Team:UCSF/lily2

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Thanks a lot to the 2011 Brown-Stanford and 2012 Lethbridge iGEM teams for snippets of their code!
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Check out their wikis at:
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https://2011.igem.org/Team:Brown-Stanford
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https://2012.igem.org/Team:Lethbridge
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<!--Abstract-->
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  <div style="float:left;"><p style="font-size:45px;line-height:45px;color:#ffffff;margin:20px 3px 0 20px;">L</p></div>
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ight has created innumerable wonders in nature. Equipped with tools and methods in optogenetic research, scientists have also achieved some truly fascinating goals in a synthetic way. This year, 2012 Peking-ECUST iGEM utilized an ultra-sensitive engineered sensor of luminescence -- the <b style="color:#ffee55;"> <i>Luminesensor</i></b>. Amazingly, the <i>Luminesensor</i> was proven to be so sensitive as to be able to detect <b style="color:#ffee55;">natural light</b> and even <b style="color:#ffee55;">bioluminescence</b>. With this sensor, spatiotemporal control of cellular behavior, such as <b style="color:#ffee55;">high-resolution 2D</b> and <b style="color:#ffee55;">3D bio-printing</b> using dim light and even the <b style="color:#ffee55;">luminescence of iPad</b> were shown to be very easy. What’s more, we successfully implemented <b style="color:#ffee55;">cell-cell signaling using light</b> for the very first time in synthetic biology, which will be of great importance for biotechnological use.
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<h2><center>Operation CRISPR: Deploying precision guided tools to target unique species in a complex microbiome</h2></center>
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  </p>
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<p>In microbial communities, bacterial populations are commonly controlled using indiscriminate, broad range antibiotics. There are few ways to target specific strains effectively without disrupting the entire microbiome and local environment. The goal of our project is to take advantage of a natural horizontal gene transfer mechanism in bacteria to precisely affect gene expression in selected strains. We combine bacterial conjugation with CRISPRi, an RNAi-like repression system developed from bacteria, to regulate gene expression in targeted strains within a complex microbial community. One possible application is to selectively repress pathogenic genes in a microbiome, leaving the community makeup unaffected. In addition, we use CRISPRi to lay the groundwork for transferring large circuits that enable complex functionality and decision-making in cells. </p>
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<div class="floatL" style="margin:0 10px 5px 0;"><table class="title_block" style="background-image:url('/wiki/images/b/be/Peking2012_Color_Title_AquaBlue.jpg');"><tr><td style="height:244px;"><p style="font-size:36px;">Abstract</p></td></tr></table></div>
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  <div class="floatL"><table class="title_block" style="background-image:url('/wiki/images/a/a4/Peking2012_Color_Title_FlameYellow.jpg');"><tr><td><a href="/Team:Peking/Project/Luminesensor" style="font-size:26px;">Luminesensor</a></tr></td></table></div>
 
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Strongly motivated to open up a new era of optogenetics, our team has utilized an ultra-sensitive sensor which is engineered for sensing luminance – named by us <i>Luminesensor</i>, enabling highly efficient spatiotemporal control of biochemical process or cellular behavior. The whole job serves as a paradigm for sensor creating.
 
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  <div class="floatL"><table class="title_block" style="background-image:url('/wiki/images/a/a2/Peking2012_Color_Title_FreshGreen.jpg');"><tr><td><a href="/Team:Peking/Project/Communication" style="font-size:26px;">Light <br /> Communication</a></tr></td></table></div>
 
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The <i>Luminesensor</i> is able to respond to very low light and meanwhile keep a wide dynamic range, which encouraged us to explore the possibility of cell-cell communication through light. We have successfully implemented, for the very first time, light-communication among cells without direct physical contact.
 
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  <div class="floatL"><table class="title_block" style="background-image:url('/wiki/images/f/fe/Peking2012_Color_Title_GrapePurple.jpg');"><tr><td><a href="/Team:Peking/Project/3D">Syn Bio in <br /> 2D & 3D</a></tr></td></table></div>
 
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3D printing is a new technology that has been rising for many years. But in the realm of synthetic biology, it is far from developed. We exploited our <i>Luminesensor</i> to implement 3D printing that can be utilized in many medical or manufacturing applications.
 
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  <div class="floatL"><table class="title_block" style="background-image:url('/wiki/images/5/50/Peking2012_Color_Title_CherryPink.jpg');"><tr><td><a href="/Team:Peking/Project/Phototaxis">Phototaxis</a></tr></td></table></div>
 
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"Phototatic" bacteria can be built by programming the chemotaxis system in <i>E. coli</i> through light. By controlling the expression level of the CheZ protein with the <i>Luminesensor</i>, the tumbling frequency is coupled to the intensity of light signals.
 
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  <div class="floatL"><table class="title_block" style="background-image:url('/wiki/images/a/a2/Peking2012_Color_Title_FreshGreen.jpg');"><tr><td><a href="/Team:Peking/HumanPractice/Sowing">Human <br /> Practice</a></tr></td></table></div>
 
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We have done a remarkable job in motivating high school students to study synthetic biology and guiding them towards future participation in the iGEM high school division. Besides, we collaborated with a lab and helped four other iGEM teams by sharing DNA materials, characterizing their parts and modeling. Furthermore, we presented all fresh iGEMers with a collection of praise for historic iGEM projects.
 
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  <div class="floatL"><table class="title_block" style="background-image:url('/wiki/images/b/be/Peking2012_Color_Title_AquaBlue.jpg');"><tr><td><a href="/Team:Peking/Modeling">Modeling</a></tr></td></table></div>
 
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Excellent stochastic simulation was conducted to describe our ultrasensitive <i>Luminesensor</i>, combining protein kinetics and reaction thermodynamics. Molecular docking was also operated. What's more, while designing our photo-taxis model, we developed a hexagonal-coordinate environment for dynamic simulation of "on-plate" system. Those who focus on cell motility will find it useful and inspirational.   
 
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    <a href="http://www.bio.pku.edu.cn"><img src="/wiki/images/a/a8/Peking2012_Sponsor_SOS.jpg" alt="" style="width:266px;" /></a>
 
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  </td><td colspan="3">
 
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    <a href="http://cqb.pku.edu.cn"><img src="/wiki/images/f/f8/Peking2012_Sponsor_CQB.jpg" alt="" style="width:530px;"/></a>
 
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    <a href="http://dean.pku.edu.cn"><img src="/wiki/images/b/be/Peking2012_Sponsor_PkuEduAdministration.jpg" alt="" style="width:170px;"/></a>
 
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  </td><td>
 
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    <a href="http://www.genscript.com"><img src="/wiki/images/9/9b/Peking2012_Sponsor_GenScript.jpg" alt="" style="width:152px;"/></a>
 
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  </td><td>
 
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    <a href="http://www.scitech-youth.org.cn"><img src="/wiki/images/3/36/Peking2012_Sponsor_BeijingTeenagerST.jpg" alt="" style="width:170px;"/></a>
 
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<p class="blank" style="width:0;height:134px;">&#32;</p>
 
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                    <div><a href="https://2013.igem.org/Team:UCSF/About_Us">
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<img src="https://static.igem.org/mediawiki/2013/2/29/2013UCSF_MainBox_Team.jpg" class="blur"></a>
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                    <a href="https://2013.igem.org/Team:UCSF/About_Us"><h3>Team</h3></a>
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                    <p>Meet our dedicated team of under-graduates who conceived of, planned, and carried out the whole project.</p></a>
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              </td>
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<td>
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              <a href="https://2013.igem.org/Team:UCSF/Project/Background"><img src="https://static.igem.org/mediawiki/2013/c/c2/UCSF2013_MainBox_Project-1.jpg" class="blur"></a>
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              <a href="https://2013.igem.org/Team:UCSF/Project/Background"><h3>Project</h3></a>
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                    <p>Discover our precision guided tools to target unique species in a complex microbiome and our groundwork for transferring large circuits that enable complex functionality and decision-making in cells.</p>           
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                    <a href="https://2013.igem.org/Team:UCSF/Modeling">
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<img src="https://static.igem.org/mediawiki/2013/a/af/UCSF2013_MainBox_Modeling-1.jpg" class="blur" />
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<!--img src="https://static.igem.org/mediawiki/2013/9/97/UCD_2013_HO_Button.jpg" class="blur"--></a>
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                    <a href="https://2013.igem.org/Team:UCSF/Modeling"><h3>Modeling</h3></a>
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                    <p>Take a look at how we use mathematical modeling to facilitate the design and construct of our project.                    </p>
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              <a href="https://2013.igem.org/Team:UCSF/Exploratorium"><img src="https://static.igem.org/mediawiki/2013/7/7c/UCSF2013_MainBox_HP.jpg" class="blur"</a>
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              <a href="https://2013.igem.org/Team:UCSF/Exploratorium"><h3>Human Practice</h3></a>
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                    <p>Examine how we teach Synthetic Biology to the general public through night event at Exploratorium and to high school students through a collaboration with Lincoln High School.</p>
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<h2><center>Special Thanks to Our 2013 iGEM Team Sponsors!</h2></center>
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<center><img style="margin-bottom:0px; width: 500px; padding:2;"src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/Logos/2012%20Sponsors.jpg" usemap="#sponsor">
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              <area shape="rect" coords="180,95,495,200" href="http://www.synberc.org/" />
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Latest revision as of 19:15, 27 September 2013

UCSF Home

UCSF iGEM 2013 Group Photo
Brainstorming project ideas during our second week of Bootcamp
Presenting a poster at the UCSF Center for Systems and Synthetic Biology retreat
Having a skype meeting with one of our mentors!
Human Practices: Speaking about Synthetic Biology at the SF Exploratorium
Having fun outside of the lab making ice cream with dry ice

Operation CRISPR: Deploying precision guided tools to target unique species in a complex microbiome

In microbial communities, bacterial populations are commonly controlled using indiscriminate, broad range antibiotics. There are few ways to target specific strains effectively without disrupting the entire microbiome and local environment. The goal of our project is to take advantage of a natural horizontal gene transfer mechanism in bacteria to precisely affect gene expression in selected strains. We combine bacterial conjugation with CRISPRi, an RNAi-like repression system developed from bacteria, to regulate gene expression in targeted strains within a complex microbial community. One possible application is to selectively repress pathogenic genes in a microbiome, leaving the community makeup unaffected. In addition, we use CRISPRi to lay the groundwork for transferring large circuits that enable complex functionality and decision-making in cells.

Team

Meet our dedicated team of under-graduates who conceived of, planned, and carried out the whole project.

Project

Discover our precision guided tools to target unique species in a complex microbiome and our groundwork for transferring large circuits that enable complex functionality and decision-making in cells.

Modeling

Take a look at how we use mathematical modeling to facilitate the design and construct of our project.

Human Practice

Examine how we teach Synthetic Biology to the general public through night event at Exploratorium and to high school students through a collaboration with Lincoln High School.

Special Thanks to Our 2013 iGEM Team Sponsors!


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