Difference between revisions of "Team:BNU-CHINA/Team"

 
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{{BNU-CHINA/article | Team | Share with you|9/95/Bnubgl}}
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                 <h2 id="attribution">Attribution</h2>
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<h2>Members <small>- WE ARE SIRENS</small></h2>
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    <li class="checked" data-filter="*"><a class="btn-filter btn">All</a></li>
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    <li data-filter=".lab"><a class="btn-filter btn">Wet Lab</a></li>
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    <li data-filter=".modeling"><a class="btn-filter btn">Modeling</a></li>
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    <li data-filter=".wiki"><a class="btn-filter btn">Wiki Construction</a></li>
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    <li data-filter=".art"><a class="btn-filter btn">Graphic Design</a></li>
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    <li data-filter=".hp"><a class="btn-filter btn">Human Practice</a></li>
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                                Under the supervision of Prof. Zhu Xudong, Prof. Yang Dong, and Prof. Xiang Benqiong etc, nearly all team members have taken part in the project designing process, especially those of wet lab group.Beichen Gao , Yuanyi Dai , Yufei Cao and Jia Li are the group leaders who mainly design the experimental patterns and guide the different parts of the experiments.
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{{BNU-CHINA/gird/item |name=Lao Kejing|info=A sophomore majoring in biology. Her work includes  plasmid purification, SDS-PAGE and nematodes synchronization. She also tried to help BIT-China with extracting membrane proteins, NhaA and NhaB.|type=lab|photo=1/14/BNU-LAOKEJING}}
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                            <h4 class="panel-title"><a data-toggle="collapse" data-parent="#accordion" href="#collapseTwo">Modeling</a></h4>
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                                Cheng Li is the leader of modeling group, who mainly enrolled in designing the device 2.0. Yuan Yin , Qiuyue Yuan and Xueting Zhao also do a great many works in the modeling group, such as information searching, paper writing and equipment appilication.
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                                Jiajun Zhang , who has led the web design group to build the wiki, together with group members Zhiyao Chen and Chengfei Peng complete the main work in database construction and maintenance.
 
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                                Lu Xu( group leader), Lee and Yalei Cao really do a fantastic work in graphic and web design. They all make great efforts in designing our team logo, website, poster, souvenir, T-shirt and so on.
 
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{{BNU-CHINA/gird/item |name=Liu Longping|info=A sophomore student who has worked on how to promote the expression rate of rMpL as well as designed the toxic test on nematodes.|type=lab|photo=8/8e/BNU-LIULONGPING}}
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                                Meng Tang , the leader of human practice group, has organized a series of activities for Policy and Practice, like survey and publicize in some middle schools etc. Some group members as Yuanyi Dai,Jia Li , Jiajun Zhang , Beichen Gao , Zhiyao Chen , Jingyu Zhao , Xiaofei Feng also play a significant role in planning and organizing the activities . Other group members also take an active part in some other activities of human practice.
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                <h2 id="collaboration">Collaboration</h2>
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                <p>Our modeling can be divided into four parts. Firstly, in order to enable our project to be applied in life, we design a device placed in soil, which can attract and kill nematodes by modified engineering bacteria inside. Secondly, assuming there is a farmland, we take advantage of nematodes’ movement analogue simulation to find the best position where the device should be placed and the best concentration of attracting substance. Thirdly, according to this concentration, we obtain the best size of the device by calculating. At last, we establish a database to enlarge applied range of our method to kill other pests. We would appreciate that new synthetic biological and environment-friendly methods can be shared and improved with the science researchers all over the world.</p>
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{{BNU-CHINA/gird/item |name=Chen Zhiyao|info=The only freshman in our team, majoring in physics. Developed the toxic and attractant database with Peng Chengfei. Also designed the UI of the database website, and took part in HP activities too!|type=modeling wiki|photo=0/09/BNU-zaixia}}
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{{BNU-CHINA/gird/item |name=Wang Yingbing|info=A junior biotech student of BNU. Mainly did some paper work for the team, and also took part in the “bace16” group work.|type=lab|photo=a/ac/BNU-FENGXIAOFEI}}
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{{BNU-CHINA/gird/item |name=Siren|info=In Greek mythology, the Sirens were dangerous yet beautiful creatures, who lured nearby sailors with their enchanting music and eat them. We call our machine Sirens as it can attract nematodes and kill them just like the Sirens do to their meals.|type=test|photo=3/31/BNU-team-siren}}
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{{BNU-CHINA/gird/item |name=Cao Yufei|info=A junior student in Liyun College of BNU, biology major. She is responsible for the parts design for expressing limonene in <em>E. coli</em> and coresponding experiments.|type=lab|photo=1/16/BNU-CAOYUFEI}}
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{{BNU-CHINA/gird/item |name=Li Jia|info=A junior bioscience student, wants to learn more about synthetic biology and makes more friends in iGEM.  Mainly worked on testifying the chemical attractants. Besides she expressed limonene and GPP synthase, and cultivated <em>C.elegans</em>.  |type=lab|photo=7/7a/BNU-LIJIA}}
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{{BNU-CHINA/gird/item |name=Yin Yuan|info=A sophomore majoring in mathematics. Helped set up the model in proposingthe solving ideas and searching the data.|type=modeling|photo=3/37/BNU-team-YINYUAN}}
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{{BNU-CHINA/gird/item |name=Zhao Xueting|info=A sophomore in mathematics. Did work of modeling section like finding out how to put equipment on farmland, writing modeling paper, doing some translation and so on.|type=modeling|photo=b/ba/BNU-ZHAOXUETING}}
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{{BNU-CHINA/gird/item |name=Liu Xinyu|info=A sophomore biology student. Is a member of the limonene group of this project, and also took part in human practice and other parts' experiments. |type=lab|photo=0/02/BNU-LIUXINYU}}
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{{BNU-CHINA/gird/item |name=Li Yuehuan|info=A sophomore bioscience student. She helped design and verify parts of the module.|type=lab |photo=c/cc/BNU-LIYUEHUAN}}
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{{BNU-CHINA/gird/item |name=Wu Zekai|info=A sophomore biology student. Designed a part of biobrick of photoinduction system, and took part in some experiments of verifing the toxicity of Bace 16.|type=lab |photo=2/29/BNU-WUZEKAI}}
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{{BNU-CHINA/gird/item |name=Yuan Qiuyue|info=A junior majoring in mathematics. Simulated the movement of nematodes, and established the model of diffusion of the attraction.|type=modeling|photo=9/96/BNU-team-YUANQIUYUE}}
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{{BNU-CHINA/gird/item |name=Lee |info=Junior biology student. Participated in graphic design of our team, such as website designing,logo of the team and T-shirt.|type=art|photo=5/5a/BNU-LIKELAI}}
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{{BNU-CHINA/gird/item |name=Zhang Jiajun|info=A junior biotech student in BNU, he has contributed to team works and wiki building. |type=wiki|photo=6/6a/BNU-ZHANGJIAJUN}}
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{{BNU-CHINA/gird/item |name=Feng Xiaofei|info=A sophomore student who has worked on how to promote the expression rate of rMpL as well as designed the toxic test on nematodes.|type=hp|photo=7/70/BNU-WANGYINGBING}}
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{{BNU-CHINA/gird/item |name=Cao Yalei|info=From school of Geography in BNU, is a member of graphic design group who designed our team logo, banner and poster. The jerseys and souvenirs were also her masterpieces.|type=art|photo=1/18/BNU-CAOYALEI}}
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{{BNU-CHINA/gird/item |name=Xu Lu|info=A junior bioscience student who is the leader of graphic design group. Did the design work for BNU-CHINA, particularly on poster and PPT design. In addition, she made a batch of uniform shirts for our team. |type=art|photo=9/9d/BNU-XULU}}
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{{BNU-CHINA/gird/item |name=Gao Beichen|info=The leader of our team, a junior biotech student of Beijing Normal University. Mainly worked for the wet lab part including constructing parts, expressing nematocidal proteins and testifying the toxicity of rMpL. |type=lab|photo=d/de/BNU-GAOBEICHEN}}
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                <h2>Acknowledgement</h2>
 
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{{BNU-CHINA/gird/item |name=Tang Meng|info=A junior Bioscience BNU student. The HP project leader who organized most activities for Policy and Practice, such as surveys, publicity and voluntary education. She also took part in nematodes cultivating. |type=hp|photo=6/68/BNU-TANGMENG}}
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{{BNU-CHINA/gird/item |name=Dai Yuanyi|info=A junior BNU student majoring in Biotech. Devoted all her energy and time in iGEM, making her a multitasking girl. Her work involves of many aspects, mainly the construction of biobricks and expriments on Bace16. |type=lab|photo=6/66/BNU-DAIYUANYI}}
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{{BNU-CHINA/gird/item |name=Li Cheng|info=A junior bioscience student.  The leader of modeling part, designed the device 2.0. Also proposes many useful ideas in this team, such as the online database and the design to improve parts. Also enrolled in Wiki and Art work. |type=modeling|photo=3/33/BNU-LICHENG}}
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                        <h5>Prof. Zhu Xudong, Prof. Yang Dong and Prof. Xiang Benqiong
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{{BNU-CHINA/gird/item |name=Zhao Jingyu|info=A sophomore majoring in biology. Took part in experiments such as the expression of the toxin rMpL, and also did some work in human practice. |type=lab|photo=a/a2/BNU-ZHAOJINGYU}}
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                        <p>Offered us much precious advice on the project.
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                        <h5>Hao Xiaoran, Chi Xiaodong, Huo Liang, Ai Ying and Wang Xuan</h5>
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                        <p>Offered us advice on our experiments and helped us solve problems.</p>
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{{BNU-CHINA/gird/item |name=Peng Chengfei|info=A sophomore student of Computer Science. Is responsible for the some technical work like constructing the database and the corresponding website and the deployment and operation of the database. |type=wiki modeling|photo=0/09/BNU-PENGMAO}}
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                        <h5>The College of Chemistry, Beijing Normal University
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                        <p>Helped us do GC-MS.
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                        <h5>Prof. Yang Chonglin of Chinese Academy of Sciences
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                        <p>Offered us C.elegens and taught us how to cultivate them.
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                        <h5>Prof. Li Hongmei of Department of Plant Pathology，Nanjing Agricultural University
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                        <p>Helped us to do Species identification of nematodes.
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                        <h5>BIT-China & ZJU-China & FAFU-CHINA
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                        <p>Offered us some helpful advice and we also had a collaboration together.
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                        <h5>Agricultural Service Center of Ceyu, Hebei Province
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                        <p>Helped us learn more information about the damage caused by local nematodes and villager’s attitude towards agricultural insecticide.
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                        <h5>Shang Zhong National Middle School of Guizhou Province
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                        <p>Supported us in our voluntary education.
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                        <h5>National Chiao Tung University &Peking University
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                        <p>Provided us opportunities to communicate with other teams.
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                        <h5>Feng Xiaofei and her family in Hebei Province
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                        <p>Helped us get soybeans samples and did a survey in the locality.
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                        <h5>Prof. Wang Yingdian
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                        <p>Discussed the bright future of our project with us.
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                    <h3 class="text-center">Sponsors</h3>
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                    <p>Beijing Normal University (BNU), is a public research university located in Beijing with strong emphasis on basic disciplines of humanities and sciences. It is one of the oldest and most prestigious universities in China. Our school supported us to our iGEM Journey and provided us adequate resources to complete the competition. Students of different colleges in our school took part in our team, and all these colleges supported us very much.</p>
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<h3 class="panel-title">Project Design and Wet Lab Experiments</h3>
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Under the supervision of <strong>Prof. Zhu Xudong</strong>, <strong>Prof. Yang Dong</strong>, and <strong>Prof. Xiang Benqiong</strong> etc, nearly all team members have taken part in the project designing process, especially those of wet lab group.<strong>Beichen Gao</strong> , <strong>Yuanyi Dai</strong> , <strong>Yufei Cao</strong> and <strong>Jia Li</strong> are the group leaders who mainly design the experimental patterns and guide the different parts of the experiments.
 
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<strong>Cheng Li</strong> is the leader of modeling group, who mainly enrolled in designing the device 2.0. <strong>Yuan Yin</strong> , <strong>Qiuyue Yuan</strong> and <strong>Xueting Zhao</strong> also do a great many works in the modeling group, such as information searching, paper writing and equipment appilication.
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<strong>Jiajun Zhang</strong> , who has led the web design group to build the wiki, together with group members <strong>Zhiyao Chen</strong> and <strong>Chengfei Peng</strong> complete the main work in database construction and maintenance.
 +
</div>
 +
</div>
 +
 
 +
<div class="panel panel-info">
 +
<div class="panel-heading">
 +
<h3 class="panel-title">Graphic design</h3>
 +
</div>
 +
 
 +
<div class="panel-body">
 +
<strong>Lu Xu</strong>( group leader), <strong>Lee</strong> and <strong>Yalei Cao</strong> really do a fantastic work in graphic and web design. They all make great efforts in designing our team logo, website, poster, souvenir, T-shirt and so on.
 +
</div>
 +
</div>
 +
 
 +
<div class="panel panel-info">
 +
<div class="panel-heading">
 +
<h3 class="panel-title">Human practice</h3>
 +
</div>
 +
 
 +
<div class="panel-body">
 +
<strong>Meng Tang</strong> , the leader of human practice group, has organized a series of activities for Policy and Practice, like survey and publicize in some middle schools etc. Some group members as <strong>Yuanyi Dai</strong>, <strong>Jia Li</strong> , <strong>Jiajun Zhang</strong> , <strong>Beichen Gao</strong> , <strong>Zhiyao Chen</strong> , <strong>Jingyu Zhao</strong> , <strong>Xiaofei Feng</strong> also play a significant role in planning and organizing the activities . Other group members also take an active part in some other activities of human practice.
 +
</div>
 +
</div>
 +
 
 +
 
 +
<h2>Details</h2>
 +
<dl class="dl-horizontal">
 +
<dt style="color: #258D79;">Team Member</dt>
 +
<dd style="color: #258D79;font-weight: bold;">Attributions</dd>
 +
 
 +
<dt>Cao Yalei</dt>
 +
<dd>Graphic Design(Design of logo, banner, poster, jersey and souvenir)</dd>
 +
 
 +
<dt>Cao Yufei</dt>
 +
<dd>Wet lab group leader(parts design for expressing lemonene in <em>E. coli</em> and coresponding experiments)</dd>
 +
 
 +
<dt>Chen Zhiyao</dt>
 +
<dd>Wiki construction(database construction; UI design)<br>Human practice</dd>
 +
 
 +
<dt>Dai Yuanyi</dt>
 +
<dd>Daily activities arrangement and personnel management<br>Wet lab group leader(biobricks construction, Bace16 expression and testification)<br>Human practice</dd>
 +
 
 +
<dt>Feng Xiaofei</dt>
 +
<dd>Wet lab experiments(limonene synthesis)<br>Human practice</dd>
 +
 
 +
<dt>Gao Beichen</dt>
 +
<dd>Team leader<br>Wet lab group leader（biobricks construction, nematocidal protein expression, rMpL's toxicity identification<br>Human practice</dd>
 +
 
 +
<dt>Lao Kejing</dt>
 +
<dd>Wet lab experiments(plasmid purification; SDS-PAGE; nematodes synchronization)<br>Helping Beijing Institute of Technology with extracting membrane proteins, NhaA and NhaB</dd>
 +
 
 +
<dt>Lee</dt>
 +
<dd>Graphic Design( website design, logo of the team and T-shirt)</dd>
 +
 
 +
<dt>Li Cheng</dt>
 +
<dd>Modeling leader(design of the device 2.0 ; parts improving)<br>Wiki<br>Graphic design</dd>
 +
 
 +
<dt>Li Jia</dt>
 +
<dd>Wet lab group leader(chemical attractants' function testification, LS and GPPS expression, <em>C.elegans</em> cultivation )<br>Human practice</dd>
 +
 
 +
<dt>Li Yuehuan</dt>
 +
<dd>Wet lab experiments(rMpL verification)</dd>
 +
 
 +
<dt>Liu Longping</dt>
 +
<dd>Wet lab experiments(exploraton of how to promote the expression rate of protein rMpL; design of the toxic test)</dd>
 +
 
 +
<dt>Liu Xinyu</dt>
 +
<dd>Wet lab experiments(limonene group and other parts' experiments)<br>Human practice</dd>
 +
 
 +
<dt>Ma Hongfei</dt>
 +
<dd>Wet lab experiments(GC-MS of limonene )<br>Modeling(device 1.0 design and creation)</dd>
 +
 
 +
<dt>Peng Chengfei</dt>
 +
<dd>Wiki construction(database construction, deployment and operation, Wiki frame construction)</dd>
 +
 
 +
<dt>Tang Meng</dt>
 +
<dd>Human practice project leader(activities planning and organization)<br>Wet lab experiments</dd>
 +
 
 +
<dt>Wang Ran</dt>
 +
<dd>Translation<br>Human practice</dd>
  
−
                    <h2>Protocol</h2>
+
<dt>Wang Yingbing</dt>
−
                    <h3>1. Cloning</h3>
+
<dd>Wet lab experiments(Bace16 group work)</dd>
−
                    <h4 class="text-center">PCR</h5>
+
−
                    <ul>
+
−
                        <li>
+
−
                            <h5>Reaction System:</h5>
+
−
                            <p>H<sub>2</sub>O 38 \(\mu\)L</p>
+
−
                            <p>10x Taq buffer 5 \(\mu\)L
+
−
                            </p>
+
−
                            <p>2.5mM dNTP 4 \(\mu\)L</p>
+
−
                            <p>Primer 1 1 \(\mu\)L</p>
+
−
                            <p>Primer 2 1 \(\mu\)L
+
−
                            </p>
+
−
                            <p>Template 0.5 \(\mu\)L
+
−
                            </p>
+
−
                            <p>Taq 0.5 \(\mu\)L
+
−
                            </p>
+
−
                        </li>
+
−
                        <li>
+
−
                            <h5>Process:</h5>
+
−
                            <p>\(\begin{equation}\left. \begin{array}{lcl} {94&#176;C\ 10min} \\ {94&#176;C\ 30s} \\{58&#176;C\ 30s} \end{array} \right\} Cycle\ 30\end {equation}\)</p>
+
−
                            <p>94&#176;C 10min
+
−
                            </p>
+
−
                            <p>94&#176;C 30s
+
−
                            </p>
+
−
                            <p>58&#176;C 30s
+
−
                            </p>
+
−
                            <p>72&#176;C 2min30s
+
−
                            </p>
+
−
                            <p>72&#176;C 10min
+
−
                            </p>
+
−
                            <p>10&#176;C ---
+
−
                            </p>
+
−
                        </li>
+
−
                        <br/>
+
  
−
                        <h5 align='center'>Electrophoresis---Gel Purification
+
<dt>Wu Zekai</dt>
−
</h5>
+
<dd>Wet lab experiments(photoinduced system design; Bace 16 functional verification)</dd>
−
                        <li>
+
−
                            <h5>Material:</h5>
+
−
                            <p>Agarose gel: 1% agarose dissolved in 1 x TAE + gelstain</p>
+
−
                        </li>
+
−
                        <li>
+
−
                            <h5>Protocol:</h5>
+
−
                            <p>We used gelstain to stain the DNA and imaged it in a Transilluminator.
+
−
                            </p>
+
−
                            <p>We used the gel extraction kit to get the objective fragment. </p>
+
−
                        </li>
+
−
                        <br/>
+
  
−
                        <h5 align='center'>Digestion</h5>
+
<dt>Xiao Shusheng</dt>
−
                        <table class="table table-condensed ">
+
<dd>Literature reading<br>Human practice</dd>
−
                            <tbody>
+
−
                                <tr>
+
−
                                    <td>50\(\mu\)L reaction system</td>
+
−
                                    <td></td>
+
−
                                    <td></td>
+
−
                                    <td></td>
+
−
                                    <td></td>
+
−
                                    <td></td>
+
−
                                </tr>
+
−
                                <tr>
+
−
                                    <td>Reagent</td>
+
−
                                    <td>10x H buffer</td>
+
−
                                    <td>EcoR I</td>
+
−
                                    <td>Pat I</td>
+
−
                                    <td>Plasmid</td>
+
−
                                    <td>H<sub>2</sub>O
+
−
                                    </td>
+
−
                                </tr>
+
−
                                <tr>
+
−
                                    <td>Dosage</td>
+
−
                                    <td>5 \(\mu\)L</td>
+
−
                                    <td>1.5 \(\mu\)L</td>
+
−
                                    <td>1.5 \(\mu\)L</td>
+
−
                                    <td>15 \(\mu\)L</td>
+
−
                                    <td>27 \(\mu\)l
+
−
                                    </td>
+
−
                                </tr>
+
−
                            </tbody>
+
−
                        </table>
+
−
                        <table class="table table-condensed ">
+
−
                            <tbody>
+
−
                                <tr>
+
−
                                    <td>10\(\mu\)L reaction system</td>
+
−
                                    <td></td>
+
−
                                    <td></td>
+
−
                                    <td></td>
+
−
                                    <td></td>
+
−
                                    <td></td>
+
−
                                </tr>
+
−
                                <tr>
+
−
                                    <td>Reagent</td>
+
−
                                    <td>10x H buffer</td>
+
−
                                    <td>EcoR I</td>
+
−
                                    <td>Pat I</td>
+
−
                                    <td>Plasmid</td>
+
−
                                    <td>H<sub>2</sub>O
+
−
                                    </td>
+
−
                                </tr>
+
−
                                <tr>
+
−
                                    <td>Dosage</td>
+
−
                                    <td>1 \(\mu\)L
+
−
                                        <td>0.3 \(\mu\)L</td>
+
−
                                        <td>0.3 \(\mu\)L</td>
+
−
                                        <td>3 \(\mu\)L</td>
+
−
                                        <td>5.4 \(\mu\)L
+
−
                                        </td>
+
−
                                </tr>
+
−
                            </tbody>
+
−
                        </table>
+
−
                        <br/>
+
  
−
                        <h5 align='center'>Ligation</h5>
+
<dt>Xu Lu</dt>
−
                        <table class="table table-condensed ">
+
<dd>Graphic design leader（mainly on poster and PPT design）</dd>
−
                            <tbody>
+
−
                                <tr>
+
−
                                    <td>Ligation reaction system</td>
+
−
                                    <td></td>
+
−
                                    <td></td>
+
−
                                    <td></td>
+
−
                                    <td></td>
+
−
                                </tr>
+
−
                                <tr>
+
−
                                    <td>Reagent</td>
+
−
                                    <td>Cph8</td>
+
−
                                    <td>PSB1C3</td>
+
−
                                    <td>T4 buffer</td>
+
−
                                    <td>T4 ligase</td>
+
−
                                </tr>
+
−
                                <tr>
+
−
                                    <td>Dosage</td>
+
−
                                    <td>14 \(\mu\)L
+
−
                                        <td>3 \(\mu\)L</td>
+
−
                                        <td>2 \(\mu\)L</td>
+
−
                                        <td>1 \(\mu\)L</td>
+
−
                                </tr>
+
−
                            </tbody>
+
−
                        </table>
+
  
−
                    </ul>
+
<dt>Yin Yuan</dt>
−
             
+
<dd>Modeling(proposing the solving ideas; searching the data)</dd>
−
           
+
−
                    <h4>5.2 Transformation</h4>
+
−
                    <ul>
+
−
                        <li>
+
−
                            <h5>Material:
+
−
                                </h5></li>
+
−
                        <table class="table table-condensed ">
+
−
                            <tbody>
+
−
                                <tr>
+
−
                                    <td>LB liquid medium</td>
+
−
                                    <td></td>
+
−
                                    <td></td>
+
−
                                    <td></td>
+
−
                                </tr>
+
−
                                <tr>
+
−
                                    <td>Reagent</td>
+
−
                                    <td>Tryptone</td>
+
−
                                    <td>Yeast extract powder</td>
+
−
                                    <td>NaCl</td>
+
−
                                </tr>
+
−
                                <tr>
+
−
                                    <td>Dosage</td>
+
−
                                    <td>10 g/L
+
−
                                        <td>5 g/L</td>
+
−
                                        <td>10 \(\mu\)L</td>
+
−
                                </tr>
+
−
                            </tbody>
+
−
                        </table>
+
−
                 
+
−
                        <li>
+
−
                            <h5>Protocol:</h5>
+
−
                            <p>preparation of the competent cells</p>
+
−
                            <p>20\(\mu\)L ligation product + 50\(\mu\)L cells
+
−
                            </p>
+
−
                            <p>Heatshock of E.coli BW25113(42&#176;C,90s)
+
−
                            </p>
+
−
                            <p>Put on ice(2min)
+
−
                            </p>
+
−
                            <p>Add 800\(\mu\)L LB media and incubate for 1.5h(37&#176;C, 150rpm)
+
−
                            </p>
+
−
                            <p>Centrifuge at 4000rpm for 1min and remove 900\(\mu\)L supernatant
+
−
                            </p>
+
−
                            <p>Resuspend the pellets using the left supernatant
+
−
                            </p>
+
−
                            <p>Spread plates(with ampicillin)
+
−
                            </p>
+
−
                            <p>Incubate for 12~16h(37&#176;C)
+
−
                            </p>
+
−
                        </li>
+
−
                    </ul>
+
−
             
+
−
           
+
−
                    <h4>5.3 Detetion</h4>
+
−
                    <br/>
+
−
                    <h5 align='center'>SDS-PAGE
+
−
</h5>
+
−
                    <ul>
+
−
                        <li>
+
−
                            <h5>Materials:</h5>
+
−
                            <table class="table table-condensed ">
+
−
                                <tbody>
+
−
                                    <tr>
+
−
                                        <td>Gel</td>
+
−
                                        <td>Tris-HCl</td>
+
−
                                        <td>Acr/Bis 30%
+
−
                                        </td>
+
−
                                        <td>SDS 10%
+
−
                                        </td>
+
−
                                        <td>ddH<sub>2</sub>O</td>
+
−
                                        <td>TEMED
+
−
                                        </td>
+
−
                                        <td>AP 10%
+
−
                                        </td>
+
−
                                    </tr>
+
−
                                    <tr>
+
−
                                        <td>Stacking Gel(4%) </td>
+
−
                                        <td>pH=6.8 500\(\mu\)L
+
−
                                        </td>
+
−
                                        <td>500 \(\mu\)L</td>
+
−
                                        <td>25 \(\mu\)L</td>
+
−
                                        <td>1350 \(\mu\)L</td>
+
−
                                        <td>2.5 \(\mu\)L</td>
+
−
                                        <td>12.5 \(\mu\)L</td>
+
  
−
                                    </tr>
+
<dt>Yuan Qiuyue</dt>
−
                                    <tr>
+
<dd>Modeling(nematode movement simulation;model of diffusion of the attraction)<br>Human practice</dd>
−
                                        <td>Running Gel(12%)
+
−
                                            <td>pH=8.8 1250 \(\mu\)L</td>
+
−
                                            <td>2000 \(\mu\)L</td>
+
−
                                            <td>50 \(\mu\)L</td>
+
−
                                            <td>1675 \(\mu\)L</td>
+
−
                                            <td>2.5 \(\mu\)L</td>
+
−
                                            <td>25 \(\mu\)L</td>
+
−
                                    </tr>
+
−
                                    <tr>
+
−
                                        <td>Running Gel(18%)
+
−
                                            <td>pH=8.8 1250 \(\mu\)L</td>
+
−
                                            <td>3000 \(\mu\)L</td>
+
−
                                            <td>50 \(\mu\)L</td>
+
−
                                            <td>675 \(\mu\)L</td>
+
−
                                            <td>2.5 \(\mu\)L</td>
+
−
                                            <td>25 \(\mu\)L</td>
+
−
                                    </tr>
+
−
                                </tbody>
+
−
                            </table>
+
−
                            <table class="table table-condensed ">
+
−
                                <tbody>
+
−
                                    <tr>
+
−
                                        <td>Running Buffer</td>
+
−
                                        <td></td>
+
−
                                        <td></td>
+
−
                                        <td></td>
+
−
                                        <td></td>
+
−
                                    </tr>
+
−
                                    <tr>
+
−
                                        <td>Reagent</td>
+
−
                                        <td>Tris-HCl</td>
+
−
                                        <td>Glycine</td>
+
−
                                        <td>(w/v) SDS</td>
+
−
                                    </tr>
+
−
                                    <tr>
+
−
                                        <td>Dosage</td>
+
−
                                        <td>25 mmol/L
+
−
                                            <td>0.192 mol/L</td>
+
−
                                            <td>0.1%</td>
+
−
                                    </tr>
+
−
                                </tbody>
+
−
                            </table>
+
−
                        </li>
+
−
                        <li>
+
−
                            <h5>Protocol:</h5>
+
−
                            <p>The SDS polyacrylamide gels are prepared in the so-called PerfectBlue™ Twin Double Gel System.</p>
+
−
                            <p>After ensuring that the equipment is waterproof, the 12 % (or 18%) running gel is mixed and filled into the chamber. Pipetting about 1 ml of H<sub>2</sub>O on top of the running gel to seal the gel. </p>
+
−
                            <p>After polymerization, the remaining H<sub>2</sub>O is removed and the 12 % stacking gel is filled on top. Insert a comb to create sample pockets.</p>
+
−
                            <p>After the stacking gel also polymerized, 1 x running buffer is used to run the Double Gel System via the SDS gel.
+
−
                            </p>
+
−
                            <p>After loading the generated pockets with the samples, the stacking gel is run at 100 V and then running gel at 120 V.
+
−
                            </p>
+
−
                        </li>
+
−
                    </ul>
+
−
                 
+
−
                    <h5 align='center'>Detection of Baiting Nematodes</h5>
+
−
                    <ul>
+
−
                        <li>
+
−
                            <h5>Materials:
+
−
</h5>
+
−
                            <p>Pure chemical compound: linalool and limonene.
+
−
                            </p>
+
−
                            <p>Solvent: DMSO
+
−
                            </p>
+
−
                            <p>Dissolve the compounds with DMSO to set a series of concentration gradient of attractant.
+
−
                            </p>
+
−
                        </li>
+
−
                    </ul>
+
−
                    <ul>
+
−
                        <li>
+
−
                            <h5>Protocol:
+
−
</h5>
+
−
                            <p>Synchronize the nematodes.
+
−
                            </p>
+
−
                            <p>Divide the NGM solid medium (d = 6 cm) equally into two parts (drawing on the surface of the culture dishes).
+
−
                            </p>
+
−
                            <p>Put 50 \(\mu\)L compound of different concentration and DMSO as contrast respectively on the two parts. Make 3 repeats of each concentration.
+
−
                            </p>
+
−
                            <p>Flush nematode from the plate with M9 and inoculate 20 \(\mu\)L (about 30 nematodes) into the center of the medium.
+
−
                            </p>
+
−
                            <p>Incubate at 20&#176;C for 1hr, and then place them at 4&#176;C refrigerator for 1hr.
+
−
                            </p>
+
−
                            <p>Count the nematodes of each part under the stereoscope.
+
−
                            </p>
+
−
                            <p>Compare the results of different compound concentration and make a conclusion.
+
−
                            </p>
+
−
                        </li>
+
−
                    </ul>
+
−
                 
+
−
                    <h5 align='center'>Detection of Killing Nematodes
+
−
</h5>
+
  
−
                    <ul>
+
<dt>Zhang Jiajun</dt>
−
                        <p>Inoculate 5mL LB liquid mediums added Chl with experimental group E.coli BW25113 (transformed with rMpl or bace16 genes) and blank control group separately. Incubate at 37&#176;C, 190 r.m.p for 3 hr.
+
<dd>Wiki leader<br>Rear services<br>Human practice</dd>
−
                        </p>
+
−
                        <p>Mix up 800\(\mu\)L control group and 200ul experimental liquid medium Inoculate 1mL mixture mentioned above to NGM plate. Incubate upside down at 37&#176;C overnight.
+
−
                        </p>
+
−
                        <p>Flush nematodes from the plate with M9, centrifugate (1500 r.p.m, 3min), abandon the supernatant and resuspend the precipitation with 3mL M9.
+
−
                        </p>
+
−
                        <p>Add 500\(\mu\)L resuspended solution to the NGM plate inoculated with mixed E.coli as mentioned above as experimental group and NGM plate with blank E.coli as control group. 37&#176;C incubate overnight.
+
−
                        </p>
+
−
                        <p>Observe and compare the activation and size of nematodes of each group and draw a conclusion.
+
−
                        </p>
+
−
                    </ul>
+
−
             
+
−
             
+
−
                    <h4>5.4 Nematode</h4>
+
−
                    <ul>
+
−
                        <li>
+
−
                            <h5>Materials:
+
−
                                </h5></li>
+
−
                        <li>
+
−
                            <p>NGM medium:</p>
+
−
                        </li>
+
−
                        <table class="table table-condensed ">
+
−
                            <tbody>
+
−
                                <tr>
+
−
                                    <td>Minimum Medium</td>
+
−
                                    <td></td>
+
−
                                    <td></td>
+
−
                                    <td></td>
+
−
                                    <td></td>
+
−
                                </tr>
+
−
                                <tr>
+
−
                                    <td>Reagent</td>
+
−
                                    <td>NaCl</td>
+
−
                                    <td>Bacto peptone（BD 4059002)</td>
+
−
                                    <td>Agar</td>
+
−
                                    <td>ddH<sub>2</sub>O</td>
+
−
                                </tr>
+
−
                                <tr>
+
−
                                    <td>Dosage</td>
+
−
                                    <td>3 g
+
−
                                        <td>2.5 g/L</td>
+
−
                                        <td>17 \(\mu\)L</td>
+
−
                                        <td>975 mL</td>
+
−
                                </tr>
+
−
                            </tbody>
+
−
                        </table>
+
−
                        <p>Prepare 1mol/L CaCl<sub>2</sub>, 1mol/L MgSO<sub>4</sub> and phosphoric acid buffer meanwhile.
+
−
                        </p>
+
−
                        <table class="table table-condensed ">
+
−
                            <tbody>
+
−
                                <tr>
+
−
                                    <td>Phosphoric Acid Buffer</td>
+
−
                                    <td></td>
+
−
                                    <td></td>
+
−
                                    <td></td>
+
−
                                </tr>
+
−
                                <tr>
+
−
                                    <td>Reagent</td>
+
−
                                    <td>KH<sub>2</sub>PO<sub>4</sub></td>
+
−
                                    <td>KHPO<sub>4</sub></td>
+
−
                                    <td>ddH<sub>2</sub>O</td>
+
−
                                </tr>
+
−
                                <tr>
+
−
                                    <td>Dosage</td>
+
−
                                    <td>108.3 g
+
−
                                        <td>35.6 g/L</td>
+
−
                                        <td>1 L</td>
+
  
−
                                </tr>
+
<dt>Zhang Tianqi</dt>
−
                            </tbody>
+
<dd>Rear services<br>Wet lab experiments(validating limonene's attracting effects on nematodes)</dd>
−
                        </table>
+
−
                        <p>Autoclave the above mentioned reagents with 120&#176;C for 30 min and then water bath them to 65&#176;C.</p>
+
−
                        <p>Dissolve the cholesterol with ethanol to 5 mg/mL.</p>
+
−
                        <p>Add 1ml cholesterol, CaCl<sub>2</sub>, MgSO<sub>4</sub> and 25 mL phosphoric acid buffer into the minimum medium in order (all at 65&#176;C, shake up).</p>
+
−
                        <p>Make plate with the NGM medium, storing at 4&#176;C.</p>
+
−
                     
+
−
                        <li>
+
−
                            <h5>OP50 E.coli deficit type (food of nematodes):</h5></li>
+
−
                        <p>Streak inoculate OP50 on LB solid medium, Incubate at 37&#176;C for 6 hr or overnight. Inoculate LB liquid medium with OP50 single colonies, and incubate (37&#176;C, 220 r.p.m) overnight.
+
−
                        </p>
+
−
                    </ul>
+
−
                 
+
−
                    <h5 align='center'>Cultivate
+
−
</h5>
+
−
                    <ul>
+
−
                        <li>
+
−
                            <h5>The incubation condition of caenorhabditis elegans N2 wild type:
+
−
</h5>
+
−
                            <p>Generally incubated at 20&#176;C. Grow slowly at 16&#176;C and grow fast at 25&#176;C while egg laying amount declines.</p>
+
−
                        </li>
+
−
                   
+
−
                        <li>
+
−
                            <h5>Protocol:
+
−
                                </h5></li>
+
−
                        <p>Inoculate NGM medium with 150~200 \(\mu\)L OP50, incubate at 37&#176;C for 12hr. Cut down a square of NGM(about 1cm x 1cm) with nematodes.
+
−
                        </p>
+
−
                        <p>Put the square on the NGM medium with OP50 and let the surface with nematodes adown to contact the medium.
+
−
                        </p>
+
−
                        <p>Seal and incubate upside down at 20&#176;C.
+
−
                        </p>
+
−
                        <p>Watch the growth condition of nematodes under the stereoscope everyday and re-inoculate every 4 to 5 days to avoid the nematodes growing too densely.
+
−
                        </p>
+
−
                        <p>For inoculating abundant nematodes rapidly, or changing plate to provide more food and better condition for them, we can flush them with M9 and centrifuge them with 1500 r.m.p for 1 min, and incubate the precipitate on a new plate. </p>
+
−
                     
+
−
                        <h5 align='center'>Synchronization</h5>
+
−
                        <li>
+
−
                            <h5>Materials:
+
−
</h5>
+
−
                            <td></td>
+
−
                            <td></td>
+
−
                            <td></td>
+
−
                            <td></td>
+
−
                            <td></td>
+
−
                        </li>
+
  
−
                        <table class="table table-condensed ">
+
<dt>Zhao Jingyu</dt>
−
                            <tbody>
+
<dd>Wet lab experiments(rMpL expression)</dd>
−
                                <tr>
+
−
                                    <td>M9 NS</td>
+
−
                                    <td></td>
+
−
                                    <td></td>
+
−
                                    <td></td>
+
−
                                    <td></td>
+
−
                                    <td></td>
+
−
                                </tr>
+
−
                                <tr>
+
−
                                    <td>Reagent</td>
+
−
                                    <td>Na<sub>2</sub>HPO<sub>4</sub></td>
+
−
                                    <td>KH<sub>2</sub>PO<sub>4</sub></td>
+
−
                                    <td>NaCl</td>
+
−
                                    <td>1M MgSO<sub>4</sub></td>
+
−
                                    <td>ddH<sub>2</sub>O
+
−
                                    </td>
+
−
                                </tr>
+
−
                                <tr>
+
−
                                    <td>Dosage</td>
+
−
                                    <td>6 g
+
−
                                        <td>3 g</td>
+
−
                                        <td>5 g</td>
+
−
                                        <td>1 mL</td>
+
−
                                        <td>1 L
+
−
                                        </td>
+
−
                                </tr>
+
−
                            </tbody>
+
−
                        </table>
+
  
−
                        <table class="table table-condensed ">
+
<dt>Zhao Xueting</dt>
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                            <tbody>
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<dd>Modeling(solving problems like how to put equipment on farmland; paper writing; translation)</dd>
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                                <tr>
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</dl>
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                                    <td>Bleach Buffer</td>
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                                    <td></td>
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                                    <td></td>
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                                    <td></td>
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                                </tr>
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                                <tr>
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                                    <td>Reagent</td>
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                                    <td>NaOCl</td>
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                                    <td>5M NaOH</td>
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                                    <td>ddH<sub>2</sub>O
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                                    </td>
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                                </tr>
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                                <tr>
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                                    <td>Dosage</td>
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                                    <td>50 \(\mu\)L
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                                        <td>100 \(\mu\)L</td>
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                                        <td>850 \(\mu\)L</td>
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                                </tr>
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                            </tbody>
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                        </table>
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                        <li>
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                            <h5>Protocols:</h5></li>
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                        <p>We have tried several methods and two of them succeed as mentioned below, we recommend the first one by comparison.
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                        </p>
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                        <p>1. Flush and incubate
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                        </p>
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                        <p>Flush the nematodes with M9 NS
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                        </p>
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                        <p>Centrifugation (3000 r.m.p, 1min)
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                        </p>
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                        <p>Abandon the supernatant, add 1 mL bleach buffer to the precipitation
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                        </p>
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                        <p>Centrifugation (3000 r.m.p, 1min), abandon the supernatant
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−
                        </p>
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                        <p>Transfer the precipitation (nematode eggs) to a NGM plate with OP50, then the eggs will incubate synchronously.
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−
                        </p>
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                        <p>2. Directly pick
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                        </p>
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                        <p>Transfer 30 nematodes that are under egg laying period to a new NGM plate with OP50. Generally, the egg laying nematodes can lay about 8 eggs per hour. Remove all nematodes after 2hr.
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                        </p>
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                        <p>
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                            Incubate the plate at 20&#176;C for 3d and therefor can get about 300 to 400 nematodes.
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−
                        </p>
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                        <p><strong>Note: all of the procedure outlined above must be conducted under sterile condition.
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                                </strong></p>
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                        <br/>
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−
                        <h5 align='center'>Isolate nematodes from soil
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</h5>
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                        <li>
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                            <h5>modified Baermann funnel method:</h5></li>
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                        <p> 1. Place a glass funnel (d = 10~15 cm) on the funnel stand linked with about 10cm rubber tube which is furnished with a flatjaw pinchcock.
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−
                        </p>
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                        <p>2. Cut the soil sample into matchstick shape. Package 10 g(wet weight) with gauze and put it into the funnel, and then add water to immersion the sample.
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−
                        </p>
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                        <p>3. After 4~24 hr, nematodes leave the plant tissue and swim in the water and ultimately precipitate at the bottom due to their gravity and hydrotaxis.
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−
                        </p>
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                        <p>4. Open the flatjaw pinchcock, adopt about 5~15 mL liquid sample from the bottom which obtains most active nematodes of the soil sample. Check under the stereoscope and count nematodes, or centrifugate(1500 r) first and check the precipitation if the nematodes are too few.
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                        </p>
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</body>
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<hr />
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<a href="https://2015.igem.org/Team:BNU-CHINA/Collaboration" class="pull-right">VIEW OUR COLLABORATIONS›</a>
  
 
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Latest revision as of 19:42, 18 September 2015

Team:BNU-CHINA - 2015.igem.org

Team Share with you

Members - WE ARE SIRENS

Lao Kejing

A sophomore majoring in biology. Her work includes plasmid purification, SDS-PAGE and nematodes synchronization. She also tried to help BIT-China with extracting membrane proteins, NhaA and NhaB.

Liu Longping

A sophomore student who has worked on how to promote the expression rate of rMpL as well as designed the toxic test on nematodes.

Chen Zhiyao

The only freshman in our team, majoring in physics. Developed the toxic and attractant database with Peng Chengfei. Also designed the UI of the database website, and took part in HP activities too!

Wang Yingbing

A junior biotech student of BNU. Mainly did some paper work for the team, and also took part in the “bace16” group work.

Siren

In Greek mythology, the Sirens were dangerous yet beautiful creatures, who lured nearby sailors with their enchanting music and eat them. We call our machine Sirens as it can attract nematodes and kill them just like the Sirens do to their meals.

Cao Yufei

A junior student in Liyun College of BNU, biology major. She is responsible for the parts design for expressing limonene in E. coli and coresponding experiments.

Li Jia

A junior bioscience student, wants to learn more about synthetic biology and makes more friends in iGEM. Mainly worked on testifying the chemical attractants. Besides she expressed limonene and GPP synthase, and cultivated C.elegans.

Yin Yuan

A sophomore majoring in mathematics. Helped set up the model in proposingthe solving ideas and searching the data.

Zhao Xueting

A sophomore in mathematics. Did work of modeling section like finding out how to put equipment on farmland, writing modeling paper, doing some translation and so on.

Liu Xinyu

A sophomore biology student. Is a member of the limonene group of this project, and also took part in human practice and other parts' experiments.

Li Yuehuan

A sophomore bioscience student. She helped design and verify parts of the module.

Wu Zekai

A sophomore biology student. Designed a part of biobrick of photoinduction system, and took part in some experiments of verifing the toxicity of Bace 16.

Yuan Qiuyue

A junior majoring in mathematics. Simulated the movement of nematodes, and established the model of diffusion of the attraction.

Lee

Junior biology student. Participated in graphic design of our team, such as website designing,logo of the team and T-shirt.

Zhang Jiajun

A junior biotech student in BNU, he has contributed to team works and wiki building.

Feng Xiaofei

A sophomore student who has worked on how to promote the expression rate of rMpL as well as designed the toxic test on nematodes.

Cao Yalei

From school of Geography in BNU, is a member of graphic design group who designed our team logo, banner and poster. The jerseys and souvenirs were also her masterpieces.

Xu Lu

A junior bioscience student who is the leader of graphic design group. Did the design work for BNU-CHINA, particularly on poster and PPT design. In addition, she made a batch of uniform shirts for our team.

Gao Beichen

The leader of our team, a junior biotech student of Beijing Normal University. Mainly worked for the wet lab part including constructing parts, expressing nematocidal proteins and testifying the toxicity of rMpL.

Tang Meng

A junior Bioscience BNU student. The HP project leader who organized most activities for Policy and Practice, such as surveys, publicity and voluntary education. She also took part in nematodes cultivating.

Dai Yuanyi

A junior BNU student majoring in Biotech. Devoted all her energy and time in iGEM, making her a multitasking girl. Her work involves of many aspects, mainly the construction of biobricks and expriments on Bace16.

Li Cheng

A junior bioscience student. The leader of modeling part, designed the device 2.0. Also proposes many useful ideas in this team, such as the online database and the design to improve parts. Also enrolled in Wiki and Art work.

Zhao Jingyu

A sophomore majoring in biology. Took part in experiments such as the expression of the toxin rMpL, and also did some work in human practice.

Peng Chengfei

A sophomore student of Computer Science. Is responsible for the some technical work like constructing the database and the corresponding website and the deployment and operation of the database.

Project Design and Wet Lab Experiments

Under the supervision of Prof. Zhu Xudong, Prof. Yang Dong, and Prof. Xiang Benqiong etc, nearly all team members have taken part in the project designing process, especially those of wet lab group.Beichen Gao , Yuanyi Dai , Yufei Cao and Jia Li are the group leaders who mainly design the experimental patterns and guide the different parts of the experiments.

Modeling

Cheng Li is the leader of modeling group, who mainly enrolled in designing the device 2.0. Yuan Yin , Qiuyue Yuan and Xueting Zhao also do a great many works in the modeling group, such as information searching, paper writing and equipment appilication.

Wiki Construction

Jiajun Zhang , who has led the web design group to build the wiki, together with group members Zhiyao Chen and Chengfei Peng complete the main work in database construction and maintenance.

Graphic design

Lu Xu( group leader), Lee and Yalei Cao really do a fantastic work in graphic and web design. They all make great efforts in designing our team logo, website, poster, souvenir, T-shirt and so on.

Human practice

Meng Tang , the leader of human practice group, has organized a series of activities for Policy and Practice, like survey and publicize in some middle schools etc. Some group members as Yuanyi Dai, Jia Li , Jiajun Zhang , Beichen Gao , Zhiyao Chen , Jingyu Zhao , Xiaofei Feng also play a significant role in planning and organizing the activities . Other group members also take an active part in some other activities of human practice.

Details

Team Member
Attributions
Cao Yalei
Graphic Design(Design of logo, banner, poster, jersey and souvenir)
Cao Yufei
Wet lab group leader(parts design for expressing lemonene in E. coli and coresponding experiments)
Chen Zhiyao
Wiki construction(database construction; UI design)
Human practice
Dai Yuanyi
Daily activities arrangement and personnel management
Wet lab group leader(biobricks construction, Bace16 expression and testification)
Human practice
Feng Xiaofei
Wet lab experiments(limonene synthesis)
Human practice
Gao Beichen
Team leader
Wet lab group leader（biobricks construction, nematocidal protein expression, rMpL's toxicity identification
Human practice
Lao Kejing
Wet lab experiments(plasmid purification; SDS-PAGE; nematodes synchronization)
Helping Beijing Institute of Technology with extracting membrane proteins, NhaA and NhaB
Lee
Graphic Design( website design, logo of the team and T-shirt)
Li Cheng
Modeling leader(design of the device 2.0 ; parts improving)
Wiki
Graphic design
Li Jia
Wet lab group leader(chemical attractants' function testification, LS and GPPS expression, C.elegans cultivation )
Human practice
Li Yuehuan
Wet lab experiments(rMpL verification)
Liu Longping
Wet lab experiments(exploraton of how to promote the expression rate of protein rMpL; design of the toxic test)
Liu Xinyu
Wet lab experiments(limonene group and other parts' experiments)
Human practice
Ma Hongfei
Wet lab experiments(GC-MS of limonene )
Modeling(device 1.0 design and creation)
Peng Chengfei
Wiki construction(database construction, deployment and operation, Wiki frame construction)
Tang Meng
Human practice project leader(activities planning and organization)
Wet lab experiments
Wang Ran
Translation
Human practice
Wang Yingbing
Wet lab experiments(Bace16 group work)
Wu Zekai
Wet lab experiments(photoinduced system design; Bace 16 functional verification)
Xiao Shusheng
Literature reading
Human practice
Xu Lu
Graphic design leader（mainly on poster and PPT design）
Yin Yuan
Modeling(proposing the solving ideas; searching the data)
Yuan Qiuyue
Modeling(nematode movement simulation;model of diffusion of the attraction)
Human practice
Zhang Jiajun
Wiki leader
Rear services
Human practice
Zhang Tianqi
Rear services
Wet lab experiments(validating limonene's attracting effects on nematodes)
Zhao Jingyu
Wet lab experiments(rMpL expression)
Zhao Xueting
Modeling(solving problems like how to put equipment on farmland; paper writing; translation)
VIEW OUR COLLABORATIONS›