Team:NCTU Formosa

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<div id="description" class="page" data-stellar-background-ratio="0.5"><div class="boxwrap" data-stellar-ratio="1.25"><div class="box"><div class="title">E.colightuner</div><span
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<div id="description" class="page" data-stellar-background-ratio="0.5"><div class="boxwrap" data-stellar-ratio="1.25"><div class="box"><div class="title"><div class="gear">NCTU_Formosa</div>E.colightuner</div><div class="team">a regulation system that does multitasking.</div><div class="wordbox"><p>Just like a smartphone that combines the functions of various devices, our genetically engineered machine can regulate multiple genes. It makes multiple genes regulation much more convenient, since it can competently regulate a number of genes in contrast to a traditional machine that controls only one gene. Such increase in convenience may ultimately decrease the cost for regulating multiple genes.</p>
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class="team">by NCTU_Formosa</span><div class="wordbox"><p>We have proven a sRNA-regulated system of our own to be an effective and competent way for regulating gene expressions. </p>
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<p>In order to build such a machine with multiple regulation, we have employed three regulated-systems, including small RNA regulated-system, light regulated-system, and temperature regulated-system, among which, small RNA regulated-system has not been widely applied to iGEM before. Although these regulated-systems may seem irrelevant, they actually form a bigger system that can precisely regulate the expression of each gene inside the system. As a matter of fact, they have created a highly potential system that can be expanded to regulate more genes than ever imagined. </p>
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<p>Recent studies have shown that sRNA-mediated regulation is an important factor to bacterial growth. sRNAs work by base pairing with limited or extended complementary target mRNAs, regulating protein productions. Using sRNA mechanism, we can control gene expression in RNA level, in contrast to common promoters that functions on DNA level. Since the existing sRNAs in Escherishia Coli have important functions in other metabolic processes, we designed an artificial sRNA with high specificity to avoid undesired base binding in vitro.</p>
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<p>By using the sRNA-regulated system, red light induced ooperator, and thirty seven degree Celsius ribosome binding site (RBS), we constructed a manipulatable system that is capable of expressing four different genes under different conditions. In other words, it is a multitask machine.</p></div></div></div></div>
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</div><div class="readmore"><span class="moret">See our project <i class="fa fa-arrow-circle-right"></i></span></div></div></div></div>
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<p class="bigtitle">Sitemap</p><p>Our wiki has 10 pages in total and each page contains several sections. There's a navigation bar sticking on the top of the page. When you want to get back to the top of the page, don't panic! Feel free to click the button on the left-bottom corner of the page anytime.</p>
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<div id="sec1" class="seclink"><a href="https://2013.igem.org/Team:NCTU_Formosa/project"><i class="icon-lightbulb"></i><p class="smalltitle">Project</p><p>A multiple regulated-system was built using three different regulation mechanisms including red light, temperature, and sRNA. In other words, it is multitasking genetic engineered machine that can express a variable genes depending on the different command given. </p></a></div>
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<div id="sec2" class="seclink"><a href="https://2013.igem.org/Team:NCTU_Formosa/results"><i class="fa fa-smile-o"></i><p class="smalltitle">Results</p><p>The current progress of our project, including detailed information of the experimental data and the overall evaluation of the practicability of this project. </p></a></div>
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<div id="sec3" class="seclink"><a href="https://2013.igem.org/Team:NCTU_Formosa/modeling"><i class="icon-bar-chart"></i><p class="smalltitle">Modeling</p><p>Modeling was our first step forward. When validated with our experimental data, modeling is also a verification of the accuracy of our experiments. </p></a></div>
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<div id="sec4" class="seclink"><a href="https://2013.igem.org/Team:NCTU_Formosa/biobricks"><i class="icon-puzzle-piece"></i><p class="smalltitle">Biobricks</p><p>To strive for the best results, we made a number of experiment. Our team always hang together in spite of many losses.</p></a></div>
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<div id="sec5" class="seclink"><a href="https://2013.igem.org/Team:NCTU_Formosa/notes"><i class="icon-pencil"></i><p class="smalltitle">Notes</p><p>The experimental log that records down the purpose, method, result and date of each experiment that we have conducted.</p></a></div>
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<div id="sec6" class="seclink"><a href="https://2013.igem.org/Team:NCTU_Formosa/human_practice"><i class="icon-magnet"></i><p class="smalltitle">Human Practice</p><p>This summer, we hosted a summer camp for high school students and held a conference for iGEMers. With these efforts, we have passed on our enthusiasm of synthetic biology to our peers and raise their interests on the topic. </p></a></div>
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<div id="sec7" class="seclink"><a href="https://2013.igem.org/Team:NCTU_Formosa/team"><i class="fa fa-group"></i> <p class="smalltitle">Team</p><p>Our team is a big family in which each member has well established tacit understanding with one another. We have 18 members, 13 advisers, and 2 professors. Perhaps, we share little in common, but all of us are willing to contribute to the successes of our team. </p></a></div>
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<div id="sec8" class="seclink"><a href="https://2013.igem.org/Team:NCTU_Formosa/safety"><i class="icon-lock"></i><p class="smalltitle">Safety</p><p>Inside a newly built, well-equipped laboratory, we conducted our experiment. Besides safety equipment, each member is well informed of the safety rules and emergency handling. </p></a></div>
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<div id="sec9" class="seclink"><a href="https://2013.igem.org/Team:NCTU_Formosa/achievement"><i class="fa fa-trophy"></i><p class="smalltitle">Achievement</p><p>We smile. We shed tears. We strive for the best. These are the little BIG things we have done.</p></a></div>
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<div id="social" class="page" data-stellar-background-ratio="0.5">
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<p class="bigtitle">Bringing back <span class="em">wiki</span> <span class="em2">the way what it was meant to be.</span></p>
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<p>The core value of wiki are the openness and its coeditable property. As people tried to beautify the pages, too often that the wiki becomes merely a work handled by one person. It digresses from the core value of wiki. Therefore, to bring back its role, we build a system not only <b>more user-friendly</b> and <b>eye-pleasing</b> but also <b>coeditable</b> and <b>smart</b>.</p>
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<p>We believe that wiki is a platform for the iGEMers and the future iGEMers.  It stands for sharing. It is meant for cooperation. It ought to be a stage that brings people together for knowledge and the value that lies with people.</p><div id="meritw" class="js-masonry" data-masonry-options='{ "columnWidth": 440, "itemSelector": ".merit" }'>
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<div class="cphoto"><img src="https://static.igem.org/mediawiki/2013/4/40/Nctu-wm1.png" width="420px"></div>
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<p class="smalltitle">Utilizing wiki markup language and BioBricks registry</p>
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<p>To layout the pages, the wiki site is often completely written by HTML rather than the expected wiki markup language. We believe that wiki language encourages users to be more involved into the project since it's easy to use. Thus, we build a website <b>letting users to edit contents by wiki language</b> but at the same time have a cleaner layout by HTML.</p>
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<p>What's more, for the <a href="https://2013.igem.org/Team:NCTU_Formosa/biobricks">Biobricks page</a>, the table is <b>directly fetched from the Biobrick Registry website</b>. Not only it gets timely updates when new parts are registered, but it intertwines wiki and part wiki into a unique iGEM-centric system.</p>
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<div class="merit">
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<div class="cphoto"><img src="https://static.igem.org/mediawiki/2013/c/ce/Nctu-wm2.png" width="420px"></div>
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<p class="smalltitle">Responsible design that re-layouts for different resolution</p>
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<p>Our wiki site implements a more modern method to create the layout. As the window size changes, <b>text reflows and layout rearranges accordingly</b>. It supports various screen size down from smartphones and up to computers. To be future-proof, it's <b>touch-friendly</b> and can even support large-width devices such as 4KTV!</p>
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<div class="cphoto"><img src="https://static.igem.org/mediawiki/2013/1/13/Nctu-wm3.png" width="420px"></div>
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<p class="smalltitle">Contents in wiki are easily editable</p>
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<p>When iGEMers log into 2013.igem.org, <b>"Edit" link for each sections appears automatically</b>. Users can click into specific section to modify it. The history log of the page (link located at the top of the screen) can <b>show the section modified and the user who modified it</b>. Since editing contents becomes so straight-forward, our team members edit it spontaneously. We believe the <b>coeditability suggests the spirit of cooperating and sharing</b>, which are what wiki ought to be and the reason why iGEM lets us show our project upon wiki. Please check out <a href="https://2013.igem.org/wiki/index.php?title=Team:NCTU_Formosa/project&action=history">the history log of our project page</a>.</p>
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<div class="cphoto"><img src="https://static.igem.org/mediawiki/2013/6/68/Nctu-wm4.png" width="420px"></div>
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<p class="smalltitle">User-friendly functions</p>
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<p>To elevate the user experience, we introduce a submenu that fix on the screen when scrolling though the page. It serves as a normal menu that links to each section. So what's special about it? It is so smart that it <b>shows the place we're currently browsing</b>, and the links to sub-section that collapsed at first will expand automatically.</p>
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<p>We also introduce <b>buttons for changing the font size</b> and a button that can back to the top of the page when page is scrolled down. This wiki is also <b>friendly for blind and visually impaired people</b> that use screen reading softwares. </p>
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<div class="cphoto"><img src="https://static.igem.org/mediawiki/2013/0/0e/Nctu-wm5.png" width="420px"></div>
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<p class="smalltitle">Auto-generated menu that powered by wiki system</p>
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<p>The submenus in our wiki are auto-generated by the Mediawiki system. Since we use the wiki markup language to <b>make our content a hierarchic structure</b>, the system can read our structure and generate a menu correspondingly. We took a step forward and made the menu even smarter. It can now collapse and expand <b>according to our mouse and the place we're browsing</b>. We believe that this is what a good customization should be.</p>
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<div class="merit">
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<div class="cphoto"><img src="https://static.igem.org/mediawiki/2013/5/56/Nctu-wm6.png" width="420px"></div>
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<p class="smalltitle">Following wiki requirements for iGEM 2013</p>
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<p>Our wiki follows <a href="https://2013.igem.org/Requirements/Wiki">the requirements</a> announced by iGEM. We understand that wiki serves as a resource for current and future iGEMers, so our code, images and files are all hosted on the 2013.igem.org server to prevent from data losing.</p>
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<p>Plus, we not only put the user editing menu on the top of the screen, <b>we also place the footer box</b> on the bottom of every page, including creative commons logo, mediawiki logo and some links, because these are useful information that shouldn't be hidden.</p>
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<div id="parchment" data-stellar-ratio="1.1"><a href="https://2013.igem.org/Team:NCTU_Formosa/project" title="Click in to know more about our project.">
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<p>E.colightuner</p>
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<p>Using sRNA, temperature and light, we want to construct a complicated regulation system.
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First, we took advantage of a powerful regulated molecules, sRNA. Bacterial small RNAs(sRNA) are small non-coding molecules, and they are highly structured and contain several stem-loops. sRNAs can either bind to protein targets, and modify the function of the bound protein , or bind to mRNA targets and regulate gene expression.
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Second, we used a Ribosome binding site which can sense change of temperature, 37oC RBS. Because this sequence has a unique secondary structure, it can’t function in room temperature. When temperature increasing, the secondary structure would change and can function.
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Third, we designed a new promoter, Pred. It is activated by red light. When removing the red light, it would be turned off, so we use this promoter to strengthen our project.
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  By these important factors, we can achieve the pathway regulation and do more applications.</p></a>
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    <p>2013 NCTU_Formosa</p>
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    <p class="author">Website designed by Calvin Hue.</p>
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    <p>Cover image credit: <a href="http://www.dvq.co.nz/" target="_blank">DVQ</a>, <a href="http://www.apple.com/" target="_blank">Apple Inc.</a></p>
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Latest revision as of 03:43, 27 October 2013

NCTU_Formosa
E.colightuner
a regulation system that does multitasking.

Just like a smartphone that combines the functions of various devices, our genetically engineered machine can regulate multiple genes. It makes multiple genes regulation much more convenient, since it can competently regulate a number of genes in contrast to a traditional machine that controls only one gene. Such increase in convenience may ultimately decrease the cost for regulating multiple genes.

In order to build such a machine with multiple regulation, we have employed three regulated-systems, including small RNA regulated-system, light regulated-system, and temperature regulated-system, among which, small RNA regulated-system has not been widely applied to iGEM before. Although these regulated-systems may seem irrelevant, they actually form a bigger system that can precisely regulate the expression of each gene inside the system. As a matter of fact, they have created a highly potential system that can be expanded to regulate more genes than ever imagined.

See our project

Sitemap

Our wiki has 10 pages in total and each page contains several sections. There's a navigation bar sticking on the top of the page. When you want to get back to the top of the page, don't panic! Feel free to click the button on the left-bottom corner of the page anytime.

Bringing back wiki the way what it was meant to be.

The core value of wiki are the openness and its coeditable property. As people tried to beautify the pages, too often that the wiki becomes merely a work handled by one person. It digresses from the core value of wiki. Therefore, to bring back its role, we build a system not only more user-friendly and eye-pleasing but also coeditable and smart.

We believe that wiki is a platform for the iGEMers and the future iGEMers. It stands for sharing. It is meant for cooperation. It ought to be a stage that brings people together for knowledge and the value that lies with people.

Utilizing wiki markup language and BioBricks registry

To layout the pages, the wiki site is often completely written by HTML rather than the expected wiki markup language. We believe that wiki language encourages users to be more involved into the project since it's easy to use. Thus, we build a website letting users to edit contents by wiki language but at the same time have a cleaner layout by HTML.

What's more, for the Biobricks page, the table is directly fetched from the Biobrick Registry website. Not only it gets timely updates when new parts are registered, but it intertwines wiki and part wiki into a unique iGEM-centric system.

Responsible design that re-layouts for different resolution

Our wiki site implements a more modern method to create the layout. As the window size changes, text reflows and layout rearranges accordingly. It supports various screen size down from smartphones and up to computers. To be future-proof, it's touch-friendly and can even support large-width devices such as 4KTV!

Contents in wiki are easily editable

When iGEMers log into 2013.igem.org, "Edit" link for each sections appears automatically. Users can click into specific section to modify it. The history log of the page (link located at the top of the screen) can show the section modified and the user who modified it. Since editing contents becomes so straight-forward, our team members edit it spontaneously. We believe the coeditability suggests the spirit of cooperating and sharing, which are what wiki ought to be and the reason why iGEM lets us show our project upon wiki. Please check out the history log of our project page.

User-friendly functions

To elevate the user experience, we introduce a submenu that fix on the screen when scrolling though the page. It serves as a normal menu that links to each section. So what's special about it? It is so smart that it shows the place we're currently browsing, and the links to sub-section that collapsed at first will expand automatically.

We also introduce buttons for changing the font size and a button that can back to the top of the page when page is scrolled down. This wiki is also friendly for blind and visually impaired people that use screen reading softwares.

Auto-generated menu that powered by wiki system

The submenus in our wiki are auto-generated by the Mediawiki system. Since we use the wiki markup language to make our content a hierarchic structure, the system can read our structure and generate a menu correspondingly. We took a step forward and made the menu even smarter. It can now collapse and expand according to our mouse and the place we're browsing. We believe that this is what a good customization should be.

Following wiki requirements for iGEM 2013

Our wiki follows the requirements announced by iGEM. We understand that wiki serves as a resource for current and future iGEMers, so our code, images and files are all hosted on the 2013.igem.org server to prevent from data losing.

Plus, we not only put the user editing menu on the top of the screen, we also place the footer box on the bottom of every page, including creative commons logo, mediawiki logo and some links, because these are useful information that shouldn't be hidden.

Retrieved from "http://2013.igem.org/Team:NCTU_Formosa"