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http://2012.igem.org/Team:OUC-China/Modeling/NoiseAnalysis
Team:OUC-China/Modeling/NoiseAnalysis
2012-10-27T04:04:54Z
<p>Dolores: </p>
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<h1 style="border:none;">Noise analysis-model</h1><br />
<p><strong>Aim:</strong><span></span>To figure out whether output is robust when presented with intrinsic noise.<br />
<br/><br />
<br/><br />
<p><strong>Steps:</strong><br />
<br/><span></span>1. Use the Gillespie algorithm to perform the stochastic analysis;<br />
<br/><span></span>2. Draw probability distribution figures (pdf);<br />
<br/><span></span>3. Compute the noise statistically.<br />
<br/><br />
<br/><br />
<p><strong>Background:</strong><span></span>After having determined the parameter range, we would make the noise analysis.According to theoretical predictions, elementary chemical reactions involved in biochemical processes exhibit substantial stochastic fluctuations when low numbers of reactant molecules are involved within the small volume of a living cell. <br />
The existence of significant stochastic fluctuations in biochemical processes has been confirmed by numerous experiments including tracking of individual protein molecules in individual cells in gene expression processes[Zhou L, Gregori G, Blackman J,Robinson J, Wanner B (2005) Stochastic activation of the response regulator PhoB by noncognate histidine kinases.J Integrative Bioinformatics 2: 11.] <br />
We refer to the most classical Gillespie algorithm and lots of improvements have been made by later generation. For example, Sagar Indurkhya et al mentioned that Dynamic Monte Carlo methods are a common means of simulating the time-evolution of chemical systems.The Gillespie Algorithm (SSA) [1] is the standard algorithm for this process, and has inspired a variety of derivative methods that speed up computation, including the Optimized Direct Method (ODM) [2] and the Next Reaction Method (NRM) [3]. These methods, however, are still computationally costly.Now,we still use the classical algorithm.:<br />
<br/><br/><br />
<p>ηij is used to describe the noise, where:<br />
<br/><span></span><br />
<a><img style="margin-left:270px;" src="https://static.igem.org/mediawiki/2012/3/32/Ouc-modeling-math20.JPG" /></a><br />
<br/><br />
<p style="text-align:center;">σ ij stands for standard deviation and <Xi> represents the mean value. If i=j then</p> <br />
<br/><a><img style="margin-left:270px;" src="https://static.igem.org/mediawiki/2012/9/9a/Math21.JPG" /></a><br />
<br/><br />
<p><span></span>The value of noise is ηi2 .<br />
If the mean([m]1:1)-mean([m]1:2) >> the value of noise, we identify the output wouldn’t be drown in noise.<br />
<br/><br />
<br/><span></span><br />
<a><img src="https://static.igem.org/mediawiki/2012/8/89/Ouc-parameter_range.png" /></a><br />
<br />
<h2>Result_Ratio sensor</h2><br />
<br/><br />
<p> <br />
<br/><br />
<a><img style="margin-left:50px;" src="https://static.igem.org/mediawiki/2012/1/1b/Ouc-R1L.jpg" /></a><br />
<a><img style="margin-left:380px; margin-top:-230px;" src="https://static.igem.org/mediawiki/2012/d/d0/Ratiop0R.jpg" /></a><br />
<a><img style="margin-left:50px; margin-top:-30px;"src="https://static.igem.org/mediawiki/2012/6/6c/Ouc-R2L.jpg" /></a><br />
<a><img style="margin-left:380px; margin-top:-230px;" src="https://static.igem.org/mediawiki/2012/7/74/Ratiop1R.jpg" /></a><br />
<a><img style="margin-left:50px; margin-top:-30px;" src="https://static.igem.org/mediawiki/2012/9/98/Ouc-R3L.jpg" /></a><br />
<a><img style="margin-left:380px; margin-top:-230px;" src="https://static.igem.org/mediawiki/2012/b/b0/Ratiop2R.jpg" /></a><br />
<br/><br />
<p style="text-align:center; font-size:90%;">Fig.1 Pdf means probability distribution frequency <br />
</p><br />
<br/><br />
<br/><br />
<p>The statistics is given below:<br />
<br/><br />
<br/><br />
<a><img src="https://static.igem.org/mediawiki/2012/5/52/Ouc-rs_analysis2.png"></a><br />
<br/><br />
<br/><br />
<br/><br />
<br/><br />
<br />
<h2>Comparator</h2><br />
<br/><br />
<br/><br />
<a><img style="margin-left:50px;" src="https://static.igem.org/mediawiki/2012/d/de/Comparator0.jpg" /></a><br />
<a><img style="margin-left:380px; margin-top:-230px;" src="https://static.igem.org/mediawiki/2012/5/51/Ouc-R1R.jpg" /></a><br />
<a><img style="margin-left:50px; margin-top:-30px;"src="https://static.igem.org/mediawiki/2012/2/27/Comparator1.jpg" /></a><br />
<a><img style="margin-left:380px; margin-top:-230px;" src="https://static.igem.org/mediawiki/2012/0/02/Ouc-R2R.jpg" /></a><br />
<a><img style="margin-left:50px; margin-top:-30px;" src="https://static.igem.org/mediawiki/2012/c/c3/Comparator2.jpg" /></a><br />
<a><img style="margin-left:380px; margin-top:-230px;" src="https://static.igem.org/mediawiki/2012/b/b8/Ouc-R3R.jpg" /></a><br />
<br />
<br/><p style="text-align:center; font-size:90%;">Fig.2 Pdf stands for probability distribution frequency.</p><br />
<br/><br />
<br/><br />
<p>The statistics is given below:<br />
<br/><br />
<br/><br />
<a><img src="https://static.igem.org/mediawiki/2012/c/c4/Ouc-c_analysis2.png"></a><br />
<br/><br />
<br/><br />
<br />
<h2>Conclusion</h2><br />
<br/><br />
<p><span></span>Both ratio sensor and comparator, the change of mRNA concentration is robust enough when presented with noise(mean([m]1:1)-mean([m]1:2) >> noise).It is rational to design our device by this parameter sets.<br />
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Dolores
http://2012.igem.org/Team:OUC-China/Modeling/NoiseAnalysis
Team:OUC-China/Modeling/NoiseAnalysis
2012-10-27T03:48:31Z
<p>Dolores: </p>
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<h1 style="border:none;">Noise analysis-model</h1><br />
<p><strong>Aim:</strong><span></span>To figure out whether output is robust when presented with intrinsic noise.<br />
<br/><br />
<br/><br />
<p><strong>Steps:</strong><br />
<br/><span></span>1. Use the Gillespie algorithm to perform the stochastic analysis;<br />
<br/><span></span>2. Draw probability distribution figures (pdf);<br />
<br/><span></span>3. Compute the noise statistically.<br />
<br/><br />
<br/><br />
<p><strong>Background:</strong><span></span>After having determined the parameter range, we would make the noise analysis.According to theoretical predictions, elementary chemical reactions involved in biochemical processes exhibit substantial stochastic fluctuations when low numbers of reactant molecules are involved within the small volume of a living cell. <br />
The existence of significant stochastic fluctuations in biochemical processes has been confirmed by numerous experiments including tracking of individual protein molecules in individual cells in gene expression processes[Zhou L, Gregori G, Blackman J,Robinson J, Wanner B (2005) Stochastic activation of the response regulator PhoB by noncognate histidine kinases.J Integrative Bioinformatics 2: 11.] <br />
We refer to the most classical Gillespie algorithm and lots of improvements have been made by later generation. For example, Sagar Indurkhya et al mentioned that Dynamic Monte Carlo methods are a common means of simulating the time-evolution of chemical systems.The Gillespie Algorithm (SSA) [1] is the standard algorithm for this process, and has inspired a variety of derivative methods that speed up computation, including the Optimized Direct Method (ODM) [2] and the Next Reaction Method (NRM) [3]. These methods, however, are still computationally costly.Now,we still use the classical algorithm.:<br />
<br/><br/><br />
<p>ηij is used to describe the noise, where:<br />
<br/><span></span><br />
<a><img style="margin-left:270px;" src="https://static.igem.org/mediawiki/2012/3/32/Ouc-modeling-math20.JPG" /></a><br />
<br/><br />
<p style="text-align:center;">σ ij stands for standard deviation and <Xi> represents the mean value. If i=j then</p> <br />
<br/><a><img style="margin-left:270px;" src="https://static.igem.org/mediawiki/2012/9/9a/Math21.JPG" /></a><br />
<br/><br />
<p><span></span>The value of noise is ηi2 .<br />
If the mean([m]1:1)-mean([m]1:2) >> the value of noise, we identify the output wouldn’t be drown in noise.<br />
<br/><br />
<br/><span></span><br />
<a><img src="https://static.igem.org/mediawiki/2012/8/89/Ouc-parameter_range.png" /></a><br />
<br />
<h2>Result_Ratio sensor</h2><br />
<br/><br />
<p> <br />
<br/><br />
<a><img style="margin-left:50px;" src="https://static.igem.org/mediawiki/2012/1/1b/Ouc-R1L.jpg" /></a><br />
<a><img style="margin-left:380px; margin-top:-230px;" src="https://static.igem.org/mediawiki/2012/d/d0/Ratiop0R.jpg" /></a><br />
<a><img style="margin-left:50px; margin-top:-30px;"src="https://static.igem.org/mediawiki/2012/6/6c/Ouc-R2L.jpg" /></a><br />
<a><img style="margin-left:380px; margin-top:-230px;" src="https://static.igem.org/mediawiki/2012/7/74/Ratiop1R.jpg" /></a><br />
<a><img style="margin-left:50px; margin-top:-30px;" src="https://static.igem.org/mediawiki/2012/9/98/Ouc-R3L.jpg" /></a><br />
<a><img style="margin-left:380px; margin-top:-230px;" src="https://static.igem.org/mediawiki/2012/b/b0/Ratiop2R.jpg" /></a><br />
<br/><br />
<p style="text-align:center; font-size:90%;">Fig.1 Pdf means probability distribution frequency <br />
</p><br />
<br/><br />
<br/><br />
<p>The statistics is given below:<br />
<br/><br />
<br/><br />
<a><img src="https://static.igem.org/mediawiki/2012/5/52/Ouc-rs_analysis2.png"></a><br />
<br/><br />
<br/><br />
<br/><br />
<br/><br />
<br />
<h2>Comparator</h2><br />
<br/><br />
<br/><br />
<a><img style="margin-left:50px;" src="https://static.igem.org/mediawiki/2012/d/de/Comparator0.jpg" /></a><br />
<a><img style="margin-left:380px; margin-top:-230px;" src="https://static.igem.org/mediawiki/2012/5/51/Ouc-R1R.jpg" /></a><br />
<a><img style="margin-left:50px; margin-top:-30px;"src="https://static.igem.org/mediawiki/2012/2/27/Comparator0.jpg" /></a><br />
<a><img style="margin-left:380px; margin-top:-230px;" src="https://static.igem.org/mediawiki/2012/0/02/Ouc-R2R.jpg" /></a><br />
<a><img style="margin-left:50px; margin-top:-30px;" src="https://static.igem.org/mediawiki/2012/c/c3/Comparator2.jpg" /></a><br />
<a><img style="margin-left:380px; margin-top:-230px;" src="https://static.igem.org/mediawiki/2012/b/b8/Ouc-R3R.jpg" /></a><br />
<br />
<br/><p style="text-align:center; font-size:90%;">Fig.2 Pdf stands for probability distribution frequency.</p><br />
<br/><br />
<br/><br />
<p>The statistics is given below:<br />
<br/><br />
<br/><br />
<a><img src="https://static.igem.org/mediawiki/2012/c/c4/Ouc-c_analysis2.png"></a><br />
<br/><br />
<br/><br />
<br />
<h2>Conclusion</h2><br />
<br/><br />
<p><span></span>Both ratio sensor and comparator, the change of mRNA concentration is robust enough when presented with noise(mean([m]1:1)-mean([m]1:2) >> noise).It is rational to design our device by this parameter sets.<br />
<br/><br />
<br/><br />
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<p>Dolores: </p>
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Dolores
http://2012.igem.org/Team:OUC-China/Team/AcknowledgementandCooperation
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<br />
<div id="organization"><br />
<h2>Organization</h2><br />
<p>Algology and algae culture laboratory of Ocean university of China</p><br />
<p><a href="http://www2.ouc.edu.cn/hysm/">College of Marine Life Science, Ocean University of China</a></p><br />
<p><a href="http://www.ouc.edu.cn">Ocean University of China</a></p><br />
<p><a href="http://jwc.ouc.edu.cn:8080/jwwz/index.html">Dean's Office of Ocean University of China</a></p><br />
<p><a href="http://english.qibebt.cas.cn/">Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences</a></p><br />
<p><a href="http://222.195.158.131/jcjxzx/">Basic teaching center basic computer department of Ocean University of China</a></p><br />
</div><br />
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<h2><span></span>Advisor</h2><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/e/eb/Ouc-team-advisor0.jpg"></a><br />
<p style="margin-top:-120px;"><strong>Xu Jian</strong><br />
<br/>Academic title: Professor<br />
<br/><br />
E-mail<a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:xujian@qibebt.ac.cn">xujian@qibebt.ac.cn</a><br />
<br/>Phone: 0532-80662654</p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/d/df/Advisor1.jpg"></a><br />
<p style="margin-top:-100px;"><strong>Bao Zhenmin</strong><br />
<br/>Academic title: Professor, Doctoral supervisor<br />
<br/>Research interest: Shellfish genetic breeding</p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/9/9f/Ouc-team-advisior2.jpg"></a><br />
<p style="width:400px; margin-top:-260px;"><strong>Mao Yunxiang</strong><br />
<br/>Academic title: Professor, Doctoral supervisor<br />
<br/>Research interest:<br />
Conservation Genetics and Germplasm Collection of Seaweed<br />
<br/>Molecular Genetic Breeding and Varity Improvement of Economical Seaweed<br />
<br/>Genomic and Genetic Dissection of Economical and Stress-tolerant Traits of Algae<br />
<br/>Reproductive Biology of Seaweed and Techniques Development of Ecological Cultivation<br />
<br/>E-mail :<a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:yxmao@ouc.edu.cn">yxmao@ouc.edu.cn</a></p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/9/9e/Ouc-team-advisor3.jpg"></a><br />
<p style="margin-top:-150px;"><strong>Gong Qingli</strong><br />
<br/>Academic title:Professor, Doctoral supervisor<br />
<br/>Research interest: Seaweed learning and algae breeding<br />
<br/>E-mail :<a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:qingli@vip.sina.com">qingli@vip.sina.com</a></p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/9/94/Ouc-team-advisor4.jpg"></a><br />
<p style="margin-top:-150px;"><strong>Yang Guanpin</strong><br />
<br/>Academic title:Professor, Doctoral supervisor<br />
<br/>Research interest: Marine economical breeding, marine microbiology<br />
<br/>E-mail :<a style="margin-left:0;margin-bottom:0; color:#444;href="yguanpin@mail.ouc.edu.cn">yguanpin@mail.ouc.edu.cn</a></p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/b/be/Ouc-team-advisor5.jpg"></a><br />
<p style="width:400px; margin-top:-260px;"><strong>Liu Chenguang</strong><br />
<br/>Academic title:Professor, Doctoral supervisor<br />
<br/>Research interest: research and application of Marine biological enzyme<br />
<br/>Molecular Genetic Breeding and Varity Improvement of Economical Seaweed<br />
<br/> Polysaccharide biological materials and drug control-released carrier enzyme<br />
<br/> Enzyme immobilization and nano biotechnology<br />
<br/>E-mail :<a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:liucg@ouc.edu.cn">liucg@ouc.edu.cn</a></p><br />
<p style="margin-top:80px; margin-left:50px; width:700px;"><strong>Ma bo</strong><br />
<br/>Academic title:Associate Professor<br />
<br/>Lead of Microfluidics Single Cell Platform Team Functional Genomics <br />
<br/>Group Qingdao Institute of BioEnergy and Bioprocess Technology Chinese Academy of Sciences<br />
<br/>E-mail: <a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:mabo@qibebt.ac.cn">mabo@qibebt.ac.cn</a></p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/b/bb/OUC-dongshugang.jpg"></a><br />
<p style="margin-top:50px; margin-left:50px; width:700px;"><strong>Dong Shugang</strong><br />
<br/>Academic title: Professor, Doctoral supervisor<br />
<br/>Research interest: Seaweed physiology and ecology<br />
<br/>E-mail: <a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:dongshg112@163.com">dongshg112@163.com</a></p><br />
</div><br />
<div id="communication"><br />
<h2>Communication with Other Teams</h2><br />
<p style="margin-bottom:0; margin-top:30px;"><span></span>It’s the second year for us to participate in iGEM, and we are lucky enough to have obtained much help from other teams. Especially, we communicate with the team of Peking University frequently. And we constructed good relationship with iGEM teams around the world through helping them in different ways.<br />
This year we started our modeling design without any experience from before. As for our noise analysis-model, ETH University helped us solve the fundamental problem of how to apply Gillespei Algorithm. And through communicating with Peking University, we have learned how to change whole biological reactions to elementary reactions and how to apply chemical mass action law.For 2012 world jamboree, Boston University buy the helium for us in advance to help our team show our project.</p> <br />
<a><img style="margin-top:10px; margin-left:100px;" src="https://static.igem.org/mediawiki/2012/b/b7/Ouc-peking.jpg" /></a><br />
<a><img style="margin-top:10px; margin-left:150px;" src="https://static.igem.org/mediawiki/2012/0/0a/Ouc-oast.jpg" /></a><br />
<a><img style="margin-top:10px; margin-left:150px;" src="https://static.igem.org/mediawiki/2012/1/15/Ouc-bo.jpg" /></a><br />
<br/><br />
<a><img style="margin-left:220px; margin-top:20px;" src="https://static.igem.org/mediawiki/2012/d/dd/Ouc-eth.jpg" /></a><br />
<br/><br />
<br/><br />
<p><span></span>OUC-China iGEM Team belongs to Ocean University of China Association of Science and Technology (OAST). We did nearly half of the experiments in the lab of OAST. The experiments of GVP were totally done in it. Besides, most human practices were done with the help of other people in the Organization. We held Hands-on experience summer camp and 2th summer camp of life science and technology in favor of OAST this summer. Almost every iGEMers in ours team are OASTers. We love iGEM, and we love OAST.<br />
</p><br />
</div><br />
<div id="special"><br />
<h2><span></span>Special Friends</h2><br />
<a><img style="margin-top:30px; margin-left:30px;" src="https://static.igem.org/mediawiki/2012/1/14/Ouc-team-Friend0.jpg"></a><br />
<p style="margin-top:-150px; margin-left:470px; width:500px;"><strong>Yang Liu</strong><br />
: He is our advisor, he is our teacher, and what’s more, he is like our elder brother. One year before, we knew nothing about synthetic biology. He taught us a lot about experiments, managing lab and how to be a REAL scientist. With his help, we did most experiment of GVP and manage lab smoothly.</p><br />
<a><img style="margin-top:30px; margin-left:30px;" src="https://static.igem.org/mediawiki/2012/a/a3/Ouc-team-Friend1.jpg"></a><br />
<p style="margin-top:-150px; margin-left:470px; margin-bottom:50px; width:500px;"><strong>Wei Liu</strong><br />
:She is our advisor and girlfriend of Yang Liu. Besides Yang Liu, she did much favor for us and helped Yang Liu to teach us Synthetic Biology. Because our team was divided into two groups and one group went to Qibebt, she helped us in qibebt about living, learning and experiment there.</p><br />
<br/><br />
<br/><br />
</div><br />
<div id="cooperator"><br />
<h2>Cooperator</h2><br />
<a><img style="margin-top:50px;" src="https://static.igem.org/mediawiki/2012/f/fd/Ouc-team-cooperator.jpg" /></a><br />
<br/><br />
<p style="margin-top:30px;"><span></span>We helped UBC to complete their survey about patent, and gave our own opinions in Nanjing university’s survey about part registry., then we forwarded the invitation for iGEM_TU_München’ survey. We also lent a hand to SUSTC Shenzhen-A and SUSTC Shenzhen-B as soon as they made contact with us. We are willing to help other teams and learn from others.<br />
<br/><br />
<span></span>When Peking university took a visit of our school in August, they showed great interest in the gelase gene discovered by professor Shi Xiaochong, which they considered to be useful in their project. So we helped them acquire the strain and send it to Peking smoothly.<br />
<br/><br />
<br/><br />
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Dolores
http://2012.igem.org/Team:OUC-China/Team/AcknowledgementandCooperation
Team:OUC-China/Team/AcknowledgementandCooperation
2012-10-27T03:42:46Z
<p>Dolores: </p>
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<br />
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<h2>Organization</h2><br />
<p>Algology and algae culture laboratory of Ocean university of China</p><br />
<p><a href="http://www2.ouc.edu.cn/hysm/">College of Marine Life Science, Ocean University of China</a></p><br />
<p><a href="http://www.ouc.edu.cn">Ocean University of China</a></p><br />
<p><a href="http://jwc.ouc.edu.cn:8080/jwwz/index.html">Dean's Office of Ocean University of China</a></p><br />
<p><a href="http://english.qibebt.cas.cn/">Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences</a></p><br />
<p><a href="http://222.195.158.131/jcjxzx/">Basic teaching center basic computer department of Ocean University of China</a></p><br />
</div><br />
<div id="advisor"><br />
<h2><span></span>Advisor</h2><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/e/eb/Ouc-team-advisor0.jpg"></a><br />
<p style="margin-top:-120px;"><strong>Xu Jian</strong><br />
<br/>Academic title: Professor<br />
<br/><br />
E-mail<a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:xujian@qibebt.ac.cn">xujian@qibebt.ac.cn</a><br />
<br/>Phone: 0532-80662654</p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/d/df/Advisor1.jpg"></a><br />
<p style="margin-top:-100px;"><strong>Bao Zhenmin</strong><br />
<br/>Academic title: Professor, Doctoral supervisor<br />
<br/>Research interest: Shellfish genetic breeding</p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/9/9f/Ouc-team-advisior2.jpg"></a><br />
<p style="width:400px; margin-top:-260px;"><strong>Mao Yunxiang</strong><br />
<br/>Academic title: Professor, Doctoral supervisor<br />
<br/>Research interest:<br />
Conservation Genetics and Germplasm Collection of Seaweed<br />
<br/>Molecular Genetic Breeding and Varity Improvement of Economical Seaweed<br />
<br/>Genomic and Genetic Dissection of Economical and Stress-tolerant Traits of Algae<br />
<br/>Reproductive Biology of Seaweed and Techniques Development of Ecological Cultivation<br />
<br/>E-mail :<a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:yxmao@ouc.edu.cn">yxmao@ouc.edu.cn</a></p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/9/9e/Ouc-team-advisor3.jpg"></a><br />
<p style="margin-top:-150px;"><strong>Gong Qingli</strong><br />
<br/>Academic title:Professor, Doctoral supervisor<br />
<br/>Research interest: Seaweed learning and algae breeding<br />
<br/>E-mail :<a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:qingli@vip.sina.com">qingli@vip.sina.com</a></p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/9/94/Ouc-team-advisor4.jpg"></a><br />
<p style="margin-top:-150px;"><strong>Yang Guanpin</strong><br />
<br/>Academic title:Professor, Doctoral supervisor<br />
<br/>Research interest: Marine economical breeding, marine microbiology<br />
<br/>E-mail :<a style="margin-left:0;margin-bottom:0; color:#444;href="yguanpin@mail.ouc.edu.cn">yguanpin@mail.ouc.edu.cn</a></p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/b/be/Ouc-team-advisor5.jpg"></a><br />
<p style="width:400px; margin-top:-260px;"><strong>Liu Chenguang</strong><br />
<br/>Academic title:Professor, Doctoral supervisor<br />
<br/>Research interest: research and application of Marine biological enzyme<br />
<br/>Molecular Genetic Breeding and Varity Improvement of Economical Seaweed<br />
<br/> Polysaccharide biological materials and drug control-released carrier enzyme<br />
<br/> Enzyme immobilization and nano biotechnology<br />
<br/>E-mail :<a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:liucg@ouc.edu.cn">liucg@ouc.edu.cn</a></p><br />
<p style="margin-top:80px; margin-left:50px; width:700px;"><strong>Ma bo</strong><br />
<br/>Academic title:Associate Professor<br />
<br/>Lead of Microfluidics Single Cell Platform Team Functional Genomics <br />
<br/>Group Qingdao Institute of BioEnergy and Bioprocess Technology Chinese Academy of Sciences<br />
<br/>E-mail: <a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:mabo@qibebt.ac.cn">mabo@qibebt.ac.cn</a></p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/b/bb/OUC-dongshugang.jpg"></a><br />
<p style="margin-top:50px; margin-left:50px; width:700px;"><strong>Dong Shugang</strong><br />
<br/>Academic title: Professor, Doctoral supervisor<br />
<br/>Research interest: Seaweed physiology and ecology<br />
<br/>E-mail: <a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:dongshg112@163.com">dongshg112@163.com</a></p><br />
</div><br />
<div id="communication"><br />
<h2>Communication with Other Teams</h2><br />
<p style="margin-bottom:0; margin-top:30px;"><span></span>It’s the second year for us to participate in iGEM, and we are lucky enough to have obtained much help from other teams. Especially, we communicate with the team of Peking University frequently. And we constructed good relationship with iGEM teams around the world through helping them in different ways.<br />
This year we started our modeling design without any experience from before. As for our noise analysis-model, ETH University helped us solve the fundamental problem of how to apply Gillespei Algorithm. And through communicating with Peking University, we have learned how to change whole biological reactions to elementary reactions and how to apply chemical mass action law.For 2012 world jamboree, Boston University buy the helium for us in advance to help our team show our project.</p> <br />
<a><img style="margin-top:10px; margin-left:100px;" src="https://static.igem.org/mediawiki/2012/b/b7/Ouc-peking.jpg" /></a><br />
<a><img style="margin-top:10px; margin-left:150px;" src="https://static.igem.org/mediawiki/2012/0/0a/Ouc-oast.jpg" /></a><br />
<a><img style="margin-top:10px; margin-left:150px;" src="https://static.igem.org/mediawiki/2012/1/15/Ouc-bo.jpg" /></a><br />
<br/><br />
<a><img style="margin-left:200px; margin-top:20px;" src="https://static.igem.org/mediawiki/2012/d/dd/Ouc-eth.jpg" /></a><br />
<br/><br />
<br/><br />
<p><span></span>OUC-China iGEM Team belongs to Ocean University of China Association of Science and Technology (OAST). We did nearly half of the experiments in the lab of OAST. The experiments of GVP were totally done in it. Besides, most human practices were done with the help of other people in the Organization. We held Hands-on experience summer camp and 2th summer camp of life science and technology in favor of OAST this summer. Almost every iGEMers in ours team are OASTers. We love iGEM, and we love OAST.<br />
</p><br />
</div><br />
<div id="special"><br />
<h2><span></span>Special Friends</h2><br />
<a><img style="margin-top:30px; margin-left:30px;" src="https://static.igem.org/mediawiki/2012/1/14/Ouc-team-Friend0.jpg"></a><br />
<p style="margin-top:-150px; margin-left:470px; width:500px;"><strong>Yang Liu</strong><br />
: He is our advisor, he is our teacher, and what’s more, he is like our elder brother. One year before, we knew nothing about synthetic biology. He taught us a lot about experiments, managing lab and how to be a REAL scientist. With his help, we did most experiment of GVP and manage lab smoothly.</p><br />
<a><img style="margin-top:30px; margin-left:30px;" src="https://static.igem.org/mediawiki/2012/a/a3/Ouc-team-Friend1.jpg"></a><br />
<p style="margin-top:-150px; margin-left:470px; margin-bottom:50px; width:500px;"><strong>Wei Liu</strong><br />
:She is our advisor and girlfriend of Yang Liu. Besides Yang Liu, she did much favor for us and helped Yang Liu to teach us Synthetic Biology. Because our team was divided into two groups and one group went to Qibebt, she helped us in qibebt about living, learning and experiment there.</p><br />
<br/><br />
<br/><br />
</div><br />
<div id="cooperator"><br />
<h2>Cooperator</h2><br />
<a><img style="margin-top:50px;" src="https://static.igem.org/mediawiki/2012/f/fd/Ouc-team-cooperator.jpg" /></a><br />
<br/><br />
<p style="margin-top:30px;"><span></span>We helped UBC to complete their survey about patent, and gave our own opinions in Nanjing university’s survey about part registry., then we forwarded the invitation for iGEM_TU_München’ survey. We also lent a hand to SUSTC Shenzhen-A and SUSTC Shenzhen-B as soon as they made contact with us. We are willing to help other teams and learn from others.<br />
<br/><br />
<span></span>When Peking university took a visit of our school in August, they showed great interest in the gelase gene discovered by professor Shi Xiaochong, which they considered to be useful in their project. So we helped them acquire the strain and send it to Peking smoothly.<br />
<br/><br />
<br/><br />
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Dolores
http://2012.igem.org/File:Comparator2.jpg
File:Comparator2.jpg
2012-10-27T03:38:00Z
<p>Dolores: </p>
<hr />
<div></div>
Dolores
http://2012.igem.org/File:Comparator1.jpg
File:Comparator1.jpg
2012-10-27T03:37:23Z
<p>Dolores: </p>
<hr />
<div></div>
Dolores
http://2012.igem.org/File:Comparator0.jpg
File:Comparator0.jpg
2012-10-27T03:35:12Z
<p>Dolores: </p>
<hr />
<div></div>
Dolores
http://2012.igem.org/Team:OUC-China/Team/AcknowledgementandCooperation
Team:OUC-China/Team/AcknowledgementandCooperation
2012-10-27T03:31:43Z
<p>Dolores: </p>
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<br />
<div id="organization"><br />
<h2>Organization</h2><br />
<p>Algology and algae culture laboratory of Ocean university of China</p><br />
<p><a href="http://www2.ouc.edu.cn/hysm/">College of Marine Life Science, Ocean University of China</a></p><br />
<p><a href="http://www.ouc.edu.cn">Ocean University of China</a></p><br />
<p><a href="http://jwc.ouc.edu.cn:8080/jwwz/index.html">Dean's Office of Ocean University of China</a></p><br />
<p><a href="http://english.qibebt.cas.cn/">Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences</a></p><br />
<p><a href="http://222.195.158.131/jcjxzx/">Basic teaching center basic computer department of Ocean University of China</a></p><br />
</div><br />
<div id="advisor"><br />
<h2><span></span>Advisor</h2><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/e/eb/Ouc-team-advisor0.jpg"></a><br />
<p style="margin-top:-120px;"><strong>Xu Jian</strong><br />
<br/>Academic title: Professor<br />
<br/><br />
E-mail<a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:xujian@qibebt.ac.cn">xujian@qibebt.ac.cn</a><br />
<br/>Phone: 0532-80662654</p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/d/df/Advisor1.jpg"></a><br />
<p style="margin-top:-100px;"><strong>Bao Zhenmin</strong><br />
<br/>Academic title: Professor, Doctoral supervisor<br />
<br/>Research interest: Shellfish genetic breeding</p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/9/9f/Ouc-team-advisior2.jpg"></a><br />
<p style="width:400px; margin-top:-260px;"><strong>Mao Yunxiang</strong><br />
<br/>Academic title: Professor, Doctoral supervisor<br />
<br/>Research interest:<br />
Conservation Genetics and Germplasm Collection of Seaweed<br />
<br/>Molecular Genetic Breeding and Varity Improvement of Economical Seaweed<br />
<br/>Genomic and Genetic Dissection of Economical and Stress-tolerant Traits of Algae<br />
<br/>Reproductive Biology of Seaweed and Techniques Development of Ecological Cultivation<br />
<br/>E-mail :<a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:yxmao@ouc.edu.cn">yxmao@ouc.edu.cn</a></p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/9/9e/Ouc-team-advisor3.jpg"></a><br />
<p style="margin-top:-150px;"><strong>Gong Qingli</strong><br />
<br/>Academic title:Professor, Doctoral supervisor<br />
<br/>Research interest: Seaweed learning and algae breeding<br />
<br/>E-mail :<a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:qingli@vip.sina.com">qingli@vip.sina.com</a></p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/9/94/Ouc-team-advisor4.jpg"></a><br />
<p style="margin-top:-150px;"><strong>Yang Guanpin</strong><br />
<br/>Academic title:Professor, Doctoral supervisor<br />
<br/>Research interest: Marine economical breeding, marine microbiology<br />
<br/>E-mail :<a style="margin-left:0;margin-bottom:0; color:#444;href="yguanpin@mail.ouc.edu.cn">yguanpin@mail.ouc.edu.cn</a></p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/b/be/Ouc-team-advisor5.jpg"></a><br />
<p style="width:400px; margin-top:-260px;"><strong>Liu Chenguang</strong><br />
<br/>Academic title:Professor, Doctoral supervisor<br />
<br/>Research interest: research and application of Marine biological enzyme<br />
<br/>Molecular Genetic Breeding and Varity Improvement of Economical Seaweed<br />
<br/> Polysaccharide biological materials and drug control-released carrier enzyme<br />
<br/> Enzyme immobilization and nano biotechnology<br />
<br/>E-mail :<a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:liucg@ouc.edu.cn">liucg@ouc.edu.cn</a></p><br />
<p style="margin-top:80px; margin-left:50px; width:700px;"><strong>Ma bo</strong><br />
<br/>Academic title:Associate Professor<br />
<br/>Lead of Microfluidics Single Cell Platform Team Functional Genomics <br />
<br/>Group Qingdao Institute of BioEnergy and Bioprocess Technology Chinese Academy of Sciences<br />
<br/>E-mail: <a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:mabo@qibebt.ac.cn">mabo@qibebt.ac.cn</a></p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/b/bb/OUC-dongshugang.jpg"></a><br />
<p style="margin-top:50px; margin-left:50px; width:700px;"><strong>Dong Shugang</strong><br />
<br/>Academic title: Professor, Doctoral supervisor<br />
<br/>Research interest: Seaweed physiology and ecology<br />
<br/>E-mail: <a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:dongshg112@163.com">dongshg112@163.com</a></p><br />
</div><br />
<div id="communication"><br />
<h2>Communication with Other Teams</h2><br />
<p style="margin-bottom:0; margin-top:30px;"><span></span>It’s the second year for us to participate in iGEM, and we are lucky enough to have obtained much help from other teams. Especially, we communicate with the team of Peking University frequently. And we constructed good relationship with iGEM teams around the world through helping them in different ways.<br />
This year we started our modeling design without any experience from before. As for our noise analysis-model, ETH University helped us solve the fundamental problem of how to apply Gillespei Algorithm. And through communicating with Peking University, we have learned how to change whole biological reactions to elementary reactions and how to apply chemical mass action law.For 2012 world jamboree, Boston University buy the helium for us in advance to help our team show our project.</p> <br />
<a><img style="margin-top:10px; margin-left:100px;" src="https://static.igem.org/mediawiki/2012/b/b7/Ouc-peking.jpg" /></a><br />
<a><img style="margin-top:10px; margin-left:150px;" src="https://static.igem.org/mediawiki/2012/0/0a/Ouc-oast.jpg" /></a><br />
<a><img style="margin-top:10px; margin-left:150px;" src="https://static.igem.org/mediawiki/2012/1/15/Ouc-bo.jpg" /></a><br />
<br/><br />
<a><img style="margin-left:185px; margin-top:20px;" src="https://static.igem.org/mediawiki/2012/d/dd/Ouc-eth.jpg" /></a><br />
<br/><br />
<br/><br />
<p><span></span>OUC-China iGEM Team belongs to Ocean University of China Association of Science and Technology (OAST). We did nearly half of the experiments in the lab of OAST. The experiments of GVP were totally done in it. Besides, most human practices were done with the help of other people in the Organization. We held Hands-on experience summer camp and 2th summer camp of life science and technology in favor of OAST this summer. Almost every iGEMers in ours team are OASTers. We love iGEM, and we love OAST.<br />
</p><br />
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<div id="special"><br />
<h2><span></span>Special Friends</h2><br />
<a><img style="margin-top:30px; margin-left:30px;" src="https://static.igem.org/mediawiki/2012/1/14/Ouc-team-Friend0.jpg"></a><br />
<p style="margin-top:-150px; margin-left:470px; width:500px;"><strong>Yang Liu</strong><br />
: He is our advisor, he is our teacher, and what’s more, he is like our elder brother. One year before, we knew nothing about synthetic biology. He taught us a lot about experiments, managing lab and how to be a REAL scientist. With his help, we did most experiment of GVP and manage lab smoothly.</p><br />
<a><img style="margin-top:30px; margin-left:30px;" src="https://static.igem.org/mediawiki/2012/a/a3/Ouc-team-Friend1.jpg"></a><br />
<p style="margin-top:-150px; margin-left:470px; margin-bottom:50px; width:500px;"><strong>Wei Liu</strong><br />
:She is our advisor and girlfriend of Yang Liu. Besides Yang Liu, she did much favor for us and helped Yang Liu to teach us Synthetic Biology. Because our team was divided into two groups and one group went to Qibebt, she helped us in qibebt about living, learning and experiment there.</p><br />
<br/><br />
<br/><br />
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<div id="cooperator"><br />
<h2>Cooperator</h2><br />
<a><img style="margin-top:50px;" src="https://static.igem.org/mediawiki/2012/f/fd/Ouc-team-cooperator.jpg" /></a><br />
<br/><br />
<p style="margin-top:30px;"><span></span>We helped UBC to complete their survey about patent, and gave our own opinions in Nanjing university’s survey about part registry., then we forwarded the invitation for iGEM_TU_München’ survey. We also lent a hand to SUSTC Shenzhen-A and SUSTC Shenzhen-B as soon as they made contact with us. We are willing to help other teams and learn from others.<br />
<br/><br />
<span></span>When Peking university took a visit of our school in August, they showed great interest in the gelase gene discovered by professor Shi Xiaochong, which they considered to be useful in their project. So we helped them acquire the strain and send it to Peking smoothly.<br />
<br/><br />
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Dolores
http://2012.igem.org/Team:OUC-China/Team/AcknowledgementandCooperation
Team:OUC-China/Team/AcknowledgementandCooperation
2012-10-27T03:30:47Z
<p>Dolores: </p>
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<section id="wrapper"><br />
<article id="main"><br />
<br />
<div id="organization"><br />
<h2>Organization</h2><br />
<p>Algology and algae culture laboratory of Ocean university of China</p><br />
<p><a href="http://www2.ouc.edu.cn/hysm/">College of Marine Life Science, Ocean University of China</a></p><br />
<p><a href="http://www.ouc.edu.cn">Ocean University of China</a></p><br />
<p><a href="http://jwc.ouc.edu.cn:8080/jwwz/index.html">Dean's Office of Ocean University of China</a></p><br />
<p><a href="http://english.qibebt.cas.cn/">Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences</a></p><br />
<p><a href="http://222.195.158.131/jcjxzx/">Basic teaching center basic computer department of Ocean University of China</a></p><br />
</div><br />
<div id="advisor"><br />
<h2><span></span>Advisor</h2><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/e/eb/Ouc-team-advisor0.jpg"></a><br />
<p style="margin-top:-120px;"><strong>Xu Jian</strong><br />
<br/>Academic title: Professor<br />
<br/><br />
E-mail<a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:xujian@qibebt.ac.cn">xujian@qibebt.ac.cn</a><br />
<br/>Phone: 0532-80662654</p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/d/df/Advisor1.jpg"></a><br />
<p style="margin-top:-100px;"><strong>Bao Zhenmin</strong><br />
<br/>Academic title: Professor, Doctoral supervisor<br />
<br/>Research interest: Shellfish genetic breeding</p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/9/9f/Ouc-team-advisior2.jpg"></a><br />
<p style="width:400px; margin-top:-260px;"><strong>Mao Yunxiang</strong><br />
<br/>Academic title: Professor, Doctoral supervisor<br />
<br/>Research interest:<br />
Conservation Genetics and Germplasm Collection of Seaweed<br />
<br/>Molecular Genetic Breeding and Varity Improvement of Economical Seaweed<br />
<br/>Genomic and Genetic Dissection of Economical and Stress-tolerant Traits of Algae<br />
<br/>Reproductive Biology of Seaweed and Techniques Development of Ecological Cultivation<br />
<br/>E-mail :<a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:yxmao@ouc.edu.cn">yxmao@ouc.edu.cn</a></p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/9/9e/Ouc-team-advisor3.jpg"></a><br />
<p style="margin-top:-150px;"><strong>Gong Qingli</strong><br />
<br/>Academic title:Professor, Doctoral supervisor<br />
<br/>Research interest: Seaweed learning and algae breeding<br />
<br/>E-mail :<a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:qingli@vip.sina.com">qingli@vip.sina.com</a></p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/9/94/Ouc-team-advisor4.jpg"></a><br />
<p style="margin-top:-150px;"><strong>Yang Guanpin</strong><br />
<br/>Academic title:Professor, Doctoral supervisor<br />
<br/>Research interest: Marine economical breeding, marine microbiology<br />
<br/>E-mail :<a style="margin-left:0;margin-bottom:0; color:#444;href="yguanpin@mail.ouc.edu.cn">yguanpin@mail.ouc.edu.cn</a></p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/b/be/Ouc-team-advisor5.jpg"></a><br />
<p style="width:400px; margin-top:-260px;"><strong>Liu Chenguang</strong><br />
<br/>Academic title:Professor, Doctoral supervisor<br />
<br/>Research interest: research and application of Marine biological enzyme<br />
<br/>Molecular Genetic Breeding and Varity Improvement of Economical Seaweed<br />
<br/> Polysaccharide biological materials and drug control-released carrier enzyme<br />
<br/> Enzyme immobilization and nano biotechnology<br />
<br/>E-mail :<a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:liucg@ouc.edu.cn">liucg@ouc.edu.cn</a></p><br />
<p style="margin-top:80px; margin-left:50px; width:700px;"><strong>Ma bo</strong><br />
<br/>Academic title:Associate Professor<br />
<br/>Lead of Microfluidics Single Cell Platform Team Functional Genomics <br />
<br/>Group Qingdao Institute of BioEnergy and Bioprocess Technology Chinese Academy of Sciences<br />
<br/>E-mail: <a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:mabo@qibebt.ac.cn">mabo@qibebt.ac.cn</a></p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/b/bb/OUC-dongshugang.jpg"></a><br />
<p style="margin-top:50px; margin-left:50px; width:700px;"><strong>Dong Shugang</strong><br />
<br/>Academic title: Professor, Doctoral supervisor<br />
<br/>Research interest: Seaweed physiology and ecology<br />
<br/>E-mail: <a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:dongshg112@163.com">dongshg112@163.com</a></p><br />
</div><br />
<div id="communication"><br />
<h2>Communication with Other Teams</h2><br />
<p style="margin-bottom:0; margin-top:30px;"><span></span>It’s the second year for us to participate in iGEM, and we are lucky enough to have obtained much help from other teams. Especially, we communicate with the team of Peking University frequently. And we constructed good relationship with iGEM teams around the world through helping them in different ways.<br />
This year we started our modeling design without any experience from before. As for our noise analysis-model, ETH University helped us solve the fundamental problem of how to apply Gillespei Algorithm. And through communicating with Peking University, we have learned how to change whole biological reactions to elementary reactions and how to apply chemical mass action law.For 2012 world jamboree, Boston University buy the helium for us in advance to help our team show our project.</p> <br />
<a><img style="margin-top:10px; margin-left:100px;" src="https://static.igem.org/mediawiki/2012/b/b7/Ouc-peking.jpg" /></a><br />
<a><img style="margin-top:10px; margin-left:150px;" src="https://static.igem.org/mediawiki/2012/0/0a/Ouc-oast.jpg" /></a><br />
<a><img style="margin-top:10px; margin-left:150px;" src="https://static.igem.org/mediawiki/2012/1/15/Ouc-bo.jpg" /></a><br />
<br/><br />
<a><img style="margin-left:175px; margin-top:10px;" src="https://static.igem.org/mediawiki/2012/d/dd/Ouc-eth.jpg" /></a><br />
<br/><br />
<br/><br />
<p><span></span>OUC-China iGEM Team belongs to Ocean University of China Association of Science and Technology (OAST). We did nearly half of the experiments in the lab of OAST. The experiments of GVP were totally done in it. Besides, most human practices were done with the help of other people in the Organization. We held Hands-on experience summer camp and 2th summer camp of life science and technology in favor of OAST this summer. Almost every iGEMers in ours team are OASTers. We love iGEM, and we love OAST.<br />
</p><br />
</div><br />
<div id="special"><br />
<h2><span></span>Special Friends</h2><br />
<a><img style="margin-top:30px; margin-left:30px;" src="https://static.igem.org/mediawiki/2012/1/14/Ouc-team-Friend0.jpg"></a><br />
<p style="margin-top:-150px; margin-left:470px; width:500px;"><strong>Yang Liu</strong><br />
: He is our advisor, he is our teacher, and what’s more, he is like our elder brother. One year before, we knew nothing about synthetic biology. He taught us a lot about experiments, managing lab and how to be a REAL scientist. With his help, we did most experiment of GVP and manage lab smoothly.</p><br />
<a><img style="margin-top:30px; margin-left:30px;" src="https://static.igem.org/mediawiki/2012/a/a3/Ouc-team-Friend1.jpg"></a><br />
<p style="margin-top:-150px; margin-left:470px; margin-bottom:50px; width:500px;"><strong>Wei Liu</strong><br />
:She is our advisor and girlfriend of Yang Liu. Besides Yang Liu, she did much favor for us and helped Yang Liu to teach us Synthetic Biology. Because our team was divided into two groups and one group went to Qibebt, she helped us in qibebt about living, learning and experiment there.</p><br />
<br/><br />
<br/><br />
</div><br />
<div id="cooperator"><br />
<h2>Cooperator</h2><br />
<a><img style="margin-top:50px;" src="https://static.igem.org/mediawiki/2012/f/fd/Ouc-team-cooperator.jpg" /></a><br />
<br/><br />
<p style="margin-top:30px;"><span></span>We helped UBC to complete their survey about patent, and gave our own opinions in Nanjing university’s survey about part registry., then we forwarded the invitation for iGEM_TU_München’ survey. We also lent a hand to SUSTC Shenzhen-A and SUSTC Shenzhen-B as soon as they made contact with us. We are willing to help other teams and learn from others.<br />
<br/><br />
<span></span>When Peking university took a visit of our school in August, they showed great interest in the gelase gene discovered by professor Shi Xiaochong, which they considered to be useful in their project. So we helped them acquire the strain and send it to Peking smoothly.<br />
<br/><br />
<br/><br />
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Dolores
http://2012.igem.org/File:Ratiop2R.jpg
File:Ratiop2R.jpg
2012-10-27T03:27:50Z
<p>Dolores: </p>
<hr />
<div></div>
Dolores
http://2012.igem.org/File:Ratiop0R.jpg
File:Ratiop0R.jpg
2012-10-27T03:26:50Z
<p>Dolores: </p>
<hr />
<div></div>
Dolores
http://2012.igem.org/File:Ratiop1R.jpg
File:Ratiop1R.jpg
2012-10-27T03:25:42Z
<p>Dolores: </p>
<hr />
<div></div>
Dolores
http://2012.igem.org/File:Ouc-eth.jpg
File:Ouc-eth.jpg
2012-10-27T03:18:47Z
<p>Dolores: uploaded a new version of &quot;File:Ouc-eth.jpg&quot;</p>
<hr />
<div></div>
Dolores
http://2012.igem.org/Team:OUC-China/Team/AcknowledgementandCooperation
Team:OUC-China/Team/AcknowledgementandCooperation
2012-10-27T03:15:36Z
<p>Dolores: </p>
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<section id="wrapper"><br />
<article id="main"><br />
<br />
<div id="organization"><br />
<h2>Organization</h2><br />
<p>Algology and algae culture laboratory of Ocean university of China</p><br />
<p><a href="http://www2.ouc.edu.cn/hysm/">College of Marine Life Science, Ocean University of China</a></p><br />
<p><a href="http://www.ouc.edu.cn">Ocean University of China</a></p><br />
<p><a href="http://jwc.ouc.edu.cn:8080/jwwz/index.html">Dean's Office of Ocean University of China</a></p><br />
<p><a href="http://english.qibebt.cas.cn/">Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences</a></p><br />
<p><a href="http://222.195.158.131/jcjxzx/">Basic teaching center basic computer department of Ocean University of China</a></p><br />
</div><br />
<div id="advisor"><br />
<h2><span></span>Advisor</h2><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/e/eb/Ouc-team-advisor0.jpg"></a><br />
<p style="margin-top:-120px;"><strong>Xu Jian</strong><br />
<br/>Academic title: Professor<br />
<br/><br />
E-mail<a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:xujian@qibebt.ac.cn">xujian@qibebt.ac.cn</a><br />
<br/>Phone: 0532-80662654</p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/d/df/Advisor1.jpg"></a><br />
<p style="margin-top:-100px;"><strong>Bao Zhenmin</strong><br />
<br/>Academic title: Professor, Doctoral supervisor<br />
<br/>Research interest: Shellfish genetic breeding</p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/9/9f/Ouc-team-advisior2.jpg"></a><br />
<p style="width:400px; margin-top:-260px;"><strong>Mao Yunxiang</strong><br />
<br/>Academic title: Professor, Doctoral supervisor<br />
<br/>Research interest:<br />
Conservation Genetics and Germplasm Collection of Seaweed<br />
<br/>Molecular Genetic Breeding and Varity Improvement of Economical Seaweed<br />
<br/>Genomic and Genetic Dissection of Economical and Stress-tolerant Traits of Algae<br />
<br/>Reproductive Biology of Seaweed and Techniques Development of Ecological Cultivation<br />
<br/>E-mail :<a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:yxmao@ouc.edu.cn">yxmao@ouc.edu.cn</a></p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/9/9e/Ouc-team-advisor3.jpg"></a><br />
<p style="margin-top:-150px;"><strong>Gong Qingli</strong><br />
<br/>Academic title:Professor, Doctoral supervisor<br />
<br/>Research interest: Seaweed learning and algae breeding<br />
<br/>E-mail :<a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:qingli@vip.sina.com">qingli@vip.sina.com</a></p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/9/94/Ouc-team-advisor4.jpg"></a><br />
<p style="margin-top:-150px;"><strong>Yang Guanpin</strong><br />
<br/>Academic title:Professor, Doctoral supervisor<br />
<br/>Research interest: Marine economical breeding, marine microbiology<br />
<br/>E-mail :<a style="margin-left:0;margin-bottom:0; color:#444;href="yguanpin@mail.ouc.edu.cn">yguanpin@mail.ouc.edu.cn</a></p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/b/be/Ouc-team-advisor5.jpg"></a><br />
<p style="width:400px; margin-top:-260px;"><strong>Liu Chenguang</strong><br />
<br/>Academic title:Professor, Doctoral supervisor<br />
<br/>Research interest: research and application of Marine biological enzyme<br />
<br/>Molecular Genetic Breeding and Varity Improvement of Economical Seaweed<br />
<br/> Polysaccharide biological materials and drug control-released carrier enzyme<br />
<br/> Enzyme immobilization and nano biotechnology<br />
<br/>E-mail :<a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:liucg@ouc.edu.cn">liucg@ouc.edu.cn</a></p><br />
<p style="margin-top:80px; margin-left:50px; width:700px;"><strong>Ma bo</strong><br />
<br/>Academic title:Associate Professor<br />
<br/>Lead of Microfluidics Single Cell Platform Team Functional Genomics <br />
<br/>Group Qingdao Institute of BioEnergy and Bioprocess Technology Chinese Academy of Sciences<br />
<br/>E-mail: <a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:mabo@qibebt.ac.cn">mabo@qibebt.ac.cn</a></p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/b/bb/OUC-dongshugang.jpg"></a><br />
<p style="margin-top:50px; margin-left:50px; width:700px;"><strong>Dong Shugang</strong><br />
<br/>Academic title: Professor, Doctoral supervisor<br />
<br/>Research interest: Seaweed physiology and ecology<br />
<br/>E-mail: <a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:dongshg112@163.com">dongshg112@163.com</a></p><br />
</div><br />
<div id="communication"><br />
<h2>Communication with Other Teams</h2><br />
<p style="margin-bottom:0; margin-top:30px;"><span></span>It’s the second year for us to participate in iGEM, and we are lucky enough to have obtained much help from other teams. Especially, we communicate with the team of Peking University frequently. And we constructed good relationship with iGEM teams around the world through helping them in different ways.<br />
This year we started our modeling design without any experience from before. As for our noise analysis-model, ETH University helped us solve the fundamental problem of how to apply Gillespei Algorithm. And through communicating with Peking University, we have learned how to change whole biological reactions to elementary reactions and how to apply chemical mass action law.For 2012 world jamboree, Boston University buy the helium for us in advance to help our team show our project.</p> <br />
<a><img style="margin-top:10px; margin-left:100px;" src="https://static.igem.org/mediawiki/2012/b/b7/Ouc-peking.jpg" /></a><br />
<a><img style="margin-top:10px; margin-left:150px;" src="https://static.igem.org/mediawiki/2012/0/0a/Ouc-oast.jpg" /></a><br />
<a><img style="margin-top:10px; margin-left:150px;" src="https://static.igem.org/mediawiki/2012/1/15/Ouc-bo.jpg" /></a><br />
<br/><br />
<br/><br />
<a><img style="margin-left:200px;" src="https://static.igem.org/mediawiki/2012/d/dd/Ouc-eth.jpg" /></a><br />
<br/><br />
<br/><br />
<p><span></span>OUC-China iGEM Team belongs to Ocean University of China Association of Science and Technology (OAST). We did nearly half of the experiments in the lab of OAST. The experiments of GVP were totally done in it. Besides, most human practices were done with the help of other people in the Organization. We held Hands-on experience summer camp and 2th summer camp of life science and technology in favor of OAST this summer. Almost every iGEMers in ours team are OASTers. We love iGEM, and we love OAST.<br />
</p><br />
</div><br />
<div id="special"><br />
<h2><span></span>Special Friends</h2><br />
<a><img style="margin-top:30px; margin-left:30px;" src="https://static.igem.org/mediawiki/2012/1/14/Ouc-team-Friend0.jpg"></a><br />
<p style="margin-top:-150px; margin-left:470px; width:500px;"><strong>Yang Liu</strong><br />
: He is our advisor, he is our teacher, and what’s more, he is like our elder brother. One year before, we knew nothing about synthetic biology. He taught us a lot about experiments, managing lab and how to be a REAL scientist. With his help, we did most experiment of GVP and manage lab smoothly.</p><br />
<a><img style="margin-top:30px; margin-left:30px;" src="https://static.igem.org/mediawiki/2012/a/a3/Ouc-team-Friend1.jpg"></a><br />
<p style="margin-top:-150px; margin-left:470px; margin-bottom:50px; width:500px;"><strong>Wei Liu</strong><br />
:She is our advisor and girlfriend of Yang Liu. Besides Yang Liu, she did much favor for us and helped Yang Liu to teach us Synthetic Biology. Because our team was divided into two groups and one group went to Qibebt, she helped us in qibebt about living, learning and experiment there.</p><br />
<br/><br />
<br/><br />
</div><br />
<div id="cooperator"><br />
<h2>Cooperator</h2><br />
<a><img style="margin-top:50px;" src="https://static.igem.org/mediawiki/2012/f/fd/Ouc-team-cooperator.jpg" /></a><br />
<br/><br />
<p style="margin-top:30px;"><span></span>We helped UBC to complete their survey about patent, and gave our own opinions in Nanjing university’s survey about part registry., then we forwarded the invitation for iGEM_TU_München’ survey. We also lent a hand to SUSTC Shenzhen-A and SUSTC Shenzhen-B as soon as they made contact with us. We are willing to help other teams and learn from others.<br />
<br/><br />
<span></span>When Peking university took a visit of our school in August, they showed great interest in the gelase gene discovered by professor Shi Xiaochong, which they considered to be useful in their project. So we helped them acquire the strain and send it to Peking smoothly.<br />
<br/><br />
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Dolores
http://2012.igem.org/File:Ouc-eth.jpg
File:Ouc-eth.jpg
2012-10-27T03:15:09Z
<p>Dolores: uploaded a new version of &quot;File:Ouc-eth.jpg&quot;</p>
<hr />
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Dolores
http://2012.igem.org/Team:OUC-China/Team/AcknowledgementandCooperation
Team:OUC-China/Team/AcknowledgementandCooperation
2012-10-27T03:13:31Z
<p>Dolores: </p>
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<section id="wrapper"><br />
<article id="main"><br />
<br />
<div id="organization"><br />
<h2>Organization</h2><br />
<p>Algology and algae culture laboratory of Ocean university of China</p><br />
<p><a href="http://www2.ouc.edu.cn/hysm/">College of Marine Life Science, Ocean University of China</a></p><br />
<p><a href="http://www.ouc.edu.cn">Ocean University of China</a></p><br />
<p><a href="http://jwc.ouc.edu.cn:8080/jwwz/index.html">Dean's Office of Ocean University of China</a></p><br />
<p><a href="http://english.qibebt.cas.cn/">Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences</a></p><br />
<p><a href="http://222.195.158.131/jcjxzx/">Basic teaching center basic computer department of Ocean University of China</a></p><br />
</div><br />
<div id="advisor"><br />
<h2><span></span>Advisor</h2><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/e/eb/Ouc-team-advisor0.jpg"></a><br />
<p style="margin-top:-120px;"><strong>Xu Jian</strong><br />
<br/>Academic title: Professor<br />
<br/><br />
E-mail<a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:xujian@qibebt.ac.cn">xujian@qibebt.ac.cn</a><br />
<br/>Phone: 0532-80662654</p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/d/df/Advisor1.jpg"></a><br />
<p style="margin-top:-100px;"><strong>Bao Zhenmin</strong><br />
<br/>Academic title: Professor, Doctoral supervisor<br />
<br/>Research interest: Shellfish genetic breeding</p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/9/9f/Ouc-team-advisior2.jpg"></a><br />
<p style="width:400px; margin-top:-260px;"><strong>Mao Yunxiang</strong><br />
<br/>Academic title: Professor, Doctoral supervisor<br />
<br/>Research interest:<br />
Conservation Genetics and Germplasm Collection of Seaweed<br />
<br/>Molecular Genetic Breeding and Varity Improvement of Economical Seaweed<br />
<br/>Genomic and Genetic Dissection of Economical and Stress-tolerant Traits of Algae<br />
<br/>Reproductive Biology of Seaweed and Techniques Development of Ecological Cultivation<br />
<br/>E-mail :<a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:yxmao@ouc.edu.cn">yxmao@ouc.edu.cn</a></p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/9/9e/Ouc-team-advisor3.jpg"></a><br />
<p style="margin-top:-150px;"><strong>Gong Qingli</strong><br />
<br/>Academic title:Professor, Doctoral supervisor<br />
<br/>Research interest: Seaweed learning and algae breeding<br />
<br/>E-mail :<a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:qingli@vip.sina.com">qingli@vip.sina.com</a></p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/9/94/Ouc-team-advisor4.jpg"></a><br />
<p style="margin-top:-150px;"><strong>Yang Guanpin</strong><br />
<br/>Academic title:Professor, Doctoral supervisor<br />
<br/>Research interest: Marine economical breeding, marine microbiology<br />
<br/>E-mail :<a style="margin-left:0;margin-bottom:0; color:#444;href="yguanpin@mail.ouc.edu.cn">yguanpin@mail.ouc.edu.cn</a></p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/b/be/Ouc-team-advisor5.jpg"></a><br />
<p style="width:400px; margin-top:-260px;"><strong>Liu Chenguang</strong><br />
<br/>Academic title:Professor, Doctoral supervisor<br />
<br/>Research interest: research and application of Marine biological enzyme<br />
<br/>Molecular Genetic Breeding and Varity Improvement of Economical Seaweed<br />
<br/> Polysaccharide biological materials and drug control-released carrier enzyme<br />
<br/> Enzyme immobilization and nano biotechnology<br />
<br/>E-mail :<a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:liucg@ouc.edu.cn">liucg@ouc.edu.cn</a></p><br />
<p style="margin-top:80px; margin-left:50px; width:700px;"><strong>Ma bo</strong><br />
<br/>Academic title:Associate Professor<br />
<br/>Lead of Microfluidics Single Cell Platform Team Functional Genomics <br />
<br/>Group Qingdao Institute of BioEnergy and Bioprocess Technology Chinese Academy of Sciences<br />
<br/>E-mail: <a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:mabo@qibebt.ac.cn">mabo@qibebt.ac.cn</a></p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/b/bb/OUC-dongshugang.jpg"></a><br />
<p style="margin-top:50px; margin-left:50px; width:700px;"><strong>Dong Shugang</strong><br />
<br/>Academic title: Professor, Doctoral supervisor<br />
<br/>Research interest: Seaweed physiology and ecology<br />
<br/>E-mail: <a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:dongshg112@163.com">dongshg112@163.com</a></p><br />
</div><br />
<div id="communication"><br />
<h2>Communication with Other Teams</h2><br />
<p style="margin-bottom:0; margin-top:30px;"><span></span>It’s the second year for us to participate in iGEM, and we are lucky enough to have obtained much help from other teams. Especially, we communicate with the team of Peking University frequently. And we constructed good relationship with iGEM teams around the world through helping them in different ways.<br />
This year we started our modeling design without any experience from before. As for our noise analysis-model, ETH University helped us solve the fundamental problem of how to apply Gillespei Algorithm. And through communicating with Peking University, we have learned how to change whole biological reactions to elementary reactions and how to apply chemical mass action law.For 2012 world jamboree, Boston University buy the helium for us in advance to help our team show our project.</p> <br />
<a><img style="margin-top:10px; margin-left:150px;" src="https://static.igem.org/mediawiki/2012/b/b7/Ouc-peking.jpg" /></a><br />
<a><img style="margin-top:10px; margin-left:150px;" src="https://static.igem.org/mediawiki/2012/0/0a/Ouc-oast.jpg" /></a><br />
<a><img style="margin-top:10px; margin-left:150px;" src="https://static.igem.org/mediawiki/2012/1/15/Ouc-bo.jpg" /></a><br />
<br/><br />
<a><img style="margin-left:250px;" src="https://static.igem.org/mediawiki/2012/d/dd/Ouc-eth.jpg" /></a><br />
<br/><br />
<br/><br />
<p><span></span>OUC-China iGEM Team belongs to Ocean University of China Association of Science and Technology (OAST). We did nearly half of the experiments in the lab of OAST. The experiments of GVP were totally done in it. Besides, most human practices were done with the help of other people in the Organization. We held Hands-on experience summer camp and 2th summer camp of life science and technology in favor of OAST this summer. Almost every iGEMers in ours team are OASTers. We love iGEM, and we love OAST.<br />
</p><br />
</div><br />
<div id="special"><br />
<h2><span></span>Special Friends</h2><br />
<a><img style="margin-top:30px; margin-left:30px;" src="https://static.igem.org/mediawiki/2012/1/14/Ouc-team-Friend0.jpg"></a><br />
<p style="margin-top:-150px; margin-left:470px; width:500px;"><strong>Yang Liu</strong><br />
: He is our advisor, he is our teacher, and what’s more, he is like our elder brother. One year before, we knew nothing about synthetic biology. He taught us a lot about experiments, managing lab and how to be a REAL scientist. With his help, we did most experiment of GVP and manage lab smoothly.</p><br />
<a><img style="margin-top:30px; margin-left:30px;" src="https://static.igem.org/mediawiki/2012/a/a3/Ouc-team-Friend1.jpg"></a><br />
<p style="margin-top:-150px; margin-left:470px; margin-bottom:50px; width:500px;"><strong>Wei Liu</strong><br />
:She is our advisor and girlfriend of Yang Liu. Besides Yang Liu, she did much favor for us and helped Yang Liu to teach us Synthetic Biology. Because our team was divided into two groups and one group went to Qibebt, she helped us in qibebt about living, learning and experiment there.</p><br />
<br/><br />
<br/><br />
</div><br />
<div id="cooperator"><br />
<h2>Cooperator</h2><br />
<a><img style="margin-top:50px;" src="https://static.igem.org/mediawiki/2012/f/fd/Ouc-team-cooperator.jpg" /></a><br />
<br/><br />
<p style="margin-top:30px;"><span></span>We helped UBC to complete their survey about patent, and gave our own opinions in Nanjing university’s survey about part registry., then we forwarded the invitation for iGEM_TU_München’ survey. We also lent a hand to SUSTC Shenzhen-A and SUSTC Shenzhen-B as soon as they made contact with us. We are willing to help other teams and learn from others.<br />
<br/><br />
<span></span>When Peking university took a visit of our school in August, they showed great interest in the gelase gene discovered by professor Shi Xiaochong, which they considered to be useful in their project. So we helped them acquire the strain and send it to Peking smoothly.<br />
<br/><br />
<br/><br />
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Dolores
http://2012.igem.org/File:Ouc-eth.jpg
File:Ouc-eth.jpg
2012-10-27T03:12:31Z
<p>Dolores: uploaded a new version of &quot;File:Ouc-eth.jpg&quot;</p>
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Dolores
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2012-10-27T03:10:26Z
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Dolores
http://2012.igem.org/Team:OUC-China/Team/AcknowledgementandCooperation
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<section id="wrapper"><br />
<article id="main"><br />
<br />
<div id="organization"><br />
<h2>Organization</h2><br />
<p>Algology and algae culture laboratory of Ocean university of China</p><br />
<p><a href="http://www2.ouc.edu.cn/hysm/">College of Marine Life Science, Ocean University of China</a></p><br />
<p><a href="http://www.ouc.edu.cn">Ocean University of China</a></p><br />
<p><a href="http://jwc.ouc.edu.cn:8080/jwwz/index.html">Dean's Office of Ocean University of China</a></p><br />
<p><a href="http://english.qibebt.cas.cn/">Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences</a></p><br />
<p><a href="http://222.195.158.131/jcjxzx/">Basic teaching center basic computer department of Ocean University of China</a></p><br />
</div><br />
<div id="advisor"><br />
<h2><span></span>Advisor</h2><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/e/eb/Ouc-team-advisor0.jpg"></a><br />
<p style="margin-top:-120px;"><strong>Xu Jian</strong><br />
<br/>Academic title: Professor<br />
<br/><br />
E-mail<a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:xujian@qibebt.ac.cn">xujian@qibebt.ac.cn</a><br />
<br/>Phone: 0532-80662654</p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/d/df/Advisor1.jpg"></a><br />
<p style="margin-top:-100px;"><strong>Bao Zhenmin</strong><br />
<br/>Academic title: Professor, Doctoral supervisor<br />
<br/>Research interest: Shellfish genetic breeding</p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/9/9f/Ouc-team-advisior2.jpg"></a><br />
<p style="width:400px; margin-top:-260px;"><strong>Mao Yunxiang</strong><br />
<br/>Academic title: Professor, Doctoral supervisor<br />
<br/>Research interest:<br />
Conservation Genetics and Germplasm Collection of Seaweed<br />
<br/>Molecular Genetic Breeding and Varity Improvement of Economical Seaweed<br />
<br/>Genomic and Genetic Dissection of Economical and Stress-tolerant Traits of Algae<br />
<br/>Reproductive Biology of Seaweed and Techniques Development of Ecological Cultivation<br />
<br/>E-mail :<a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:yxmao@ouc.edu.cn">yxmao@ouc.edu.cn</a></p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/9/9e/Ouc-team-advisor3.jpg"></a><br />
<p style="margin-top:-150px;"><strong>Gong Qingli</strong><br />
<br/>Academic title:Professor, Doctoral supervisor<br />
<br/>Research interest: Seaweed learning and algae breeding<br />
<br/>E-mail :<a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:qingli@vip.sina.com">qingli@vip.sina.com</a></p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/9/94/Ouc-team-advisor4.jpg"></a><br />
<p style="margin-top:-150px;"><strong>Yang Guanpin</strong><br />
<br/>Academic title:Professor, Doctoral supervisor<br />
<br/>Research interest: Marine economical breeding, marine microbiology<br />
<br/>E-mail :<a style="margin-left:0;margin-bottom:0; color:#444;href="yguanpin@mail.ouc.edu.cn">yguanpin@mail.ouc.edu.cn</a></p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/b/be/Ouc-team-advisor5.jpg"></a><br />
<p style="width:400px; margin-top:-260px;"><strong>Liu Chenguang</strong><br />
<br/>Academic title:Professor, Doctoral supervisor<br />
<br/>Research interest: research and application of Marine biological enzyme<br />
<br/>Molecular Genetic Breeding and Varity Improvement of Economical Seaweed<br />
<br/> Polysaccharide biological materials and drug control-released carrier enzyme<br />
<br/> Enzyme immobilization and nano biotechnology<br />
<br/>E-mail :<a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:liucg@ouc.edu.cn">liucg@ouc.edu.cn</a></p><br />
<p style="margin-top:80px; margin-left:50px; width:700px;"><strong>Ma bo</strong><br />
<br/>Academic title:Associate Professor<br />
<br/>Lead of Microfluidics Single Cell Platform Team Functional Genomics <br />
<br/>Group Qingdao Institute of BioEnergy and Bioprocess Technology Chinese Academy of Sciences<br />
<br/>E-mail: <a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:mabo@qibebt.ac.cn">mabo@qibebt.ac.cn</a></p><br />
<a><img style="margin-top:30px;" src="https://static.igem.org/mediawiki/2012/b/bb/OUC-dongshugang.jpg"></a><br />
<p style="margin-top:50px; margin-left:50px; width:700px;"><strong>Dong Shugang</strong><br />
<br/>Academic title: Professor, Doctoral supervisor<br />
<br/>Research interest: Seaweed physiology and ecology<br />
<br/>E-mail: <a style="margin-left:0;margin-bottom:0; color:#444;"href="mailto:dongshg112@163.com">dongshg112@163.com</a></p><br />
</div><br />
<div id="communication"><br />
<h2>Communication with Other Teams</h2><br />
<p style="margin-bottom:0; margin-top:30px;"><span></span>It’s the second year for us to participate in iGEM, and we are lucky enough to have obtained much help from other teams. Especially, we communicate with the team of Peking University frequently. And we constructed good relationship with iGEM teams around the world through helping them in different ways.<br />
This year we started our modeling design without any experience from before. As for our noise analysis-model, ETH University helped us solve the fundamental problem of how to apply Gillespei Algorithm. And through communicating with Peking University, we have learned how to change whole biological reactions to elementary reactions and how to apply chemical mass action law.For 2012 world jamboree, Boston University buy the helium for us in advance to help our team show our project.</p> <br />
<a><img style="margin-top:10px; margin-left:80px;" src="https://static.igem.org/mediawiki/2012/b/b7/Ouc-peking.jpg" /></a><br />
<a><img style="margin-top:10px; margin-left:80px;" src="https://static.igem.org/mediawiki/2012/d/dd/Ouc-eth.jpg" /></a><br />
<a><img style="margin-top:10px; margin-left:80px;" src="https://static.igem.org/mediawiki/2012/0/0a/Ouc-oast.jpg" /></a><br />
<a><img style="margin-top:10px; margin-left:80px;" src="https://static.igem.org/mediawiki/2012/1/15/Ouc-bo.jpg" /></a><br />
<br/><br />
<br/><br />
<p><span></span>OUC-China iGEM Team belongs to Ocean University of China Association of Science and Technology (OAST). We did nearly half of the experiments in the lab of OAST. The experiments of GVP were totally done in it. Besides, most human practices were done with the help of other people in the Organization. We held Hands-on experience summer camp and 2th summer camp of life science and technology in favor of OAST this summer. Almost every iGEMers in ours team are OASTers. We love iGEM, and we love OAST.<br />
</p><br />
</div><br />
<div id="special"><br />
<h2><span></span>Special Friends</h2><br />
<a><img style="margin-top:30px; margin-left:30px;" src="https://static.igem.org/mediawiki/2012/1/14/Ouc-team-Friend0.jpg"></a><br />
<p style="margin-top:-150px; margin-left:470px; width:500px;"><strong>Yang Liu</strong><br />
: He is our advisor, he is our teacher, and what’s more, he is like our elder brother. One year before, we knew nothing about synthetic biology. He taught us a lot about experiments, managing lab and how to be a REAL scientist. With his help, we did most experiment of GVP and manage lab smoothly.</p><br />
<a><img style="margin-top:30px; margin-left:30px;" src="https://static.igem.org/mediawiki/2012/a/a3/Ouc-team-Friend1.jpg"></a><br />
<p style="margin-top:-150px; margin-left:470px; margin-bottom:50px; width:500px;"><strong>Wei Liu</strong><br />
:She is our advisor and girlfriend of Yang Liu. Besides Yang Liu, she did much favor for us and helped Yang Liu to teach us Synthetic Biology. Because our team was divided into two groups and one group went to Qibebt, she helped us in qibebt about living, learning and experiment there.</p><br />
<br/><br />
<br/><br />
</div><br />
<div id="cooperator"><br />
<h2>Cooperator</h2><br />
<a><img style="margin-top:50px;" src="https://static.igem.org/mediawiki/2012/f/fd/Ouc-team-cooperator.jpg" /></a><br />
<br/><br />
<p style="margin-top:30px;"><span></span>We helped UBC to complete their survey about patent, and gave our own opinions in Nanjing university’s survey about part registry., then we forwarded the invitation for iGEM_TU_München’ survey. We also lent a hand to SUSTC Shenzhen-A and SUSTC Shenzhen-B as soon as they made contact with us. We are willing to help other teams and learn from others.<br />
<br/><br />
<span></span>When Peking university took a visit of our school in August, they showed great interest in the gelase gene discovered by professor Shi Xiaochong, which they considered to be useful in their project. So we helped them acquire the strain and send it to Peking smoothly.<br />
<br/><br />
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Dolores
http://2012.igem.org/File:Ouc-bo.jpg
File:Ouc-bo.jpg
2012-10-27T03:02:14Z
<p>Dolores: </p>
<hr />
<div></div>
Dolores
http://2012.igem.org/File:Ouc-oast.jpg
File:Ouc-oast.jpg
2012-10-27T02:53:53Z
<p>Dolores: </p>
<hr />
<div></div>
Dolores
http://2012.igem.org/File:Ouc-eth.jpg
File:Ouc-eth.jpg
2012-10-27T02:53:15Z
<p>Dolores: </p>
<hr />
<div></div>
Dolores
http://2012.igem.org/File:Ouc-peking.jpg
File:Ouc-peking.jpg
2012-10-27T02:52:01Z
<p>Dolores: </p>
<hr />
<div></div>
Dolores
http://2012.igem.org/Team:OUC-China/Modeling/NoiseAnalysis
Team:OUC-China/Modeling/NoiseAnalysis
2012-10-27T02:40:11Z
<p>Dolores: </p>
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<h1 style="border:none;">Noise analysis-model</h1><br />
<p><strong>Aim:</strong><span></span>To figure out whether output is robust when presented with intrinsic noise.<br />
<br/><br />
<br/><br />
<p><strong>Steps:</strong><br />
<br/><span></span>1. Use the Gillespie algorithm to perform the stochastic analysis;<br />
<br/><span></span>2. Draw probability distribution figures (pdf);<br />
<br/><span></span>3. Compute the noise statistically.<br />
<br/><br />
<br/><br />
<p><strong>Background:</strong><span></span>After having determined the parameter range, we would make the noise analysis.According to theoretical predictions, elementary chemical reactions involved in biochemical processes exhibit substantial stochastic fluctuations when low numbers of reactant molecules are involved within the small volume of a living cell. <br />
The existence of significant stochastic fluctuations in biochemical processes has been confirmed by numerous experiments including tracking of individual protein molecules in individual cells in gene expression processes[Zhou L, Gregori G, Blackman J,Robinson J, Wanner B (2005) Stochastic activation of the response regulator PhoB by noncognate histidine kinases.J Integrative Bioinformatics 2: 11.] <br />
We refer to the most classical Gillespie algorithm and lots of improvements have been made by later generation. For example, Sagar Indurkhya et al mentioned that Dynamic Monte Carlo methods are a common means of simulating the time-evolution of chemical systems.The Gillespie Algorithm (SSA) [1] is the standard algorithm for this process, and has inspired a variety of derivative methods that speed up computation, including the Optimized Direct Method (ODM) [2] and the Next Reaction Method (NRM) [3]. These methods, however, are still computationally costly.Now,we still use the classical algorithm.:<br />
<br/><br/><br />
<p>ηij is used to describe the noise, where:<br />
<br/><span></span><br />
<a><img style="margin-left:270px;" src="https://static.igem.org/mediawiki/2012/3/32/Ouc-modeling-math20.JPG" /></a><br />
<br/><br />
<p style="text-align:center;">σ ij stands for standard deviation and <Xi> represents the mean value. If i=j then</p> <br />
<br/><a><img style="margin-left:270px;" src="https://static.igem.org/mediawiki/2012/9/9a/Math21.JPG" /></a><br />
<br/><br />
<p><span></span>The value of noise is ηi2 .<br />
If the mean([m]1:1)-mean([m]1:2) >> the value of noise, we identify the output wouldn’t be drown in noise.<br />
<br/><br />
<br/><span></span><br />
<a><img src="https://static.igem.org/mediawiki/2012/8/89/Ouc-parameter_range.png" /></a><br />
<br />
<h2>Result_Ratio sensor</h2><br />
<br/><br />
<p> <br />
<br/><br />
<a><img src="https://static.igem.org/mediawiki/2012/a/a2/Ouc-rs2.png"></a><br />
<br/><br />
<p style="text-align:center; font-size:90%;">Fig.1 Pdf means probability distribution frequency <br />
</p><br />
<br/><br />
<br/><br />
<p>The statistics is given below:<br />
<br/><br />
<br/><br />
<a><img src="https://static.igem.org/mediawiki/2012/5/52/Ouc-rs_analysis2.png"></a><br />
<br/><br />
<br/><br />
<br/><br />
<br/><br />
<br />
<h2>Comparator</h2><br />
<br/><br />
<br/><br />
<a><img style="margin-left:50px;" src="https://static.igem.org/mediawiki/2012/1/1b/Ouc-R1L.jpg" /></a><br />
<a><img style="margin-left:380px; margin-top:-230px;" src="https://static.igem.org/mediawiki/2012/5/51/Ouc-R1R.jpg" /></a><br />
<a><img style="margin-left:50px; margin-top:-30px;"src="https://static.igem.org/mediawiki/2012/6/6c/Ouc-R2L.jpg" /></a><br />
<a><img style="margin-left:380px; margin-top:-230px;" src="https://static.igem.org/mediawiki/2012/0/02/Ouc-R2R.jpg" /></a><br />
<a><img style="margin-left:50px; margin-top:-30px;" src="https://static.igem.org/mediawiki/2012/9/98/Ouc-R3L.jpg" /></a><br />
<a><img style="margin-left:380px; margin-top:-230px;" src="https://static.igem.org/mediawiki/2012/b/b8/Ouc-R3R.jpg" /></a><br />
<br />
<br/><p style="text-align:center; font-size:90%;">Fig.2 Pdf stands for probability distribution frequency.</p><br />
<br/><br />
<br/><br />
<p>The statistics is given below:<br />
<br/><br />
<br/><br />
<a><img src="https://static.igem.org/mediawiki/2012/c/c4/Ouc-c_analysis2.png"></a><br />
<br/><br />
<br/><br />
<br />
<h2>Conclusion</h2><br />
<br/><br />
<p><span></span>Both ratio sensor and comparator, the change of mRNA concentration is robust enough when presented with noise(mean([m]1:1)-mean([m]1:2) >> noise).It is rational to design our device by this parameter sets.<br />
<br/><br />
<br/><br />
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Dolores
http://2012.igem.org/Team:OUC-China/Modeling/NoiseAnalysis
Team:OUC-China/Modeling/NoiseAnalysis
2012-10-27T02:39:13Z
<p>Dolores: </p>
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<h1 style="border:none;">Noise analysis-model</h1><br />
<p><strong>Aim:</strong><span></span>To figure out whether output is robust when presented with intrinsic noise.<br />
<br/><br />
<br/><br />
<p><strong>Steps:</strong><br />
<br/><span></span>1. Use the Gillespie algorithm to perform the stochastic analysis;<br />
<br/><span></span>2. Draw probability distribution figures (pdf);<br />
<br/><span></span>3. Compute the noise statistically.<br />
<br/><br />
<br/><br />
<p><strong>Background:</strong><span></span>After having determined the parameter range, we would make the noise analysis.According to theoretical predictions, elementary chemical reactions involved in biochemical processes exhibit substantial stochastic fluctuations when low numbers of reactant molecules are involved within the small volume of a living cell. <br />
The existence of significant stochastic fluctuations in biochemical processes has been confirmed by numerous experiments including tracking of individual protein molecules in individual cells in gene expression processes[Zhou L, Gregori G, Blackman J,Robinson J, Wanner B (2005) Stochastic activation of the response regulator PhoB by noncognate histidine kinases.J Integrative Bioinformatics 2: 11.] <br />
We refer to the most classical Gillespie algorithm and lots of improvements have been made by later generation. For example, Sagar Indurkhya et al mentioned that Dynamic Monte Carlo methods are a common means of simulating the time-evolution of chemical systems.The Gillespie Algorithm (SSA) [1] is the standard algorithm for this process, and has inspired a variety of derivative methods that speed up computation, including the Optimized Direct Method (ODM) [2] and the Next Reaction Method (NRM) [3]. These methods, however, are still computationally costly.Now,we still use the classical algorithm.:<br />
<br/><br/><br />
<p>ηij is used to describe the noise, where:<br />
<br/><span></span><br />
<a><img style="margin-left:270px;" src="https://static.igem.org/mediawiki/2012/3/32/Ouc-modeling-math20.JPG" /></a><br />
<br/><br />
<p style="text-align:center;">σ ij stands for standard deviation and <Xi> represents the mean value. If i=j then</p> <br />
<br/><a><img style="margin-left:270px;" src="https://static.igem.org/mediawiki/2012/9/9a/Math21.JPG" /></a><br />
<br/><br />
<p><span></span>The value of noise is ηi2 .<br />
If the mean([m]1:1)-mean([m]1:2) >> the value of noise, we identify the output wouldn’t be drown in noise.<br />
<br/><br />
<br/><span></span><br />
<a><img src="https://static.igem.org/mediawiki/2012/8/89/Ouc-parameter_range.png" /></a><br />
<br />
<h2>Result_Ratio sensor</h2><br />
<br/><br />
<p> <br />
<br/><br />
<a><img src="https://static.igem.org/mediawiki/2012/a/a2/Ouc-rs2.png"></a><br />
<br/><br />
<p style="text-align:center; font-size:90%;">Fig.1 Pdf means probability distribution frequency <br />
</p><br />
<br/><br />
<br/><br />
<p>The statistics is given below:<br />
<br/><br />
<br/><br />
<a><img src="https://static.igem.org/mediawiki/2012/5/52/Ouc-rs_analysis2.png"></a><br />
<br/><br />
<br/><br />
<br/><br />
<br/><br />
<br />
<h2>Comparator</h2><br />
<br/><br />
<br/><br />
<a><img style="margin-left:50px;" src="https://static.igem.org/mediawiki/2012/1/1b/Ouc-R1L.jpg" /></a><br />
<a><img style="margin-left:380px; margin-top:-30px;" src="https://static.igem.org/mediawiki/2012/5/51/Ouc-R1R.jpg" /></a><br />
<a><img style="margin-left:50px; margin-top:-30px;"src="https://static.igem.org/mediawiki/2012/6/6c/Ouc-R2L.jpg" /></a><br />
<a><img style="margin-left:380px; margin-top:-30px;" src="https://static.igem.org/mediawiki/2012/0/02/Ouc-R2R.jpg" /></a><br />
<a><img style="margin-left:50px; margin-top:-30px;" src="https://static.igem.org/mediawiki/2012/9/98/Ouc-R3L.jpg" /></a><br />
<a><img style="margin-left:380px; margin-top:-30px;" src="https://static.igem.org/mediawiki/2012/b/b8/Ouc-R3R.jpg" /></a><br />
<br />
<br/><p style="text-align:center; font-size:90%;">Fig.2 Pdf stands for probability distribution frequency.</p><br />
<br/><br />
<br/><br />
<p>The statistics is given below:<br />
<br/><br />
<br/><br />
<a><img src="https://static.igem.org/mediawiki/2012/c/c4/Ouc-c_analysis2.png"></a><br />
<br/><br />
<br/><br />
<br />
<h2>Conclusion</h2><br />
<br/><br />
<p><span></span>Both ratio sensor and comparator, the change of mRNA concentration is robust enough when presented with noise(mean([m]1:1)-mean([m]1:2) >> noise).It is rational to design our device by this parameter sets.<br />
<br/><br />
<br/><br />
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Dolores
http://2012.igem.org/Team:OUC-China/Modeling/NoiseAnalysis
Team:OUC-China/Modeling/NoiseAnalysis
2012-10-27T02:37:58Z
<p>Dolores: </p>
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<h1 style="border:none;">Noise analysis-model</h1><br />
<p><strong>Aim:</strong><span></span>To figure out whether output is robust when presented with intrinsic noise.<br />
<br/><br />
<br/><br />
<p><strong>Steps:</strong><br />
<br/><span></span>1. Use the Gillespie algorithm to perform the stochastic analysis;<br />
<br/><span></span>2. Draw probability distribution figures (pdf);<br />
<br/><span></span>3. Compute the noise statistically.<br />
<br/><br />
<br/><br />
<p><strong>Background:</strong><span></span>After having determined the parameter range, we would make the noise analysis.According to theoretical predictions, elementary chemical reactions involved in biochemical processes exhibit substantial stochastic fluctuations when low numbers of reactant molecules are involved within the small volume of a living cell. <br />
The existence of significant stochastic fluctuations in biochemical processes has been confirmed by numerous experiments including tracking of individual protein molecules in individual cells in gene expression processes[Zhou L, Gregori G, Blackman J,Robinson J, Wanner B (2005) Stochastic activation of the response regulator PhoB by noncognate histidine kinases.J Integrative Bioinformatics 2: 11.] <br />
We refer to the most classical Gillespie algorithm and lots of improvements have been made by later generation. For example, Sagar Indurkhya et al mentioned that Dynamic Monte Carlo methods are a common means of simulating the time-evolution of chemical systems.The Gillespie Algorithm (SSA) [1] is the standard algorithm for this process, and has inspired a variety of derivative methods that speed up computation, including the Optimized Direct Method (ODM) [2] and the Next Reaction Method (NRM) [3]. These methods, however, are still computationally costly.Now,we still use the classical algorithm.:<br />
<br/><br/><br />
<p>ηij is used to describe the noise, where:<br />
<br/><span></span><br />
<a><img style="margin-left:270px;" src="https://static.igem.org/mediawiki/2012/3/32/Ouc-modeling-math20.JPG" /></a><br />
<br/><br />
<p style="text-align:center;">σ ij stands for standard deviation and <Xi> represents the mean value. If i=j then</p> <br />
<br/><a><img style="margin-left:270px;" src="https://static.igem.org/mediawiki/2012/9/9a/Math21.JPG" /></a><br />
<br/><br />
<p><span></span>The value of noise is ηi2 .<br />
If the mean([m]1:1)-mean([m]1:2) >> the value of noise, we identify the output wouldn’t be drown in noise.<br />
<br/><br />
<br/><span></span><br />
<a><img src="https://static.igem.org/mediawiki/2012/8/89/Ouc-parameter_range.png" /></a><br />
<br />
<h2>Result_Ratio sensor</h2><br />
<br/><br />
<p> <br />
<br/><br />
<a><img src="https://static.igem.org/mediawiki/2012/a/a2/Ouc-rs2.png"></a><br />
<br/><br />
<p style="text-align:center; font-size:90%;">Fig.1 Pdf means probability distribution frequency <br />
</p><br />
<br/><br />
<br/><br />
<p>The statistics is given below:<br />
<br/><br />
<br/><br />
<a><img src="https://static.igem.org/mediawiki/2012/5/52/Ouc-rs_analysis2.png"></a><br />
<br/><br />
<br/><br />
<br/><br />
<br/><br />
<br />
<h2>Comparator</h2><br />
<br/><br />
<br/><br />
<a><img style="margin-left:50px;" src="https://static.igem.org/mediawiki/2012/1/1b/Ouc-R1L.jpg" /></a><br />
<a><img style="margin-left:380px; margin-top:-230px;" src="https://static.igem.org/mediawiki/2012/5/51/Ouc-R1R.jpg" /></a><br />
<a><img style="margin-left:50px; margin-top:-230px;"src="https://static.igem.org/mediawiki/2012/6/6c/Ouc-R2L.jpg" /></a><br />
<a><img style="margin-left:380px; margin-top:-230px;" src="https://static.igem.org/mediawiki/2012/0/02/Ouc-R2R.jpg" /></a><br />
<a><img style="margin-left:50px; margin-top:-230px;" src="https://static.igem.org/mediawiki/2012/9/98/Ouc-R3L.jpg" /></a><br />
<a><img style="margin-left:380px; margin-top:-230px;" src="https://static.igem.org/mediawiki/2012/b/b8/Ouc-R3R.jpg" /></a><br />
<br />
<br/><p style="text-align:center; font-size:90%;">Fig.2 Pdf stands for probability distribution frequency.</p><br />
<br/><br />
<br/><br />
<p>The statistics is given below:<br />
<br/><br />
<br/><br />
<a><img src="https://static.igem.org/mediawiki/2012/c/c4/Ouc-c_analysis2.png"></a><br />
<br/><br />
<br/><br />
<br />
<h2>Conclusion</h2><br />
<br/><br />
<p><span></span>Both ratio sensor and comparator, the change of mRNA concentration is robust enough when presented with noise(mean([m]1:1)-mean([m]1:2) >> noise).It is rational to design our device by this parameter sets.<br />
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Dolores
http://2012.igem.org/Team:OUC-China/Modeling/NoiseAnalysis
Team:OUC-China/Modeling/NoiseAnalysis
2012-10-27T02:36:32Z
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<h1 style="border:none;">Noise analysis-model</h1><br />
<p><strong>Aim:</strong><span></span>To figure out whether output is robust when presented with intrinsic noise.<br />
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<p><strong>Steps:</strong><br />
<br/><span></span>1. Use the Gillespie algorithm to perform the stochastic analysis;<br />
<br/><span></span>2. Draw probability distribution figures (pdf);<br />
<br/><span></span>3. Compute the noise statistically.<br />
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<p><strong>Background:</strong><span></span>After having determined the parameter range, we would make the noise analysis.According to theoretical predictions, elementary chemical reactions involved in biochemical processes exhibit substantial stochastic fluctuations when low numbers of reactant molecules are involved within the small volume of a living cell. <br />
The existence of significant stochastic fluctuations in biochemical processes has been confirmed by numerous experiments including tracking of individual protein molecules in individual cells in gene expression processes[Zhou L, Gregori G, Blackman J,Robinson J, Wanner B (2005) Stochastic activation of the response regulator PhoB by noncognate histidine kinases.J Integrative Bioinformatics 2: 11.] <br />
We refer to the most classical Gillespie algorithm and lots of improvements have been made by later generation. For example, Sagar Indurkhya et al mentioned that Dynamic Monte Carlo methods are a common means of simulating the time-evolution of chemical systems.The Gillespie Algorithm (SSA) [1] is the standard algorithm for this process, and has inspired a variety of derivative methods that speed up computation, including the Optimized Direct Method (ODM) [2] and the Next Reaction Method (NRM) [3]. These methods, however, are still computationally costly.Now,we still use the classical algorithm.:<br />
<br/><br/><br />
<p>ηij is used to describe the noise, where:<br />
<br/><span></span><br />
<a><img style="margin-left:270px;" src="https://static.igem.org/mediawiki/2012/3/32/Ouc-modeling-math20.JPG" /></a><br />
<br/><br />
<p style="text-align:center;">σ ij stands for standard deviation and <Xi> represents the mean value. If i=j then</p> <br />
<br/><a><img style="margin-left:270px;" src="https://static.igem.org/mediawiki/2012/9/9a/Math21.JPG" /></a><br />
<br/><br />
<p><span></span>The value of noise is ηi2 .<br />
If the mean([m]1:1)-mean([m]1:2) >> the value of noise, we identify the output wouldn’t be drown in noise.<br />
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<br/><span></span><br />
<a><img src="https://static.igem.org/mediawiki/2012/8/89/Ouc-parameter_range.png" /></a><br />
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<h2>Result_Ratio sensor</h2><br />
<br/><br />
<p> <br />
<br/><br />
<a><img src="https://static.igem.org/mediawiki/2012/a/a2/Ouc-rs2.png"></a><br />
<br/><br />
<p style="text-align:center; font-size:90%;">Fig.1 Pdf means probability distribution frequency <br />
</p><br />
<br/><br />
<br/><br />
<p>The statistics is given below:<br />
<br/><br />
<br/><br />
<a><img src="https://static.igem.org/mediawiki/2012/5/52/Ouc-rs_analysis2.png"></a><br />
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<h2>Comparator</h2><br />
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<a><img style="margin-left:50px;" src="https://static.igem.org/mediawiki/2012/1/1b/Ouc-R1L.jpg" /></a><br />
<a><img style="margin-left:380px; margin-top:-30px;" src="https://static.igem.org/mediawiki/2012/5/51/Ouc-R1R.jpg" /></a><br />
<a><img style="margin-left:50px;" src="https://static.igem.org/mediawiki/2012/6/6c/Ouc-R2L.jpg" /></a><br />
<a><img style="margin-left:380px; margin-top:-30px;" src="https://static.igem.org/mediawiki/2012/0/02/Ouc-R2R.jpg" /></a><br />
<a><img style="margin-left:50px;" src="https://static.igem.org/mediawiki/2012/9/98/Ouc-R3L.jpg" /></a><br />
<a><img style="margin-left:380px; margin-top:-30px;" src="https://static.igem.org/mediawiki/2012/b/b8/Ouc-R3R.jpg" /></a><br />
<br />
<br/><p style="text-align:center; font-size:90%;">Fig.2 Pdf stands for probability distribution frequency.</p><br />
<br/><br />
<br/><br />
<p>The statistics is given below:<br />
<br/><br />
<br/><br />
<a><img src="https://static.igem.org/mediawiki/2012/c/c4/Ouc-c_analysis2.png"></a><br />
<br/><br />
<br/><br />
<br />
<h2>Conclusion</h2><br />
<br/><br />
<p><span></span>Both ratio sensor and comparator, the change of mRNA concentration is robust enough when presented with noise(mean([m]1:1)-mean([m]1:2) >> noise).It is rational to design our device by this parameter sets.<br />
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Dolores
http://2012.igem.org/Team:OUC-China/Modeling/NoiseAnalysis
Team:OUC-China/Modeling/NoiseAnalysis
2012-10-27T02:29:51Z
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<h1 style="border:none;">Noise analysis-model</h1><br />
<p><strong>Aim:</strong><span></span>To figure out whether output is robust when presented with intrinsic noise.<br />
<br/><br />
<br/><br />
<p><strong>Steps:</strong><br />
<br/><span></span>1. Use the Gillespie algorithm to perform the stochastic analysis;<br />
<br/><span></span>2. Draw probability distribution figures (pdf);<br />
<br/><span></span>3. Compute the noise statistically.<br />
<br/><br />
<br/><br />
<p><strong>Background:</strong><span></span>After having determined the parameter range, we would make the noise analysis.According to theoretical predictions, elementary chemical reactions involved in biochemical processes exhibit substantial stochastic fluctuations when low numbers of reactant molecules are involved within the small volume of a living cell. <br />
The existence of significant stochastic fluctuations in biochemical processes has been confirmed by numerous experiments including tracking of individual protein molecules in individual cells in gene expression processes[Zhou L, Gregori G, Blackman J,Robinson J, Wanner B (2005) Stochastic activation of the response regulator PhoB by noncognate histidine kinases.J Integrative Bioinformatics 2: 11.] <br />
We refer to the most classical Gillespie algorithm and lots of improvements have been made by later generation. For example, Sagar Indurkhya et al mentioned that Dynamic Monte Carlo methods are a common means of simulating the time-evolution of chemical systems.The Gillespie Algorithm (SSA) [1] is the standard algorithm for this process, and has inspired a variety of derivative methods that speed up computation, including the Optimized Direct Method (ODM) [2] and the Next Reaction Method (NRM) [3]. These methods, however, are still computationally costly.Now,we still use the classical algorithm.:<br />
<br/><br/><br />
<p>ηij is used to describe the noise, where:<br />
<br/><span></span><br />
<a><img style="margin-left:270px;" src="https://static.igem.org/mediawiki/2012/3/32/Ouc-modeling-math20.JPG" /></a><br />
<br/><br />
<p style="text-align:center;">σ ij stands for standard deviation and <Xi> represents the mean value. If i=j then</p> <br />
<br/><a><img style="margin-left:270px;" src="https://static.igem.org/mediawiki/2012/9/9a/Math21.JPG" /></a><br />
<br/><br />
<p><span></span>The value of noise is ηi2 .<br />
If the mean([m]1:1)-mean([m]1:2) >> the value of noise, we identify the output wouldn’t be drown in noise.<br />
<br/><br />
<br/><span></span><br />
<a><img src="https://static.igem.org/mediawiki/2012/8/89/Ouc-parameter_range.png" /></a><br />
<br />
<h2>Result_Ratio sensor</h2><br />
<br/><br />
<p> <br />
<br/><br />
<a><img src="https://static.igem.org/mediawiki/2012/a/a2/Ouc-rs2.png"></a><br />
<br/><br />
<p style="text-align:center; font-size:90%;">Fig.1 Pdf means probability distribution frequency <br />
</p><br />
<br/><br />
<br/><br />
<p>The statistics is given below:<br />
<br/><br />
<br/><br />
<a><img src="https://static.igem.org/mediawiki/2012/5/52/Ouc-rs_analysis2.png"></a><br />
<br/><br />
<br/><br />
<br/><br />
<br/><br />
<br />
<h2>Comparator</h2><br />
<br/><br />
<br/><br />
<a><img style="margin-left:50px;" src="https://static.igem.org/mediawiki/2012/1/1b/Ouc-R1L.jpg" /></a><br />
<a><img style="margin-left:380px; margin-top:-230px;" src="https://static.igem.org/mediawiki/2012/5/51/Ouc-R1R.jpg" /></a><br />
<a><img style="margin-left:50px;" src="https://static.igem.org/mediawiki/2012/6/6c/Ouc-R2L.jpg" /></a><br />
<a><img style="margin-left:380px; margin-top:-230px;" src="https://static.igem.org/mediawiki/2012/0/02/Ouc-R2R.jpg" /></a><br />
<a><img style="margin-left:50px;" src="https://static.igem.org/mediawiki/2012/9/98/Ouc-R3L.jpg" /></a><br />
<a><img style="margin-left:380px; margin-top:-230px;" src="https://static.igem.org/mediawiki/2012/b/b8/Ouc-R3R.jpg" /></a><br />
<br />
<br/><p style="text-align:center; font-size:90%;">Fig.2 Pdf stands for probability distribution frequency.</p><br />
<br/><br />
<br/><br />
<p>The statistics is given below:<br />
<br/><br />
<br/><br />
<a><img src="https://static.igem.org/mediawiki/2012/c/c4/Ouc-c_analysis2.png"></a><br />
<br/><br />
<br/><br />
<br />
<h2>Conclusion</h2><br />
<br/><br />
<p><span></span>Both ratio sensor and comparator, the change of mRNA concentration is robust enough when presented with noise(mean([m]1:1)-mean([m]1:2) >> noise).It is rational to design our device by this parameter sets.<br />
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<h1 style="border-bottom:none;">ODE Model</h1><br />
<h2>ODE simulation</h2><br />
<p><strong>Aim:</strong> To verify feasibility of ratio sensor & comparator theoretically<br />
<br/><br />
<br/><br />
<p><strong>Steps:</strong><br />
<p><span></span>1. Establish ODE equations based on Mass-action law;<br />
<br/><span></span>2. Investigate reasonable parameter sets from previous researches;<br />
<br/><span></span>3. Simulation;<br />
<br/><span></span>4. Verify the feasibility of devices.<br />
<br/><br />
<br/><br />
<p><strong>Results:</strong><span></span>Both Ratio Sensor and Comparator are feasible within the affordable range in vivo. However, the parameter space of Ratio sensor is not wide enough, which adds uncertainty on constructing such a device.<br />
<br/><br />
<br/><br />
<h2>Background</h2><br />
<p><span></span>Simulation based on mass-action law is a common method of modeling sRNA regulation[1].<br />
Generally, we perform our simulation under the guidance given below<br />
<br/><br />
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<a><img src="https://static.igem.org/mediawiki/2012/a/a5/Ouc-modelfc.png" /></a><br />
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<p><span></span>The differences on design between ratio sensor and comparator is noted in the <a href="https://2012.igem.org/Team:OUC-China/Project/DesignMaking/GoalandDesign">project</a> page. <br />
<br/><br />
Considering the RNA pairing reaction as chemical reaction,we will see the probability of collision is determined by their concentration, and the probability of pairing after collision is determined by their affinity(that is reaction constant k in mass-action law).<br />
<br/><br />
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<a><img style="margin-left:25px;" src="https://static.igem.org/mediawiki/2012/8/83/Ouc-project-designmaking-design0.jpg" /></a><br />
<br/><br />
<br/><br />
<p><span></span>Noting that the input(extra inducer concentration) controls alphas & alpham(RNA synthesis rate), we formulated the mechanism above quantitatively via a simple kinetic model(ODE model) for three RNA interaction. The model is cast in terms of two mass-action equations for the cellular concentrations of the sRNA ([s1],[s2]) and its target GFP mRNA ([m]):<br />
<a><img style="margin-left:175px;" src="https://static.igem.org/mediawiki/2012/1/15/Ouc-project-designmaking-design3.JPG" /></a><br />
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<br/><br />
<p><strong>Is it feasible?</strong><span></span>In this ternary system,there are at least 6 parameters uncertain,we verified the feasibility of constructing such a device through ODE simulation using parameter set from previous researches, fortunately,it is viable theoretically within the affordable parameter range in cell, and the apparent enough with the presence of noise<br />
<br/><br />
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<a><img style="margin-left:80px;" src="https://static.igem.org/mediawiki/2012/5/59/Ouc-project-designmaking-design6.JPG" /></a><br />
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<br/><br />
<p><strong>Comparator</strong><span></span>For comparator, simple conclusions could be drawn:<br />
<br/><br />
<br/><br />
<p style="text-align:center;"> When as1/as2>1, [m]steady state=0;<br />
<br/> When as1/as2<1, [m]steady-state=60</p><br />
<br/><br />
<br />
<p><span></span>Considering the mechanism of comparator as a molecular titration,we also expect a ultra-sensitivity behavior at the switch point(as1/as2=1),which will contribute to the “comparing” decision-making behavior.<br />
<br/><br />
<br/><br />
<p><strong>Ratio sensor</strong><span></span>For ratio sensor, an apparent peak can be observed when as1/as2=1<br />
We run a supplementary simulation at point of as1:as2=1, making comparisons when as1:as2=1:1 and as1:as2=1:2(Fig.3)<br />
<br/><br />
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<a><img style="margin-left:170px;" src="https://static.igem.org/mediawiki/2012/1/1d/Ouc-mo1.jpg" /></a><br />
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<a><img style="margin-left:170px;" src="https://static.igem.org/mediawiki/2012/c/c7/Ouc-mo2.jpg" /></a><br />
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<a><img style="margin-left:170px;" src="https://static.igem.org/mediawiki/2012/f/f8/Ouc-mo3.jpg" /></a><br />
<br/><br />
<br/><br />
<p style="font-size:90%; text-align:center;">Fig 3.</p><br />
<br/><br />
<br/><br />
<p><span></span>Discussion: The three differential equations are established based on Erel Levine et al and we have made a further development. In addition, our model has changed from the one for single interaction between sRNA and mRNA to the one for three kinds of interaction (s1RNA and s2RNA, s1RNA and mRNA, s2RNA and mRNA ). Therefore the latter model would come as a meaningful example for researchers to explore more interactions among RNAs. Of course, we can get the model, to a large degree, due to the creative achievement of Erel Levine et al and others.<br />
<br/><br/><br />
<p><strong>References</strong><br />
<br/>[1] Levine, E., et al., Quantitative characteristics of gene regulation by small RNA. PLoS biology, 2007. 5(9)<br />
<br/>[2] Nicolas E. Buchler1, Matthieu Louis, Molecular Titration and Ultrasensitivity in<br />
Regulatory Networks, J. Mol. Biol. (2008) 384, 1106–1119 <br />
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<h1 style="border-bottom:none;">ODE Model</h1><br />
<h2>ODE simulation</h2><br />
<p><strong>Aim:</strong> To verify feasibility of ratio sensor & comparator theoretically<br />
<br/><br />
<br/><br />
<p><strong>Steps:</strong><br />
<p><span></span>1. Establish ODE equations based on Mass-action law;<br />
<br/><span></span>2. Investigate reasonable parameter sets from previous researches;<br />
<br/><span></span>3. Simulation;<br />
<br/><span></span>4. Verify the feasibility of devices.<br />
<br/><br />
<br/><br />
<p><strong>Results:</strong><span></span>Both Ratio Sensor and Comparator are feasible within the affordable range in vivo. However, the parameter space of Ratio sensor is not wide enough, which adds uncertainty on constructing such a device.<br />
<br/><br />
<br/><br />
<h2>Background</h2><br />
<p><span></span>Simulation based on mass-action law is a common method of modeling sRNA regulation[1].<br />
Generally, we perform our simulation under the guidance given below<br />
<br/><br />
<br/><br />
<a><img src="https://static.igem.org/mediawiki/2012/a/a5/Ouc-modelfc.png" /></a><br />
<br/><br />
<br/><br />
<p><span></span>The differences on design between ratio sensor and comparator is noted in the <a href="https://2012.igem.org/Team:OUC-China/Project/DesignMaking/GoalandDesign">project</a> page. <br />
<br/><br />
Considering the RNA pairing reaction as chemical reaction,we will see the probability of collision is determined by their concentration, and the probability of pairing after collision is determined by their affinity(that is reaction constant k in mass-action law).<br />
<br/><br />
<br/><br />
<a><img style="margin-left:25px;" src="https://static.igem.org/mediawiki/2012/8/83/Ouc-project-designmaking-design0.jpg" /></a><br />
<br/><br />
<br/><br />
<p><span></span>Noting that the input(extra inducer concentration) controls alphas & alpham(RNA synthesis rate), we formulated the mechanism above quantitatively via a simple kinetic model(ODE model) for three RNA interaction. The model is cast in terms of two mass-action equations for the cellular concentrations of the sRNA ([s1],[s2]) and its target GFP mRNA ([m]):<br />
<a><img style="margin-left:175px;" src="https://static.igem.org/mediawiki/2012/1/15/Ouc-project-designmaking-design3.JPG" /></a><br />
<br/><br />
<br/><br />
<a><img src="https://static.igem.org/mediawiki/2012/0/0b/Ouc-project-designmaking-design4.jpg" /></a><br />
<br/><br />
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<a><img src="https://static.igem.org/mediawiki/2012/6/6a/Ouc-modeling-math3.jpg" /></a><br />
<br/><br />
<br/><br />
<p><strong>Is it feasible?</strong><span></span>In this ternary system,there are at least 6 parameters uncertain,we verified the feasibility of constructing such a device through ODE simulation using parameter set from previous researches, fortunately,it is viable theoretically within the affordable parameter range in cell, and the apparent enough with the presence of noise<br />
<br/><br />
<br/><br />
<a><img style="margin-left:80px;" src="https://static.igem.org/mediawiki/2012/5/59/Ouc-project-designmaking-design6.JPG" /></a><br />
<br/><br />
<br/><br />
<p><strong>Comparator</strong><span></span>For comparator, simple conclusions could be drawn:<br />
<br/><br />
<br/><br />
<p style="text-align:center;"> When as1/as2>1, [m]steady state=0;<br />
<br/> When as1/as2<1, [m]steady-state=60</p><br />
<br/><br />
<br />
<p><span></span>Considering the mechanism of comparator as a molecular titration,we also expect a ultra-sensitivity behavior at the switch point(as1/as2=1),which will contribute to the “comparing” decision-making behavior.<br />
<br/><br />
<br/><br />
<p><strong>Ratio sensor</strong><span></span>For ratio sensor, an apparent peak can be observed when as1/as2=1<br />
We run a supplementary simulation at point of as1:as2=1, making comparisons when as1:as2=1:1 and as1:as2=1:2(Fig.3)<br />
<br/><br />
<br/><br />
<a><img style="margin-left:170px;" src="https://static.igem.org/mediawiki/2012/1/1d/Ouc-mo1.jpg" /></a><br />
<br/><br />
<a><img style="margin-left:170px;" src="https://static.igem.org/mediawiki/2012/c/c7/Ouc-mo2.jpg" /></a><br />
<br/><br />
<a><img style="margin-left:170px;" src="https://static.igem.org/mediawiki/2012/f/f8/Ouc-mo3.jpg" /></a><br />
<br/><br />
<br/><br />
<p style="font-size:90%; text-align:center;">Fig 3.</p><br />
<br/><br />
<br/><br />
<p><span></span>Discussion: The three differential equations are established based on Erel Levine et al and we have made a further development. In addition, our model has changed from the one for single interaction between sRNA and mRNA to the one for three kinds of interaction (s1RNA and s2RNA, s1RNA and mRNA, s2RNA and mRNA ). Therefore the latter model would come as a meaningful example for researchers to explore more interactions among RNAs. Of course, we can get the model, to a large degree, due to the creative achievement of Erel Levine et al and others.<br />
<br/><br/><br />
<p><strong>References</strong><br />
<br/>[1] Levine, E., et al., Quantitative characteristics of gene regulation by small RNA. PLoS biology, 2007. 5(9)<br />
<br/>[2] Nicolas E. Buchler1, Matthieu Louis, Molecular Titration and Ultrasensitivity in<br />
Regulatory Networks, J. Mol. Biol. (2008) 384, 1106–1119 <br />
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http://2012.igem.org/Team:OUC-China/Modeling/ODEModel
Team:OUC-China/Modeling/ODEModel
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<h1 style="border-bottom:none;">ODE Model</h1><br />
<h2>ODE simulation</h2><br />
<p><strong>Aim:</strong> To verify feasibility of ratio sensor & comparator theoretically<br />
<br/><br />
<br/><br />
<p><strong>Steps:</strong><br />
<p><span></span>1. Establish ODE equations based on Mass-action law;<br />
<br/><span></span>2. Investigate reasonable parameter sets from previous researches;<br />
<br/><span></span>3. Simulation;<br />
<br/><span></span>4. Verify the feasibility of devices.<br />
<br/><br />
<br/><br />
<p><strong>Results:</strong><span></span>Both Ratio Sensor and Comparator are feasible within the affordable range in vivo. However, the parameter space of Ratio sensor is not wide enough, which adds uncertainty on constructing such a device.<br />
<br/><br />
<br/><br />
<h2>Background</h2><br />
<p><span></span>Simulation based on mass-action law is a common method of modeling sRNA regulation[1].<br />
Generally, we perform our simulation under the guidance given below<br />
<br/><br />
<br/><br />
<a><img src="https://static.igem.org/mediawiki/2012/a/a5/Ouc-modelfc.png" /></a><br />
<br/><br />
<br/><br />
<p><span></span>The differences on design between ratio sensor and comparator is noted in the <a href="https://2012.igem.org/Team:OUC-China/Project/DesignMaking/GoalandDesign">project</a> page. <br />
<br/><br />
Considering the RNA pairing reaction as chemical reaction,we will see the probability of collision is determined by their concentration, and the probability of pairing after collision is determined by their affinity(that is reaction constant k in mass-action law).<br />
<br/><br />
<br/><br />
<a><img style="margin-left:25px;" src="https://static.igem.org/mediawiki/2012/8/83/Ouc-project-designmaking-design0.jpg" /></a><br />
<br/><br />
<br/><br />
<p><span></span>Noting that the input(extra inducer concentration) controls alphas & alpham(RNA synthesis rate), we formulated the mechanism above quantitatively via a simple kinetic model(ODE model) for three RNA interaction. The model is cast in terms of two mass-action equations for the cellular concentrations of the sRNA ([s1],[s2]) and its target GFP mRNA ([m]):<br />
<a><img style="margin-left:175px;" src="https://static.igem.org/mediawiki/2012/1/15/Ouc-project-designmaking-design3.JPG" /></a><br />
<br/><br />
<br/><br />
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<br/><br />
<br/><br />
<a><img src="https://static.igem.org/mediawiki/2012/6/6a/Ouc-modeling-math3.jpg" /></a><br />
<br/><br />
<br/><br />
<p><strong>Is it feasible?</strong><span></span>In this ternary system,there are at least 6 parameters uncertain,we verified the feasibility of constructing such a device through ODE simulation using parameter set from previous researches, fortunately,it is viable theoretically within the affordable parameter range in cell, and the apparent enough with the presence of noise<br />
<br/><br />
<br/><br />
<a><img style="margin-left:80px;" src="https://static.igem.org/mediawiki/2012/5/59/Ouc-project-designmaking-design6.JPG" /></a><br />
<br/><br />
<br/><br />
<p><strong>Comparator</strong><span></span>For comparator, simple conclusions could be drawn:<br />
<br/><br />
<br/><br />
<p style="text-align:center;"> When as1/as2>1, [m]steady state=0;<br />
<br/> When as1/as2<1, [m]steady-state=60</p><br />
<br/><br />
<br />
<p><span></span>Considering the mechanism of comparator as a molecular titration,we also expect a ultra-sensitivity behavior at the switch point(as1/as2=1),which will contribute to the “comparing” decision-making behavior.<br />
<br/><br />
<br/><br />
<p><strong>Ratio sensor</strong><span></span>For ratio sensor, an apparent peak can be observed when as1/as2=1<br />
We run a supplementary simulation at point of as1:as2=1, making comparisons when as1:as2=1:1 and as1:as2=1:2(Fig.3)<br />
<br/><br />
<br/><br />
<a><img style="margin-left:170px;" src="https://static.igem.org/mediawiki/2012/1/1d/Ouc-mo1.jpg" /></a><br />
<br/><br />
<a><img style="margin-left:170px;" src="https://static.igem.org/mediawiki/2012/c/c7/Ouc-mo2.jpg" /></a><br />
<br/><br />
<a><img style="margin-left:170px;" src="https://static.igem.org/mediawiki/2012/f/f8/Ouc-mo3.jpg" /></a><br />
<br/><br />
<br/><br />
<p style="font-size:90%; text-align:center;">Fig 3.</p><br />
<br/><br />
<br/><br />
<p><span></span>Discussion: The three differential equations are established based on Erel Levine et al and we have made a further development. In addition, our model has changed from the one for single interaction between sRNA and mRNA to the one for three kinds of interaction (s1RNA and s2RNA, s1RNA and mRNA, s2RNA and mRNA ). Therefore the latter model would come as a meaningful example for researchers to explore more interactions among RNAs. Of course, we can get the model, to a large degree, due to the creative achievement of Erel Levine et al and others.<br />
<br/><br/><br />
<p><strong>References</strong><br />
<br/>[1] Levine, E., et al., Quantitative characteristics of gene regulation by small RNA. PLoS biology, 2007. 5(9)<br />
<br/>[2] Nicolas E. Buchler1, Matthieu Louis, Molecular Titration and Ultrasensitivity in<br />
Regulatory Networks, J. Mol. Biol. (2008) 384, 1106–1119 <br />
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http://2012.igem.org/Team:OUC-China/Modeling/ODEModel
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<h1 style="border-bottom:none;">ODE Model</h1><br />
<h2>ODE simulation</h2><br />
<p><strong>Aim:</strong> To verify feasibility of ratio sensor & comparator theoretically<br />
<br/><br />
<br/><br />
<p><strong>Steps:</strong><br />
<p><span></span>1. Establish ODE equations based on Mass-action law;<br />
<br/><span></span>2. Investigate reasonable parameter sets from previous researches;<br />
<br/><span></span>3. Simulation;<br />
<br/><span></span>4. Verify the feasibility of devices.<br />
<br/><br />
<br/><br />
<p><strong>Results:</strong><span></span>Both Ratio Sensor and Comparator are feasible within the affordable range in vivo. However, the parameter space of Ratio sensor is not wide enough, which adds uncertainty on constructing such a device.<br />
<br/><br />
<br/><br />
<h2>Background</h2><br />
<p><span></span>Simulation based on mass-action law is a common method of modeling sRNA regulation[1].<br />
Generally, we perform our simulation under the guidance given below<br />
<br/><br />
<br/><br />
<a><img src="https://static.igem.org/mediawiki/2012/a/a5/Ouc-modelfc.png" /></a><br />
<br/><br />
<br/><br />
<p><span></span>The differences on design between ratio sensor and comparator is noted in the <a href="https://2012.igem.org/Team:OUC-China/Project/DesignMaking/GoalandDesign">project</a> page. <br />
<br/><br />
Considering the RNA pairing reaction as chemical reaction,we will see the probability of collision is determined by their concentration, and the probability of pairing after collision is determined by their affinity(that is reaction constant k in mass-action law).<br />
<br/><br />
<br/><br />
<a><img style="margin-left:25px;" src="https://static.igem.org/mediawiki/2012/8/83/Ouc-project-designmaking-design0.jpg" /></a><br />
<br/><br />
<br/><br />
<p><span></span>Noting that the input(extra inducer concentration) controls alphas & alpham(RNA synthesis rate), we formulated the mechanism above quantitatively via a simple kinetic model(ODE model) for three RNA interaction. The model is cast in terms of two mass-action equations for the cellular concentrations of the sRNA ([s1],[s2]) and its target GFP mRNA ([m]):<br />
<a><img style="margin-left:175px;" src="https://static.igem.org/mediawiki/2012/1/15/Ouc-project-designmaking-design3.JPG" /></a><br />
<br/><br />
<br/><br />
<a><img src="https://static.igem.org/mediawiki/2012/0/0b/Ouc-project-designmaking-design4.jpg" /></a><br />
<br/><br />
<br/><br />
<a><img src="https://static.igem.org/mediawiki/2012/6/6a/Ouc-modeling-math3.jpg" /></a><br />
<br/><br />
<br/><br />
<p><strong>Is it feasible?</strong><span></span>In this ternary system,there are at least 6 parameters uncertain,we verified the feasibility of constructing such a device through ODE simulation using parameter set from previous researches, fortunately,it is viable theoretically within the affordable parameter range in cell, and the apparent enough with the presence of noise<br />
<br/><br />
<br/><br />
<a><img style="margin-left:80px;" src="https://static.igem.org/mediawiki/2012/5/59/Ouc-project-designmaking-design6.JPG" /></a><br />
<br/><br />
<br/><br />
<p><strong>Comparator</strong><span></span>For comparator, simple conclusions could be drawn:<br />
<br/><br />
<br/><br />
<p style="text-align:center;"> When as1/as2>1, [m]steady state=0;<br />
<br/> When as1/as2<1, [m]steady-state=60</p><br />
<br/><br />
<br />
<p><span></span>Considering the mechanism of comparator as a molecular titration,we also expect a ultra-sensitivity behavior at the switch point(as1/as2=1),which will contribute to the “comparing” decision-making behavior.<br />
<br/><br />
<br/><br />
<p><strong>Ratio sensor</strong><span></span>For ratio sensor, an apparent peak can be observed when as1/as2=1<br />
We run a supplementary simulation at point of as1:as2=1, making comparisons when as1:as2=1:1 and as1:as2=1:2(Fig.3)<br />
<br/><br />
<br/><br />
<a><img style="margin-left:170px;" src="https://static.igem.org/mediawiki/2012/1/1d/Ouc-mo1.jpg" /></a><br />
<br/><br />
<a><img style="margin-left:170px;" src="https://static.igem.org/mediawiki/2012/c/c7/Ouc-mo2.jpg" /></a><br />
<br/><br />
<a><img style="margin-left:170px;" src="https://static.igem.org/mediawiki/2012/f/f8/Ouc-mo3.jpg" /></a><br />
<br/><br />
<br/><br />
<p style="font-size:90%; text-align:center;">Fig 3.</p><br />
<br/><br />
<br/><br />
<p><span></span>Discussion: The three differential equations are established based on Erel Levine et al and we have made a further development. In addition, our model has changed from the one for single interaction between sRNA and mRNA to the one for three kinds of interaction (s1RNA and s2RNA, s1RNA and mRNA, s2RNA and mRNA ). Therefore the latter model would come as a meaningful example for researchers to explore more interactions among RNAs. Of course, we can get the model, to a large degree, due to the creative achievement of Erel Levine et al and others.<br />
<br/><br/><br />
<p><strong>References</strong><br />
<br/>[1] Levine, E., et al., Quantitative characteristics of gene regulation by small RNA. PLoS biology, 2007. 5(9)<br />
<br/>[2] Nicolas E. Buchler1, Matthieu Louis, Molecular Titration and Ultrasensitivity in<br />
Regulatory Networks, J. Mol. Biol. (2008) 384, 1106–1119 <br />
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Dolores
http://2012.igem.org/Team:OUC-China/Modeling/ODEModel
Team:OUC-China/Modeling/ODEModel
2012-10-27T02:04:23Z
<p>Dolores: </p>
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<h1 style="border-bottom:none;">ODE Model</h1><br />
<h2>ODE simulation</h2><br />
<p><strong>Aim:</strong> To verify feasibility of ratio sensor & comparator theoretically<br />
<br/><br />
<br/><br />
<p><strong>Steps:</strong><br />
<p><span></span>1. Establish ODE equations based on Mass-action law;<br />
<br/><span></span>2. Investigate reasonable parameter sets from previous researches;<br />
<br/><span></span>3. Simulation;<br />
<br/><span></span>4. Verify the feasibility of devices.<br />
<br/><br />
<br/><br />
<p><strong>Results:</strong><span></span>Both Ratio Sensor and Comparator are feasible within the affordable range in vivo. However, the parameter space of Ratio sensor is not wide enough, which adds uncertainty on constructing such a device.<br />
<br/><br />
<br/><br />
<h2>Background</h2><br />
<p><span></span>Simulation based on mass-action law is a common method of modeling sRNA regulation[1].<br />
Generally, we perform our simulation under the guidance given below<br />
<br/><br />
<br/><br />
<a><img src="https://static.igem.org/mediawiki/2012/a/a5/Ouc-modelfc.png" /></a><br />
<br/><br />
<br/><br />
<p><span></span>The differences on design between ratio sensor and comparator is noted in the <a href="https://2012.igem.org/Team:OUC-China/Project/DesignMaking/GoalandDesign">project</a> page. <br />
<br/><br />
Considering the RNA pairing reaction as chemical reaction,we will see the probability of collision is determined by their concentration, and the probability of pairing after collision is determined by their affinity(that is reaction constant k in mass-action law).<br />
<br/><br />
<br/><br />
<a><img style="margin-left:25px;" src="https://static.igem.org/mediawiki/2012/8/83/Ouc-project-designmaking-design0.jpg" /></a><br />
<br/><br />
<br/><br />
<p><span></span>Noting that the input(extra inducer concentration) controls alphas & alpham(RNA synthesis rate), we formulated the mechanism above quantitatively via a simple kinetic model(ODE model) for three RNA interaction. The model is cast in terms of two mass-action equations for the cellular concentrations of the sRNA ([s1],[s2]) and its target GFP mRNA ([m]):<br />
<a><img style="margin-left:175px;" src="https://static.igem.org/mediawiki/2012/1/15/Ouc-project-designmaking-design3.JPG" /></a><br />
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<a><img src="https://static.igem.org/mediawiki/2012/0/0b/Ouc-project-designmaking-design4.jpg" /></a><br />
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<a><img src="https://static.igem.org/mediawiki/2012/6/6a/Ouc-modeling-math3.jpg" /></a><br />
<br/><br />
<br/><br />
<p><strong>Is it feasible?</strong><span></span>In this ternary system,there are at least 6 parameters uncertain,we verified the feasibility of constructing such a device through ODE simulation using parameter set from previous researches, fortunately,it is viable theoretically within the affordable parameter range in cell, and the apparent enough with the presence of noise<br />
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<a><img style="margin-left:80px;" src="https://static.igem.org/mediawiki/2012/5/59/Ouc-project-designmaking-design6.JPG" /></a><br />
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<br/><br />
<p><strong>Comparator</strong><span></span>For comparator, simple conclusions could be drawn:<br />
<br/><br />
<br/><br />
<p style="text-align:center;"> When as1/as2>1, [m]steady state=0;<br />
<br/> When as1/as2<1, [m]steady-state=60</p><br />
<br/><br />
<br />
<p><span></span>Considering the mechanism of comparator as a molecular titration,we also expect a ultra-sensitivity behavior at the switch point(as1/as2=1),which will contribute to the “comparing” decision-making behavior.<br />
<br/><br />
<br/><br />
<p><strong>Ratio sensor</strong><span></span>For ratio sensor, an apparent peak can be observed when as1/as2=1<br />
We run a supplementary simulation at point of as1:as2=1, making comparisons when as1:as2=1:1 and as1:as2=1:2(Fig.3)<br />
<br/><br />
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<a><img style="margin-left:170px;" src="https://static.igem.org/mediawiki/2012/1/1d/Ouc-mo1.jpg" /></a><br />
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<a><img style="margin-left:170px;" src="https://static.igem.org/mediawiki/2012/c/c7/Ouc-mo2.jpg" /></a><br />
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<a><img style="margin-left:170px;" src="https://static.igem.org/mediawiki/2012/f/f8/Ouc-mo3.jpg" /></a><br />
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<br/><br />
<p style="font-size:90%; text-align:center;">Fig 3.</p><br />
<br/><br />
<br/><br />
<p><span></span>Discussion: The three differential equations are established based on Erel Levine et al and we have made a further development. In addition, our model has changed from the one for single interaction between sRNA and mRNA to the one for three kinds of interaction (s1RNA and s2RNA, s1RNA and mRNA, s2RNA and mRNA ). Therefore the latter model would come as a meaningful example for researchers to explore more interactions among RNAs. Of course, we can get the model, to a large degree, due to the creative achievement of Erel Levine et al and others.<br />
<br/><br/><br />
<p><strong>References</strong><br />
<br/>[1] Levine, E., et al., Quantitative characteristics of gene regulation by small RNA. PLoS biology, 2007. 5(9)<br />
<br/>[2] Nicolas E. Buchler1, Matthieu Louis, Molecular Titration and Ultrasensitivity in<br />
Regulatory Networks, J. Mol. Biol. (2008) 384, 1106–1119 <br />
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<h1 style="border-bottom:none;">ODE Model</h1><br />
<h2>ODE simulation</h2><br />
<p><strong>Aim:</strong> To verify feasibility of ratio sensor & comparator theoretically<br />
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<p><strong>Steps:</strong><br />
<p><span></span>1. Establish ODE equations based on Mass-action law;<br />
<br/><span></span>2. Investigate reasonable parameter sets from previous researches;<br />
<br/><span></span>3. Simulation;<br />
<br/><span></span>4. Verify the feasibility of devices.<br />
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<p><strong>Results:</strong><span></span>Both Ratio Sensor and Comparator are feasible within the affordable range in vivo. However, the parameter space of Ratio sensor is not wide enough, which adds uncertainty on constructing such a device.<br />
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<h2>Background</h2><br />
<p><span></span>Simulation based on mass-action law is a common method of modeling sRNA regulation[1].<br />
Generally, we perform our simulation under the guidance given below<br />
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<a><img src="https://static.igem.org/mediawiki/2012/a/a5/Ouc-modelfc.png" /></a><br />
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<p><span></span>The differences on design between ratio sensor and comparator is noted in the <a href="https://2012.igem.org/Team:OUC-China/Project/DesignMaking/GoalandDesign">project</a> page. <br />
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Considering the RNA pairing reaction as chemical reaction,we will see the probability of collision is determined by their concentration, and the probability of pairing after collision is determined by their affinity(that is reaction constant k in mass-action law).<br />
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<a><img style="margin-left:25px;" src="https://static.igem.org/mediawiki/2012/8/83/Ouc-project-designmaking-design0.jpg" /></a><br />
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<p><span></span>Noting that the input(extra inducer concentration) controls alphas & alpham(RNA synthesis rate), we formulated the mechanism above quantitatively via a simple kinetic model(ODE model) for three RNA interaction. The model is cast in terms of two mass-action equations for the cellular concentrations of the sRNA ([s1],[s2]) and its target GFP mRNA ([m]):<br />
<a><img style="margin-left:175px;" src="https://static.igem.org/mediawiki/2012/1/15/Ouc-project-designmaking-design3.JPG" /></a><br />
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<a><img src="https://static.igem.org/mediawiki/2012/0/0b/Ouc-project-designmaking-design4.jpg" /></a><br />
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<a><img src="https://static.igem.org/mediawiki/2012/6/6a/Ouc-modeling-math3.jpg" /></a><br />
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<p><strong>Is it feasible?</strong><span></span>In this ternary system,there are at least 6 parameters uncertain,we verified the feasibility of constructing such a device through ODE simulation using parameter set from previous researches, fortunately,it is viable theoretically within the affordable parameter range in cell, and the apparent enough with the presence of noise<br />
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<a><img style="margin-left:80px;" src="https://static.igem.org/mediawiki/2012/5/59/Ouc-project-designmaking-design6.JPG" /></a><br />
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<p><strong>Comparator</strong><span></span>For comparator, simple conclusions could be drawn:<br />
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<p style="text-align:center;"> When as1/as2>1, [m]steady state=0;<br />
<br/> When as1/as2<1, [m]steady-state=60</p><br />
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<p><span></span>Considering the mechanism of comparator as a molecular titration,we also expect a ultra-sensitivity behavior at the switch point(as1/as2=1),which will contribute to the “comparing” decision-making behavior.<br />
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<p><strong>Ratio sensor</strong><span></span>For ratio sensor, an apparent peak can be observed when as1/as2=1<br />
We run a supplementary simulation at point of as1:as2=1, making comparisons when as1:as2=1:1 and as1:as2=1:2(Fig.3)<br />
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<a><img style="margin-left:170px;" src="https://static.igem.org/mediawiki/2012/1/1d/Ouc-mo1.jpg" /></a><br />
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<a><img style="margin-left:170px;" src="https://static.igem.org/mediawiki/2012/c/c7/Ouc-mo2.jpg" /></a><br />
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<a><img style="margin-left:170px;" src="https://static.igem.org/mediawiki/2012/f/f8/Ouc-mo3.jpg" /></a><br />
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<p style="font-size:90%; text-align:center;">Fig 3.</p><br />
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<p><span></span>Discussion: The three differential equations are established based on Erel Levine et al and we have made a further development. In addition, our model has changed from the one for single interaction between sRNA and mRNA to the one for three kinds of interaction (s1RNA and s2RNA, s1RNA and mRNA, s2RNA and mRNA ). Therefore the latter model would come as a meaningful example for researchers to explore more interactions among RNAs. Of course, we can get the model, to a large degree, due to the creative achievement of Erel Levine et al and others.<br />
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<p><strong>References</strong><br />
<br/>[1] Levine, E., et al., Quantitative characteristics of gene regulation by small RNA. PLoS biology, 2007. 5(9)<br />
<br/>[2] Nicolas E. Buchler1, Matthieu Louis, Molecular Titration and Ultrasensitivity in<br />
Regulatory Networks, J. Mol. Biol. (2008) 384, 1106–1119 <br />
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Dolores
http://2012.igem.org/Team:OUC-China/Modeling/ODEModel
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2012-10-27T01:41:24Z
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<h1 style="border-bottom:none;">ODE Model</h1><br />
<h2>ODE simulation</h2><br />
<p><strong>Aim:</strong> To verify feasibility of ratio sensor & comparator theoretically<br />
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<p><strong>Steps:</strong><br />
<p><span></span>1. Establish ODE equations based on Mass-action law;<br />
<br/><span></span>2. Investigate reasonable parameter sets from previous researches;<br />
<br/><span></span>3. Simulation;<br />
<br/><span></span>4. Verify the feasibility of devices.<br />
<br/><br />
<br/><br />
<p><strong>Results:</strong><span></span>Both Ratio Sensor and Comparator are feasible within the affordable range in vivo. However, the parameter space of Ratio sensor is not wide enough, which adds uncertainty on constructing such a device.<br />
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<br/><br />
<h2>Background</h2><br />
<p><span></span>Simulation based on mass-action law is a common method of modeling sRNA regulation[1].<br />
Generally, we perform our simulation under the guidance given below<br />
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<a><img src="https://static.igem.org/mediawiki/2012/a/a5/Ouc-modelfc.png" /></a><br />
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<p><span></span>The differences on design between ratio sensor and comparator is noted in the <a href="https://2012.igem.org/Team:OUC-China/Project/DesignMaking/GoalandDesign">project</a> page. <br />
<br/><br />
Considering the RNA pairing reaction as chemical reaction,we will see the probability of collision is determined by their concentration, and the probability of pairing after collision is determined by their affinity(that is reaction constant k in mass-action law).<br />
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<a><img style="margin-left:25px;" src="https://static.igem.org/mediawiki/2012/8/83/Ouc-project-designmaking-design0.jpg" /></a><br />
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<p><span></span>Noting that the input(extra inducer concentration) controls alphas & alpham(RNA synthesis rate), we formulated the mechanism above quantitatively via a simple kinetic model(ODE model) for three RNA interaction. The model is cast in terms of two mass-action equations for the cellular concentrations of the sRNA ([s1],[s2]) and its target GFP mRNA ([m]):<br />
<a><img style="margin-left:175px;" src="https://static.igem.org/mediawiki/2012/1/15/Ouc-project-designmaking-design3.JPG" /></a><br />
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<p><strong>Is it feasible?</strong><span></span>In this ternary system,there are at least 6 parameters uncertain,we verified the feasibility of constructing such a device through ODE simulation using parameter set from previous researches, fortunately,it is viable theoretically within the affordable parameter range in cell, and the apparent enough with the presence of noise<br />
<br/><br />
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<a><img style="margin-left:80px;" src="https://static.igem.org/mediawiki/2012/5/59/Ouc-project-designmaking-design6.JPG" /></a><br />
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<p><strong>Comparator</strong><span></span>For comparator, simple conclusions could be drawn:<br />
<br/><br />
<br/><br />
<p style="text-align:center;"> When as1/as2>1, [m]steady state=0;<br />
<br/> When as1/as2<1, [m]steady-state=60</p><br />
<br/><br />
<br />
<p><span></span>Considering the mechanism of comparator as a molecular titration,we also expect a ultra-sensitivity behavior at the switch point(as1/as2=1),which will contribute to the “comparing” decision-making behavior.<br />
<br/><br />
<br/><br />
<p><strong>Ratio sensor</strong><span></span>For ratio sensor, an apparent peak can be observed when as1/as2=1<br />
We run a supplementary simulation at point of as1:as2=1, making comparisons when as1:as2=1:1 and as1:as2=1:2(Fig.3)<br />
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<p style="font-size:90%; text-align:center;">Fig 3.</p><br />
<br/><br />
<br/><br />
<p><span></span>Discussion: The three differential equations are established based on Erel Levine et al and we have made a further development. In addition, our model has changed from the one for single interaction between sRNA and mRNA to the one for three kinds of interaction (s1RNA and s2RNA, s1RNA and mRNA, s2RNA and mRNA ). Therefore the latter model would come as a meaningful example for researchers to explore more interactions among RNAs. Of course, we can get the model, to a large degree, due to the creative achievement of Erel Levine et al and others.<br />
<br/><br/><br />
<p><strong>References</strong><br />
<br/>[1] Levine, E., et al., Quantitative characteristics of gene regulation by small RNA. PLoS biology, 2007. 5(9)<br />
<br/>[2] Nicolas E. Buchler1, Matthieu Louis, Molecular Titration and Ultrasensitivity in<br />
Regulatory Networks, J. Mol. Biol. (2008) 384, 1106–1119 <br />
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<li class="meet"><a href="https://2012.igem.org/Team:OUC-China"><span>Back</span></a></li><br />
<li class="sensor"><a href="https://2012.igem.org/Team:OUC-China/Project/GVP/GasandBackground"><span></span>Background</a></li><br />
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<h1 style="border-bottom:none;">Design and Result</h1><br />
<h2>Cloning strategy</h2><br />
<p><strong>1. Gene cluster</strong><span></span>For our <i>gvp</i> gene cluster we use the specificity primer form Walsby 2002 and add the necessary restriction sites that annealed these pieces of DNA have EcoRI and SpeI sticky ends. We use the vector psb4K5 because the uncoordinated expression of the entire <i>gvp</i>A/C cluster from its own constitutive promoter when carried on a high-copy number vector could result in the accumulation of lethal quantities of gas vesicle proteins in the host cells.Hence we use the low-copy number vector to ensure that the gene cluster can in the host to the normal expression.[3] so we use The vector pSB4K5 containing <i>gvp</i> gene cluster was cut with EcoRI and PstI and was ligated with B0015. ( Figure 4 5) After PCR inspection by using Specific primer we get the target fragment. ( Figure7)<br />
On the other hand, In order to prove that the integrity of the <i>gvp</i> gene cluster we use a set of genetic circuit controlled by the methods OMPR promoter reverse connection in the back of the K73710 using another light controlled element in laser under excitation of start OMPR promoter that the expression of gene cluster is restrained to prove <i>gvp</i> gene cluster integrity. ( Figure 23)<br />
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<a><img src="https://static.igem.org/mediawiki/2012/c/c2/Ouc-project-gvp3.jpg" /></a><br />
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<p style="text-align:center; font-size:90%;">Figure 4 This 1 kbp part contains 2 open reading frames coding for gas vesicle genes (<i>gvp</i>A and <i>gvp</i>-20) and the <i>Cyanobacteria</i> gene promoter and RBS (BBa_K737019 and BBa_K737020) from <i>Bacillus Planktothrix rubescens</i> strain BC-Pla 9402. Promotion of the sequence results in expression of gas vesicles, organelles made entirely out of protein. These organelles contain gas and therefore provide buoyancy to the cell. <br />
</p><br />
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<a><img style="margin-left:112px;" src="https://static.igem.org/mediawiki/2012/7/7c/Ouc-project-gvp4.jpg" /></a><br />
<a><img style="margin-left:93px;" src="https://static.igem.org/mediawiki/2012/5/55/Ouc-project-gvp5.jpg" /></a><br />
<br/><br />
<p style="text-align:center; font-size:90%;">Figure 5 and 6The cloning strategy of buoyancy device and light control device. Because the uncoordinated expression of the entire <i>gvp</i>A/C cluster with its own constitutive promoter could result in the accumulation of lethal quantities of gas vesicle proteins when carried on a high-copy number vector in the host cells. <br />
</p><br/><br />
<a><img style="margin-left:50px;" src="https://static.igem.org/mediawiki/2012/a/af/Ouc-gvp2.jpg" /></a><br />
<p style="margin-left:360px; margin-top:-280px;">Use the low-copy number vector pSB4A to ensure that the gene cluster can in the normal expression in the host<br />
The light control gene circuit from our iGEM lab is based on UC-iGEM 2005.we use part BBa_ I15008 (ho1) and BBa_I15009 and Cph1 / EnvZ FP redesigned photosensitive gene line, fixed iGEM part library of the BBa_I150010 Cph1 / EnvZ FP mistakes, successful synthesis of 660 nm red light sensitive gene expression device, which in the red light input conditions closed gas vesicle expression. (Figure7)<br />
<br/></p><br />
<br/><br />
<p style="font-size:90%; margin-top:50px;">(Figure7) the 660 nm laser induced device<br />
It is made up of three 660 nm wavelength of<br />
laser device and a cooling fan composition can<br />
be fixed a root tube that nutrient solution to<br />
get full sunshine has reached laser induced effect<br />
( OUC-China team)</p><br />
<br/><br />
<br/><br />
<br/><br />
<p><strong>2.<i>gvp</i>A and <i>gvp</i>C genes</strong><span></span>It’s out second step to take out the <i>gvp</i>A and <i>gvp</i>C gene from <i>Planktothrix rubescens</i> 9402 strain (CCAP 1460/9). Since there is no sequence information in NCBI about Pla 9402, we decided to take advantages of its translocation mechanism. So we use the Pla 9401 (GenBank: AJ132354.1) and Pla 9402/b (GenBank: AJ494991.1) gene sequence as the template to design primers for <i>gvp</i>A, <i>gvp</i>C-20psi and <i>gvp</i>C-16omega. In consideration of Pla 9402’s repetitive sequences of gvp gene, we took two different approaches to take out the genes: one is directly doing PCR with the genome of Pla 9402 as template, while the other is PCRed on the BssSI-enzymed template of Pla 9402 genome. The gene <i>gvp</i>A and <i>gvp</i>C-20psi was successfully cloned through both these pathways, but the attempts to clone <i>gvp</i>C-16omega gene failed. <br />
<br/><br />
<br/><br />
<br/><br />
<p><strong>3.Synthetic <i>gvpA/C</i> gene cluster</strong><br />
<span></span>In order to realize the gas vesicle as the decision making output actuator, we clone the gvp structure gene gvpA and gvpC from the natural gvp gene cluster and ligate the promoter(<a href="http://partsregistry.org/Part:BBa_J23106">BBa-J23106</a>)RBS(<a href="http://partsregistry.org/Part:BBa_B0034">BBa-B0034</a>)and terminator(<a href="http://partsregistry.org/Part:BBa_B0015">BBa-B0015</a>)of the E.coli expression system. Because we use the standardized promoter and RBS in this part, so this part can be used in more expression system and control its expression by ourselves as the decision making output actuator. It may extend the applicability of gvp floating device.<br />
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<br/><br />
<a><img style="margin-left:97px;" src="https://static.igem.org/mediawiki/2012/7/77/Ouc-gvp4.png" /></a><br />
<p style="font-size:90%; text-align:center;">Fig 7: We want to recombine the gvpA/C cluster and control its expression by ourselves to realize the decision making output.</p><br />
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<a><img style="margin-left:160px;" src="https://static.igem.org/mediawiki/2012/b/bc/Ouc-gvp4.jpg" /></a><br />
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<p style="font-size:90%; text-align:center;">Fig 8:the expression situation of th e Gas vesicle synthetic gene cluster in escherichia coli JM109,from the picture, we can see obviously gas vesicle due to the expression of bacteria produce clear separation phenomenon.</p><br />
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<br/><br />
<h2>Floating <i>E.Coli</i></h2><br />
<br/><br />
<p><span></span> We transformed 1Kbp <i>gvp</i> gene cluster into JM109 and stationary culture for 36 hours. You can find the E.Coli floating on the surface! (Figure 10 and 11)<br />
<br/><span></span>The expression situation of the Gas Vesicle gene cluster in Escherichia coli JM109, from the picture, we can see obviously gas vesicle due to the expression of bacteria produce clear separation phenomenon. The picture on the right of the experimental group were liquid surface layer and intermediate layer of fluid sampling results, we can see that the fluid layer surface bacteria volume density is obviously higher than that of the middle layer of fluid.<br />
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<a><img style="margin-left:110px;" src="https://static.igem.org/mediawiki/2012/9/97/Ouc-project-gvp7.jpg" /></a><br />
<br/><br />
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<p style="text-align:center; font-size:90%;">Figure 10 and 11. The expression situation of the Gas vesicle gene cluster in <i>Escherichia coli</i> JM109, from the picture, we can see obviously gas vesicle due to the expression of bacteria produce clear separation phenomenon. The picture on the right of the experimental group were liquid surface layer and intermediate layer of fluid sampling results, we can see that the fluid layer surface bacteria volume density is obviously higher than that of the middle layer of fluid.<br />
</p><br />
<br/><br />
<br/><br />
<p><span></span> The buoyancy of Gvp was tested by using the buoyancy test protocol. The cells were grown in a test tube with LB medium for 36 hours (Figure 10) and were left for a while before detected in order to give the cells time to sink or float.<br />
Trace stratified take liquid apparatus. It is made up of a 10 ml volumetric syringe and five a 1 ml volumetric syringe composition. It can be used as a culture cell containers and can be performed every layer of the synchronous sampling the aim is to avoid the sampling process caused by vibration caused by fluid layer surface thallus under. The whole device can make quantitative analysis more accurate.<br />
<br/><br />
<br/><br />
<a><img style="margin-left:170px;" src="https://static.igem.org/mediawiki/2012/c/cb/Ouc-project-gvp8.jpg" /></a><br/><br/><br />
<p style="text-align:center; font-size:90%;">Figure 12. Trace stratified take liquid apparatus. It is made up of a 10 ml volumetric syringe and five a 1 ml volumetric syringe composition. It can be used as a culture cell containers and can be performed every layer of the synchronous sampling the aim is to avoid the sampling process caused by vibration caused by fluid layer surface thallus under. The whole device can make quantitative analysis more accurate. (OUC-China team)<br />
</p><br />
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<br/><br />
<br/><br />
<p><span></span> Because when the bacteria die, it may float on the surface. There is a question, do the bacteria floating on the surface die or not So we made a microscopic examination. We use a vital stain to examine the bacteria die or not. Dead bacteria can’t decompose the stain, so they appear blue, while the living cells turn to be transparent (Figure 11 and 12).<br />
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<br/> <br />
<a><img style="margin-left:70px;" src="https://static.igem.org/mediawiki/2012/9/9e/Ouc-project-gvp9.jpg" /></a><br />
<br/><br />
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<p style="text-align:center; font-size:90%;">Figure 13 and 14. The left picture shows that most of surface bacteria are living because there are few blue spot here. The right picture is dead bacteria as control. We can see that, almost all the bacteria are dead.<br />
</p><br/><br />
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<a><img style="margin-left:72px;" src="https://static.igem.org/mediawiki/2012/6/6f/Ouc-gvp10.jpg" /></a><br />
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<p style="text-align:center; font-size:90%;">Figure 15 and 16. Under the microscope, we use the blood count method to observe the different liquid layer cell capacity, the left is from the liquid layer on the surface of the samples taken from the experimental group, and the right is middle layer of fluid samples. Through the under the microscope observation can obviously observed as the cells expressed in the gas vesicle that cells in the culture solution of concentrated in the surface layer of fluid.<br />
</p><br/><br />
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<a><img style="margin-left:70px;" src="https://static.igem.org/mediawiki/2012/d/d2/Ouc-project-gvp11.jpg" /></a><br />
<br/><br />
<br/><br />
<p style="text-align:center; font-size:90%;">Figure 17 and 18. Under the microscope we use the blood count method to observe the different liquid layer cell capacity, the cell from the bottom of the control samples taken from control group(left)the surface layer of fluid samples.(right) Because the control group cells without expression of Gas vesicle that the force of gravity has a large number of somatic settlement in the test tube through the bottom under the microscope observation we can clear observation the samples of bottom and the difference between the surface sample.</p><br />
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<p><span></span> According to the different layer accurately sampling, the samples blood count determine different height body effusion layer cell number so as to reflect the situation of gas vesicle expression. The results were best visible with and cell density of OD600=2.382 in Liquid surface. And we find that in the test tube, in addition to liquid layer surface and bottom cell is dense in the rest of the liquid layer densities and roughly the same and surface bacteria volume density difference of an order of magnitude. From the control group of counting the results to the distribution of cells with normal cells in the test tube, the distribution so can also explain the experimental results is due to gas vesicle expression in cells. We also do each liquid layer absorbance inspection results and cell number experimental results high similarity from the side proved the correctness of blood count experiment.<br />
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<a><img style="margin-left:79px;" src="https://static.igem.org/mediawiki/2012/3/3e/Ouc-ode1.jpg" /></a><br />
<br/><br />
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<p style="text-align:center; font-size:90%;">Figure 19. The picture shows the gas vesicle in the cells after expressed in the overall trend. We in the cultivation of the cells into logarithmic phase after transferring them to test tube, quiet place and culture 36 hours after using Trace stratified take liquid apparatus at the same time to each liquid layer for sampling. Then each layer of fluid samples of blood count the number of cells with statistics. Results show that gas vesicle due to the existence of the cell concentration in the test tube surface layer of fluid, and control group due to the action of gravity that most cells sedimentation in the test tube bottom.<br />
</p><br/><br />
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<a><img style="margin-left:79px;" src="https://static.igem.org/mediawiki/2012/2/25/Ouc-ode2.jpg" /></a><br />
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<p style="text-align:center; font-size:90%;">Figure 20. Graph of OD measurements at 600nm of both experience group and control group. From the experimental results can be seen in the liquid surface can see cell number have significant abrupt transformation.<br />
</p><br />
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<a><img style="margin-left:10px;" src="https://static.igem.org/mediawiki/2012/7/7e/Ouc-project-gvp14.JPG" /></a><br />
<a><img style="margin-left:370px; margin-top:-520px;" src="https://static.igem.org/mediawiki/2012/7/74/Ouc-project-gvp15.JPG" /></a><br />
<p style="margin-left:400px; margin-top:-100px; font-size:90%">Figure21. Fitting function that function relation is y=25300x4-4726000x3+30515000x2-7.7444000x+70902000. In the picture X axis representative distance test tube bottom every centimeter liquid column and ordinate for cell number.</p><br />
</p><br/><br />
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<p><span></span>Through experiment data f and significant t test. We draw conclusion that in the experimental group and control group on the surface of the liquid layer cell count there exist significant differences this difference is due to the experimental group cells express gas vesicle.<br />
<br/><br />
<br/><a><img style="margin-left:10px; margin-top:-3px;" src="https://static.igem.org/mediawiki/2012/d/d6/Ouc-project-gvp16.JPG" /></a><br />
<p style="margin-left:140px; margin-top:-310px; width:600px;"><span></span>Besides detecting OD/600, we use blood counting method to get cell number in different water-courses. With the help of MATLAB analysis,we can get fitting function of cell number in different water-courses.<br />
<br/><br />
<br/><span></span>Fitting function that function relation is y=25300x4-4726000x3+30515000x2-7.7444000x+70902000. In the picture X axis representative distance test tube bottom every centimeter liquid column and ordinate for cell number.<br />
<br/><br/><span></span>After getting the plasmids of constitutive GvpA and GFP generator, constitutive GvpC and GFP generator, we transform the two plasmids into E.Coli to see if they can float. As expected, they float! It shows that the <i>gvp</i>A and <i>gvp</i>C genes work. In other word, only two genes (about 700bp) can make bacteria floating.<br />
<br/><br/><br />
<p style="font-size:90%; margin-left:10px;"> Figure 22.Floating bacteria with double plasmids.</p><br />
<br/><br />
<br/><br />
<h2>Gas vesicle protein and Expressive inspection</h2><br />
<br/><br />
<p><span></span>We cloned the <i>gvp</i> gene cluster and <i>gvp</i> coding gene form <i>Planktothrix rubescens</i>, which can make the protein GvpA and GvpC-20.The two types of gas vesicle structure protein can be assembled into an empty bubble structure of the Protein polymers which can be in the electron microscope observation under.<br />
<br/><span></span>After successfully transform the BBa_K737010 into the Expression strains JM109, the experiment results show that gas vesicle gene can be expressed in <i>E.coli</i> when gas vesicle gene expression in cells it can make floating bacteria in nutrient solution layer surface. The results showed that some of our speculations include that the <i>gvp</i> genes in prokaryotes of generality.<br />
<br/><br />
<br/><br />
<a><img style="margin-left:4px;" src="https://static.igem.org/mediawiki/2012/d/d2/Ouc-project-gvp17.JPG" /></a><br />
<br/><br/><br />
<p style="font-size:90%; width:200px; margin-left:20px; margin-top:-10px;">Figure 23. Gas vesicles in a freeze-fractured cell of Prosthecomicrobium<br />
Pneumaticum showing the straight –sided cone (Micrograph by<br />
D. Branton and A.E. Walsby) Magnification 210000x)<br />
<p style="font-size:90%; width:200px; margin-left:250px; margin-top:-160px;">Figure 24.Gas vesicles in E.coli protoplasts (BBa_K190033).<br />
The cells were treated with Lysozyme and SDS to<br />
create the protoplasts, uranyl acetate was used for<br />
staining. Magnification: 11500x.(2009 Groningen iGEM )<br />
<p style="font-size:90%; margin-top:-150px; width:250px; margin-left:470px;">Figure 25.The <i>gvp</i> gene cluster in 1% agarose gel form 1 to 4<br />
1 and 2 representative gvp gene cluster + B0015 + R0082 + B0034<br />
3 and 4 gvp representing gene cluster + B0015 and gvp gene cluster<br />
</p><br />
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<br/><br />
<br/><br />
<br/><br />
<p><span></span>To check whether gas vesicles really were present in the cells we did some electron microscopy. In Figure 28 a picture of gas vesicles in a protoplast can be seen. This protoplast comes from an <i>E. coli</i> cell that contained a plasmid with the <i>gvp</i> gene cluster (<a href="http://partsregistry.org/Part:BBa_K737010">BBa_K737010</a>). Figure 29 a picture of blank plasmid in the <i>E. coli</i> JM109 in electron microscope.<br />
</p><br />
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<a><img style="margin-left:220px;" src="https://static.igem.org/mediawiki/2012/4/4f/Ouc-gvp1.jpg" /></a><br />
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<p style="font-size:90%; text-align:center;">Figure 26. Gas vesicles in <i>E. coli</i> protoplasts (<a href="http://partsregistry.org/Part:BBa_K737010">BBa_K737010</a>). The cells were treated with Lysozyme and SDS to create the protoplasts, uranyl acetate was used for staining. Magnification: 60k x.</p><br />
<br/><br />
<a><img style="margin-left:220px;" src="https://static.igem.org/mediawiki/2012/b/bb/Gvp2.jpg" /></a><br />
<br/><br />
<br/><br />
<p style="font-size:90%; text-align:center;">Figure 27. A blank plasmid in the <i>E. coli</i> JM109 The cells were treated with Lysozyme and SDS to create the protoplasts, uranyl acetate was used for staining. Magnification: x 60k</p><br />
<br/><br />
<br/><br />
<h2>Gas vesicle protein quantitative analysis</h2><br />
<br/><br />
<p><span></span>In order to quantitative analyze the expression of gvp gene inside the cell, we design a genetic circuit that could be realized by inserting the <i>gvp</i> gene alongside GFP as a polycistron[5]. Using this part, we can know the expression level of Gvp protein by the detecting the fluorescence of GFP.It will be transcribed into an mRNA and the two genes each have a same promoter (BBa_ J23106). So we can through the expression of GFP to detect gvp gene expression of roughly quantitative. GFP expression can through the determination expression of the specific excitation wavelength of fluorescence value to calculate. [5][6]<br />
<br/><span></span>We made 2 polycistron circuits of gvpA/C and gfp genes. <br />
<br/><span></span>Our devices are:<br />
<br/><span></span>Constitutive GvpA and GFP generator (BBa_K737006):<br />
<br/><span></span>Promoter (BBa_J23106) + RBS (BBa_B0034) + gvpA + RBS + GFP + terminator (BBa_E0840)<br />
<br/><span></span>Constitutive GvpC and GFP generator (BBa-_K737007):<br />
<br/><span></span>Promoter (BBa_J23106) + RBS (BBa_B0034) + gvpC + RBS + GFP + terminator (BBa_E0840)<br />
<br/><br />
<br/><br />
<a><img style="margin-left:140px;" src="https://static.igem.org/mediawiki/2012/2/25/Ouc-project-gvp18.JPG" /></a><br />
<br/><br />
<br/><br />
<p><span></span>In order to check out the expression of polycistronic genetic circuit .We use the SDS-PAGE(protocol)to get the intracellular total protein. Here is the result of SDS-polyacrylamide gel electrophoresis. (Figure22) We can see GFP and GvpC protein directly. Lane 4 is top10 control group, lane 3 is constitutive GvpA and GFP generator, lane 5 is constitutive GvpC and GFP generator. The upper blue and red boxes are in the position about 26KD are GFP protein (25.8KD). The lower red box in the position of about 20KD is GvpC-20 (20KD). Because the MW(molecular weight) of GvpA protein is too small, it’s very difficult to see it on the SDS-polyacrylamide gel. But the expression of GFP suggests it may be expressed.<br />
<br/><span></span>Some papers say that GvpA is difficult to see is that GvpA is too hydrophobic to run out of sample hole. Because the gas vesicle is multimodal protein so it cannot isolate by using SDS-PAGE, too. (Figure28)<br />
<br/><span></span>Finally, we consider that GVP as exogenous protein may be in escherichia coli form inclusion body so we through the Wilkinson–Harrison solubility model to predict GVP protein solubility and judgment GVP protein formation the possibility of inclusion body.<br />
<br/><span></span>The revised Wilkinson–Harrison solubility model involves calculating[9]<br />
<br/><span></span>a canonical variable (CV) or composite parameter for the protein for which<br />
<br/><span></span>the solubility is being predicted. The canonical variable in the two parameter model is defined as:<br />
<br/><br/><br />
<a><img style="margin-left:190px;" src="https://static.igem.org/mediawiki/2012/1/15/Ouc-project-gvp19.JPG" /></a><br />
<br/><br/><br />
<p>where: n 4 number of amino acids in protein<br />
<br/>N,G,P,S 4 number of Asn, Gly, Pro, or Ser residues, respectively.<br />
<br/>R,K,D,E 4 number of Arg, Lys, Asp, or Glu residues, respectively.<br />
<br/>λ1 andλ2 coefficients (15.43 and 29.56, respectively)<br />
<br/>The probability of the protein solubility is based on the parameter CV-CV8,<br />
<br/>where CV8 is the discriminant equal to 1.71. If CV-CV8 is positive, the<br />
<br/>protein is predicted to be insoluble, while if CV-CV8 is negative, the<br />
<br/>protein is predicted to be soluble. The probability of solubility or insolubility can be predicted from the following equation:<br />
<br/>Probability of solubility or insolubility =<br />
<br/><br />
<a><img style="margin-left:220px;" src="https://static.igem.org/mediawiki/2012/4/4f/Ouc-project-gvp20.JPG" /></a><br />
<br/><br />
<p><span></span>The Calculation results show that the gas vesicle protein is insoluble protein.it may be form the <br />
inclusion body in the escherichia coli expression system.( Table 2)<br />
<br/><br />
<br/><br />
<a><img src="https://static.igem.org/mediawiki/2012/9/90/Ouc-project-gvp21.JPG" /></a><br />
<br/><br />
<br/><br />
<a><img style="margin-left:280px" src="https://static.igem.org/mediawiki/2012/1/17/Ouc-project-gvp22.jpg" /></a><br />
<p style="margin-left:20px; margin-top:20px; width:700px; font-size:90%;">Figure 28.the result of 10% SDS-polyacrylamide gel electrophoresis.<br />
the expression of protein gas vesicle in E. coli JM109 analyzed by<br />
SDS-PAGE and quantitative measurement. Equal amount of sample<br />
from cell lysate was fractioned into the pellet and subjected<br />
to SDS-PAGE. 1 and 2 bands in pellet represent respectively the<br />
JM109 blank control and import GVP gene cluster strains.<br />
</p><br />
<br/><br/><br />
<a><img style="margin-left:100px;" src="https://static.igem.org/mediawiki/2012/b/b6/Ouc-project-gvp23.JPG" /></a><br />
<br/><br/><br />
<p style="text-align:center; font-size:90%;">Figure 29.The result of SDS-polyacrylamide gel electrophoresis. Lane 4 is top10 control group, lane 3 is constitutive GvpA and GFP generator, lane 5 is constitutive GvpC and GFP generator. The upper blue and red boxes are in the position about 26kDa are GFP protein (25.8kDa). The lower red box in the position of about 20kDa is GvpC-20 (20kDa).<br />
</p><br />
<br/><br />
<br/><br />
<p><span></span>Because the GvpA protein can’t be seen on the SDS-polyacrylamide gel electrophoresis, we wanted to use GFP to detect the expression of GvpA. We use a polycistron of gvpA (gvpC) and gfp to detect the RFU. We can see that, the RFU of Gvp and GFP Generator is about 2000, and the RFU of Gvp and GFP Generator is about 4000, while top 10 is about 0 as control. (Figure26)First, the RFU of these parts are rather high. Second, the E.Coli with these two plasmids can float. Third, we can see GvpC on the SDS-polyacrylamide gel. So, we can see the two parts can express Gvp Protein and work well.<br />
<br/><br />
<br/><br />
<a><img style="margin-left: 120px;" src="https://static.igem.org/mediawiki/2012/7/7d/Ouc-project-gvp24.JPG" /></a><br />
<br/><br />
<p style="margin-left:20px; margin-top:10px;margin-bottom:20px; font-size:90%;">Figure 30.We can see that, the RFU of Gvp and GFP Generator is about 2000, and the RFU of Gvp and GFP Generator is about 4000, while top 10 is about 0 as control. <br />
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Dolores
http://2012.igem.org/File:Ouc-gvp4.jpg
File:Ouc-gvp4.jpg
2012-10-27T01:14:49Z
<p>Dolores: uploaded a new version of &quot;File:Ouc-gvp4.jpg&quot;</p>
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Dolores
http://2012.igem.org/Team:OUC-China/Project/GVP/DesignandResult
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2012-10-27T01:12:08Z
<p>Dolores: </p>
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<h1 style="border-bottom:none;">Design and Result</h1><br />
<h2>Cloning strategy</h2><br />
<p><strong>1. Gene cluster</strong><span></span>For our <i>gvp</i> gene cluster we use the specificity primer form Walsby 2002 and add the necessary restriction sites that annealed these pieces of DNA have EcoRI and SpeI sticky ends. We use the vector psb4K5 because the uncoordinated expression of the entire <i>gvp</i>A/C cluster from its own constitutive promoter when carried on a high-copy number vector could result in the accumulation of lethal quantities of gas vesicle proteins in the host cells.Hence we use the low-copy number vector to ensure that the gene cluster can in the host to the normal expression.[3] so we use The vector pSB4K5 containing <i>gvp</i> gene cluster was cut with EcoRI and PstI and was ligated with B0015. ( Figure 4 5) After PCR inspection by using Specific primer we get the target fragment. ( Figure7)<br />
On the other hand, In order to prove that the integrity of the <i>gvp</i> gene cluster we use a set of genetic circuit controlled by the methods OMPR promoter reverse connection in the back of the K73710 using another light controlled element in laser under excitation of start OMPR promoter that the expression of gene cluster is restrained to prove <i>gvp</i> gene cluster integrity. ( Figure 23)<br />
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<br/><br />
<p style="text-align:center; font-size:90%;">Figure 4 This 1 kbp part contains 2 open reading frames coding for gas vesicle genes (<i>gvp</i>A and <i>gvp</i>-20) and the <i>Cyanobacteria</i> gene promoter and RBS (BBa_K737019 and BBa_K737020) from <i>Bacillus Planktothrix rubescens</i> strain BC-Pla 9402. Promotion of the sequence results in expression of gas vesicles, organelles made entirely out of protein. These organelles contain gas and therefore provide buoyancy to the cell. <br />
</p><br />
<br/><br />
<br/><br />
<a><img style="margin-left:112px;" src="https://static.igem.org/mediawiki/2012/7/7c/Ouc-project-gvp4.jpg" /></a><br />
<a><img style="margin-left:93px;" src="https://static.igem.org/mediawiki/2012/5/55/Ouc-project-gvp5.jpg" /></a><br />
<br/><br />
<p style="text-align:center; font-size:90%;">Figure 5 and 6The cloning strategy of buoyancy device and light control device. Because the uncoordinated expression of the entire <i>gvp</i>A/C cluster with its own constitutive promoter could result in the accumulation of lethal quantities of gas vesicle proteins when carried on a high-copy number vector in the host cells. <br />
</p><br/><br />
<a><img style="margin-left:50px;" src="https://static.igem.org/mediawiki/2012/a/af/Ouc-gvp2.jpg" /></a><br />
<p style="margin-left:360px; margin-top:-280px;">Use the low-copy number vector pSB4A to ensure that the gene cluster can in the normal expression in the host<br />
The light control gene circuit from our iGEM lab is based on UC-iGEM 2005.we use part BBa_ I15008 (ho1) and BBa_I15009 and Cph1 / EnvZ FP redesigned photosensitive gene line, fixed iGEM part library of the BBa_I150010 Cph1 / EnvZ FP mistakes, successful synthesis of 660 nm red light sensitive gene expression device, which in the red light input conditions closed gas vesicle expression. (Figure7)<br />
<br/></p><br />
<br/><br />
<p style="font-size:90%; margin-top:50px;">(Figure7) the 660 nm laser induced device<br />
It is made up of three 660 nm wavelength of<br />
laser device and a cooling fan composition can<br />
be fixed a root tube that nutrient solution to<br />
get full sunshine has reached laser induced effect<br />
( OUC-China team)</p><br />
<br/><br />
<br/><br />
<br/><br />
<p><strong>2.<i>gvp</i>A and <i>gvp</i>C genes</strong><span></span>It’s out second step to take out the <i>gvp</i>A and <i>gvp</i>C gene from <i>Planktothrix rubescens</i> 9402 strain (CCAP 1460/9). Since there is no sequence information in NCBI about Pla 9402, we decided to take advantages of its translocation mechanism. So we use the Pla 9401 (GenBank: AJ132354.1) and Pla 9402/b (GenBank: AJ494991.1) gene sequence as the template to design primers for <i>gvp</i>A, <i>gvp</i>C-20psi and <i>gvp</i>C-16omega. In consideration of Pla 9402’s repetitive sequences of gvp gene, we took two different approaches to take out the genes: one is directly doing PCR with the genome of Pla 9402 as template, while the other is PCRed on the BssSI-enzymed template of Pla 9402 genome. The gene <i>gvp</i>A and <i>gvp</i>C-20psi was successfully cloned through both these pathways, but the attempts to clone <i>gvp</i>C-16omega gene failed. <br />
<br/><br />
<br/><br />
<br/><br />
<p><strong>3.Synthetic <i>gvpA/C</i> gene cluster</strong><br />
<span></span>In order to realize the gas vesicle as the decision making output actuator, we clone the gvp structure gene gvpA and gvpC from the natural gvp gene cluster and ligate the promoter(<a href="http://partsregistry.org/Part:BBa_J23106">BBa-J23106</a>)RBS(<a href="http://partsregistry.org/Part:BBa_B0034">BBa-B0034</a>)and terminator(<a href="http://partsregistry.org/Part:BBa_B0015">BBa-B0015</a>)of the E.coli expression system. Because we use the standardized promoter and RBS in this part, so this part can be used in more expression system and control its expression by ourselves as the decision making output actuator. It may extend the applicability of gvp floating device.<br />
<br/><br />
<br/><br />
<a><img style="margin-left:97px;" src="https://static.igem.org/mediawiki/2012/7/77/Ouc-gvp4.png" /></a><br />
<p style="font-size:90%; text-align:center;">Fig 7: We want to recombine the gvpA/C cluster and control its expression by ourselves to realize the decision making output.</p><br />
<br/><br />
<a><img style="margin-left:70px;" src="https://static.igem.org/mediawiki/2012/b/bc/Ouc-gvp4.jpg" /></a><br />
<br/><br />
<br/><br />
<p style="text-font:90%; text-align:center;">Fig 8:the expression situation of th e Gas vesicle synthetic gene cluster in escherichia coli JM109,from the picture, we can see obviously gas vesicle due to the expression of bacteria produce clear separation phenomenon.</p><br />
<br/><br />
<br/><br />
<h2>Floating <i>E.Coli</i></h2><br />
<br/><br />
<p><span></span> We transformed 1Kbp <i>gvp</i> gene cluster into JM109 and stationary culture for 36 hours. You can find the E.Coli floating on the surface! (Figure 10 and 11)<br />
<br/><span></span>The expression situation of the Gas Vesicle gene cluster in Escherichia coli JM109, from the picture, we can see obviously gas vesicle due to the expression of bacteria produce clear separation phenomenon. The picture on the right of the experimental group were liquid surface layer and intermediate layer of fluid sampling results, we can see that the fluid layer surface bacteria volume density is obviously higher than that of the middle layer of fluid.<br />
<br/><br />
<br/><br />
<a><img style="margin-left:110px;" src="https://static.igem.org/mediawiki/2012/9/97/Ouc-project-gvp7.jpg" /></a><br />
<br/><br />
<br/><br />
<p style="text-align:center; font-size:90%;">Figure 10 and 11. The expression situation of the Gas vesicle gene cluster in <i>Escherichia coli</i> JM109, from the picture, we can see obviously gas vesicle due to the expression of bacteria produce clear separation phenomenon. The picture on the right of the experimental group were liquid surface layer and intermediate layer of fluid sampling results, we can see that the fluid layer surface bacteria volume density is obviously higher than that of the middle layer of fluid.<br />
</p><br />
<br/><br />
<br/><br />
<p><span></span> The buoyancy of Gvp was tested by using the buoyancy test protocol. The cells were grown in a test tube with LB medium for 36 hours (Figure 10) and were left for a while before detected in order to give the cells time to sink or float.<br />
Trace stratified take liquid apparatus. It is made up of a 10 ml volumetric syringe and five a 1 ml volumetric syringe composition. It can be used as a culture cell containers and can be performed every layer of the synchronous sampling the aim is to avoid the sampling process caused by vibration caused by fluid layer surface thallus under. The whole device can make quantitative analysis more accurate.<br />
<br/><br />
<br/><br />
<a><img style="margin-left:170px;" src="https://static.igem.org/mediawiki/2012/c/cb/Ouc-project-gvp8.jpg" /></a><br/><br/><br />
<p style="text-align:center; font-size:90%;">Figure 12. Trace stratified take liquid apparatus. It is made up of a 10 ml volumetric syringe and five a 1 ml volumetric syringe composition. It can be used as a culture cell containers and can be performed every layer of the synchronous sampling the aim is to avoid the sampling process caused by vibration caused by fluid layer surface thallus under. The whole device can make quantitative analysis more accurate. (OUC-China team)<br />
</p><br />
<br/><br />
<br/><br />
<br/><br />
<p><span></span> Because when the bacteria die, it may float on the surface. There is a question, do the bacteria floating on the surface die or not So we made a microscopic examination. We use a vital stain to examine the bacteria die or not. Dead bacteria can’t decompose the stain, so they appear blue, while the living cells turn to be transparent (Figure 11 and 12).<br />
<br/><br />
<br/> <br />
<a><img style="margin-left:70px;" src="https://static.igem.org/mediawiki/2012/9/9e/Ouc-project-gvp9.jpg" /></a><br />
<br/><br />
<br/><br />
<p style="text-align:center; font-size:90%;">Figure 13 and 14. The left picture shows that most of surface bacteria are living because there are few blue spot here. The right picture is dead bacteria as control. We can see that, almost all the bacteria are dead.<br />
</p><br/><br />
<br/><br />
<br />
<a><img style="margin-left:72px;" src="https://static.igem.org/mediawiki/2012/6/6f/Ouc-gvp10.jpg" /></a><br />
<br/><br />
<br/><br />
<p style="text-align:center; font-size:90%;">Figure 15 and 16. Under the microscope, we use the blood count method to observe the different liquid layer cell capacity, the left is from the liquid layer on the surface of the samples taken from the experimental group, and the right is middle layer of fluid samples. Through the under the microscope observation can obviously observed as the cells expressed in the gas vesicle that cells in the culture solution of concentrated in the surface layer of fluid.<br />
</p><br/><br />
<br/><br />
<a><img style="margin-left:70px;" src="https://static.igem.org/mediawiki/2012/d/d2/Ouc-project-gvp11.jpg" /></a><br />
<br/><br />
<br/><br />
<p style="text-align:center; font-size:90%;">Figure 17 and 18. Under the microscope we use the blood count method to observe the different liquid layer cell capacity, the cell from the bottom of the control samples taken from control group(left)the surface layer of fluid samples.(right) Because the control group cells without expression of Gas vesicle that the force of gravity has a large number of somatic settlement in the test tube through the bottom under the microscope observation we can clear observation the samples of bottom and the difference between the surface sample.</p><br />
<br/><br />
<br/><br />
<p><span></span> According to the different layer accurately sampling, the samples blood count determine different height body effusion layer cell number so as to reflect the situation of gas vesicle expression. The results were best visible with and cell density of OD600=2.382 in Liquid surface. And we find that in the test tube, in addition to liquid layer surface and bottom cell is dense in the rest of the liquid layer densities and roughly the same and surface bacteria volume density difference of an order of magnitude. From the control group of counting the results to the distribution of cells with normal cells in the test tube, the distribution so can also explain the experimental results is due to gas vesicle expression in cells. We also do each liquid layer absorbance inspection results and cell number experimental results high similarity from the side proved the correctness of blood count experiment.<br />
<br/><br />
<br/><br />
<a><img style="margin-left:79px;" src="https://static.igem.org/mediawiki/2012/3/3e/Ouc-ode1.jpg" /></a><br />
<br/><br />
<br/><br />
<p style="text-align:center; font-size:90%;">Figure 19. The picture shows the gas vesicle in the cells after expressed in the overall trend. We in the cultivation of the cells into logarithmic phase after transferring them to test tube, quiet place and culture 36 hours after using Trace stratified take liquid apparatus at the same time to each liquid layer for sampling. Then each layer of fluid samples of blood count the number of cells with statistics. Results show that gas vesicle due to the existence of the cell concentration in the test tube surface layer of fluid, and control group due to the action of gravity that most cells sedimentation in the test tube bottom.<br />
</p><br/><br />
<br/><br />
<a><img style="margin-left:79px;" src="https://static.igem.org/mediawiki/2012/2/25/Ouc-ode2.jpg" /></a><br />
<br/><br />
<br/><br />
<p style="text-align:center; font-size:90%;">Figure 20. Graph of OD measurements at 600nm of both experience group and control group. From the experimental results can be seen in the liquid surface can see cell number have significant abrupt transformation.<br />
</p><br />
<br/><br />
<br/><br />
<a><img style="margin-left:10px;" src="https://static.igem.org/mediawiki/2012/7/7e/Ouc-project-gvp14.JPG" /></a><br />
<a><img style="margin-left:370px; margin-top:-520px;" src="https://static.igem.org/mediawiki/2012/7/74/Ouc-project-gvp15.JPG" /></a><br />
<p style="margin-left:400px; margin-top:-100px; font-size:90%">Figure21. Fitting function that function relation is y=25300x4-4726000x3+30515000x2-7.7444000x+70902000. In the picture X axis representative distance test tube bottom every centimeter liquid column and ordinate for cell number.</p><br />
</p><br/><br />
<br/><br />
<br/><br />
<br/><br />
<p><span></span>Through experiment data f and significant t test. We draw conclusion that in the experimental group and control group on the surface of the liquid layer cell count there exist significant differences this difference is due to the experimental group cells express gas vesicle.<br />
<br/><br />
<br/><a><img style="margin-left:10px; margin-top:-3px;" src="https://static.igem.org/mediawiki/2012/d/d6/Ouc-project-gvp16.JPG" /></a><br />
<p style="margin-left:140px; margin-top:-310px; width:600px;"><span></span>Besides detecting OD/600, we use blood counting method to get cell number in different water-courses. With the help of MATLAB analysis,we can get fitting function of cell number in different water-courses.<br />
<br/><br />
<br/><span></span>Fitting function that function relation is y=25300x4-4726000x3+30515000x2-7.7444000x+70902000. In the picture X axis representative distance test tube bottom every centimeter liquid column and ordinate for cell number.<br />
<br/><br/><span></span>After getting the plasmids of constitutive GvpA and GFP generator, constitutive GvpC and GFP generator, we transform the two plasmids into E.Coli to see if they can float. As expected, they float! It shows that the <i>gvp</i>A and <i>gvp</i>C genes work. In other word, only two genes (about 700bp) can make bacteria floating.<br />
<br/><br/><br />
<p style="font-size:90%; margin-left:10px;"> Figure 22.Floating bacteria with double plasmids.</p><br />
<br/><br />
<br/><br />
<h2>Gas vesicle protein and Expressive inspection</h2><br />
<br/><br />
<p><span></span>We cloned the <i>gvp</i> gene cluster and <i>gvp</i> coding gene form <i>Planktothrix rubescens</i>, which can make the protein GvpA and GvpC-20.The two types of gas vesicle structure protein can be assembled into an empty bubble structure of the Protein polymers which can be in the electron microscope observation under.<br />
<br/><span></span>After successfully transform the BBa_K737010 into the Expression strains JM109, the experiment results show that gas vesicle gene can be expressed in <i>E.coli</i> when gas vesicle gene expression in cells it can make floating bacteria in nutrient solution layer surface. The results showed that some of our speculations include that the <i>gvp</i> genes in prokaryotes of generality.<br />
<br/><br />
<br/><br />
<a><img style="margin-left:4px;" src="https://static.igem.org/mediawiki/2012/d/d2/Ouc-project-gvp17.JPG" /></a><br />
<br/><br/><br />
<p style="font-size:90%; width:200px; margin-left:20px; margin-top:-10px;">Figure 23. Gas vesicles in a freeze-fractured cell of Prosthecomicrobium<br />
Pneumaticum showing the straight –sided cone (Micrograph by<br />
D. Branton and A.E. Walsby) Magnification 210000x)<br />
<p style="font-size:90%; width:200px; margin-left:250px; margin-top:-160px;">Figure 24.Gas vesicles in E.coli protoplasts (BBa_K190033).<br />
The cells were treated with Lysozyme and SDS to<br />
create the protoplasts, uranyl acetate was used for<br />
staining. Magnification: 11500x.(2009 Groningen iGEM )<br />
<p style="font-size:90%; margin-top:-150px; width:250px; margin-left:470px;">Figure 25.The <i>gvp</i> gene cluster in 1% agarose gel form 1 to 4<br />
1 and 2 representative gvp gene cluster + B0015 + R0082 + B0034<br />
3 and 4 gvp representing gene cluster + B0015 and gvp gene cluster<br />
</p><br />
<br/><br />
<br/><br />
<br/><br />
<br/><br />
<p><span></span>To check whether gas vesicles really were present in the cells we did some electron microscopy. In Figure 28 a picture of gas vesicles in a protoplast can be seen. This protoplast comes from an <i>E. coli</i> cell that contained a plasmid with the <i>gvp</i> gene cluster (<a href="http://partsregistry.org/Part:BBa_K737010">BBa_K737010</a>). Figure 29 a picture of blank plasmid in the <i>E. coli</i> JM109 in electron microscope.<br />
</p><br />
<br/><br />
<a><img style="margin-left:220px;" src="https://static.igem.org/mediawiki/2012/4/4f/Ouc-gvp1.jpg" /></a><br />
<br/><br />
<br/><br />
<p style="font-size:90%; text-align:center;">Figure 26. Gas vesicles in <i>E. coli</i> protoplasts (<a href="http://partsregistry.org/Part:BBa_K737010">BBa_K737010</a>). The cells were treated with Lysozyme and SDS to create the protoplasts, uranyl acetate was used for staining. Magnification: 60k x.</p><br />
<br/><br />
<a><img style="margin-left:220px;" src="https://static.igem.org/mediawiki/2012/b/bb/Gvp2.jpg" /></a><br />
<br/><br />
<br/><br />
<p style="font-size:90%; text-align:center;">Figure 27. A blank plasmid in the <i>E. coli</i> JM109 The cells were treated with Lysozyme and SDS to create the protoplasts, uranyl acetate was used for staining. Magnification: x 60k</p><br />
<br/><br />
<br/><br />
<h2>Gas vesicle protein quantitative analysis</h2><br />
<br/><br />
<p><span></span>In order to quantitative analyze the expression of gvp gene inside the cell, we design a genetic circuit that could be realized by inserting the <i>gvp</i> gene alongside GFP as a polycistron[5]. Using this part, we can know the expression level of Gvp protein by the detecting the fluorescence of GFP.It will be transcribed into an mRNA and the two genes each have a same promoter (BBa_ J23106). So we can through the expression of GFP to detect gvp gene expression of roughly quantitative. GFP expression can through the determination expression of the specific excitation wavelength of fluorescence value to calculate. [5][6]<br />
<br/><span></span>We made 2 polycistron circuits of gvpA/C and gfp genes. <br />
<br/><span></span>Our devices are:<br />
<br/><span></span>Constitutive GvpA and GFP generator (BBa_K737006):<br />
<br/><span></span>Promoter (BBa_J23106) + RBS (BBa_B0034) + gvpA + RBS + GFP + terminator (BBa_E0840)<br />
<br/><span></span>Constitutive GvpC and GFP generator (BBa-_K737007):<br />
<br/><span></span>Promoter (BBa_J23106) + RBS (BBa_B0034) + gvpC + RBS + GFP + terminator (BBa_E0840)<br />
<br/><br />
<br/><br />
<a><img style="margin-left:140px;" src="https://static.igem.org/mediawiki/2012/2/25/Ouc-project-gvp18.JPG" /></a><br />
<br/><br />
<br/><br />
<p><span></span>In order to check out the expression of polycistronic genetic circuit .We use the SDS-PAGE(protocol)to get the intracellular total protein. Here is the result of SDS-polyacrylamide gel electrophoresis. (Figure22) We can see GFP and GvpC protein directly. Lane 4 is top10 control group, lane 3 is constitutive GvpA and GFP generator, lane 5 is constitutive GvpC and GFP generator. The upper blue and red boxes are in the position about 26KD are GFP protein (25.8KD). The lower red box in the position of about 20KD is GvpC-20 (20KD). Because the MW(molecular weight) of GvpA protein is too small, it’s very difficult to see it on the SDS-polyacrylamide gel. But the expression of GFP suggests it may be expressed.<br />
<br/><span></span>Some papers say that GvpA is difficult to see is that GvpA is too hydrophobic to run out of sample hole. Because the gas vesicle is multimodal protein so it cannot isolate by using SDS-PAGE, too. (Figure28)<br />
<br/><span></span>Finally, we consider that GVP as exogenous protein may be in escherichia coli form inclusion body so we through the Wilkinson–Harrison solubility model to predict GVP protein solubility and judgment GVP protein formation the possibility of inclusion body.<br />
<br/><span></span>The revised Wilkinson–Harrison solubility model involves calculating[9]<br />
<br/><span></span>a canonical variable (CV) or composite parameter for the protein for which<br />
<br/><span></span>the solubility is being predicted. The canonical variable in the two parameter model is defined as:<br />
<br/><br/><br />
<a><img style="margin-left:190px;" src="https://static.igem.org/mediawiki/2012/1/15/Ouc-project-gvp19.JPG" /></a><br />
<br/><br/><br />
<p>where: n 4 number of amino acids in protein<br />
<br/>N,G,P,S 4 number of Asn, Gly, Pro, or Ser residues, respectively.<br />
<br/>R,K,D,E 4 number of Arg, Lys, Asp, or Glu residues, respectively.<br />
<br/>λ1 andλ2 coefficients (15.43 and 29.56, respectively)<br />
<br/>The probability of the protein solubility is based on the parameter CV-CV8,<br />
<br/>where CV8 is the discriminant equal to 1.71. If CV-CV8 is positive, the<br />
<br/>protein is predicted to be insoluble, while if CV-CV8 is negative, the<br />
<br/>protein is predicted to be soluble. The probability of solubility or insolubility can be predicted from the following equation:<br />
<br/>Probability of solubility or insolubility =<br />
<br/><br />
<a><img style="margin-left:220px;" src="https://static.igem.org/mediawiki/2012/4/4f/Ouc-project-gvp20.JPG" /></a><br />
<br/><br />
<p><span></span>The Calculation results show that the gas vesicle protein is insoluble protein.it may be form the <br />
inclusion body in the escherichia coli expression system.( Table 2)<br />
<br/><br />
<br/><br />
<a><img src="https://static.igem.org/mediawiki/2012/9/90/Ouc-project-gvp21.JPG" /></a><br />
<br/><br />
<br/><br />
<a><img style="margin-left:280px" src="https://static.igem.org/mediawiki/2012/1/17/Ouc-project-gvp22.jpg" /></a><br />
<p style="margin-left:20px; margin-top:20px; width:700px; font-size:90%;">Figure 28.the result of 10% SDS-polyacrylamide gel electrophoresis.<br />
the expression of protein gas vesicle in E. coli JM109 analyzed by<br />
SDS-PAGE and quantitative measurement. Equal amount of sample<br />
from cell lysate was fractioned into the pellet and subjected<br />
to SDS-PAGE. 1 and 2 bands in pellet represent respectively the<br />
JM109 blank control and import GVP gene cluster strains.<br />
</p><br />
<br/><br/><br />
<a><img style="margin-left:100px;" src="https://static.igem.org/mediawiki/2012/b/b6/Ouc-project-gvp23.JPG" /></a><br />
<br/><br/><br />
<p style="text-align:center; font-size:90%;">Figure 29.The result of SDS-polyacrylamide gel electrophoresis. Lane 4 is top10 control group, lane 3 is constitutive GvpA and GFP generator, lane 5 is constitutive GvpC and GFP generator. The upper blue and red boxes are in the position about 26kDa are GFP protein (25.8kDa). The lower red box in the position of about 20kDa is GvpC-20 (20kDa).<br />
</p><br />
<br/><br />
<br/><br />
<p><span></span>Because the GvpA protein can’t be seen on the SDS-polyacrylamide gel electrophoresis, we wanted to use GFP to detect the expression of GvpA. We use a polycistron of gvpA (gvpC) and gfp to detect the RFU. We can see that, the RFU of Gvp and GFP Generator is about 2000, and the RFU of Gvp and GFP Generator is about 4000, while top 10 is about 0 as control. (Figure26)First, the RFU of these parts are rather high. Second, the E.Coli with these two plasmids can float. Third, we can see GvpC on the SDS-polyacrylamide gel. So, we can see the two parts can express Gvp Protein and work well.<br />
<br/><br />
<br/><br />
<a><img style="margin-left: 120px;" src="https://static.igem.org/mediawiki/2012/7/7d/Ouc-project-gvp24.JPG" /></a><br />
<br/><br />
<p style="margin-left:20px; margin-top:10px;margin-bottom:20px; font-size:90%;">Figure 30.We can see that, the RFU of Gvp and GFP Generator is about 2000, and the RFU of Gvp and GFP Generator is about 4000, while top 10 is about 0 as control. <br />
</p><br />
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Dolores
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2012-10-27T00:54:50Z
<p>Dolores: </p>
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Dolores