family:Cambria;margin-top:10px;line-height:80%">Technology</span></center><br />
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<br />
=Replace of RBS in Plasmid=<br />
[[file:TJU2012-Proj-LMR-fig-21.png|thumb|500px|center|'''Figure 1.''' The process of introducing the O-RBS to plasmid (from TJU iGEM Team 2012)]]<br />
Here, how did we introduce the O-Lock, we just use two primers to build pcr. Those two primers have about 20bp overhands on their 5' end, which contain the O-Locks or other mutations. Then we directly transform those PCR products to E. coli by electroporation-mediated method. Then those PCR productions could cyclize and form the complete plasmids.<br />
<br />
=Yeast Assembler=<br />
===History===<br />
Yeast Assembler is based on in vivo homologous recombination in yeast. As for its high efficiency and ease to work with, in vivo homologous recombination in yeast has been widely used for gene cloning, plasmid construction and library creation. In the early of 2008, Zengyi Shao from University of lllinois at Urbana-Champaign, Urbana, used such a method to construct biochemical pathways. Such a method, for its high efficiency in assembling multiple genes, received great popularity since its appearance.<br />
<br />
===The Difficulty of Large Fragments Assembly===<br />
The general digestion connection will leave scar and will be limited by the specific cleavage sequences.<br />
[[file:TJU2012-Proj-LMR-fig-2.png|thumb|150px|center|'''Figure 2.''' Enzyme digestion (from the website of dnaQ]]<br />
Long PCR fragment will suffer the decline of success rate and distortion, etc. <br />
[[file:TJU2012-Proj-LMR-fig-3.png|thumb|500px|center|'''Figure 3.''' PCR Recombinant & PCR Machine (from the website of dnaQ]]<br />
However, the construction of some large fragments cannot be avoided, so the development of a low-cost, simple operation, good fidelity, a little limiting factor large DNA fragment assembly method is particularly important.<br />
<br />
===Principles===<br />
One step assembly into a vector.<br />
[[file:TJU2012-Proj-LMR-fig-4.png|thumb|500px|center|'''Figure 4.''' Principles of Yeast assembler (from "DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways")]]<br />
When parts are transformed all parts into Yeast, homologous recombination occurs at the site “x”, and then all little parts are integrated into a vector.<br />
<br />
===Advantages and Disadvantages===<br />
Compared with other methods,the “Yeast assembler” are more efficient and useful for large gene assemble.<br />
<br />
<center><b>Table 1.</b> Advantages compared to the other two methods (from TJU iGEM Team 2012)</center><br />
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<th style="background:#fbb181;">&nbsp;</th><br />
<th style="background:#fbb181;">Yeast Assembler</th><br />
<th style="background:#fbb181;">SLIC</th><br />
<th style="background:#fbb181;">Domino Method</th><br />
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<td style="background:#fbb181;">Advantages</td><br />
<td style="background:#fdd8c0;">High efficient, Fit for large gene assemble rapid</td><br />
<td style="background:#fdd8c0;">Fit for many little parts into overall</td><br />
<td style="background:#fdd8c0;">Fit for two large gene parts integration</td><br />
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<td>Process is complex</td><br />
<td>Success rate is low, The size of recombinant is relatively small(<8kb)</td><br />
<td>Require a great amount of time and labor. Process is sequential</td><br />
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===Completely Synthesizing the Genome of Mycoplasma Genitalium using Yeast Assembler===<br />
In 2008, Gibson from the J. Craig Venter Institute, published an article “one-step assembly in Yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome”. In the article, the author transformed 25 overlapping DNA fragments into Yeast, homologous recombination occurs, and then the whole genome is synthesized.<br />
[[file:TJU2012-Proj-LMR-fig-6.png|thumb|500px|center|'''Figure 5.''' Synthetic Mycoplasma genitalium genome (from "One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic ''Mycoplasma genitalium'' genome")]]<br />
Construction of a synthetic M. genitalium genome in yeast. Yeast cells were transformed with 25 different overlapping A-series DNA segments (blue arrows; ~17 kb to35 kb each) composing the M. genitalium genome. To assemble these into a complete genome, a single yeast cell (tan) must take up at least one representative of the 25 different DNA fragments and incorporate them in the nucleus (yellow), where homologous recombination occurs. This assembled genome, called JCVI-1.1, is 590,011 bp, including the vector sequence (red triangle) shown internal to A86 – 89.<br />
<br />
=MAGE=<br />
We thought that now that we could introduce O-Lock into a cell, could we introduce O-Lock to the whole system. Theoretically speaking, we could make it come true because there is a technology called MAGE (Multiplex Automated Genomic Engineering) which comes from Harvard University. We could use this technology to replace all the N-RBS to O-RBS of the genome. Then we could regulate the metabolic network more freely and accurately by many AND gates which come from the O-Locks.<br />
[[file:TJU2012-Proj-LMR-fig-22.png|thumb|500px|center|'''Figure 6.''' The basic principle of MAGE (from TJU iGEM Team 2012)]]<br />
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{{:Team:Tianjin/footer}}</div>Helengoodhttp://2012.igem.org/Team:Tianjin/Project/TechnologyTeam:Tianjin/Project/Technology2012-10-27T01:12:48Z<p>Helengood: /* Replace of RBS in Plasmid */</p>
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<a href="https://2012.igem.org/Team:Tianjin/Project/Gene">Future Work</a><br />
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<a href="#Replace_of_RBS_in_Plasmid">Replace of RBS in Plasmid</a><br />
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<center><span style="font-size:46px;font-family:Cambria;margin-top:10px;line-height:80%">Technology</span></center><br />
<br><br />
<br />
=Replace of RBS in Plasmid=<br />
[[file:TJU2012-Proj-LMR-fig-21.png|thumb|500px|center|'''Figure 1.''' The process of introducing the O-RBS to plasmid (from TJU iGEM Team 2012)]]<br />
Here, how did we introduce the O-Lock, we just use two primers to build pcr. Those two primers have about 20bp overhands on their 5' end, which contain the O-Locks or other mutations. Then we directly transform those PCR products to E. coli by electroporation-mediated method. Then those PCR productions could cyclize and form the complete plasmids.<br />
<br />
=Yeast Assembler=<br />
===History===<br />
Yeast Assembler is based on in vivo homologous recombination in yeast. As for its high efficiency and ease to work with, in vivo homologous recombination in yeast has been widely used for gene cloning, plasmid construction and library creation. In the early of 2008, Zengyi Shao from University of lllinois at Urbana-Champaign, Urbana, used such a method to construct biochemical pathways. Such a method, for its high efficiency in assembling multiple genes, received great popularity since its appearance.<br />
<br />
===The Difficulty of Large Fragments Assembly===<br />
The general digestion connection will leave scar and will be limited by the specific cleavage sequences.<br />
[[file:TJU2012-Proj-LMR-fig-2.png|thumb|150px|center|'''Figure 2.''' Enzyme digestion (from the website of dnaQ]]<br />
Long PCR fragment will suffer the decline of success rate and distortion, etc. <br />
[[file:TJU2012-Proj-LMR-fig-3.png|thumb|500px|center|'''Figure 3.''' PCR Recombinant & PCR Machine (from the website of dnaQ]]<br />
However, the construction of some large fragments cannot be avoided, so the development of a low-cost, simple operation, good fidelity, a little limiting factor large DNA fragment assembly method is particularly important.<br />
<br />
===Principles===<br />
One step assembly into a vector.<br />
[[file:TJU2012-Proj-LMR-fig-4.png|thumb|500px|center|'''Figure 4.''' Principles of Yeast assembler (from "DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways")]]<br />
When parts are transformed all parts into Yeast, homologous recombination occurs at the site “x”, and then all little parts are integrated into a vector.<br />
<br />
===Advantages and Disadvantages===<br />
Compared with other methods,the “Yeast assembler” are more efficient and useful for large gene assemble.<br />
<br />
<center><b>Table 1.</b> Advantages compared to the other two methods (from TJU iGEM Team 2012)</center><br />
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<th style="background:#fbb181;">&nbsp;</th><br />
<th style="background:#fbb181;">Yeast Assembler</th><br />
<th style="background:#fbb181;">SLIC</th><br />
<th style="background:#fbb181;">Domino Method</th><br />
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<td style="background:#fbb181;">Advantages</td><br />
<td style="background:#fdd8c0;">High efficient, Fit for large gene assemble rapid</td><br />
<td style="background:#fdd8c0;">Fit for many little parts into overall</td><br />
<td style="background:#fdd8c0;">Fit for two large gene parts integration</td><br />
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<td>Process is complex</td><br />
<td>Success rate is low, The size of recombinant is relatively small(<8kb)</td><br />
<td>Require a great amount of time and labor. Process is sequential</td><br />
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===Completely Synthesizing the Genome of Mycoplasma Genitalium using Yeast Assembler===<br />
In 2008, Gibson from the J. Craig Venter Institute, published an article “one-step assembly in Yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome”. In the article, the author transformed 25 overlapping DNA fragments into Yeast, homologous recombination occurs, and then the whole genome is synthesized.<br />
[[file:TJU2012-Proj-LMR-fig-6.png|thumb|500px|center|'''Figure 5.''' Synthetic Mycoplasma genitalium genome (from "One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic ''Mycoplasma genitalium'' genome")]]<br />
Construction of a synthetic M. genitalium genome in yeast. Yeast cells were transformed with 25 different overlapping A-series DNA segments (blue arrows; ~17 kb to35 kb each) composing the M. genitalium genome. To assemble these into a complete genome, a single yeast cell (tan) must take up at least one representative of the 25 different DNA fragments and incorporate them in the nucleus (yellow), where homologous recombination occurs. This assembled genome, called JCVI-1.1, is 590,011 bp, including the vector sequence (red triangle) shown internal to A86 – 89.<br />
<br />
=MAGE=<br />
We thought that now that we could introduce O-Lock cell, could we introduce O-Lock to the whole system. Theoretically speaking, we could make it come true because there is a technology called MAGE (Multiplex Automated Genomic Engineering) which comes from Harvard University. We could use this technology to replace all the N-RBS to O-RBS of the genomic. Then we could regulate the metabolic network more freely and accurately by many AND gates which come from the O-Locks.<br />
[[file:TJU2012-Proj-LMR-fig-22.png|thumb|500px|center|'''Figure 6.''' The basic principle of MAGE (from TJU iGEM Team 2012)]]<br />
<br />
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{{:Team:Tianjin/footer}}</div>Helengoodhttp://2012.igem.org/Team:Tianjin/Project/GeneTeam:Tianjin/Project/Gene2012-09-27T03:55:24Z<p>Helengood: /* References */</p>
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<center><span style="font-size:46px;font-family:Cambria;margin-top:10px;line-height:80%">Genetic Pollution Prevention and Genetic Encryption</span></center><br />
<br><br />
<br />
=Background=<br />
[[file:Tianjin_SynBio_Museum.jpg|thumb|250px|right|'''Figure 1.''' Poster of SynBio Museum (by TJU iGEM Team 2012)]]<br />
===Genetic Pollution===<br />
Genetic pollution is the term of genetics in which the genetic information is transferred in to the organisms where it is not needed or where this information never existed before. This flow of genetic information is usually undesired and cannot be controlled. The flow of genetic information usually takes place between the genetically modified organisms into the organisms which are not genetically modified.<br />
<br />
Genetic pollution occurs when domesticated or genetically engineered species interbreed with their wild cousins, thus polluting the wild species gene pool. It is seen as negative because it affects the wild population's evolved capability to survive, as well as spreading genes that are not found in nature.<br />
<br />
One of the main issues of genetic pollution lies in the fact that man has tampered with the genetic structure of these species and has created a situation that would not be found naturally. Some people find no issue with genetic pollution however, stating that it is the natural course of events. One thing is certain, genetic pollution irrevocably alters a species, for better or worse.<br />
<br />
Genetic pollution doesn't exist in theories or novels anymore. It is happening in our world. For example, "gold rice" event in China where genetically engineered rice with β-carotene was fed to children for research recently attracted people's large attention. The serious situation calls for new way to prevent genetic pollution. For more imformation, go to our [[Team:Tianjin/HumanPractice|Human Practice]] page.<br />
<br />
===Genetic Encryption===<br />
[[file:TJU2012-Proj-SE-fig-1.png|thumb|200px|left|'''Figure 2.''' Genetic Encryption (from TJU iGEM Team 2012)]]In the information time, data encryption have always been a vital part of commerce, informatics and Internets. It has become a major research and investment field.<br />
<br />
After the establishment of DNA double helix model, scientists have always been trying to store data through gene. Just as other forms of information flows, if we want to communicate through gene, we have to encrypt and decipher. Many scientists developed some other methods to encrypt in gene. For example, some researchers thought of encrypting through specific inducer. Only adding this inducer, the cell could transcript the gene and express the stored information. Here we offer one new method to encrypt through orthogonal system, and it works well.<br />
<br />
===Pollution Prevention===<br />
[[file:TJU2012-Proj-SE-fig-2.png|thumb|200px|right|'''Figure 3.''' Logo of TJU iGEM Team 2012 (from TJU iGEM Team 2012)]]Biologists across the globe have proposed various solutions to conquer genetic pollution, such as kill-switch. These approaches have their advantages in one way or another, but certain defects too. In this year's project, we come up with a distinctive thinking. We want to construct a new system of orthogonal transcription-translation network, i.e. O-Key. Any genes in O-Key cannot be expressed in normal environment, and then decomposed. In this way, the O-Key can prevent the horizontal gene transfer. In our project this year, we propose several methods to construct orthogonal creature, the phages, such as T7, and φX174. What is more, we have begun to execute the plan of creating the orthogonal φX174. Although this is just a beginning, the future of orthogonal organism and O-Key is sure to be promising.<br />
<br />
=Principles=<br />
===Preventing Genetic Pollution and Genetic Encryption===<br />
In order to express a certain gene in an orthogonal transcription-translation system, we need both the o-ribosome and o-mRNA to form the O-Key. We are able to rationally design the SD sequence of an mRNA, to make it inscrutable to canonical ribosome. In the meantime, a plasmid manufacturing orthogonal ribosome can be transformed into the cell to help express the o-mRNA: just like a key opens a lock. This mechanism is highly effective in controlling protein expression. <br />
<br />
What if we want to limit the expression of certain protein? What if we need to accurately regulate the expression under certain circumstances? The O-Key offers us a great choice. We can put an o-RBS to any gene that codes for hazardous protein. By controlling the existence of the O-Key, we can precisely control the expression of this protein. In this way, the synthesis of dangerous proteins can be strictly restricted and controlled by O-Key, thus preventing genetic pollution. The O-Key serves as a safe to contain <br />
<br />
To take one step further O-Key can be applied into biological product. Say we are a pharmaceutical company, and we have a brand new bacterium that can produce an antibiotics. We want to lease bacterium to some companies, but we don't want them to resell it or spread it out. In order to protect our intellectual property, we can use a new encryption technology using the O-Key. <br />
<br />
The RBS of the mRNA of some essential protein that sustains cells' life are switched to O-Lock, and we embedded the gene that manufacture O-Key in the cells to decipher the O-Luck. However, the gene for O-Lock needs special inducer. Thus, our company needs to constantly provide the inducer when the contract is valid. The inducer will result in O-Key. Together with the O-Lock, they serve as the O-Key System to produce the essential protein that sustains cells' life. When the contract expires, we'll stop providing the inducer, and the bacteria will stop manufacturing the antibiotics. <br />
<br />
As demonstrated previously, we can use the O-Key System to restrict genetic pollution, and construct an encryption system that protects intellectual property.<br />
<br />
===Constructing the Orthogonal Phages===<br />
If we could apply the O-Key System to one particular regulation. Why can't we apply it to the entire organism? At first, we wanted to build a fully orthogonal cells. But minimal genome for a cell is more than 300, which is obviously beyond our abilities. Therefore, we chose phages as the creature we work on. The reason why we choose phages are mainly based on its simple replication process and relatively small genome.<br />
<br />
However, different phages have different genome, so we should adopt different methods. For the phages with large genome(more than 20kb), we could divide the whole genome into several little parts, mutate the genome one by one and then assembly with "Yest Assembler". For the phages with small genome, we could mutate the gene directly or firstly divide the genome into small parts and then assembly in Gibson assembly method. As the mutation methods are all site-specific mutations, we just take φX174 as an example. <br />
<br />
We will mutate the genome one by one. Once we mutate one gene, we will transform the mutated phage DNA into orthogonal and normal cells to check whether the phage could still replicate, which is revealed by phage plaques. For the overlap gene in the phage DNA, if mutated RBS does affect other genes, we will put this gene before gene A and close the original gene by changing its start codon.<br />
<br />
For the limited time, we just plan to construct fully orthogonal φX174. Why we choose φx174 are based on following facts.<br />
# The first creature that was sequenced whole genome;<br />
# The second artificially synthesized viral;<br />
# We have knew clearly about it(if searching in goggle scholar, articles>300);<br />
# The replication process is simple and clear.<br />
# The genome is small, containing only 11 gene.<br />
# φX174 will not affect the common ''E. coli''.<br />
<br />
=Experiment=<br />
===Ampr RBS Mutation===<br />
We used the orthogonal principle described in the previous section to mutate the Ampr RBS, and constructed an orthogonal transcription-translation system that is independent of the existing system. <br />
<br />
The SD sequence of Ampr RBS is GAGAAA, and we rationally designed the orthogonal sequence to be GTTCCG. We further mutated the Ampr RBS of the RFP operon, and transformed plasmid into ''E coli''. <br />
<br />
Here, we chose two distinct competent cell: the normal competent cells; the orthogonal competent cells containing o-16S rRNA, and plate the cells on Amp LB plates. As we can predict, the normal competent cells would not be able to express the Amp resistance protein, thus cannot survive. On the contrary, the orthogonal cells can resist Amp in the plate and express the RFP.<br />
<br />
====Process==== <br />
# Using PCR to mutate 16sRNA on the P15a plasmid to get the mutated P15a with O-16sRNA.<br />
# Changing RBS of Ampr gene on PBR322 to O-RBS.<br />
# Cotransfomating the above two mutated plasmids into cells, plating Amp LB plates, cultivating for 12-24hours.<br />
<br />
Both of the plasmids used above contain the RFP gene to display the results and the Pbad promoter induced by Ala; only if Ampr gene could be expressed, cell will reproduce, RFP gene be expressed and the colony turned red.<br />
<br />
====Results====<br />
[[file:TJU2012-Proj-SE-fig-3.png|thumb|500px|center|'''Figure 4.''' Photo of two plates showing the normal cells (left) and orthogonal cells (right)(from TJU iGEM Team 2012)]]<br />
[[file:TJU2012-Proj-SE-fig-4.png|thumb|371px|center|'''Figure 5.''' Chart showing the results (from TJU iGEM Team 2012)]]<br />
From the two flats, we could easily find that the left plant plated without Ala,which means cells only containing normal ribosome. There is no colony on the plate. The reason is that without no orthogonal ribosome, Ampr gene could not be transcripted and translated,then cells could not survive on LB flat with Amp. On the other hand, the right flat, added Ala, containing orthogonal ribosome, have red colonies. Existing orthogonal ribosome means that cells could transcript and translate the Amp r gene, survive in Amp situation, the RFP could also be expressed with the help of normal ribosome.<br />
<br />
===Plan of φx174===<br />
[[file:TJU2012-Proj-SE-fig-5.png|thumb|371px|center|'''Figure 6.''' φX174 assemble process (from TJU iGEM Team 2012)]]<br />
As for the limited time, we just do some preliminary experiments and design the primers needed for latter work.<br />
<br />
=Modeling=<br />
To describe the process of genetic pollution, we have established a model inspired by the popular economical Bass model combined with the biological special conditions, for example the change number of bacteria under ideal and real condition, the spatial diffusion of exogenous gene. This model can predict the time when the critical concentration of bacteria is reached at a specific condition. For more details, see our [[Team:Tianjin/Modeling|Model Part]].<br />
[[file:TJU2012-Mode-HGT-fig-7.png|thumb|500px|center|'''Figure 7.''' Prediction of genetic pollution (from TJU iGEM Team 2012)]]<br />
<br />
=Prospect=<br />
Some people say that 21 century is the bio-century. With the full development of biology, genetic pollution will be a topic that could not be avoided in future. Some method on preventing genetic pollution will receive more and more attention. Our O-Key System, for its robustness,universality,is simple and effective. In the near future, the O-Key System will play a vital role in genetic pollution prevention. What is more, the O-Key System also works well in genetic encryption. Today, we are facing a world, full of information. Of all the parts of statistics flow, data encryption is an essential fragment. Orthogonal encryption system provide a good method to mask information. To our pleasure, we have been contacting with some related companies for application and received some good results. We have confidence that such a system will achieve a good success. <br />
<br />
Finally, we all think building orthogonal creature is a perfect idea. Since we could put orthogonal system in one regulation, why don't we apply it to the whole cell. Just as J C Venter. Other scientists all focused on assembly of a small gene, but he assembled the whole genome of bacterium ''Mycoplasma mycoides''. When we use the orthogonal phages, they could not affect normal cells. Phage pollution is usually common condition in laboratory and need several weeks to disinfect. Orthogonal cells have great advantages in real practice, such as more easily adjusted,never polluting normal cells. We believe that in the future, more orthogonal creatures will be built, and then construct an indispensable system, separate from existing translation and transcription system. Such a system, for its advantages, is more suitable for application in industry and research, blocking the possibility of genetic pollution. However, admittedly, building up such a huge system still require a lots of time and source, we have faith such day will finally come, when real orthogonal system is set up.<br />
<br />
=References=<br />
#Lon M. Chubiz and Christopher V. Rao(2008). Computational design of orthogonal ribosomes, vol.36 no.12<br />
#Wenlin An and Jason W. Chinl(2009). Synthesis of orthogonal transcriptiontranslation networks, vol.106 no.21<br />
#Howard M Salis, Ethan A Mirsky & Christopher A Voigt(2009).Automated design of synthetic ribosome binding sites to control protein expression, doi:10.1038/nbt.1568<br />
#George H.McArthur IV and Stephen S. Fong, Toward Engineering Synthetic Microbial Metabolism<br />
#WANG Haisheng,ZHANG Xiaoxia, et al., Recent research progress of bacterial violacein <br />
#Carotenoid Crystal Formation in Arabidopsis and Carrot Roots Caused by Increased Phytoene Synthase Protein Levels<br />
#Guoyin Kai, Pan Liao, Tong Zhang, Wei Zhou, Jing Wang, Hui Xu, Yuanyun Liu, and Lin Zhang. Characterization,Expression Profiling, and Functional Identification of a Gene Encoding Geranylgeranyl Diphosphate Synthase from Salvia miltiorrhiza<br />
<br />
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{{:Team:Tianjin/footer}}</div>Helengoodhttp://2012.igem.org/Team:Tianjin/SafetyTeam:Tianjin/Safety2012-09-27T03:53:15Z<p>Helengood: </p>
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<br><center><span style="font-size:46px;font-family:Cambria;margin-top:10px">Biosafety Handbook</span></center><br />
<br><br />
<br />
Biosafety handbook is one of most important part of our human practice. Our handbook is based on the iGEM programs, from which we select the teams whose safety parts are beneficial and fruitful. And we also made reference to some related papers. [[file:Labsafety.jpg|thumb|250px|left|Biosafety should be the primary concern in the laboratory]]At last, we summarized and wrote this biosafety handbook. We hope our handbook can help people with the work of gene pollution prevention. And we believe our biosafety handbook will provide reference to other iGEM teams in the future.<br />
<br />
Genetic pollution refers to the unintended or uncontrolled gene flow of native species gene pool. In 21th century, the recombinant organisms begin to spread into the environment extensively. Admittedly, scientists and international groups have already started to seriously consider the safety of transgenosis, but there are still a lot of limitations and a lack of long-term data. Although genetic engineering can bring huge benefits to us, but the potential threats it cause can never be ignored. Like DDT, which won a Nobel Prize in the year when it was created, but caused great injury to both human beings and the environment after 50 years. We can't stop this kind of things totally, but at least we can make efforts to prevent it. Considering the specialty of our program, it can be creatively used in the career of the gene pollution prevention, we will show the possibilities and examples in the third part. <br />
We divided our handbook into three parts:<br />
<br />
=Operation=<br />
'''Laboratory Practices Followed By Our Team'''<br />
:1. Always wear appropriate personal protective equipment. Feet and legs should be covered; sandals and open-toed shoes should not be worn in laboratories. Wear appropriate gloves while handling infectious or toxic materials and animals. Do not wear lab coats, gloves or other personal protective equipment outside the laboratory. Change gloves when contaminated, and dispose of used gloves with other contaminated laboratory waste.<br />
[[file:Safety-goggle.jpg|thumb|250px|right|A safety goggle]]<br />
:2. Do not eat, drink, smoke, handle contact lenses, apply cosmetics, or store food for human consumption in the laboratory.<br />
:3. Wash your hands after working with potentially hazardous materials and before leaving the laboratory.<br />
:4. Follow the institutional policies regarding safe handling of sharps (i.e., needles, scalpels, pipettes, and broken glassware). Be careful with needles and syringes. Use only when alternative methods are not feasible. Syringes, needles, Pasteur pipettes, etc, should be placed in rigid, leak-proof containers (Sharps Safe) and discarded following the waste rules.<br />
:5. Take care to minimize the creation of aerosols and/or splashes.<br />
:6.Decontaminate all work surfaces before and after your experiments, and immediately after any spill or splash of potentially infectious material with an appropriate disinfectant. Clean laboratory equipment routinely, even if it is not contaminated.<br />
:7. Decontaminate all potentially infectious materials before disposal.<br />
:8. Report any incidents that may result in exposure to infectious materials to appropriate personnel (e.g., laboratory supervisor, safety officer).<br />
:9. Know where the nearest eyewash, safety shower, and fire extinguisher are located. Know how to use them. <br />
:10. Insist upon good housekeeping in your laboratory.<br />
:11. Check for insects and rodents. Keep all areas clean.<br />
:12. Secure all gas cylinders.<br />
:13. Use a biological safety cabinet for handling infectious materials or materials requiring protection from contamination and a fume hood for toxic materials; mixed hazards need to be evaluated case by case.[[file:Labsafety2.jpg|thumb|250px|right|Use fume hoods]]<br />
:14. Fume hoods should be used for laboratory activities that could result in chemical explosions or fires, for experiments involving toxic, hazardous or carcinogenic compounds, and use of strong acids and bases. 9Biological safety cabinets should not be used for this kind of work. Fume hoods are workstations, not storage cabinets. Vented storage areas may be located under the fume hood work area. However, these are not for storage of flammables.<br />
:15. Respect chemicals and radionuclides. Know their hazards and follow appropriate safety precautions. Chemical and radioactive waste must not be poured down the drain.<br />
:16. All equipment must be documented to be free of chemical, biological, and radiological contamination before repair work is done or before moving equipment for storage or elsewhere.<br />
:17. Never mouth pipette anything. Use mechanical pipetting devices only!<br />
:18. Close laboratory doors while experiments are in progress. Restrict access to laboratory.<br />
:19. Put liquid traps and in-line vacuum filters on all vacuum lines.<br />
:20. Minimize or contain all aerosol-producing activities, large-volume work, concentrated solutions or cultures. These activities include centrifugation (use safety cups), vortex missing (stopper tube), blending (use metal safety blender), sonication, grinding, opening containers of infectious material, inoculating culture flasks, inoculating animals, harvesting infectious materials from cultures or animals, and weighing or reconstructing toxic powders, etc.<br />
[[file:LabSafety3.jpg|thumb|250px|left|Avoid leaking]]<br />
:21. Place biological safety cabinets in low-traffic areas and minimize activities that disrupt air flow in or around cabinet.<br />
:22. Decontaminate all work surfaces daily, and decontaminate all spills immediately.<br />
:23. Decontaminate (by autoclaving or chemical disinfection) all biologically contaminated materials – glassware, animal cages, laboratory equipment, etc. – before washing, reuse or disposal. Discard materials via proper waste stream.<br />
:24. Broken glassware and disposable pipettes (after decontamination) should be placed in a “Disposable Labware and Broken Glass Box” and discarded following the waste rules.<br />
:25. Place contaminated biological materials in covered, leak-proof containers before removing them from the laboratory.<br />
:26. Wash your hands after handling chemicals, infectious materials, animals, after removing gloves and before leaving the laboratory.<br />
<br />
=Social=<br />
:'''1. Everyone should be prudent'''<br />
DDT, the inventor of which won the Nobel Prize, was used as a pesticide at early time, but after 50 years we found out that it caused irreparable damage to human beings and environment. Therefore, it is necessary to slow the development of genetic engineering and focus on improving its basic research. We should make sure it won't cause side effects to the environment and human beings before its promotion.<br />
:'''2. Establish and improve the related laws and regulations, and strictly implement them'''<br />
[[file:Slide0263_image223.jpg|thumb|250px|left|Wild type plant (left) compared with genetically engineered plant (right)]]<br />
In the past two decades, Chinese government also put forward a lot of related laws and regulations. In 1993, the former State Science and Technology Commission issued a regulation called "genetic engineering safety management measures". In 1996 the Ministry of Agriculture issued the “Agricultural Biological Genetic Engineering Safety Management Implementation Approach". In May 23, 2001, the State Council announced “Agricultural Genetically Modified Organisms' (GMOs') Safety Management Regulations". On January 5, 2002, the Ministry of Agriculture announced “Safety Assessment of Agricultural GMO", "Measures for the Administration of the Import of Agricultural Transgenic Living Things", “Agricultural GMO Identity Management Approach ". These laws and regulations help organizations to stick to principles to prevent genetic pollution.<br />
:'''3. Improve the examination and approval system of gene engineering technology application'''<br />
The system should require the genetic engineering technology pass the microbiology, plant and animal experiments, environmental experiments and human trials before put into application. We should prevent the abuse and industrialization or commercialization of genetic engineered product rashly. For example, some governments have made announcements to prohibit the production and sale of any crops with antibiotic resistance gene.<br />
:'''4. Carry out public science education'''<br />
The lack of the biological safety awareness is one of the biggest reasons of the genetic pollution. The majority of Chinese people whose daily life are closely related to genetically modified food can't ever understand the genetic pollution. So it's necessary for us to carry out the popular science education so that more and more people can pay attention to the genetic engineering knowledge.<br />
:'''5. Implementation of a labelling system for genetically modified food'''<br />
[[file:6301.jpg|thumb|200px|right|Food containing genetically engineered organisms]]<br />
United Nations announce if we take people's health and the environment into account, every country has the right to restrict the import of genetically modified food. All genetically modified products in the shipment should be labeled, indicating “this product contains genetically modified material ". International Consumers Association believe that although it is uncertain that genetically modified food is unsafe, but in order to prevent potential hazard to human, we should take preventive measures and establish an identification system. The identification of GMOs can help consumers to make choices. Genetic pollution is really a big problem in the application of genetic engineering. But we must realize the great benefit of genetic engineering. It is likely to bring the best choice for us to solve the global food shortage. Therefore we cannot give up improving gene engineering technology for fear of a little trouble.<br />
:'''6. Risk assessment and management'''<br />
Conduct the risk assessment and management of transgenic technique and analysis the adverse effects of its products in the trans-boundary movement process so that the importer can make choices easily.<br />
<br />
=Synthetic Biology=<br />
When it comes to our iGEM project this year, the regulation of gene expression systems can not only introduces a new way for protein-specific expression but also plays an important role in preventing genetic pollution. For example, if you want to transfer some exogenous genes that are harmful to the environment or human beings into cells, then biological safety is one thing we must consider about. To prevent harmful genes being expressed in uncontrolled cases, we must do something to prevent possible genetic pollution. And this year our project can do a lot on this problem. Our o-ribosome device allows translation only when the combination of the o-16s ribosome and o-RBS, so if we put the device at the upstream of the target genes, we can control the expression of target genes precisely. At the same time, RBS sequences are necessary in almost every cell,therefore an extensive application can be performed by our o-ribosomal. [[file:Tianjin_Model_hand3.jpg|thumb|300px|right|Our teammate is performing gel-cutting.]]Not only can our project regulate gene expression and prevent genetic pollution, but also it will not consume any extra nutrients, and have no influence on the normal life activities of bacteria. <br />
On the other hand, different RBS sequences can influence the efficiency of the translation, so we can use a series of RBS sequences to regulate gene expression with a gradient rate. The possibility of genetic pollution can also be reduced in this accurate process.<br />
<br />
Finally, the o-ribosomal devices can be used to establish a orthogonal system, in which cells have specific o-ribosomal devices instead of the original ones. Being different from other ordinary cells, they cannot be expressed in normal cells even if the target genes from orthogonal system spread out,which leads to a strong protection against genetic pollution. It is obvious that genetic pollution can be completely prevented in this orthogonal system.<br />
There were also several projects which were related to gene expression regulation in iGEM last year. For example, the SJTU-BioX-Shanghai team designed a set of Codon-Switches that regulate target protein biosynthesis (translation).In their rare-codon switch, the translation of the protein can be finely turned up/down with the control of rare tRNA amount, aaRS that charges the rare tRNA and rare codons. Besides they also made other two switches that could be turned on/off without background noise. One called the stop-codon switch was to use stop codon as the controlling element. The other one called the initial-codon switch was to use any codon but the original start codon to initiate translation. What's more, the projects of the BYU Provo team, USTC-China team, Peking-R team and some other teams were all related to gene expression regulation too. We believe that maybe the principles of these projects can also be used in the prevention to genetic pollution. So if you are interested in this, you can know more through their wiki.<br />
<br />
As iGEM teams are from different countries which may have different regulations for biosaftey. So on the one hand, it's necessary to collect information and make standard biosafety rules for basic synthetic biology experiments. On the other hand, our simple biosafety handbook cannot be suitable for all teams. But we believe our work must be useful for many iGEM teams and other researchers.<br />
<br />
<br><center><span style="font-size:46px;font-family:Cambria;margin-top:10px">Regulation Summary</span></center><br />
<br><br />
The creature differs from each other due to the patterns of gene expression,because most genes differ in their level of the cell cycle.The activity of genes is also keyed to the functions of the cell;The expression of the protein can influence the whole cell.The main role in gene regulation is the level of transcription,either through signals originating within the cell itself or in response to external conditions.Many gene products are needed only on ocassion ,and transcription can be regulated in an on-off manner that enables such products to ve present only when external conditions demand them .Five main control points for gene expression include:<br />
<br />
# Transcriptional regulation of the synthesis of RNA transcrips by controling initiation or termination.<br />
# RNA processing or regulation through RNA splicing or alternative patterns of splicing.<br />
# Translational control of polypeptide synthesis.<br />
# Stability of mRNA,because mRNAs that persist in the cell have longer-lasting effects than those that are degraded rapidly.<br />
# Posttranslational control,which includes a great variety of mechanisms that affect enzyme activity, activation,stability, and so on.<br />
# DNA rearrangements,in which gene expression changes depending on the position of DNA sequencs in the genome.<br />
<br />
The regulatory systems of prokayotes and eukaryotes differ from each other in many details.Because the project in the iGEM 's platforms are mostly prokayotes,we just focus on the prokayotes' gene regulation.Prokayotes are generally free-living unicellular organisms that grow and divice indefinitely as long as environmental conditions are suitable and the supply of nutrients is adequate.Their regulatory systems are often geared to provide the maximum growth rate in a particular environment .In contrast ,the cells in a developing muticellular organism modulate their growth rate as they undergo dramatic,coordinated differentiation in morphology and metabolism.In an adult animal,growth and division of most cell types has ceased,and each type of cell needs to maintain its identity through time.<br />
<br />
Synthetic biology is a brand new field of biological research which combines science and engineering. Now more and more people are familiar with this promising and appealing field. Gene expression regulation can expand the regulating tools for synthetic biology. We can control protein biosynthesis through things like riboswitch. Different combinations of these regulating tools can bring different outcomes in protein expression levels. And they can be applied to real life to solve many difficult practical problems.<br />
<br />
According to some of the championship projects in2011 igem,we find some are intresting and develpmental.Gene regulation can be called as the core for most of the projects.<br />
<br />
For example, As BYU's first iGEM team, BYU team proposed constructing a molecular AND gate in E. coli. To detect their chosen inputs they investigated the OxyR promoter and a thermo-sensitive riboswitch. The OxyR protein activates transcription in the presence of hydrogen peroxide, a reactive oxygen speesscies (ROS). The riboswitch allows translation only above a specific temperature. Both inputs activate a Cre/Lox system to remove a terminator sequence and allow transcription of a molecular signal. And they think a similar system, in theory, could be used for early detection of colorectal cancer.<br />
<br />
Another team is the SJTU-BioX-Shanghai, they designed a set of Codon-Switches that regulate target protein biosynthesis (translation).In their rare-codon switch, the translation of the protein can be finely turned up/down with the control of rare tRNA amount,aaRS that charges the rare tRNA and rare codons. Besides, their also made other two switches that can be turned on/off without background noise . One is to use stop codon as the controlling element, the stop-codon switch.The other is to use any codon but the original start codon to initiate translation, the initial-codon switch.<br />
<br />
Various methods of regulation are provide.Followings are the typical ones.<br />
=Regulation with density: XMU gold medal,Advance to Championship=<br />
[[file:TJU1201.jpg|center]]<br />
They have developed a series of devices which program a bacteria population to maintain at different cell densities. They 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 using RBSes of different strength and mutated luxR promoters (lux pr). They are working on builting up a database for a series of mutation sites and RBSes corresponding to different steady-state cell densities. An artificial neural network will be 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. <br />
<br />
=Regulation with Light=<br />
===WHU, Gold medal, Advance to Championship===<br />
Their project focuses on constructing colorful E.coli, which includes two parts. They plan to construct two systems consisting of several strains of E.coli: one produces different pigments due to the change of time, and the other produces different pigments with the change of position.<br />
<br />
In the first part, the strain of E.coli works as an oscillator which can yield different kinds of pigment periodically with the help of a signal transformation system.<br />
<br />
In the second part, They came up with the idea of “colorful E.film”. In hope to create a colorful film, They will construct three E.coli strains which can produce and secrete three primary colors respectively in the presence of the three primary lights. <br />
[[file:TJU1202.jpg|center]]<br />
<br />
===UC Davis, gold medal===<br />
They set out to develop a quick, easy process for the expansion of basic parts into a part families. Our method employs a suped-up mutagenic PCR protocol that uses standard VF2 and VR primers and materials most iGEM teams already have on hand. They chose to prototype this process by creating a part family from the LacI promoter BBa_R0010, and to mutate GFP to visually assess our ability to create functional protein mutants.we have a functioning part family generation process and seven well-characterized LacI promoter mutants and eight GFP mutants (two of which have been lovingly named Orange-Mutated Green Fluorescent Protein or [OMGfp] 1 and 2) which await further characterization.<br />
<br />
=Regulation with temperature, UTP-Panama, Gold medal=<br />
To develop flexible and better sensors for environmental, agricultural and engineering applications are the aims of the UTP-Panama Team “SynBio Engineering Tool Kit”. In this way they work with Nitrate Biosensor (PyeaR - GFP composite) developed by Team BCCS-Bristol 2010, which expresses fluorescent signals upon nutrient detection, producing a high-resolution map of arable land. To achieve this goal they use the collateral effect of the AOX enzyme (Alternative oxidase) mainly designed to generate heat in response to a cold-shock, using the hybB promoter. This effect increases the bacteria growth at temperatures below 20°C. Finally we design a prototype device with a better cold shock promoter (CspA promoter) developed by UNAM-CINVESTAV Team in 2010, in order to give our E. coli a “Intelligent Coat", which means that not to only survive a cold-shock but to also still been able to keep up with his duties due to improve their expression mechanism at low temperature. <br />
<br />
=Regulation with Quorum-Sensing, THU,Gold medal=<br />
They dedicate in pursuing the goal of the construction of a biological oscillator, which they call 'ECHO', the abbreviation of 'the ''E. coli'' Homochronous Oscillator'.<br />
With two Escherichia coli populations expressing gene one after another, they give red and green fluorescent light alternately. E.coli populations communicate bi-directionally by a class of signaling molecules involves in bacteria quorum sensing, that is, N-Acyl homoserine lactones (AHL), to regulate the gene expression of each other. By engineering their gene circuits, two groups (name as CELL-A and CELL-B) will form a network, with B inducing A and A restricting B, thus able to realize oscillation. A mechanism is set up to change the rate of an AHL expression, allowing us to control the period and the phase of the oscillatory cycle.<br />
[[file:TJU1203.jpg|center]]<br />
<br />
As a translational regulatory tool, our device achieves more precise tuning of protein expression when compared with transcriptional tools. The controlling elements we use in this device are codons and tRNAs, the major participants of translation process. Thus manipulating these elements exert direct effects on protein biosynthesis. We just try to summarize something useful for more teams to refer to.<br />
<br />
=References=<br />
[1] ZHANG Zhen-tian, HUANG Guo-feng, ZHONG Liu-zhu. Genetic pollution and ecological and environmental safety[J]. Ecology and Environment 2005, 14(6): 987-989<br />
<br />
[2] Dalton. R. Transgenic corn found growing in Mexico, Nature, 2011, 413:337<br />
<br />
[3]QIAN Yingqian, WEI Wei, MA Keping. Thinking about the problems of biological safety. Impact of Science on Society, 2002(4):24-26<br />
<br />
[4] WANG Xiu-mei. Gene Contamination, Biosafety and the Protection of International Environment——“The Protocol on Biosafety”and the New Development of International Environment Law[J]. Journal of Chang ′an University ( Social Science Edition) 2002, Vol. 4 No. 1<br />
<br />
[5] LIU San-mao, CHEN Jin-xiang. Progress of transgene crop gene floating and it’ s gene pollution[J], JIANGXI COTTON 2005, Vol. 27, No. 6<br />
<br />
[6] WEI Wei, Ma Keping. How Should We Face the Problems of Gene Flow and Gene Contamination[J], Review of China Agricul tural Science and Technology 2002, Vol. 4(4)<br />
<br />
[7] LIANG Zhao. The current situation and problems of gene therapy[J]. Chinese Medical Ethics 2003(1):16-18<br />
<br />
[8] WEI Xiaozhou. Genetic pollution---new century hardship[J]. Digest of Science and Technology 2004(7):10-11<br />
<br />
[9] Daniel L. Hartl. Elizabeth W. Jones. Genetics. Jones and Bartlett Publishers. 2005<br />
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{{:Team:Tianjin/footer}}</div>Helengoodhttp://2012.igem.org/File:TJU1203.jpgFile:TJU1203.jpg2012-09-27T03:52:58Z<p>Helengood: </p>
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<div></div>Helengoodhttp://2012.igem.org/Team:Tianjin/SafetyTeam:Tianjin/Safety2012-09-27T03:49:56Z<p>Helengood: /* Regulation with Quorum-Sensing, THU,Gold medal */</p>
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<a href="https://2012.igem.org/Team:Tianjin/Safety/Question"><center><span style="font-size:72px;font-family:Cambria;line-height:80%">?</span><br>Safety Questions</center></a></div><br />
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<br />
<br><center><span style="font-size:46px;font-family:Cambria;margin-top:10px">Biosafety Handbook</span></center><br />
<br><br />
<br />
Biosafety handbook is one of most important part of our human practice. Our handbook is based on the iGEM programs, from which we select the teams whose safety parts are beneficial and fruitful. And we also made reference to some related papers. [[file:Labsafety.jpg|thumb|250px|left|Biosafety should be the primary concern in the laboratory]]At last, we summarized and wrote this biosafety handbook. We hope our handbook can help people with the work of gene pollution prevention. And we believe our biosafety handbook will provide reference to other iGEM teams in the future.<br />
<br />
Genetic pollution refers to the unintended or uncontrolled gene flow of native species gene pool. In 21th century, the recombinant organisms begin to spread into the environment extensively. Admittedly, scientists and international groups have already started to seriously consider the safety of transgenosis, but there are still a lot of limitations and a lack of long-term data. Although genetic engineering can bring huge benefits to us, but the potential threats it cause can never be ignored. Like DDT, which won a Nobel Prize in the year when it was created, but caused great injury to both human beings and the environment after 50 years. We can't stop this kind of things totally, but at least we can make efforts to prevent it. Considering the specialty of our program, it can be creatively used in the career of the gene pollution prevention, we will show the possibilities and examples in the third part. <br />
We divided our handbook into three parts:<br />
<br />
=Operation=<br />
'''Laboratory Practices Followed By Our Team'''<br />
:1. Always wear appropriate personal protective equipment. Feet and legs should be covered; sandals and open-toed shoes should not be worn in laboratories. Wear appropriate gloves while handling infectious or toxic materials and animals. Do not wear lab coats, gloves or other personal protective equipment outside the laboratory. Change gloves when contaminated, and dispose of used gloves with other contaminated laboratory waste.<br />
[[file:Safety-goggle.jpg|thumb|250px|right|A safety goggle]]<br />
:2. Do not eat, drink, smoke, handle contact lenses, apply cosmetics, or store food for human consumption in the laboratory.<br />
:3. Wash your hands after working with potentially hazardous materials and before leaving the laboratory.<br />
:4. Follow the institutional policies regarding safe handling of sharps (i.e., needles, scalpels, pipettes, and broken glassware). Be careful with needles and syringes. Use only when alternative methods are not feasible. Syringes, needles, Pasteur pipettes, etc, should be placed in rigid, leak-proof containers (Sharps Safe) and discarded following the waste rules.<br />
:5. Take care to minimize the creation of aerosols and/or splashes.<br />
:6.Decontaminate all work surfaces before and after your experiments, and immediately after any spill or splash of potentially infectious material with an appropriate disinfectant. Clean laboratory equipment routinely, even if it is not contaminated.<br />
:7. Decontaminate all potentially infectious materials before disposal.<br />
:8. Report any incidents that may result in exposure to infectious materials to appropriate personnel (e.g., laboratory supervisor, safety officer).<br />
:9. Know where the nearest eyewash, safety shower, and fire extinguisher are located. Know how to use them. <br />
:10. Insist upon good housekeeping in your laboratory.<br />
:11. Check for insects and rodents. Keep all areas clean.<br />
:12. Secure all gas cylinders.<br />
:13. Use a biological safety cabinet for handling infectious materials or materials requiring protection from contamination and a fume hood for toxic materials; mixed hazards need to be evaluated case by case.[[file:Labsafety2.jpg|thumb|250px|right|Use fume hoods]]<br />
:14. Fume hoods should be used for laboratory activities that could result in chemical explosions or fires, for experiments involving toxic, hazardous or carcinogenic compounds, and use of strong acids and bases. 9Biological safety cabinets should not be used for this kind of work. Fume hoods are workstations, not storage cabinets. Vented storage areas may be located under the fume hood work area. However, these are not for storage of flammables.<br />
:15. Respect chemicals and radionuclides. Know their hazards and follow appropriate safety precautions. Chemical and radioactive waste must not be poured down the drain.<br />
:16. All equipment must be documented to be free of chemical, biological, and radiological contamination before repair work is done or before moving equipment for storage or elsewhere.<br />
:17. Never mouth pipette anything. Use mechanical pipetting devices only!<br />
:18. Close laboratory doors while experiments are in progress. Restrict access to laboratory.<br />
:19. Put liquid traps and in-line vacuum filters on all vacuum lines.<br />
:20. Minimize or contain all aerosol-producing activities, large-volume work, concentrated solutions or cultures. These activities include centrifugation (use safety cups), vortex missing (stopper tube), blending (use metal safety blender), sonication, grinding, opening containers of infectious material, inoculating culture flasks, inoculating animals, harvesting infectious materials from cultures or animals, and weighing or reconstructing toxic powders, etc.<br />
[[file:LabSafety3.jpg|thumb|250px|left|Avoid leaking]]<br />
:21. Place biological safety cabinets in low-traffic areas and minimize activities that disrupt air flow in or around cabinet.<br />
:22. Decontaminate all work surfaces daily, and decontaminate all spills immediately.<br />
:23. Decontaminate (by autoclaving or chemical disinfection) all biologically contaminated materials – glassware, animal cages, laboratory equipment, etc. – before washing, reuse or disposal. Discard materials via proper waste stream.<br />
:24. Broken glassware and disposable pipettes (after decontamination) should be placed in a “Disposable Labware and Broken Glass Box” and discarded following the waste rules.<br />
:25. Place contaminated biological materials in covered, leak-proof containers before removing them from the laboratory.<br />
:26. Wash your hands after handling chemicals, infectious materials, animals, after removing gloves and before leaving the laboratory.<br />
<br />
=Social=<br />
:'''1. Everyone should be prudent'''<br />
DDT, the inventor of which won the Nobel Prize, was used as a pesticide at early time, but after 50 years we found out that it caused irreparable damage to human beings and environment. Therefore, it is necessary to slow the development of genetic engineering and focus on improving its basic research. We should make sure it won't cause side effects to the environment and human beings before its promotion.<br />
:'''2. Establish and improve the related laws and regulations, and strictly implement them'''<br />
[[file:Slide0263_image223.jpg|thumb|250px|left|Wild type plant (left) compared with genetically engineered plant (right)]]<br />
In the past two decades, Chinese government also put forward a lot of related laws and regulations. In 1993, the former State Science and Technology Commission issued a regulation called "genetic engineering safety management measures". In 1996 the Ministry of Agriculture issued the “Agricultural Biological Genetic Engineering Safety Management Implementation Approach". In May 23, 2001, the State Council announced “Agricultural Genetically Modified Organisms' (GMOs') Safety Management Regulations". On January 5, 2002, the Ministry of Agriculture announced “Safety Assessment of Agricultural GMO", "Measures for the Administration of the Import of Agricultural Transgenic Living Things", “Agricultural GMO Identity Management Approach ". These laws and regulations help organizations to stick to principles to prevent genetic pollution.<br />
:'''3. Improve the examination and approval system of gene engineering technology application'''<br />
The system should require the genetic engineering technology pass the microbiology, plant and animal experiments, environmental experiments and human trials before put into application. We should prevent the abuse and industrialization or commercialization of genetic engineered product rashly. For example, some governments have made announcements to prohibit the production and sale of any crops with antibiotic resistance gene.<br />
:'''4. Carry out public science education'''<br />
The lack of the biological safety awareness is one of the biggest reasons of the genetic pollution. The majority of Chinese people whose daily life are closely related to genetically modified food can't ever understand the genetic pollution. So it's necessary for us to carry out the popular science education so that more and more people can pay attention to the genetic engineering knowledge.<br />
:'''5. Implementation of a labelling system for genetically modified food'''<br />
[[file:6301.jpg|thumb|200px|right|Food containing genetically engineered organisms]]<br />
United Nations announce if we take people's health and the environment into account, every country has the right to restrict the import of genetically modified food. All genetically modified products in the shipment should be labeled, indicating “this product contains genetically modified material ". International Consumers Association believe that although it is uncertain that genetically modified food is unsafe, but in order to prevent potential hazard to human, we should take preventive measures and establish an identification system. The identification of GMOs can help consumers to make choices. Genetic pollution is really a big problem in the application of genetic engineering. But we must realize the great benefit of genetic engineering. It is likely to bring the best choice for us to solve the global food shortage. Therefore we cannot give up improving gene engineering technology for fear of a little trouble.<br />
:'''6. Risk assessment and management'''<br />
Conduct the risk assessment and management of transgenic technique and analysis the adverse effects of its products in the trans-boundary movement process so that the importer can make choices easily.<br />
<br />
=Synthetic Biology=<br />
When it comes to our iGEM project this year, the regulation of gene expression systems can not only introduces a new way for protein-specific expression but also plays an important role in preventing genetic pollution. For example, if you want to transfer some exogenous genes that are harmful to the environment or human beings into cells, then biological safety is one thing we must consider about. To prevent harmful genes being expressed in uncontrolled cases, we must do something to prevent possible genetic pollution. And this year our project can do a lot on this problem. Our o-ribosome device allows translation only when the combination of the o-16s ribosome and o-RBS, so if we put the device at the upstream of the target genes, we can control the expression of target genes precisely. At the same time, RBS sequences are necessary in almost every cell,therefore an extensive application can be performed by our o-ribosomal. [[file:Tianjin_Model_hand3.jpg|thumb|300px|right|Our teammate is performing gel-cutting.]]Not only can our project regulate gene expression and prevent genetic pollution, but also it will not consume any extra nutrients, and have no influence on the normal life activities of bacteria. <br />
On the other hand, different RBS sequences can influence the efficiency of the translation, so we can use a series of RBS sequences to regulate gene expression with a gradient rate. The possibility of genetic pollution can also be reduced in this accurate process.<br />
<br />
Finally, the o-ribosomal devices can be used to establish a orthogonal system, in which cells have specific o-ribosomal devices instead of the original ones. Being different from other ordinary cells, they cannot be expressed in normal cells even if the target genes from orthogonal system spread out,which leads to a strong protection against genetic pollution. It is obvious that genetic pollution can be completely prevented in this orthogonal system.<br />
There were also several projects which were related to gene expression regulation in iGEM last year. For example, the SJTU-BioX-Shanghai team designed a set of Codon-Switches that regulate target protein biosynthesis (translation).In their rare-codon switch, the translation of the protein can be finely turned up/down with the control of rare tRNA amount, aaRS that charges the rare tRNA and rare codons. Besides they also made other two switches that could be turned on/off without background noise. One called the stop-codon switch was to use stop codon as the controlling element. The other one called the initial-codon switch was to use any codon but the original start codon to initiate translation. What's more, the projects of the BYU Provo team, USTC-China team, Peking-R team and some other teams were all related to gene expression regulation too. We believe that maybe the principles of these projects can also be used in the prevention to genetic pollution. So if you are interested in this, you can know more through their wiki.<br />
<br />
As iGEM teams are from different countries which may have different regulations for biosaftey. So on the one hand, it's necessary to collect information and make standard biosafety rules for basic synthetic biology experiments. On the other hand, our simple biosafety handbook cannot be suitable for all teams. But we believe our work must be useful for many iGEM teams and other researchers.<br />
<br />
<br><center><span style="font-size:46px;font-family:Cambria;margin-top:10px">Regulation Summary</span></center><br />
<br><br />
The creature differs from each other due to the patterns of gene expression,because most genes differ in their level of the cell cycle.The activity of genes is also keyed to the functions of the cell;The expression of the protein can influence the whole cell.The main role in gene regulation is the level of transcription,either through signals originating within the cell itself or in response to external conditions.Many gene products are needed only on ocassion ,and transcription can be regulated in an on-off manner that enables such products to ve present only when external conditions demand them .Five main control points for gene expression include:<br />
<br />
# Transcriptional regulation of the synthesis of RNA transcrips by controling initiation or termination.<br />
# RNA processing or regulation through RNA splicing or alternative patterns of splicing.<br />
# Translational control of polypeptide synthesis.<br />
# Stability of mRNA,because mRNAs that persist in the cell have longer-lasting effects than those that are degraded rapidly.<br />
# Posttranslational control,which includes a great variety of mechanisms that affect enzyme activity, activation,stability, and so on.<br />
# DNA rearrangements,in which gene expression changes depending on the position of DNA sequencs in the genome.<br />
<br />
The regulatory systems of prokayotes and eukaryotes differ from each other in many details.Because the project in the iGEM 's platforms are mostly prokayotes,we just focus on the prokayotes' gene regulation.Prokayotes are generally free-living unicellular organisms that grow and divice indefinitely as long as environmental conditions are suitable and the supply of nutrients is adequate.Their regulatory systems are often geared to provide the maximum growth rate in a particular environment .In contrast ,the cells in a developing muticellular organism modulate their growth rate as they undergo dramatic,coordinated differentiation in morphology and metabolism.In an adult animal,growth and division of most cell types has ceased,and each type of cell needs to maintain its identity through time.<br />
<br />
Synthetic biology is a brand new field of biological research which combines science and engineering. Now more and more people are familiar with this promising and appealing field. Gene expression regulation can expand the regulating tools for synthetic biology. We can control protein biosynthesis through things like riboswitch. Different combinations of these regulating tools can bring different outcomes in protein expression levels. And they can be applied to real life to solve many difficult practical problems.<br />
<br />
According to some of the championship projects in2011 igem,we find some are intresting and develpmental.Gene regulation can be called as the core for most of the projects.<br />
<br />
For example, As BYU's first iGEM team, BYU team proposed constructing a molecular AND gate in E. coli. To detect their chosen inputs they investigated the OxyR promoter and a thermo-sensitive riboswitch. The OxyR protein activates transcription in the presence of hydrogen peroxide, a reactive oxygen speesscies (ROS). The riboswitch allows translation only above a specific temperature. Both inputs activate a Cre/Lox system to remove a terminator sequence and allow transcription of a molecular signal. And they think a similar system, in theory, could be used for early detection of colorectal cancer.<br />
<br />
Another team is the SJTU-BioX-Shanghai, they designed a set of Codon-Switches that regulate target protein biosynthesis (translation).In their rare-codon switch, the translation of the protein can be finely turned up/down with the control of rare tRNA amount,aaRS that charges the rare tRNA and rare codons. Besides, their also made other two switches that can be turned on/off without background noise . One is to use stop codon as the controlling element, the stop-codon switch.The other is to use any codon but the original start codon to initiate translation, the initial-codon switch.<br />
<br />
Various methods of regulation are provide.Followings are the typical ones.<br />
=Regulation with density: XMU gold medal,Advance to Championship=<br />
They have developed a series of devices which program a bacteria population to maintain at different cell densities. They 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 using RBSes of different strength and mutated luxR promoters (lux pr). They are working on builting up a database for a series of mutation sites and RBSes corresponding to different steady-state cell densities. An artificial neural network will be 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. <br />
<br />
=Regulation with Light=<br />
===WHU, Gold medal, Advance to Championship===<br />
Their project focuses on constructing colorful E.coli, which includes two parts. They plan to construct two systems consisting of several strains of E.coli: one produces different pigments due to the change of time, and the other produces different pigments with the change of position.<br />
<br />
In the first part, the strain of E.coli works as an oscillator which can yield different kinds of pigment periodically with the help of a signal transformation system.<br />
<br />
In the second part, They came up with the idea of “colorful E.film”. In hope to create a colorful film, They will construct three E.coli strains which can produce and secrete three primary colors respectively in the presence of the three primary lights. <br />
<br />
===UC Davis, gold medal===<br />
They set out to develop a quick, easy process for the expansion of basic parts into a part families. Our method employs a suped-up mutagenic PCR protocol that uses standard VF2 and VR primers and materials most iGEM teams already have on hand. They chose to prototype this process by creating a part family from the LacI promoter BBa_R0010, and to mutate GFP to visually assess our ability to create functional protein mutants.we have a functioning part family generation process and seven well-characterized LacI promoter mutants and eight GFP mutants (two of which have been lovingly named Orange-Mutated Green Fluorescent Protein or [OMGfp] 1 and 2) which await further characterization.<br />
<br />
=Regulation with temperature, UTP-Panama, Gold medal=<br />
To develop flexible and better sensors for environmental, agricultural and engineering applications are the aims of the UTP-Panama Team “SynBio Engineering Tool Kit”. In this way they work with Nitrate Biosensor (PyeaR - GFP composite) developed by Team BCCS-Bristol 2010, which expresses fluorescent signals upon nutrient detection, producing a high-resolution map of arable land. To achieve this goal they use the collateral effect of the AOX enzyme (Alternative oxidase) mainly designed to generate heat in response to a cold-shock, using the hybB promoter. This effect increases the bacteria growth at temperatures below 20°C. Finally we design a prototype device with a better cold shock promoter (CspA promoter) developed by UNAM-CINVESTAV Team in 2010, in order to give our E. coli a “Intelligent Coat", which means that not to only survive a cold-shock but to also still been able to keep up with his duties due to improve their expression mechanism at low temperature. <br />
<br />
=Regulation with Quorum-Sensing, THU,Gold medal=<br />
They dedicate in pursuing the goal of the construction of a biological oscillator, which they call 'ECHO', the abbreviation of 'the ''E. coli'' Homochronous Oscillator'.<br />
With two Escherichia coli populations expressing gene one after another, they give red and green fluorescent light alternately. E.coli populations communicate bi-directionally by a class of signaling molecules involves in bacteria quorum sensing, that is, N-Acyl homoserine lactones (AHL), to regulate the gene expression of each other. By engineering their gene circuits, two groups (name as CELL-A and CELL-B) will form a network, with B inducing A and A restricting B, thus able to realize oscillation. A mechanism is set up to change the rate of an AHL expression, allowing us to control the period and the phase of the oscillatory cycle.<br />
<br />
As a translational regulatory tool, our device achieves more precise tuning of protein expression when compared with transcriptional tools. The controlling elements we use in this device are codons and tRNAs, the major participants of translation process. Thus manipulating these elements exert direct effects on protein biosynthesis. We just try to summarize something useful for more teams to refer to.<br />
<br />
=References=<br />
[1] ZHANG Zhen-tian, HUANG Guo-feng, ZHONG Liu-zhu. Genetic pollution and ecological and environmental safety[J]. Ecology and Environment 2005, 14(6): 987-989<br />
<br />
[2] Dalton. R. Transgenic corn found growing in Mexico, Nature, 2011, 413:337<br />
<br />
[3]QIAN Yingqian, WEI Wei, MA Keping. Thinking about the problems of biological safety. Impact of Science on Society, 2002(4):24-26<br />
<br />
[4] WANG Xiu-mei. Gene Contamination, Biosafety and the Protection of International Environment——“The Protocol on Biosafety”and the New Development of International Environment Law[J]. Journal of Chang ′an University ( Social Science Edition) 2002, Vol. 4 No. 1<br />
<br />
[5] LIU San-mao, CHEN Jin-xiang. Progress of transgene crop gene floating and it’ s gene pollution[J], JIANGXI COTTON 2005, Vol. 27, No. 6<br />
<br />
[6] WEI Wei, Ma Keping. How Should We Face the Problems of Gene Flow and Gene Contamination[J], Review of China Agricul tural Science and Technology 2002, Vol. 4(4)<br />
<br />
[7] LIANG Zhao. The current situation and problems of gene therapy[J]. Chinese Medical Ethics 2003(1):16-18<br />
<br />
[8] WEI Xiaozhou. Genetic pollution---new century hardship[J]. Digest of Science and Technology 2004(7):10-11<br />
<br />
[9] Daniel L. Hartl. Elizabeth W. Jones. Genetics. Jones and Bartlett Publishers. 2005<br />
<br />
{{:Team:Tianjin/footer}}</div>Helengoodhttp://2012.igem.org/Team:Tianjin/SafetyTeam:Tianjin/Safety2012-09-27T03:48:34Z<p>Helengood: </p>
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<a href="#Operation">Operation</a><br />
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<a href="#Social">Social</a><br />
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<a href="#Synthetic_Biology">Synthetic Biology</a><br />
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<a href="https://2012.igem.org/Team:Tianjin/Safety/Question"><center><span style="font-size:72px;font-family:Cambria;line-height:80%">?</span><br>Safety Questions</center></a></div><br />
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<br><center><span style="font-size:46px;font-family:Cambria;margin-top:10px">Biosafety Handbook</span></center><br />
<br><br />
<br />
Biosafety handbook is one of most important part of our human practice. Our handbook is based on the iGEM programs, from which we select the teams whose safety parts are beneficial and fruitful. And we also made reference to some related papers. [[file:Labsafety.jpg|thumb|250px|left|Biosafety should be the primary concern in the laboratory]]At last, we summarized and wrote this biosafety handbook. We hope our handbook can help people with the work of gene pollution prevention. And we believe our biosafety handbook will provide reference to other iGEM teams in the future.<br />
<br />
Genetic pollution refers to the unintended or uncontrolled gene flow of native species gene pool. In 21th century, the recombinant organisms begin to spread into the environment extensively. Admittedly, scientists and international groups have already started to seriously consider the safety of transgenosis, but there are still a lot of limitations and a lack of long-term data. Although genetic engineering can bring huge benefits to us, but the potential threats it cause can never be ignored. Like DDT, which won a Nobel Prize in the year when it was created, but caused great injury to both human beings and the environment after 50 years. We can't stop this kind of things totally, but at least we can make efforts to prevent it. Considering the specialty of our program, it can be creatively used in the career of the gene pollution prevention, we will show the possibilities and examples in the third part. <br />
We divided our handbook into three parts:<br />
<br />
=Operation=<br />
'''Laboratory Practices Followed By Our Team'''<br />
:1. Always wear appropriate personal protective equipment. Feet and legs should be covered; sandals and open-toed shoes should not be worn in laboratories. Wear appropriate gloves while handling infectious or toxic materials and animals. Do not wear lab coats, gloves or other personal protective equipment outside the laboratory. Change gloves when contaminated, and dispose of used gloves with other contaminated laboratory waste.<br />
[[file:Safety-goggle.jpg|thumb|250px|right|A safety goggle]]<br />
:2. Do not eat, drink, smoke, handle contact lenses, apply cosmetics, or store food for human consumption in the laboratory.<br />
:3. Wash your hands after working with potentially hazardous materials and before leaving the laboratory.<br />
:4. Follow the institutional policies regarding safe handling of sharps (i.e., needles, scalpels, pipettes, and broken glassware). Be careful with needles and syringes. Use only when alternative methods are not feasible. Syringes, needles, Pasteur pipettes, etc, should be placed in rigid, leak-proof containers (Sharps Safe) and discarded following the waste rules.<br />
:5. Take care to minimize the creation of aerosols and/or splashes.<br />
:6.Decontaminate all work surfaces before and after your experiments, and immediately after any spill or splash of potentially infectious material with an appropriate disinfectant. Clean laboratory equipment routinely, even if it is not contaminated.<br />
:7. Decontaminate all potentially infectious materials before disposal.<br />
:8. Report any incidents that may result in exposure to infectious materials to appropriate personnel (e.g., laboratory supervisor, safety officer).<br />
:9. Know where the nearest eyewash, safety shower, and fire extinguisher are located. Know how to use them. <br />
:10. Insist upon good housekeeping in your laboratory.<br />
:11. Check for insects and rodents. Keep all areas clean.<br />
:12. Secure all gas cylinders.<br />
:13. Use a biological safety cabinet for handling infectious materials or materials requiring protection from contamination and a fume hood for toxic materials; mixed hazards need to be evaluated case by case.[[file:Labsafety2.jpg|thumb|250px|right|Use fume hoods]]<br />
:14. Fume hoods should be used for laboratory activities that could result in chemical explosions or fires, for experiments involving toxic, hazardous or carcinogenic compounds, and use of strong acids and bases. 9Biological safety cabinets should not be used for this kind of work. Fume hoods are workstations, not storage cabinets. Vented storage areas may be located under the fume hood work area. However, these are not for storage of flammables.<br />
:15. Respect chemicals and radionuclides. Know their hazards and follow appropriate safety precautions. Chemical and radioactive waste must not be poured down the drain.<br />
:16. All equipment must be documented to be free of chemical, biological, and radiological contamination before repair work is done or before moving equipment for storage or elsewhere.<br />
:17. Never mouth pipette anything. Use mechanical pipetting devices only!<br />
:18. Close laboratory doors while experiments are in progress. Restrict access to laboratory.<br />
:19. Put liquid traps and in-line vacuum filters on all vacuum lines.<br />
:20. Minimize or contain all aerosol-producing activities, large-volume work, concentrated solutions or cultures. These activities include centrifugation (use safety cups), vortex missing (stopper tube), blending (use metal safety blender), sonication, grinding, opening containers of infectious material, inoculating culture flasks, inoculating animals, harvesting infectious materials from cultures or animals, and weighing or reconstructing toxic powders, etc.<br />
[[file:LabSafety3.jpg|thumb|250px|left|Avoid leaking]]<br />
:21. Place biological safety cabinets in low-traffic areas and minimize activities that disrupt air flow in or around cabinet.<br />
:22. Decontaminate all work surfaces daily, and decontaminate all spills immediately.<br />
:23. Decontaminate (by autoclaving or chemical disinfection) all biologically contaminated materials – glassware, animal cages, laboratory equipment, etc. – before washing, reuse or disposal. Discard materials via proper waste stream.<br />
:24. Broken glassware and disposable pipettes (after decontamination) should be placed in a “Disposable Labware and Broken Glass Box” and discarded following the waste rules.<br />
:25. Place contaminated biological materials in covered, leak-proof containers before removing them from the laboratory.<br />
:26. Wash your hands after handling chemicals, infectious materials, animals, after removing gloves and before leaving the laboratory.<br />
<br />
=Social=<br />
:'''1. Everyone should be prudent'''<br />
DDT, the inventor of which won the Nobel Prize, was used as a pesticide at early time, but after 50 years we found out that it caused irreparable damage to human beings and environment. Therefore, it is necessary to slow the development of genetic engineering and focus on improving its basic research. We should make sure it won't cause side effects to the environment and human beings before its promotion.<br />
:'''2. Establish and improve the related laws and regulations, and strictly implement them'''<br />
[[file:Slide0263_image223.jpg|thumb|250px|left|Wild type plant (left) compared with genetically engineered plant (right)]]<br />
In the past two decades, Chinese government also put forward a lot of related laws and regulations. In 1993, the former State Science and Technology Commission issued a regulation called "genetic engineering safety management measures". In 1996 the Ministry of Agriculture issued the “Agricultural Biological Genetic Engineering Safety Management Implementation Approach". In May 23, 2001, the State Council announced “Agricultural Genetically Modified Organisms' (GMOs') Safety Management Regulations". On January 5, 2002, the Ministry of Agriculture announced “Safety Assessment of Agricultural GMO", "Measures for the Administration of the Import of Agricultural Transgenic Living Things", “Agricultural GMO Identity Management Approach ". These laws and regulations help organizations to stick to principles to prevent genetic pollution.<br />
:'''3. Improve the examination and approval system of gene engineering technology application'''<br />
The system should require the genetic engineering technology pass the microbiology, plant and animal experiments, environmental experiments and human trials before put into application. We should prevent the abuse and industrialization or commercialization of genetic engineered product rashly. For example, some governments have made announcements to prohibit the production and sale of any crops with antibiotic resistance gene.<br />
:'''4. Carry out public science education'''<br />
The lack of the biological safety awareness is one of the biggest reasons of the genetic pollution. The majority of Chinese people whose daily life are closely related to genetically modified food can't ever understand the genetic pollution. So it's necessary for us to carry out the popular science education so that more and more people can pay attention to the genetic engineering knowledge.<br />
:'''5. Implementation of a labelling system for genetically modified food'''<br />
[[file:6301.jpg|thumb|200px|right|Food containing genetically engineered organisms]]<br />
United Nations announce if we take people's health and the environment into account, every country has the right to restrict the import of genetically modified food. All genetically modified products in the shipment should be labeled, indicating “this product contains genetically modified material ". International Consumers Association believe that although it is uncertain that genetically modified food is unsafe, but in order to prevent potential hazard to human, we should take preventive measures and establish an identification system. The identification of GMOs can help consumers to make choices. Genetic pollution is really a big problem in the application of genetic engineering. But we must realize the great benefit of genetic engineering. It is likely to bring the best choice for us to solve the global food shortage. Therefore we cannot give up improving gene engineering technology for fear of a little trouble.<br />
:'''6. Risk assessment and management'''<br />
Conduct the risk assessment and management of transgenic technique and analysis the adverse effects of its products in the trans-boundary movement process so that the importer can make choices easily.<br />
<br />
=Synthetic Biology=<br />
When it comes to our iGEM project this year, the regulation of gene expression systems can not only introduces a new way for protein-specific expression but also plays an important role in preventing genetic pollution. For example, if you want to transfer some exogenous genes that are harmful to the environment or human beings into cells, then biological safety is one thing we must consider about. To prevent harmful genes being expressed in uncontrolled cases, we must do something to prevent possible genetic pollution. And this year our project can do a lot on this problem. Our o-ribosome device allows translation only when the combination of the o-16s ribosome and o-RBS, so if we put the device at the upstream of the target genes, we can control the expression of target genes precisely. At the same time, RBS sequences are necessary in almost every cell,therefore an extensive application can be performed by our o-ribosomal. [[file:Tianjin_Model_hand3.jpg|thumb|300px|right|Our teammate is performing gel-cutting.]]Not only can our project regulate gene expression and prevent genetic pollution, but also it will not consume any extra nutrients, and have no influence on the normal life activities of bacteria. <br />
On the other hand, different RBS sequences can influence the efficiency of the translation, so we can use a series of RBS sequences to regulate gene expression with a gradient rate. The possibility of genetic pollution can also be reduced in this accurate process.<br />
<br />
Finally, the o-ribosomal devices can be used to establish a orthogonal system, in which cells have specific o-ribosomal devices instead of the original ones. Being different from other ordinary cells, they cannot be expressed in normal cells even if the target genes from orthogonal system spread out,which leads to a strong protection against genetic pollution. It is obvious that genetic pollution can be completely prevented in this orthogonal system.<br />
There were also several projects which were related to gene expression regulation in iGEM last year. For example, the SJTU-BioX-Shanghai team designed a set of Codon-Switches that regulate target protein biosynthesis (translation).In their rare-codon switch, the translation of the protein can be finely turned up/down with the control of rare tRNA amount, aaRS that charges the rare tRNA and rare codons. Besides they also made other two switches that could be turned on/off without background noise. One called the stop-codon switch was to use stop codon as the controlling element. The other one called the initial-codon switch was to use any codon but the original start codon to initiate translation. What's more, the projects of the BYU Provo team, USTC-China team, Peking-R team and some other teams were all related to gene expression regulation too. We believe that maybe the principles of these projects can also be used in the prevention to genetic pollution. So if you are interested in this, you can know more through their wiki.<br />
<br />
As iGEM teams are from different countries which may have different regulations for biosaftey. So on the one hand, it's necessary to collect information and make standard biosafety rules for basic synthetic biology experiments. On the other hand, our simple biosafety handbook cannot be suitable for all teams. But we believe our work must be useful for many iGEM teams and other researchers.<br />
<br />
<br><center><span style="font-size:46px;font-family:Cambria;margin-top:10px">Regulation Summary</span></center><br />
<br><br />
The creature differs from each other due to the patterns of gene expression,because most genes differ in their level of the cell cycle.The activity of genes is also keyed to the functions of the cell;The expression of the protein can influence the whole cell.The main role in gene regulation is the level of transcription,either through signals originating within the cell itself or in response to external conditions.Many gene products are needed only on ocassion ,and transcription can be regulated in an on-off manner that enables such products to ve present only when external conditions demand them .Five main control points for gene expression include:<br />
<br />
# Transcriptional regulation of the synthesis of RNA transcrips by controling initiation or termination.<br />
# RNA processing or regulation through RNA splicing or alternative patterns of splicing.<br />
# Translational control of polypeptide synthesis.<br />
# Stability of mRNA,because mRNAs that persist in the cell have longer-lasting effects than those that are degraded rapidly.<br />
# Posttranslational control,which includes a great variety of mechanisms that affect enzyme activity, activation,stability, and so on.<br />
# DNA rearrangements,in which gene expression changes depending on the position of DNA sequencs in the genome.<br />
<br />
The regulatory systems of prokayotes and eukaryotes differ from each other in many details.Because the project in the iGEM 's platforms are mostly prokayotes,we just focus on the prokayotes' gene regulation.Prokayotes are generally free-living unicellular organisms that grow and divice indefinitely as long as environmental conditions are suitable and the supply of nutrients is adequate.Their regulatory systems are often geared to provide the maximum growth rate in a particular environment .In contrast ,the cells in a developing muticellular organism modulate their growth rate as they undergo dramatic,coordinated differentiation in morphology and metabolism.In an adult animal,growth and division of most cell types has ceased,and each type of cell needs to maintain its identity through time.<br />
<br />
Synthetic biology is a brand new field of biological research which combines science and engineering. Now more and more people are familiar with this promising and appealing field. Gene expression regulation can expand the regulating tools for synthetic biology. We can control protein biosynthesis through things like riboswitch. Different combinations of these regulating tools can bring different outcomes in protein expression levels. And they can be applied to real life to solve many difficult practical problems.<br />
<br />
According to some of the championship projects in2011 igem,we find some are intresting and develpmental.Gene regulation can be called as the core for most of the projects.<br />
<br />
For example, As BYU's first iGEM team, BYU team proposed constructing a molecular AND gate in E. coli. To detect their chosen inputs they investigated the OxyR promoter and a thermo-sensitive riboswitch. The OxyR protein activates transcription in the presence of hydrogen peroxide, a reactive oxygen speesscies (ROS). The riboswitch allows translation only above a specific temperature. Both inputs activate a Cre/Lox system to remove a terminator sequence and allow transcription of a molecular signal. And they think a similar system, in theory, could be used for early detection of colorectal cancer.<br />
<br />
Another team is the SJTU-BioX-Shanghai, they designed a set of Codon-Switches that regulate target protein biosynthesis (translation).In their rare-codon switch, the translation of the protein can be finely turned up/down with the control of rare tRNA amount,aaRS that charges the rare tRNA and rare codons. Besides, their also made other two switches that can be turned on/off without background noise . One is to use stop codon as the controlling element, the stop-codon switch.The other is to use any codon but the original start codon to initiate translation, the initial-codon switch.<br />
<br />
Various methods of regulation are provide.Followings are the typical ones.<br />
=Regulation with density: XMU gold medal,Advance to Championship=<br />
They have developed a series of devices which program a bacteria population to maintain at different cell densities. They 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 using RBSes of different strength and mutated luxR promoters (lux pr). They are working on builting up a database for a series of mutation sites and RBSes corresponding to different steady-state cell densities. An artificial neural network will be 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. <br />
<br />
=Regulation with Light=<br />
===WHU, Gold medal, Advance to Championship===<br />
Their project focuses on constructing colorful E.coli, which includes two parts. They plan to construct two systems consisting of several strains of E.coli: one produces different pigments due to the change of time, and the other produces different pigments with the change of position.<br />
<br />
In the first part, the strain of E.coli works as an oscillator which can yield different kinds of pigment periodically with the help of a signal transformation system.<br />
<br />
In the second part, They came up with the idea of “colorful E.film”. In hope to create a colorful film, They will construct three E.coli strains which can produce and secrete three primary colors respectively in the presence of the three primary lights. <br />
<br />
===UC Davis, gold medal===<br />
They set out to develop a quick, easy process for the expansion of basic parts into a part families. Our method employs a suped-up mutagenic PCR protocol that uses standard VF2 and VR primers and materials most iGEM teams already have on hand. They chose to prototype this process by creating a part family from the LacI promoter BBa_R0010, and to mutate GFP to visually assess our ability to create functional protein mutants.we have a functioning part family generation process and seven well-characterized LacI promoter mutants and eight GFP mutants (two of which have been lovingly named Orange-Mutated Green Fluorescent Protein or [OMGfp] 1 and 2) which await further characterization.<br />
<br />
=Regulation with temperature, UTP-Panama, Gold medal=<br />
To develop flexible and better sensors for environmental, agricultural and engineering applications are the aims of the UTP-Panama Team “SynBio Engineering Tool Kit”. In this way they work with Nitrate Biosensor (PyeaR - GFP composite) developed by Team BCCS-Bristol 2010, which expresses fluorescent signals upon nutrient detection, producing a high-resolution map of arable land. To achieve this goal they use the collateral effect of the AOX enzyme (Alternative oxidase) mainly designed to generate heat in response to a cold-shock, using the hybB promoter. This effect increases the bacteria growth at temperatures below 20°C. Finally we design a prototype device with a better cold shock promoter (CspA promoter) developed by UNAM-CINVESTAV Team in 2010, in order to give our E. coli a “Intelligent Coat", which means that not to only survive a cold-shock but to also still been able to keep up with his duties due to improve their expression mechanism at low temperature. <br />
<br />
=Regulation with Quorum-Sensing, THU,Gold medal=<br />
They dedicate in pursuing the goal of the construction of a biological oscillator, which they call ‘ECHO’, the abbreviation of ‘the E.Coli Homochronous Oscillator’.<br />
With two Escherichia coli populations expressing gene one after another, they give red and green fluorescent light alternately. E.coli populations communicate bi-directionally by a class of signaling molecules involves in bacteria quorum sensing, that is, N-Acyl homoserine lactones (AHL), to regulate the gene expression of each other. By engineering their gene circuits, two groups (name as CELL-A and CELL-B) will form a network, with B inducing A and A restricting B, thus able to realize oscillation. A mechanism is set up to change the rate of an AHL expression, allowing us to control the period and the phase of the oscillatory cycle.<br />
<br />
As a translational regulatory tool, our device achieves more precise tuning of protein expression when compared with transcriptional tools. The controlling elements we use in this device are codons and tRNAs, the major participants of translation process. Thus manipulating these elements exert direct effects on protein biosynthesis. We just try to summarize something useful for more teams to refer to.<br />
<br />
=References=<br />
[1] ZHANG Zhen-tian, HUANG Guo-feng, ZHONG Liu-zhu. Genetic pollution and ecological and environmental safety[J]. Ecology and Environment 2005, 14(6): 987-989<br />
<br />
[2] Dalton. R. Transgenic corn found growing in Mexico, Nature, 2011, 413:337<br />
<br />
[3]QIAN Yingqian, WEI Wei, MA Keping. Thinking about the problems of biological safety. Impact of Science on Society, 2002(4):24-26<br />
<br />
[4] WANG Xiu-mei. Gene Contamination, Biosafety and the Protection of International Environment——“The Protocol on Biosafety”and the New Development of International Environment Law[J]. Journal of Chang ′an University ( Social Science Edition) 2002, Vol. 4 No. 1<br />
<br />
[5] LIU San-mao, CHEN Jin-xiang. Progress of transgene crop gene floating and it’ s gene pollution[J], JIANGXI COTTON 2005, Vol. 27, No. 6<br />
<br />
[6] WEI Wei, Ma Keping. How Should We Face the Problems of Gene Flow and Gene Contamination[J], Review of China Agricul tural Science and Technology 2002, Vol. 4(4)<br />
<br />
[7] LIANG Zhao. The current situation and problems of gene therapy[J]. Chinese Medical Ethics 2003(1):16-18<br />
<br />
[8] WEI Xiaozhou. Genetic pollution---new century hardship[J]. Digest of Science and Technology 2004(7):10-11<br />
<br />
[9] Daniel L. Hartl. Elizabeth W. Jones. Genetics. Jones and Bartlett Publishers. 2005<br />
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{{:Team:Tianjin/footer}}</div>Helengoodhttp://2012.igem.org/Team:Tianjin/Project/OrthogonalSystemTeam:Tianjin/Project/OrthogonalSystem2012-09-27T03:36:44Z<p>Helengood: /* References */</p>
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<a href="#The_Orthogonal_System_of_Regulating_Translation:_the_AegiSafe.E2.84.A2_O-Key">the AegiSafe™ O-Key</a><br />
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<center><span style="font-size:46px;font-family:Cambria;margin-top:10px;line-height:80%">Orthogonal System</span></center><br />
<br><br />
=<span style="line-height:110%">The Orthogonal System of Regulating Translation: the AegiSafe™ O-Key</span>=<br />
[[file:TJU2012-Proj-OS-fig-1.png|thumb|300px|right|'''Figure 1.''' Simulation figure of ribosome (from עדה יונת)]]The synthesis of protein relies on the transcription-translation network. In transcription, mRNA is synthesized through complementary base pairing by RNA polymerase from the DNA template, and is followed by translation. Translation is the third stage of protein biosynthesis. In translation, mRNA produced by transcription is decoded by the ribosome to produce a specific amino acid chain, or polypeptide, that will later fold into an active protein. Therefore, we can say that translation is one of most important of activities in a cell. <br />
<br />
Due to its importance of protein synthesis, there are intricate and delicate regulation systems. To regulate transcription, cells alter the gene expression levels. This is called transcriptional regulation. Many means of transcriptional regulation, such as various mechanisms as specificity factors, activators, etc., are presented in a cell. There are also inducible and repressible systems, and transcription factor that can determine the initiation rate of transcription.<br />
<br />
While a number of genetic tools exist for regulating transcription in cells, far fewer tools exist for translation. Of the tools available in bacteria, the most popular are riboregulators, both cis- and trans-activating, and '''orthogonal ribosomes''' (o-ribosomes). [[file:TJU2012-Proj-OS-fig-2.png|thumb|300px|left|'''Figure 2.''' Simulation figure of 16S (from Johns Hopkins Medical Institutions)]]In terms of reprograming translation, o-ribosomes are especially powerful as they enable one to partially decouple translation from the native protein synthesis machinery. In particular, o-ribosomes can translate genes with altered '''Shine-Dalgarno''' (SD) sequences not recognized by host ribosomes. Therefore, o-ribosomes can be used to explore gene expression dynamics as they potentially provide a method for tuning translation rates. Furthermore, o-ribosomes may have application in synthetic biology as they introduce new functionality within cells.<br />
<br />
In this year's project, we focus on modifying the Sine-Dalgarno (SD) sequence of the mRNA and the anti-Shine-Dalgarno (ASD) sequence of the 16S rRNA of the ribosome to construct an orthogonal translation system called the AegiSafe™ O-Key. '''Aegis''' was originally the shield that was associated with Zeus and Athena, which offers protection. '''AegiSafe™''' means our orthogonal system secure the environment from potential biosafety issue. '''O-Key''' stands for orthogonal system that includes orthogonal ribosome (o-ribosome, '''O-Key''') and orthogonal RBS (o-RBS, '''O-Lock'''), which indicates that our system can not only shut down contamination, but also using the orthogonal system to selectively open our translation pathway like a key to a lcok. This is a truly amazing system for two independent translation systems co-existing harmoniously and working effectively in one single cell. In the following sections, we will elaborate on the AegiSafe™ O-Key about the orthogonal system and its application.<br />
<br />
=The Overview of Orthogonal Ribosome (O-Key)=<br />
===The Canonical Ribosome===<br />
Ribosome is the protein factory of a cell, an organelle without membrane. Its sophisticated structure guarantees the accurate information flow from mRNA to protein. Ribosomes consist of two subunits that fit together and work as one to translate the mRNA into a polypeptide chain during protein synthesis. <br />
<br />
Prokaryotes have 70S ribosomes, each consisting of a small (30S) and a large (50S) subunit. The smaller subunit binds to the mRNA pattern, while the larger subunit binds to the tRNA and the amino acids. Their small subunit has a '''16S RNA subunit''' (consisting of 1540 nucleotides) bound to 21 proteins. The large subunit is composed of a 5S RNA subunit (120 nucleotides), a 23S RNA subunit (2900 nucleotides) and 31 proteins. Crystallographic work has shown that there are no ribosomal proteins close to the reaction site for polypeptide synthesis. This suggests that the protein components of ribosomes act as a scaffold that may enhance the ability of rRNA to synthesize protein rather than directly participating in catalysis, while the rRNA reacts with the mRNA and catalyze the synthesis. <br />
<br />
Multiple sequences of 16S rRNA can exist within a single bacterium. <br />
[[file:TJU2012-Proj-OS-fig-3.png|thumb|500px|center|'''Figure 3.''' Biochemistry fourth edition (from Reginald H.Garrett & Charles M.Grisham)]]<br />
It has several functions:<br />
* Like the large (23S) ribosomal RNA, it has a structural role, acting as a scaffold defining the positions of the rebosomal proteins.<br />
* The 3' end contains the anti-Shine-Dalgarno sequence, which binds upstream to the AUG start codon on the mRNA. The 3'-end of 16S RNA binds to the proteins S1 and S21 known to be involved in initiation of protein synthesis<br />
*Interacts with 23S, aiding in the binding of the two ribosomal subunits (50S+30S)<br />
*Stabilizes correct codon-anticodon pairing in the A site, via a hydrogen bond formation between the N1 atom of Adenine (see image of Purine chemical structure) residues 1492 and 1493 and the 2'OH group of the mRNA backbone.<br />
<br />
In bacterial cells, ribosomes are synthesized in the cytoplasm through the transcription of multiple ribosome gene operons.<br />
<br />
The rRNAs that make up the ribosome are directly translated from the rRNA operon rrnB. The three E. coli rRNA molecules – 23S, 16S, and 5S – are derived from a single 30S rRNA precursor transcript that also includes several tRNAs.<br />
<br />
===The Orthogonal Ribosome===<br />
The previous section described the structure of a canonical ribosome. As for the orthogonal ribosome (O-Key), the primary structure remains the same. The only difference lies in the ASD sequence close the 3' of the 16S rRNA. This altered sequence will not recognize the canonical SD sequence, thus pausing translation, just like a key cannot open a mismatched lock. The O-Key can only pair with its corresponding RBS, i.e. O-Lock. The O-Key (orthogonal) system serves as a powerful tool in regulating inner cellular metabolism. We will elaborate on its application in the following chapter.<br />
<br />
=Gibson Free Energy in the O-Key System=<br />
The strength of the interaction between SD and ASD sequence is thought to influence translational efficiency as mutations in either the SD or ASD sequence that weaken the interaction reduce the amount of protein made. The mechanism of protein expression is primarily determined by the delta Gibbs free energy of the combination of SD sequence on ribosome and the ASD sequence on RBS of the mRNA. Therefore, it is necessary to investigate the property of ΔG.<br />
[[file:TJU2012-Proj-OS-fig-4.png|thumb|500px|center|'''Figure 4.''' The two states of 16S binding mRNA (from "Automated design of synthetic ribosome binding sites to control protein expression")]]<br />
[[file:TJU2012-Proj-OS-fig-6.png|thumb|500px|center|'''Figure 5.''' Process of translation (from "Automated design of synthetic ribosome binding sites to control protein expression")]]<br />
ΔG<sub>tot</sub>=ΔG<sub>mRNA:rRNA</sub>+ΔG<sub>start</sub>+ΔG<sub>spacing</sub>-ΔG<sub>standby</sub>-ΔG<sub>mRNA</sub><br />
<br />
ΔG<sub>mRNA:rRNA</sub> is the energy released when the last nine nucleotides(nt) of the E. coli 16S rRNA (3′-AUUCCUCCA-5′) hybridizes and co-folds to the mRNA sub-sequence (ΔG<sub>mRNA:rRNA</sub><0). Intramolecular folding within the mRNA is allowed. All possible hybridizations between the mRNA and 16S rRNA are considered to find the highest affinity 16S rRNA binding site. The binding site minimizes the sum of the hybridization free energy ΔG<sub>mRNA:rRNA</sub> and the penalty for nonoptimal spacing, ΔG<sub>spacing</sub>. Thus, the algorithm can identify the 16S rRNA binding site regardless of its similarity to the consensus Shine-Dalgarno sequence.<br />
<br />
*ΔG<sub>start</sub> is the energy released when the start codon hybridizes to the initiating tRNA anticodon loop (3'-UAC-5').<br />
*ΔG<sub>spacing</sub> is the free energy penalty caused by a nonoptimal physical distance between the 16S rRNA binding site and the start codon (ΔG<sub>spacing</sub>>0). When this distance is increased or decreased from an optimum of 5 nt (or ~17A), the 30S complex becomes distorted, resulting in a decreased translation initiation rate.<br />
*Δ<sub>GmRNA</sub> is the work required to unfold the mRNA sub-sequence when it folds to its most stable secondary structure, called the minimum free energy structure (ΔG<sub>mRNA</sub><0).<br />
*ΔG<sub>standby</sub> is the work required to unfold any secondary structures sequestering the standby site (ΔG<sub>standby</sub><0) after the 30S complex assembly. We define the standby site as the four nucleotides upstream of the 16S rRNA binding site, which is its location in a previously studied mRNA.<br />
<br />
To calculate ΔG<sub>mRNA:rRNA</sub>, ΔG<sub>start</sub>, ΔG<sub>mRNA</sub> and ΔG<sub>standby</sub>, we use the NUPACK suite of algorithms with the Mfold 3.0 RNA energy parameters. These free energy calculations do not have any additional fitting or training parameters and explicitly depend on the mRNA sequence. In addition, the free energy terms are not orthogonal; changing a single nucleotide can potentially affect multiple energy terms. The relationship between the spacing and the ΔG<sub>spacing</sub> was empirically determined by measuring the protein expression level driven by synthetic RBSs of varying spacing and fitting a quantitative model to this data.<br />
[[file:TJU2012-Proj-OS-fig-5.png|thumb|500px|center|'''Figure 6.''' Orthogonal sequences of different ΔG (from "Computational design of orthogonal ribosomes")]]<br />
<br />
=Orthogonality Verification Experiment=<br />
<br />
If orthogonal RBS is safe, why don't we change all the canonical 16s into orthogonal 16s? The answer is no. That is because if we change all the base 16s, the other housekeeping genes will stop expressing. This will produce orthogonal rivalry, leading to bacterial death. So we are bound to face competition between canonical and orthogonal 16s. Then we design the following experiment to research this problem. We designed three operons to verify the orthogonality of our system. First, our first experiment is based on an assumption that the fluorescent light intensity can represent the amount of the expression of fluorescent protein. The relevant literature indicates that the fluorescent light intensity represents the amount of the expression of fluorescent protein and the assumption can be right if the experimental precision is not sensitive.<br />
<br />
We constructed two sets of plasmid co-transformed into E. coli to achieve the purpose. One set is induced by the promoter then transcripts the O-key's vector, which is equivalent to the key. The other set is O-RBS/RFP+RBS/GFP, it is constructed to compare the orthogonality between the O-RBS and N-RBS by GFP and RFP.<br />
[[file:TJU2012-Proj-OS-fig-8.png|thumb|200px|center|'''Figure 7.''' Possible combination of 16S and mRNA(from TJU iGEM Team 2012)]]<br />
From this figure, we can see that there are four competition relationships in the orthogonal cell system, the ideal state is the 1th and 2th path exists while the 3th and 4th path weaken. That means our system has good orthogonality. We did multiple sets of pre-experiments of different O-16s then decided to use this set.<br />
[[file:TJU2012-Proj-OS-fig-7.png|thumb|500px|center|'''Figure 8.''' the Operon: RBS/RFP+RBS/RFP, n-RBS. n-RBS binds to the original RBS to translate RFP and GFP. (from TJU iGEM Team 2012)]]<br />
[[file:TJU2012-Proj-OS-fig-9.png|thumb|500px|center|'''Figure 9.''' the Operon: RBS/RFP+RBS/GFP, n-RBS and O-RBS. n-RBS binds to the original RBS to translate RFP and GFP, O-RBS can’t bind to the original RBS and translate RFP and GRP. (from TJU iGEM Team 2012)]]<br />
[[file:TJU2012-Proj-OS-fig-10.png|thumb|500px|center|'''Figure 10.''' the Operon: RBS/RFP+RBS/GFP, n-RBS and O-RBS. n-RBS binds to the original RBS to translate RFP and GFP, O-RBS can’t bind to the original RBS and translate RFP and GRP. (from TJU iGEM Team 2012)]]<br />
[[file:TJU2012-Proj-OS-fig-11.png|thumb|500px|center|'''Figure 11.''' the Operon: O-RBS/RFP+RBS/GFP, n-RBS and O-RBS. n-RBS binds to the original RBS and O-RBS binds to the O-RBS then translate RFP and GFP. (from TJU iGEM Team 2012)]]<br />
[[file:TJU2012-Proj-OS-fig-12.png|thumb|500px|center|'''Figure 12.''' The figure shows the bacteria that product fluorescent protein. (from TJU iGEM Team 2012)]]<br />
[[file:TJU2012-Proj-OS-fig-13.png|thumb|500px|center|'''Figure 10.''' The result of the experiment of the orthogonality verification. (from TJU iGEM Team 2012)]]<br />
<br />
=Modeling=<br />
In order to design the orthogonality and to predict the protein expression level, we have established the protein expression model which has strong relationship with the wet lab. The model is based on detailed study of the effects of changing Gibbs free energy on the translation process.<br />
<br />
In the process of translation, the initiation rate is the rate determine step. The protein expression amount is consequently direct proportional to the initial translation speed. Furthermore, the initial translation speed is strongly related to the delta Gibbs free energy, which can be calculated out through results of many newly published papers and various commercialized software such as the Vienna RNA Package, RBS-Calculator, and Nucleic Acid Package.<br />
In our model, we calculated the delta Gibbs energy. Ideal results can be obtained from the model. The orthogonality predicted by our model before the wet lab is similar to our prediction. When combined with some wet lab result, we can finally predict the spectroscope curve of RFP and GFP under three designed experimental state. For more details, see our [[Team:Tianjin/Modeling|Model Part]].<br />
[[file:TJU2012-Proj-OS-fig-14.png|thumb|500px|center|'''Figure 14.''' RFP expression level under four pathways (from TJU iGEM Team 2012)]]<br />
<br />
=Future Work=<br />
Previous experiments and modeling has described that the orthogonality of our expression system is very tight, but we are still not satisfied with the current state, then we design and do the following experiment.<br />
The following experiment includes:<br />
#We are using λRed technology to integrate the O-16s biobrick into the genome for constructing the orthogonal cells, so as to solve the revertants as well as stability problems caused by plasmid instability. <br />
#We are trying to build other groups of different orthogonal (O-16s-RBS) system, so as to achieve the different orthogonality switch effect, and attempt to make them corporate. <br />
#We also consult with some biological gene enterprises to make our results put into production in the life full of modern technology, such as genetic pollution control, gene encryption and metabolic regulation, etc.<br />
<br />
=References=<br />
1.http://en.wikipedia.org/wiki/16S_ribosomal_RNA <br />
<br />
2.Lon M. Chubiz and Christopher V. Rao(2008). Computational design of orthogonal ribosomes, vol.36 no.12<br />
<br />
3.Howard M Salis, Ethan A Mirsky & Christopher A Voigt(2009).Automated design of synthetic ribosome binding sites to control protein expression, doi:10.1038/nbt.1568<br />
<br />
4.Wenlin An and Jason W. Chinl(2009).Synthesis of orthogonal transcription-translation networks,vol.106 no.21 <br />
<br />
5.George H.McArthur IV and Stephen S. Fong, Toward Engineering Synthetic Microbial Metabolism<br />
<br />
6.Kevin Clancy and Christopher A Voigt, Programming cells: towards an automated ‘Genetic Compiler’<br />
<br />
7.WANG Haisheng, ZHANG Xiaoxia, et al., Recent research progress of bacterial violacein <br />
<br />
8.Carotenoid Crystal Formation in Arabidopsis and Carrot Roots Caused by Increased Phytoene Synthase Protein<br />
Levels<br />
<br />
9.Guoyin Kai, Pan Liao, Tong Zhang, Wei Zhou, Jing Wang, Hui Xu, Yuanyun Liu, and Lin Zhang, Characterization, Expression Profiling, and Functional Identification of a Gene Encoding Geranylgeranyl Diphosphate Synthase from Salvia miltiorrhiza.<br />
<br />
10.crtB Masaki Fujisawa,Mio Watanabe,Song-Kang Choi,Maki Teramoto,Kanji Ohyama,and Norihiko Misawa, Enrichment of Carotenoids in Flaxseed (Linum usitatissimum) by Metabolic Engineering with Introduction of Bacterial Phytoene Synthase Gene <br />
<br />
11. William R. Farmer and James C. Liao, Improving lycopene production in Escherichia coli by engineering metabolic control.<br />
<br />
{{:Team:Tianjin/footer}}</div>Helengoodhttp://2012.igem.org/Team:Tianjin/Project/RegulationTeam:Tianjin/Project/Regulation2012-09-27T03:35:23Z<p>Helengood: /* References */</p>
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<p class="menu_head">Project Contents</p><br />
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<a href="https://2012.igem.org/Team:Tianjin/Project">Project Home</a><br />
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<a href="https://2012.igem.org/Team:Tianjin/Project/OrthogonalSystem">Orthogonal System</a><br />
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<a href="https://2012.igem.org/Team:Tianjin/Project/Gene">Safety Encryption</a><br />
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<a href="#Overview">Overview</a><br />
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<a href="#Orthogonal_System">Orthogonal System</a><br />
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<a href="#Logic_Metabolism_Regulation">Logic Metabolism Regulation</a><br />
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<center><span style="font-size:46px;font-family:Cambria;margin-top:10px;line-height:80%">Logic Metabolism Regulation</span></center><br />
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<br />
=Background=<br />
[[file:TJU2012-Proj-LMR-fig-1.png|thumb|300px|right|'''Figure 1.''' ''E. coli'' (from the website of dnaQ)]]<br />
===Metabolic Regulation===<br />
Cell metabolism is the foundation of cell growth, secretion, differentiation, etc. as well as the core process of the modern fermentation technology that can make large impact on the quality and output of product.<br />
<br />
However the modern metabolic regulation of strains has a large amount of areas for improvement. Take the most common E. coli as example. At present, most of the regulation means is to use a single promoter to construct specific operon gene cluster to achieve the regulation with the addition of certain inducers induction of a specific protein. But this induced expression is typically unidirectional, irreversible and it needs to build many complex operons’ gene structure to construct multiple logical regulation, this will produce a plenty of limitation. <br />
<br />
If we add our O-Key into the expression system, a novel regulation means will exist on the level of translation. Meanwhile, we can combine O-Key with the traditional transcription regulation to create logic gate regulation structure like “AND” gate. The logic gate working with normal close and normal open promoter can constitute multiple “AND/OR/NOR” logic gate control system which has more simple structure compared to traditional regulation.<br />
<br />
===The Difficulty of Large Fragments Assembly===<br />
The general digestion connection will leave scar and will be limited by the specific cleavage sequences.<br />
[[file:TJU2012-Proj-LMR-fig-2.png|thumb|150px|center|'''Figure 2.''' Enzyme digestion (from the website of dnaQ]]<br />
Long PCR fragment will suffer the decline of success rate and distortion, etc. <br />
[[file:TJU2012-Proj-LMR-fig-3.png|thumb|500px|center|'''Figure 3.''' PCR Recombinant & PCR Machine (from the website of dnaQ]]<br />
However, the construction of some large fragments cannot be avoided, so the development of a low-cost, simple operation, good fidelity, a little limiting factor large DNA fragment assembly method is particularly important.<br />
<br />
=Yeast Assembler=<br />
===History===<br />
Yeast Assembler is based on in vivo homologous recombination in yeast. As for its high efficiency and ease to work with, in vivo homologous recombination in yeast has been widely used for gene cloning, plasmid construction and library creation. In the early of 2008, Zengyi Shao from University of lllinois at Urbana-Champaign, Urbana, used such a method to construct biochemical pathways. Such a method, for its high efficiency in assembling multiple genes, received great popularity since its appearance.<br />
<br />
===Principles===<br />
One step assembly into a vector.<br />
[[file:TJU2012-Proj-LMR-fig-4.png|thumb|500px|center|'''Figure 4.''' Principles of Yeast assembler (from "DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways")]]<br />
When parts are transformed all parts into Yeast, homologous recombination occurs at the site “x”, and then all little parts are integrated into a vector.<br />
<br />
===Advantages and Disadvantages===<br />
Compared with other methods,the “Yeast assembler” are more efficient and useful for large gene assemble.<br />
[[file:TJU2012-Proj-LMR-fig-5.png|thumb|500px|center|'''Figure 5.''' Advantages and disadvantages of three assemble methods (from "DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways")]]<br />
<br />
===Completely Synthesizing the Genome of Mycoplasma Genitalium using Yeast Assembler===<br />
In 2008, Gibson from the J. Craig Venter Institute, published an article “one-step assembly in Yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome”. In the article, the author transformed 25 overlapping DNA fragments into Yeast, homologous recombination occurs, and then the whole genome is synthesized.<br />
[[file:TJU2012-Proj-LMR-fig-6.png|thumb|500px|center|'''Figure 6.''' Synthetic Mycoplasma genitalium genome (from "One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic ''Mycoplasma genitalium'' genome")]]<br />
Construction of a synthetic M. genitalium genome in yeast. Yeast cells were transformed with 25 different overlapping A-series DNA segments (blue arrows; ~17 kb to35 kb each) composing the M. genitalium genome. To assemble these into a complete genome, a single yeast cell (tan) must take up at least one representative of the 25 different DNA fragments and incorporate them in the nucleus (yellow), where homologous recombination occurs. This assembled genome, called JCVI-1.1, is 590,011 bp, including the vector sequence (red triangle) shown internal to A86 – 89.<br />
<br />
=Synthesizing the Pathway Needed for Synthesizing Violacein=<br />
===Background===<br />
In order to verify the abilities of orthogonal system to adjust metabolism, we chose the metabolic pathway of Violacein. The reason why we chose this one are based on the facts that the pathway is suitable to adjust, and has been deeply learned.<br />
<br />
Violacei, the major pigment produced by Chromobacterium violaceum, is a bactericide, a trypanocide, a tumoricide and in addition it has anti-viral activity.<br />
[[file:TJU2012-Proj-LMR-fig-7.png|thumb|500px|center|'''Figure 7.''' Violacein's structure (from "Production, extraction and purification of violacein: an antibiotic pigment produced by Chromobacterium violaceum")]]<br />
The metabolic pathways to produce Violacein are revealed in the following picture.<br />
[[file:TJU2012-Proj-LMR-fig-8.png|thumb|500px|center|'''Figure 8.''' Pathway of Violacein (from BBa_K274002)]]<br />
From the pathway, we can know that except for the desire product, Violacein, the pathway will also produce side product, deoxyviolacein.<br />
<br />
===Principle===<br />
In order to verify the feasibility of the orthogonal system in adjusting metabolism, we mutated the RBS of the gene encoding VioD by MAGE, and assembled in Yeast Assembler. The VioD gene and the O-Key gene with pBad promoter were finally transformed into the cell. Because the cell itself doesn’t have the O-Key, the gene is stringently shut down. When we added Ala to induce pBad, the O-Key were produced to open the O-Lock, so the cell could produce violacin.<br />
<br />
===Experiment===<br />
#MAGE mutate the RBS of the gene coding VioD to o-RBS<br />
#We construct different parts of Vio operons, and transformed into yeast for assembly(In this part, we also assembly the original genes without mutation)[[file:TJU2012-Proj-LMR-fig-9.png|thumb|500px|center|'''Figure 9.''' Assembler of Violacein (from TJU iGEM Team 2012)]]<br />
#Extracted the plasmid of Yeast and then transformed into our O-E.coli on LB plates.<br />
#Verify through Cpcr and inculcated the right colony into liquid LB overnight.<br />
#Extracted the plasmid of E.coli and verified through digestion of ligase.<br />
<br />
===Results and Analysis===<br />
[[file:TJU2012-Proj-LMR-fig-10.png|thumb|500px|center|'''Figure 10.''' Process of experiments (from TJU iGEM Team 2012)]]<br />
#From the above picture, the process is finished smoothly and the result of Digested verification is right.[[file:TJU2012-Proj-LMR-fig-11.png|thumb|500px|center|'''Figure 11.''' Results of the normal pathway (from TJU iGEM Team 2012)]]<br />
#From this picture, we could find that the test tube with the normal pathway, the liquid is purple. In such condition, for PVA have the larger potential to turn into violacein, violacein stand for a large part and liquid is purple.[[file:TJU2012-Proj-LMR-fig-12.png|thumb|500px|center|'''Figure 12.''' Results of the mutated pathway without adding Ala (from TJU iGEM Team 2012)]]<br />
#In this picture, we could find that liquid is blue. As we didn’t add Ala into the liquid, the cells didn’t produce O-ribosome, then the vioD could not be expressed. The PVA could only become deoxyviolacein, which is blue. Therefore the liquid is blue.[[file:TJU2012-Proj-LMR-fig-13.png|thumb|500px|center|'''Figure 13.''' Results of the mutated pathway adding Ala (from TJU iGEM Team 2012)]]<br />
#In this picture, the liquid is lavender. For this tube, we added Ala, which could induce the production of O-ribosome, then PVA could turn into violacein, then the liquid is lavender.<br />
#From the results of this experiment, we could find that the orthogonal system could work well when used to adjust metabolism, and the effect is satisfied. In the fourth part, we will further discuss the application of the orthogonal system in regulating the metabolism.<br />
<br />
=Logic Gate Metabolic Regulation=<br />
Biological logic gate has been described as the most advanced “biological circuit” ever built. This year, we used the orthogonal system to achieve metabolic regulation by logic gate – the O-Key. Our technology is a translational regulation. It not only introduce a new “AND gate” regulation to cells, but also works perfect with transcriptional regulation, waste no sequence resources and has certain potential of encryption.<br />
[[file:TJU2012-Proj-LMR-fig-14.png|thumb|500px|center|'''Figure 14.''' Theory figure of logic gate metabolic regulation(from TJU iGEM Team 2012)]]<br />
The core of our O-Key consists of two part: the o-ribosome and o-mRNA. Their roles in metabolic regulation can be described as key and lock. O-ribosome serves as key, while o-mRNA is the lock. We use the o-RBS to “lock” the target sequence, and make it decipherable only under o-ribosome. They altogether forms an AND gate.<br />
[[file:TJU2012-Proj-LMR-fig-15.png|thumb|500px|center|'''Figure 15.''' The method of controling O-Key synthesis (from TJU iGEM Team 2012)]]<br />
The regulation of o-ribosome can be achieved by four ways: constitutive promoter, chemical inducible systems, temperature-inducible systems, quorum sensing systems。We can chose different pathways according various conditions.<br />
[[file:TJU2012-Proj-LMR-fig-16.png|thumb|500px|center|'''Figure 16.''' Orthoganol regulation of metabolism network (from KEGG)]]<br />
We use modeling fitting to predict the key nodes in the metabolism network. MAGE can be used to mutate the RBS of target gene to o-RBS thus locking the target gene. Compared with the conventional way of regulating by overexpression and gene knockout, our O-Key avoids decreasing cell activity and slowing growth rate because of partial adjustment of regulation networks by altering multiple cell native control transcription simultaneously. This technology saves time and boost efficiency.<br />
[[file:TJU2012-Proj-LMR-fig-17.png|thumb|500px|center|'''Figure 17.''' The difference between original regulation and orthogonal regulation (from TJU iGEM Team 2012)]]<br />
We will elaborate on the function of O-Key in the following examples.<br />
[[file:TJU2012-Proj-LMR-fig-18.png|thumb|500px|center|'''Figure 18.''' The first example of metabolism regulation (from TJU iGEM Team 2012)]]<br />
This pathway has two branches. If we put an O-Lock between C and D, we can adjust the metabolic pathway according to the cell growth cycle. Say I is the primary metabolites, and the bacteria need it for growth, we can close the O-Lock to shut down pathway D. When the bacteria is in stationary phase and in sufficient quantity, we can open the O-Lock to turn on pathway D, and increase the secondary metabolites F by its competitive advantage.<br />
[[file:TJU2012-Proj-LMR-fig-19.png|thumb|500px|center|'''Figure 19.''' The second example of metabolism regulation (from TJU iGEM Team 2012)]]<br />
If the natural branch competitive advantage does not exist, or we need precise regulation of the metabolism of the two pathway, we can install different O-Key system on the two pathway, and use the O-Key to achieve accurate control.<br />
<br />
In a word, the O-Key system has two advantages. On the one hand, it can achieve the same function of other complex operons using much more concise sequence.<br />
[[file:TJU2012-Proj-LMR-fig-20.png|thumb|500px|center|'''Figure 20.''' One example of logic metabolism regulation (from "Synthesis of orthogonal transcription-translation networks")]]<br />
Moreover, with the combination of different O-Key system we are able to construct more complicated logic networks using in a much simpler way. Currently, we have demonstrated that bacteria and DNA molecules can “copy” logic gate, and started constructing more complicated logic gates.<br />
<br />
We wish this research would result in a new generation biological processor, and they have the same importance in information processing as other electric devices. Although there is still a long way before constructing a biological computer, we have the faith that our O-Key logic gate will be applied as the fundamental module in the computer.<br />
<br />
=References=<br />
# Lon M. Chubiz and Christopher V. Rao(2008). Computational design of orthogonal ribosomes, vol.36 no.12<br />
# Daniel G. Gibsona,1, Gwynedd A. Bendersb, Kevin C. Axelrod PNAS(2008). One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome, vol. 105 no. 51 <br />
# Daniel G. Gibson(2009).Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides. vol.37 no.20Zengyi Shao, Hua Zhao1and Huimin Zhao(2009). DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways. vol.37 no.2<br />
# Zengyi Shao, Hua Zhao1and Huimin Zhao(2009). DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways. vol.37 no.2Daniel G. Gibsona, Gwynedd A. Bendersb, et al., Next-generation synthetic gene network<br />
# Howard M Salis, Ethan A Mirsky & Christopher A Voigt(2009).Automated design of synthetic ribosome binding sites to control protein expression, doi:10.1038/nbt.1568<br />
# Howard M Salis, Ethan A Mirsky & Christopher A Voigt(2009).Automated design of synthetic ribosome binding sites to control protein expression, doi:10.1038/nbt.1568<br />
# Wenlin An and Jason W. Chinl(2009).Synthesis of orthogonal transcriptiontranslation networks vol.106 no.21 <br />
# George H.McArthur IV and Stephen S. Fong, Toward Engineering Synthetic Microbial Metabolism <br />
<br />
<br />
{{:Team:Tianjin/footer}}</div>Helengood