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| − | <a href="https://2015.igem.org/"><img src="https://static.igem.org/mediawiki/2014/0/09/Aalto_Helsinki_Logov_iGEM.png" class="img-responsive igem-logo"></a>
| + | <img class="img-responsive center-block" src="https://static.igem.org/mediawiki/2015/4/4b/EPF_Lausanne_Home1.png" alt="First slide"> |
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| − | <h1>EPF Lausanne<br>
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| − | <small>Bio LOGIC</small></h1>
| + | |
| − | <!--<img src="https://static.igem.org/mediawiki/2014/d/dc/Aalto_Helsinki_Logov_Oma.png" class="img-responsive omalogo center-block" >--> | + | |
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| − | Single cell computing
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| − | <a href="#Abstract">
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| − | Scroll down to read more
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| − | </a>
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| − | | + | <img class="img-responsive center-block" src="https://static.igem.org/mediawiki/2015/4/4b/EPF_Lausanne_Home2.png" alt="Third slide"> |
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| − | <p class="transp"> | + | |
| − | <a href="http://i-see-faces.deviantart.com/">Photo © Tanja Maria</a>
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| − | <div class="link" id="Abstract"></div> | + | |
| − | <h2>EPF-Lausanne<br>
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| − | <small>An orthogonal complex system in a single cell</small></h2>
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| − | | + | |
| − | <h3>Project Description</h3>
| + | |
| − | <p>
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| − | Logic gates are the main components of every modern digital circuit. Digital circuits work with binary values that are either 0 or 1 and we can think of this values as representing a false or true state respectively; physically 0 and 1 (false or true), are represented by 0V or 5V. Logic gates are ‘’black boxes’’ that can take many binary inputs and gives generally one binary output. For example the NOT gate takes one binary input and invert it: if the input is 0 the output will be 1, while if the input is 1 the output will be 0. The NOT gate is one of the simplest logic gates we can imagine but many other gates with different functionalities exists. For example the AND gate takes two inputs and gives an output: the output is true (i.e. the output value is 1) if both the inputs are true, otherwise the output is false (i.e. the output value is 0). Another common example is the OR gate, which takes two inputs and gives an output: the output is false if both inputs are false, otherwise the output is true. By combining different logic gates in sequence and in parallel (each gate having its own characteristic truth table) it is possible to create digital circuits with complex behaviours.
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| − | </p>
| + | |
| − | <p>
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| − | The aim of our project, is to create a general framework allowing simple design of digital circuits inside living cells, using dCas9 proteins with specific gRNAs as activators or inhibitors of gene transcription.
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| − | </p>
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| − | <p>
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| − | Cas9 (CRISPR associated protein 9) is an RNA-guided DNA endonuclease enzyme which can target nearly any DNA sequence complementary to its guide RNA (gRNA). The original function of the CRISPR-Cas9 system in bacteria is to cleave foreign DNA after positive match. However, a dead version of Cas9 (dCas9) unable to cut the DNA can be used as a repressor (by preventing the binding of the RNA polymerase to promoter sequences) or as an activator (our dCas9 is fused with a a polymerase recruiting element).
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| − | </p>
| + | |
| − | | + | |
| − | <p>Our project relies on a three plasmids system. The first one will produce dCas9, another will gather gates acting like a gate array and the last one will act as a linker for the gates and can represent the programm.
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| − | </p>
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| − | <p>This modified Cas9 will form a complex with a chosen produced gRNA (guideRNA) that will allow the complex to complementary bind to the plasmids. That way dCas9 will induce the production of other gRNAs or inhibit them. The output of a gate would then be the production or not of gRNA that will go back to the linker that will induce also a gRNA to continue the program etc…
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| − | </p>
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| − | <!--<div class="row">
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| − | <a href="https://www.youtube.com/watch?v=Fa6qf7avM1s" target="_blank"><img src="https://static.igem.org/mediawiki/2014/7/79/Aaltohelsinki_pitc_capture.png" class="img-responsive smallerimg"></img></a>
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| − | <p class="kuvateksti">
| + | |
| − | Vidéo descriptive de Logic Gates ou dCas9?
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| − | </p>
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| | </div> | | </div> |
| − | </div>-->
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| − | <!--<img src="https://static.igem.org/mediawiki/2014/7/7e/Aalto_Helsinki_Logot_Oma.png" class="img-responsive center-block omalogot" >--> | + | <img class="img-responsive center-block" src="https://static.igem.org/mediawiki/ 2015/ 9/ 9b/ EPF_Lausanne_Home3.png" alt=" Fourth slide"> |
| − | | + | |
| − | </article>
| + | |
| − | <!--<article class="abg-pcb">
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| − | | + | |
| − | <h2>The Story of Aalto-Helsinki Bioworks</h2>
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| − | <div class="row">
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| − | <div class="col-md-6 text-col-left">
| + | |
| − | <p>
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| − | We are Aalto-Helsinki Bioworks, the first-ever Finnish iGEM Team and one of the four teams in the new Entrepreneurship Track. Our <a href="https://2014.igem.org/Team:Aalto-Helsinki/Team">team</a> consists of nine students from Aalto University and the University of Helsinki and we are combining our interdisciplinary forces to develop something new and fascinating. We want to put Finland on the map of synthetic biology and improve undergraduate research opportunities in our universities.
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| − | </p>
| + | |
| − | <p>
| + | |
| − | We have <a href="https://2014.igem.org/Team:Aalto-Helsinki/Research">designed</a> a three-channel gene switch that would make it possible to control three user-defined genes with blue light intensity. We are using <a href="https://2014.igem.org/Team:Aalto-Helsinki/Research#yf1-title">YF1</a> as our light receptor protein and the signal is mediated to lambda repressor protein (CI) production via phosphorylation pathway. The concentration of the CI protein defines the gene that should be active at a time. The secret behind this function is our modified version of the <a href="https://2014.igem.org/Team:Aalto-Helsinki/Research#lambda-title">lambda repressor</a> mechanism.
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| − | </p>
| + | |
| − | <p>
| + | |
| − | We constructed a mathematical <a href="https://2014.igem.org/Team:Aalto-Helsinki/Modeling">model</a> that simulates the interactions of the molecules and function of the gene switch we designed. This revealed interesting phenomena in the dynamics of our system which helps us to better understand the capabilities and limitations of the gene switch. We also made an <a href="http://igem-qsf.github.io/SimCircus/WebUI/">interactive simulation</a> available to everybody to best illustrate how our idea actually works.
| + | |
| − | </p>
| + | |
| − | <p>
| + | |
| − | To control the amount of blue light on our cell cultures, we created the <a href="https://2014.igem.org/Team:Aalto-Helsinki/Research#ledrig-title">LED rig</a> device. This enabled us to perform diverse experiments in order to characterize our light response element. These <a href="https://2014.igem.org/Team:Aalto-Helsinki/Research#Results">results</a> show that our light response element is able to regulate the downstream gene expression precisely. In addition, the response time is in a ten-minute-scale, which enables constant and nearly real-time control over bacterial cultures. In addition, we hypothesize that this system is also applicable to bioreactors, which would enable higher level of control in industrial bioprocesses. However, our fully functional prototype is still under ongoing development.
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| − | </p>
| + | |
| − | <p>
| + | |
| − | We have developed an open approach to <a href="https://2014.igem.org/Team:Aalto-Helsinki/Business">biotech business</a> inspired by the business models for open source software. Following the Open Source philosophy, we will distribute open Aalto-Helsinki Bioworks technologies for free to everybody - as long as they share the improvements made on the technology. Therefore, we empower our users to participate in product development. Our <a href="https://2014.igem.org/Team:Aalto-Helsinki/Business#canvas-title">business model</a> is based on hardware and wide range of services offered to our customers.
| + | |
| − | </p>
| + | |
| − | <p>
| + | |
| − | During the summer we participated in Aalto Entrepreneurship Society’s <a href="https://2014.igem.org/Team:Aalto-Helsinki/Business#Sos">Summer of Startups 2014</a> incubator programme to learn the essential entrepreneurial skills, such as pitching, investor relations, customer-driven development and <a href="https://2014.igem.org/Team:Aalto-Helsinki/Business#pitch-title">explaining</a> the science for general audience. See our Demo Day video for details.
| + | |
| − | </p>
| + | |
| − | <p>
| + | |
| − | iGEM is an international experience and as the first Finnish team, we went to find advice and experience around the globe. We contributed to the iGEM community by building a <a href="https://2014.igem.org/Team:Aalto-Helsinki/Cooperation#Seekers">BioBrick Seeker</a> tool which makes it easy to find parts of your interest in the 2014 BioBrick distribution. This tool has been used by iGEM teams all over the world! We also did a lot of <a href="https://2014.igem.org/Team:Aalto-Helsinki/Cooperation#Interteam">cooperation</a>, including filling out surveys and having skype conversations and live meetings with current and previous iGEM teams from France, Colombia, Switzerland, USA and the Netherlands. We even made a <a href="http://www.youtube.com/embed/icPgP3OOVOQ?rel=0">video</a> together with ETH Zürich team to Colombia team’s challenge.
| + | |
| − | </p>
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| − | <p>
| + | |
| − | We wanted to <a href="https://2014.igem.org/Team:Aalto-Helsinki/Outreach">raise awareness</a> about synthetic biology in Finland and also showcase researchers’ work to young people and undergraduate students. Therefore, we have been reaching out to general public, especially young people via <a href="https://2014.igem.org/Team:Aalto-Helsinki/Outreach#SoMe">social media</a>, including <a href="http://www.facebook.com/AaltoHelsinki">Facebook</a>, <a href="http://twitter.com/AaltoHelsinki">Twitter</a>, <a href="http://www.youtube.com/channel/UCEZliqjLu86CRpQlk57FfSw">Youtube</a>, <a href="http://www.flickr.com/photos/aaltohelsinki/">Flickr</a> and our own blog. We’ve shared stories, pictures, videos and experiences to our followers. In addition, we have been featured in radio interviews and articles on magazines and webzines. We also made a silly game: <a href="https://2014.igem.org/Team:Aalto-Helsinki/Flappycoli">Flappy Coli</a>. We have a public team webpage, <a href="http://2014.aaltohelsinki.com/">aaltohelsinki.com</a>, where you can find the latest stories of Aalto Helsinki also in the future. We lifted some of the highlights of this project on a <a href="https://2014.igem.org/Team:Aalto-Helsinki/Journal#Timeline">timeline</a>: the story of Aalto-Helsinki Bioworks is there for you to see!
| + | |
| − | </p>
| + | |
| − | </div>
| + | |
| − | <div class="col-md-6 img-100">
| + | |
| − | <img src="https://static.igem.org/mediawiki/2014/a/a2/Aalto_Helsinki_Banner.png" class="img-responsive">
| + | |
| − | </div>
| + | |
| − | </div>
| + | |
| − | | + | |
| − | | + | |
| − | </article>-->
| + | |
| − | <article>
| + | |
| − | | + | |
| − | <h2 class="kakspaddingbot">Accomplishments</h2>
| + | |
| − | <ul>
| + | |
| − | <li>Incoming</li>
| + | |
| − | </ul>
| + | |
| − | | + | |
| − | </article>
| + | |
| − | <article>
| + | |
| − | | + | |
| − | <h2>Categories</h2>
| + | |
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| − | <div class="row row-eq-height">
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| + | |
| − | <p class="feattext-p">
| + | |
| − | <big><big><big>Team</big></big></big><br>
| + | |
| − | We are a team of twelve students with a multicultural background.
| + | |
| − | </p>
| + | |
| − | </div>
| + | |
| | </div> | | </div> |
| − | </a>
| + | |
| − | </div>
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| + | |
| − | <p class="feattext-p">
| + | |
| − | <big><big><big>Business</big></big></big><br>
| + | |
| − | We explored the possibilities of biotech and synthetic biology business.
| + | |
| − | </p>
| + | |
| − | </div>
| + | |
| | </div> | | </div> |
| | + | </div> |
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| − | <p class="feattext-p">
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| − | <big><big><big>Research</big></big></big><br>
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| − | We engineered a three-channel switch that can be controlled with the intensity of blue light.
| |
| − | </p>
| |
| − | </div>
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| − | </div>
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| − | </a>
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| − | <big><big><big>Modeling</big></big></big><br>
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| − | We made mathematic models of the interactions behind our gene switch.
| |
| − | </p>
| |
| − | </div>
| |
| − | </div>
| |
| − | </a>
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| − | </div>
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| − | <div class="col-md-6 bg feat feat-right bg-cooperation">
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| − | <big><big><big>Cooperation</big></big></big><br>
| |
| − | We got to know other iGEM teams and developed tools for everyone to use.
| |
| − | </p>
| |
| − | </div>
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| − | </a>
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| − | <div class="row row-eq-height">
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| − | <big><big><big>Outreach</big></big></big><br>
| |
| − | We spread the word about iGEM and synthetic biology especially in Finland.
| |
| − | </p>
| |
| − | </div>
| |
| − | </div>
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| − | </a>
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| − | <p class="feattext-p">
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| − | <big><big><big>Journal</big></big></big><br>
| |
| − | We documented the project well.
| |
| − | </p>
| |
| − | </div>
| |
| − | </div>
| |
| − | </a>
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| − | </div>
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