Team:SJTU-BioX-Shanghai

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<li ><a href="/Team:SJTU-BioX-Shanghai/Project">Overview</a>
<li ><a href="/Team:SJTU-BioX-Shanghai/Project">Overview</a>
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<li ><a href="/Team:SJTU-BioX-Shanghai/Project/Luminous_device/Design">luminous device</a>
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<li ><a href="/Team:SJTU-BioX-Shanghai/Project/Luminous_device/Design">Luminous System</a>
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<li ><a href="/Team:SJTU-BioX-Shanghai/Project/Light_sensor/Red">Light sensor</a>
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<li ><a href="/Team:SJTU-BioX-Shanghai/Project/Light_sensor/Red">Light Sensors</a>
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<li ><a href="/Team:SJTU-BioX-Shanghai/Project/project/Design_criteria">Actuator</a>
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<li ><a href="/Team:SJTU-BioX-Shanghai/Project/Regulator/Design_criteria">Regulator-CRISPRi</a>
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<li ><a href="/Team:SJTU-BioX-Shanghai/Project">Feed back protocol</a>
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<li><a href="/Team:SJTU-BioX-Shanghai/Modeling">Modeling</a><li>
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<li><a href="/Team:SJTU-BioX-Shanghai/Modeling">Modeling</a>
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<li><a href="/Team:SJTU-BioX-Shanghai/Modeling/Light_sensor_characteristic">Light sensor characteristic</a></li>
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<li><a href="/Team:SJTU-BioX-Shanghai/Modeling/Report_gene_prediction">Report gene prediction</a></li>
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<li><a href="/Team:SJTU-BioX-Shanghai/Modeling/Metabolize_optimization">Metabolize optimization</a></li>
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<li><a href="/Team:SJTU-BioX-Shanghai/Parts">Parts</a></li>
<li><a href="/Team:SJTU-BioX-Shanghai/Parts">Parts</a></li>
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<li><a href="/Team:SJTU-BioX-Shanghai/Prospect/CRISPRi-on">Prospect</a>
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<li><a href="/Team:SJTU-BioX-Shanghai/Prospect/CRISPRi-on">CRISPRi-on</a></li>
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<li><a href="/Team:SJTU-BioX-Shanghai/Prospect/Smaller_light_sensors">Samaller Light Sensor</a></li>
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<li><a href="/Team:SJTU-BioX-Shanghai/Prospect/Absolutely_automatic">Absolutely Automatic</a></li>
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<li><a href="/Team:SJTU-BioX-Shanghai/Team">Team</a>
<li><a href="/Team:SJTU-BioX-Shanghai/Team">Team</a>
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<li><a href="/Team:SJTU-BioX-Shanghai/Team">Members</a></li>
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<li><a href="/Team:SJTU-BioX-Shanghai/Team/members">Members</a></li>
<li><a href="/Team:SJTU-BioX-Shanghai/Team">Attributions</a></li>
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<li><a href="/Team:SJTU-BioX-Shanghai/Notebook/protocol">Notebook</a>
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<li><a href="/Team:SJTU-BioX-Shanghai/protocol">Protocol</a>
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<li><a href="/Team:SJTU-BioX-Shanghai/Notebook/protocol">Protocol</a>
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<li><a href="/Team:SJTU-BioX-Shanghai/Notebook/protocol">Lablog</a>
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<li><a href="/Team:SJTU-BioX-Shanghai/Notebook/Lab_log/July">Lablog</a>
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<li><a href="/Team:SJTU-BioX-Shanghai/Consideration/human">Human Practice</a></li>
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<li><a href="/Team:SJTU-BioX-Shanghai/Consideration/human">Human Practice</a>
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<ul><li><a href="/Team:SJTU-BioX-Shanghai/Consideration/human">BioCraft</a></li>
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<li><a href="/Team:SJTU-BioX-Shanghai/Consideration/human/CC">Communications on Campus</a></li>
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<li><a href="/Team:SJTU-BioX-Shanghai/Consideration/human/RSB">Reserch on Synthetic Biology</a></li>
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<li><a href="/Team:SJTU-BioX-Shanghai/Consideration/human/Cooperation">Cooperation</a></li>
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<li><a href="/Team:SJTU-BioX-Shanghai/Consideration/safety">Safety</a></li>
<li><a href="/Team:SJTU-BioX-Shanghai/Consideration/safety">Safety</a></li>
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<div id="abstract-title"><p><strong style="color:rgb(255,102,102); font-size:60px;">A</strong>bstract</p></div>
<div id="abstract-title"><p><strong style="color:rgb(255,102,102); font-size:60px;">A</strong>bstract</p></div>
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<p>Few researches have been done to regulate gene expression levels in genomic scale so far. This year we aim to combine two systems together in order to provide a universal and convenient tool which can be used to regulate different genomic genes simultaneously and independently in a quantitative way. </p>
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<p>How to regulate an <strong>entire metabolic pathway</strong> <font style="font-style:italic;">in vivo</font>, delicately, <strong>accurately and conveniently</strong>, simultaneously controlling the expression of <strong>several</strong> genes? And how to <strong>optimize metabolic fluxes so as to maximize desired products</strong>? For decades, these questions remain haunting to “bioengineers”(especially synthetic biologists) who would like to have certain metabolites produced in live cells. The difficulty is again raised up when target genes endogenously reside on the <strong>genome</strong>, or have been implemented into the genome.</p>
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<p>Our project involves the newly developed gene regulating tool CRISPRi and three light-controlled expression systems induced by red, green, and blue light respectively. Simply by changing the regulating parts in CRISPRi system towards mRFP, luciferase, and three enzymes, we hope to prove our system can be used qualitatively, quantitatively and practically step by step. </p>
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<p>So this year, our team, SJTU-BioX-Shanghai, is dedicated to solve the problem. By integrating <strong>CRISPRi</strong>, the newly developed expression interference tool, with three <strong>light sensors</strong> (namely <font color=red>red light sensor</font>, <font color=green>green light sensor</font> and <font color=blue>blue light sensor</font>), we expect to provide a <strong>versatile</strong> platform on which researchers are able to quantitatively adjust the expression of any three enzymes in whatever pathway – to <strong>change the target, simply change the small guide RNA</strong> (sgRNA)!</p>
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<p>We have also designed a box and written a software as our experiment measurements. Simply by typing in several parameters, different gene expression levels can be controlled. This system can also be improved to predict the maximized producing efficiency after some simple tests in future. </p>
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<p>In addition, with the <strong>luminous device and accompanying software</strong>, one could simply enter metabolomics data (catalytic rates of related enzymes) into our User Interface. The software will automatically conduct <strong>flux balance analysis (FBA)</strong>, giving out suggestions for optimal expression value of different enzymes. Then, the expression value would be converted into <strong>intensity of lights</strong> that are finally to be exerted on cell cultures. It is -- just convenient! :)</p>
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                                 <p>Luminous Device provide us a tool to easily adjust genetic expression. With this tool, we can also regulate 3 genes at the same time.</p>
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                                 <p>Luminous System provide us a fascinating tool to adjust expression </p>
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                                 <p>Use date collected from experiments, we can optimize the metabolic system after several circles.</p>
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<div id="achievements-title"><p><strong style="color:rgb(102,102,255); font-size:60px;">A</strong>chievements</p></div>
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<p><strong><img src="/wiki/images/7/73/12SJTU_r.png"><font face="Cambria, serif " size="4"> The honors we won:</font></strong> Gold Medal, Best New BioBrick Part or Device Engineered (BBa_K771001) and Regional Winner at Asia Jamboree; Advanced to World Championship.</p>
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<p><strong><font face="Wingdings " size="4">ü</font><font face="Cambria, serif " size="4"> The breakthrough we made:</font></strong> Redefinition of scaffold in Synthetic Biology by recruiting <i>E.coli’</i>s inner membrane as a natural two-dimensional scaffold. </p>
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<p><strong><img src="/wiki/images/7/73/12SJTU_r.png"><font face="Cambria, serif " size="4"><font face="Wingdings " size="4"></font><font face="Cambria, serif " size="4"> The breakthrough we made:</font></strong> Redefinition of scaffold in Synthetic Biology by recruiting <i>E.coli’</i>s inner membrane as a natural two-dimensional scaffold. </p>
<p><strong><font face="Wingdings " size="4">ü</font><font face="Cambria, serif " size="4"> The system we built:</font></strong> 6 membrane proteins orderly organized on the inner membrane of <i>E.coli</i>, the efficiency of which has been proved by fluorescence complementation assay and biosynthesis experiment.</p>
<p><strong><font face="Wingdings " size="4">ü</font><font face="Cambria, serif " size="4"> The system we built:</font></strong> 6 membrane proteins orderly organized on the inner membrane of <i>E.coli</i>, the efficiency of which has been proved by fluorescence complementation assay and biosynthesis experiment.</p>
<p><strong><font face="Wingdings " size="4">ü</font><font face="Cambria, serif " size="4"> The device we created – Membrane Accelerator:</font></strong> A universal tool that serves to accelerate biochemical reactions in <i>E.coli</i>; Rate of fatty acids synthesis was increased by 24 fold compared to wild-type <i>E.coli </i>and 9 fold compared to that with overexpressed cytoplasmic enzymes.</p>
<p><strong><font face="Wingdings " size="4">ü</font><font face="Cambria, serif " size="4"> The device we created – Membrane Accelerator:</font></strong> A universal tool that serves to accelerate biochemical reactions in <i>E.coli</i>; Rate of fatty acids synthesis was increased by 24 fold compared to wild-type <i>E.coli </i>and 9 fold compared to that with overexpressed cytoplasmic enzymes.</p>
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<div align="center" id="footer"> (c)  <a href="" target="_self">SJTU_BioX_iGEM2012</a> Powered by huanan1991</div>
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<div align="center" id="footer"> (c)  <a href="" target="_self">SJTU_BioX_iGEM2013</a> Powered by LukeLiu</div>
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Revision as of 19:17, 27 September 2013

'Bold text'

Abstract

How to regulate an entire metabolic pathway in vivo, delicately, accurately and conveniently, simultaneously controlling the expression of several genes? And how to optimize metabolic fluxes so as to maximize desired products? For decades, these questions remain haunting to “bioengineers”(especially synthetic biologists) who would like to have certain metabolites produced in live cells. The difficulty is again raised up when target genes endogenously reside on the genome, or have been implemented into the genome.

So this year, our team, SJTU-BioX-Shanghai, is dedicated to solve the problem. By integrating CRISPRi, the newly developed expression interference tool, with three light sensors (namely red light sensor, green light sensor and blue light sensor), we expect to provide a versatile platform on which researchers are able to quantitatively adjust the expression of any three enzymes in whatever pathway – to change the target, simply change the small guide RNA (sgRNA)!

In addition, with the luminous device and accompanying software, one could simply enter metabolomics data (catalytic rates of related enzymes) into our User Interface. The software will automatically conduct flux balance analysis (FBA), giving out suggestions for optimal expression value of different enzymes. Then, the expression value would be converted into intensity of lights that are finally to be exerted on cell cultures. It is -- just convenient! :)

Luminous System provide us a fascinating tool to adjust expression

Achievements

The breakthrough we made: Redefinition of scaffold in Synthetic Biology by recruiting E.coli’s inner membrane as a natural two-dimensional scaffold.

ü The system we built: 6 membrane proteins orderly organized on the inner membrane of E.coli, the efficiency of which has been proved by fluorescence complementation assay and biosynthesis experiment.

ü The device we created – Membrane Accelerator: A universal tool that serves to accelerate biochemical reactions in E.coli; Rate of fatty acids synthesis was increased by 24 fold compared to wild-type E.coli and 9 fold compared to that with overexpressed cytoplasmic enzymes.

ü device we created – Membrane Rudder: A universal tool used to dynamically and artificially control biochemical reactions in E.coli; the direction of Violacein and Deoxyviolacein synthetic pathway was successfully switched.

ü New direction we proposed: The application of scaffold system in accelerating biodegradation pathway using our Membrane Accelerator.

ü Parts we submitted: 42 well-characterized parts that could either be used directly or serve as a universal tool readily for potential scientific or engineering use.

ü A club we established – BioCraft: The headquarter of our human practice programs, having come a long way in propagandizing Synthetic Biology and iGEM. Warmly-received activities have been held in and outside the campus. Several celebrities in different fields have shown support for us, laying a cornerstone for our future development.

Sponsors


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