Difference between revisions of "Team:Ain Shams-Egypt"

 
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<title>WATTS-APTAMER - UP_PRETORIA iGEM</title>
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<h1>Ain Shams-Egypt<br>
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<IMG SRC="https://static.igem.org/mediawiki/2016/e/e6/Ain_Shams-Egypt--Logo.png" width="50%">
<small> 2016 IGEM Team</small></h1>
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<h5 style="position:relative;top:-4em;">Targeting Circular RNA Deregulation In Hepatocellular carcinoma  </h5>
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Figuring out how to combine business with science.
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                Scroll down to read more
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            <a href="http://i-see-faces.deviantart.com/">Photo © Tanja Maria</a>
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<h2>Ain Shams-Egypt 2016 IGEM Team<br>
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<small>Hepatocellular Carcinoma And circular DNA</small></h2>
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<h3>Project Description</h3>
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Liver cancer in adult men is the fifth most frequently diagnosed cancer worldwide, and is the second leading cause of cancer-related death in the world. In adult women, it is the seventh most commonly diagnosed cancer and the sixth leading cause of cancer death.
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The burden has been increasing in Egypt with a doubling in incidence rates in the last 10 years, Egypt has a one of the highest incidence of in hepatocellular carcinoma (HCC) in the world
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Treatment options for HCC are limited and often inefficient. Anti-cancer therapy faces major challenges, particularly in terms of specificity of treatment. The ideal therapy would eradicate tumor cells selectively with minimum side effects on normal tissue
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So as a team that believes in synthetic biology we searched how could we help our community regarding this problem & we found that it’s been shown that circular RNA (circ.RNA) is associated with human cancers, & some studies have been reported in HCC. Circular RNA will be delivered as it is a new area of research with around 130 circular RNA sequence detected in HCC only less than 10% of these has been investigated and characterized through previous studies.
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Circular RNA is a type of RNA which, that forms a covalently closed continuous loop. This feature confers numerous properties to circular RNAs, many of which have only recently been identified. Circular RNAs have recently shown potential as gene regulators. Like many other alternative noncoding isoforms, the biological function of most circular RNAs are unclear, circular RNAs do not have 5' or 3' ends so they are resistant to exonuclease-mediated degradation and more stable than most linear RNAs in cells.
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We are using mammalian cells to see the expression of the circular RNA in the deregulated micro RNA environment of the cancer cells in tissue cultures, prove their role and detect if they can serve as a biomarker in HCC, Detect the relation between its expression levels and rate of progression and the possibility of using it as a potential novel target for the treatment of HCC.
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            <a href="http://youtu.be/tlc7MPY9SE8"><img src="https://static.igem.org/mediawiki/2014/7/79/Aaltohelsinki_pitc_capture.png" class="img-responsive smallerimg"></img></a>
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                Our pitch video on August 6th, Summer of Startups Demo Day.
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<h2>The Story of Aalto-Helsinki Bioworks</h2>
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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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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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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.
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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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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.
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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.
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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.
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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!
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<h2 class="kakspaddingbot">Accomplishments</h2>
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<li>Best undergraduate wiki 2014</li>
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<li>Poster</li>
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<li>Presentation at the Giant Jamboree in Boston</li>
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<li>Background research, design and the creation of a <a href="https://2014.igem.org/Team:Aalto-Helsinki/Research">Three-Channel Gene Switch</a></li>
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<li>Submission of <a href="https://2014.igem.org/Team:Aalto-Helsinki/Research#Parts">three new BioBricks and two new primers to the Registry</a></li>
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<li>Creation of <a href="https://2014.igem.org/Team:Aalto-Helsinki/Business#Plan">an Open Source business model and a business plan</a> for Synthetic Biology Entrepreneurship</li>
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<li>Logo and brand design</li>
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<li><a href="http://youtu.be/tlc7MPY9SE8">Pitch</a> to an audience of 1000+ people</li>
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<li>Participation in the <a href="https://2014.igem.org/Team:Aalto-Helsinki/Business#Sos">Summer of Startups</a>, a startup incubator program</li>
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<li>Connecting with <a href="https://2014.igem.org/Team:Aalto-Helsinki/Outreach">investors and general public</a></li>
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<li>Received 45 000€ in <a href="https://2014.igem.org/Team:Aalto-Helsinki/Team#Sponsors">funding</a></li>
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<li>Drawing attention <a href="https://2014.igem.org/Team:Aalto-Helsinki/Outreach#Media">in the media</a></li>
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<li>BioBrick and Team <a href="https://2014.igem.org/Team:Aalto-Helsinki/Cooperation#Seekers">Seekers</a></li>
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<li>Collaboration with other <a href="https://2014.igem.org/Team:Aalto-Helsinki/Cooperation#Interteam">iGEM teams</a></li>
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<li>Participation in the <a href="https://2014.igem.org/Team:Aalto-Helsinki/Cooperation#Interlab">Measurement Interlab Study</a></li>
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<h2>Categories</h2>
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Our wiki has seven different categories in addition to this main page. On each of them you can just scroll through the content until you're finished reading. Everything about the subject can be found on one page, additional material is provided when possible and pages discussing similar topics are linked to each other. A submenu will also appear when you start scrolling through the other pages: see the top of the page as you advance in the wiki!
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<big><big><big>Team</big></big></big><br>
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We are a team of nine Finnish students and we've gotten amazing support during this project.
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<video class="bgvid" preload="auto" loop="loop" autoplay="false" muted="muted" volume="0"><source src="https://static.igem.org/mediawiki/2016/e/e0/PretoriaUP_Okra_Seedling_Time_Lapse.webm" type="video/webm" responsive-src="https://2015.igem.org/Team:William_and_Mary/rubik_responsive.jpg"><source src="https://static.igem.org/mediawiki/2016/1/19/PretoriaUP_Okra_Seedling_Time_Lapse.mp4" type="video/mp4">Video not supported</video>
 
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We explored the possibilities of biotech and synthetic biology business.
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<p>Liver cancer in adult men is the fifth most frequently diagnosed cancer worldwide, and is the second leading cause of cancer-related death in the world. In adult women, it is the seventh most commonly diagnosed cancer and the sixth leading cause of cancer death.
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<p><a href="https://2016.igem.org/Team:Ain_Shams-Egypt/Description">Read more on our Project Description page.</a>
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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.
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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.
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<p>We would like to extend special thanks to the following organizations for their support:</p>
<big><big><big>Cooperation</big></big></big><br>
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We got to know other iGEM teams and developed tools for everyone to use.
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<a href="http://eu.idtdna.com/site"><IMG SRC="https://static.igem.org/mediawiki/2016/5/5e/IDT-Logo_pasteur.jpg" height=100px style="max-width:100%"></a>
We spread the word about iGEM and synthetic biology especially in Finland.
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<a href="http://i-see-faces.deviantart.com/">Photos © Tanja Maria</a>
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If you find yourself lost (or simply don't know where to start looking for what you'd want to find), <a href="https://static.igem.org/mediawiki/2014/7/73/Aalto_Helsinki_Wiki_Sitemap.png" target="_blank">here's a sitemap to help with the task</a>!
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                e2.setAttribute("href","#"+e.id);
+
                if (e2.innerHTML == "."){
+
                    e2.innerHTML = "Figure " + (index+1);
+
                } else {
+
                    e2.innerHTML = "figure " + (index+1);
+
                }
+
            });
+
            $.each($('span[ref="'+referenceName+'"]'), function(j, e2){
+
                e2.setAttribute("href","#"+e.id);
+
                if (e2.innerHTML == "."){
+
                    e2.innerHTML = "Figure " + (index+1);
+
                } else {
+
                    e2.innerHTML = "figure " + (index+1);
+
                }
+
            });
+
        }
+
    );
+
 
+
    // Table reference script
+
    /*
+
    USAGE:
+
    tag table with a tab that is connected to the table, such as:
+
    <table ref="intensities" />
+
    When you insert a reference in text, put a tag with a ref attribute:
+
    <a tab="intensities"></a>
+
    Do not put href attribute, it will be replaced with a link to the image.
+
    Moreover, inner html of the anchor tag will be "table x" where x is the
+
    correct table number. If span or anchor has "." as the inner html, the
+
    caption will be capitalized.
+
    */
+
    var tables = $('table[tab], img[tab]');
+
    $.each(tables, function(index, e){
+
            var tableName = e.getAttribute("tab");
+
            if (!e.id){
+
                e.setAttribute("id","table"+(index+1));
+
            }
+
            $.each($('a[tab="'+tableName+'"]'), function(j, e2){
+
                e2.setAttribute("href","#"+e.id);
+
                if (e2.innerHTML == "."){
+
                    e2.innerHTML = "Table " + (index+1);
+
                } else {
+
                    e2.innerHTML = "table " + (index+1);
+
                }
+
            });
+
            $.each($('span[tab="'+tableName+'"]'), function(j, e2){
+
                e2.setAttribute("href","#"+e.id);
+
                if (e2.innerHTML == "."){
+
                    e2.innerHTML = "Table " + (index+1);
+
                } else {
+
                    e2.innerHTML = "table " + (index+1);
+
                }
+
            });
+
        }
+
    );
+
</script>
+
 
</html>
 
</html>
 +
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Latest revision as of 03:57, 20 October 2016

WATTS-APTAMER - UP_PRETORIA iGEM

WATTS-APTAMER - UP_PRETORIA iGEM