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| | + | Human Practices |
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| | + | <button class="tablinks" onclick="openTab(event, 'High School Workshop')" id="defaultOpen">High School Workshop</button> |
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| − | text-align: left;
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| + | <div id="High School Workshop" class="tabcontent"> |
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| + | <article> |
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| + | |
| − | /*this above textalig is only for the homepage*/
| + | |
| | | | |
| − | }
| + | |
| | + | <p class="section-content"> |
| | + | The NYUAD iGEM team invited high school students and teachers from Brighton College in Abu Dhabi, UAE, to experience an iGEM research environment. This one-day workshop provided the students with the opportunity to channel their interest in both biology and engineering. This is the first high school workshop that is tailored towards exposing talented high school students to iGEM in the UAE, and future NYU Abu Dhabi iGEM teams will continue hosting this workshop for students in and around Abu Dhabi. All of the materials we used are provided below. |
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| | + | </div> |
| | + | </div> |
| | + | <br> |
| | + | <p class="section-content"> |
| | + | The workshop was kicked off by a presentation on iGEM and emphasized how the students can get involved by potentially joining future NYUAD teams or by creating their own team. Throughout this presentation, the students also learned the important connection between biology and engineering in the context of iGEM and the field of synthetic biology. This presentation was followed by the first workshop of the day: <i>GLO, Bacteria, GLO</i>, which taught the students how to transform pGLO DNA into DH5α <i>E. coli</i> using the heat shock method. The NYUAD team walked them through basic laboratory techniques including, lab safety, basic pipetting techniques and bacterial transformation, which is integral to an iGEM team’s success. The students then experienced the engineering environment through the second workshop <i>Arduino + LED</i>, which taught the students how to integrate many elements to create a device that included interactive design, programming, and circuitry. The students learned the basics of programming and circuit design by creating their own simple circuit using LEDs and Arduino, an open source electronic platform. After completing the workshop, the students also received a copy of the NYUAD team’s magazine <i>Synthetic Biology 101</i> as a source for further information about recent advances in synthetic biology. |
| | + | </p> |
| | + | <p class="section-content"> |
| | + | The NYUAD team is proud to have pioneered the first iGEM-specific workshop for high school students in the UAE. The workshop achieved the original aim of propagating the impact of iGEM in the region and encouraging interest in scientific research among high school students. In the future, the NYUAD team envisions similar workshops that can reach a larger audience in the UAE. |
| | + | </p> |
| | | | |
| | + | <p class="section-content"> |
| | + | For further details, please download our <a href="https://static.igem.org/mediawiki/2017/c/c2/Hsworkshop_ppt.pdf">powerpoint slides</a> and the <a href="https://static.igem.org/mediawiki/2017/a/a9/Hswkshpcode.pdf">protocols</a> we used for both engineering and biology workshops. |
| | + | </p> |
| | + | </article> |
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| | | | |
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| + | <p class="section-content">NYUAD iGEM team wrote and printed <i>Synthetic Biology 101</i>, a magazine on synthetic biology that deals not only with an overview of synthetic biology, but also a variety of topics ranging from iGEM competition, importance of food safety, NYUAD iGEM team project in 2017, and many more. We distributed the magazine personally to people who participated in our various human practices activities. The pdf version of our magazine was also shared online.</p> |
| − | background-image: url(https://static.igem.org/mediawiki/2017/5/5c/T--NYU_Abu_Dhabi--group2.jpg);
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| − | home-bg{
| + | One Saturday evening, inspired by a TED talk that he recently watched on iGEM, a student from NYU New York emailed us,<i> How can I start my own iGEM team?</i>. For a freshman minoring in genetics, iGEM must have seemed like Disneyland; a Jamboree of 4000 outstanding minds, representing 300 teams from five different continents, all gathered at the same place to share what they’ve accomplished in the past year. Moreover, when we hosted a <a href="https://2017.igem.org/Team:NYU_Abu_Dhabi/Engagement"> high school workshop </a> with students and teachers from Brighton College Abu Dhabi, we sensed a great interest from them in iGEM. What is the best advice we can give these potential iGEM participants? |
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| | | | |
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| + | Firstly, it should be noted that this competition is open to a diverse group of educational institutions. iGEM reunites synthetic biology enthusiasts all the way from the high school level up to graduate students and researchers. This mixture of people of varying expertise on this interdisciplinary field provides a perfect opportunity to learn from one another. A high school or an undergraduate student who is starting to learn about synthetic biology and desires to start an iGEM team should reach out to faculty or researchers who work in this field in order to obtain helpful guidance. Nonetheless, if an institution does not count with a group specifically dedicated to synthetic biology, it is still perfectly possible to participate. In this case, biology and engineering faculty can act as mentors. |
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| − | a:visited { | + | Another important aspect to take into account is funding. Despite research in STEM generally requires access to costly equipment, reagents, and facilities, iGEM teams with heterogeneous access to resources have participated successfully in the competition. A concrete example of a team with scarce resources who succeeded at the Giant Jamboree is <a href="https://2014.igem.org/Team:Sumbawagen"> Team Sumbawagen </a>, who did not have access to a key piece of equipment for their project, but still worked hard in order to solve a significant issue of their community. Collaboration with other teams is key to overcome problems as the one Team Sumbawagen experienced; other institutions may have the required resources to test parts or perform other experiments for another group. |
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| + | Of course, one of the most important parts of starting an iGEM team is having a good idea for a project. iGEM enthusiasts need to think about this carefully: what problem that affects a given community, large or small, can they solve by applying synthetic biology concepts? A large amount of research needs to go into how the project will impact everyone involved and the environment. Working closely with those who the project aims to benefit will help to understand what are their needs and how they should be addressed. |
| − | }
| + | </p> |
| | | | |
| − | | + | <p class="section-content"> |
| − | #top-section {
| + | What’s next? Apply on behalf of your school for the contest, come up with a cool project idea involving Biobricks, keep dedications high, and take it a step further to Boston to show the world what you’ve accomplished! |
| − | border: none;
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| + | <div id=" La La LAMP" class=" tabcontent"> |
| − | | + | <article> |
| − | <!-- NAVIGATION -->
| + | <h2 class="section-header">Overview</h2> |
| − | <nav role="navigation">
| + | <p class="section-content"> Our portable device enables users to detect the impurities in their food on-the-go. The WHO estimated that 1 in 10 individuals are affected by foodborne diseases globally each year. We have developed <i>La La LAMP</i>, a program which allows individuals to record and share their device results. Each experiment can be recorded by scanning its unique QR code, which is provided on the PDMS chip. We envision that this information sharing would enable scientists and researchers to better track trends in food safety, as well as enable the general public to take control of their food safety wherever they are in the world. |
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| − | <li><a class="page-link" href="#labnotebook" style="color: white;">Lab Notebook<i class="fa fa-pencil"></i></a></li>
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| − | <div class="copyright" style="color: white;">Connect with us on <a href="https://www.facebook.com/iGEMNYUAD/">Facebook</a><br>
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| − | Or email us at nyuad.igem@nyu.edu</div>
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| − | <h3><span class="color-default">स्वागतम्</span></h3>
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| − | <h3><font face="Helvetica" color="red">Welcome</font></h3>
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| − | <h3><font face="Helvetica" color="blue">Hola!</font></h3>
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| − | <h3> <font face="Helvetica" color="orange">Bonjour</font></h3>
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| − | <div class="pw1"> | + | <h2 class="section-header">Installation Manual</h2> |
| − | <img src="https://static.igem.org/mediawiki/2017/a/a3/T--NYU_Abu_Dhabi--logo1.png" height=600 width=600 align="middle">
| + | <p class="section-content"> |
| − | <br><br><br><br>
| + | <div class="shadow-bottom"> |
| − | <div class="page-head">Project Description</div>
| + | <div id="pdf"> |
| − | <div class="page-bodyy"><p>The most common type of bacterial infection stems from contact with Escherichia coli, which when ingested can cause a variety of symptoms ranging from nausea to diarrhea.
| + | <object data="https://static.igem.org/mediawiki/2017/7/7a/Nyuad_application_manual.pdf#toolbar=1&navpanes=0&scrollbar=1&page=1&view=FitH" |
| − | Shiga toxin-producing E. coli (STECs) are responsible for the majority of foodborne E. coli infections because the shiga toxin produced inhibits protein synthesis in all cells.
| + | type="application/pdf" |
| − | While most countries now have stringent food safety regulations in place to prevent the sale of contaminated foods, small scale manufacturers, particularly street food vendors, often do not have access, time or pressure to consult laboratories about the safety of their food.
| + | width="100%" |
| − | Therefore, STEC-illnesses are still a major problem in countries that revolve around street food.</p>
| + | position: fixed; |
| − | <p>Our project aims to produce a portable device that allows for the detection of STEC through the use of loop-mediated isothermal amplification (LAMP), a technique that is similar to, but more sensitive than, polymerase chain reaction (PCR). The end goal of our project is to provide food vendors an opportunity to easily and quickly detect for the presence of STEC in their products to ensure that they are complying with government standards efficiently and conveniently. The results of each test will be uploaded into a database that provides consumers with the date, location and result of each STEC test. This will ensure that both vendor and consumer are safe, leading to a decreased incidence of foodborne E.coli infections.</p>
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| | </div> | | </div> |
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| | + | </p> |
| | + | <h2 class="section-header">Changelog</h2> |
| | + | <p class="section-content">The base starting file, which is also available on the first link below, is <b>Beta 3</b>. In Beta 4, users can now check the database of their previous logfile simply by uploading it to the application. The application with display all results in a rich textbox format. This version is available in the second link below.</p> |
| | + | <h2 class="section-header">Download</h2> |
| | + | <p class="section-content"> [External] You can download the beta version of our app <b>[Beta 3]</b> via this <a href="https://drive.google.com/file/d/0B1a_uY3cfYrDTUpiQklpMGlNYkk/view?usp=sharing">link.</a><br> Also, latest updates to the app will be periodically added <a href="https://drive.google.com/open?id=0BwQJfFRaPiBJMUFTLUZQRDlxZ0k">here.</a> <br>We highly encourage you to download the latest beta files from the <b>second</b> link, as we'll periodically keep updating it. Future changelogs will also be added there. |
| | + | </p> |
| | + | <h2 class="section-header">Future Directions and Goals</h2> |
| | + | <p class="section-content"> We envision our program to be accessible on mobile devices (iOS/Android). To this regard, we are working to export the records to a more navigable datasheet that can be categorized according to time, location, and other variables and accessed via the Cloud. |
| | + | </p> |
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| − | </section>
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| − | | + | |
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| − | <div class="col-lg-10 col-lg-offset-1">
| + | |
| − | <br><br><br><br><br><br><br><br><br>
| + | |
| − | <div class="fancy">Meet the team.</div>
| + | |
| − | <br><br><br><br><br><br><br><br><br><br><br><br>
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| − | <img src="https://static.igem.org/mediawiki/2017/6/66/T--NYU_Abu_Dhabi--adrienne.jpg" class="img-responsive center-block" alt=""> | + | |
| | </div> | | </div> |
| − | <div class="col-md-6 col-box bg-gray-light">
| + | |
| − | <div class="page-header">
| + | |
| − | <h3 class="page-head">Adrienne Chang</h3>
| + | |
| − | </div>
| + | |
| − | <p style="text-align:left">
| + | |
| − | Major: Chemistry (Biochemistry)<br>
| + | |
| − | Year: 2018 <br>
| + | |
| − | Where are you from: US/Taiwan <br>
| + | |
| − | Something interesting about yourself: My spirit animal is a sloth. <br>
| + | |
| − | Why do you want to participate in iGEM? I’ve always been interested in engineering and was curious to see how I could combine both passions.
| + | |
| − | </p>
| + | |
| | </div> | | </div> |
| − | </div><!-- .row -->
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| − | <h3 class="page-head">Alex Cho</h3>
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| − | <p style="text-align:left">
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| − | Major: Biology<br>
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| − | Year: 2020 <br>
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| − | Where are you from: South Korea <br>
| |
| − | Something interesting about yourself: I’m a South Korean soldier next year. <br>
| |
| − | Why do you want to participate in iGEM? You don’t say no to these things.
| |
| − | </p>
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| − | </div>
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| − | <div class="col-md-6 no-padding">
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| − | <img src="https://static.igem.org/mediawiki/2017/8/8f/T--NYU_Abu_Dhabi--alex.jpg" class="img-responsive center-block" alt="">
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| − | <img src="https://static.igem.org/mediawiki/2017/5/52/T--NYU_Abu_Dhabi--diego.jpg" class="img-responsive center-block" alt="">
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| − | </div>
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| − | <div class="col-md-6 col-box bg-gray-light">
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| − | <div class="page-header">
| |
| − | <h3 class="page-head">Diego Kleiman</h3>
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| − | </div>
| |
| − | <p style="text-align:left">
| |
| − | Major: Biology<br>
| |
| − | Year: 2020 <br>
| |
| − | Where are you from: Argentina <br>
| |
| − | Something interesting about yourself: I am interested in exploring what can be learnt at the interface between biology and other disciplines. <br>
| |
| − | Why do you want to participate in iGEM? I think that iGEM is a great opportunity to develop an interdisciplinary project that draws upon biological knowledge to solve a real-world problem.
| |
| − | </p>
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| − | </div>
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| − | <h3 class="page-head">Fathurur Said</h3>
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| − | </div>
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| − | <p style="text-align:left">
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| − | Major: Electrical Engineering<br>
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| − | Year: 2019 <br>
| |
| − | Where are you from: Indonesia <br>
| |
| − | Something interesting about yourself: I was 5 days away from getting struck by Tsunami.<br>
| |
| − | Why do you want to participate in iGEM? Who says engineers can’t join a Biology competition?
| |
| − | </p>
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| − | </div>
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| − | <div class="col-md-6 no-padding">
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| − | <img src="https://static.igem.org/mediawiki/2017/3/3c/T--NYU_Abu_Dhabi--said.jpg" class="img-responsive center-block" alt="">
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| − | <img src="https://static.igem.org/mediawiki/2017/0/0c/T--NYU_Abu_Dhabi--nisa.jpg" class="img-responsive center-block" alt="">
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| − | <div class="col-md-6 col-box bg-gray-light">
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| − | <div class="page-header">
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| − | <h3 class="page-head">Khairunnisa Mentari Semesta</h3>
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| − | </div>
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| − | <p style="text-align:left">
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| − | Major: Biology<br>
| |
| − | Year: 2018<br>
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| − | Where are you from: Indonesia <br>
| |
| − | Something interesting about yourself: In my life I’ve survived multiple earthquakes and volcanic eruptions… #Indonesian<br>
| |
| − | Why do you want to participate in iGEM? My synthetic biology class introduced me to iGEM - I couldn’t wait to get hands-on experience in my final year!
| |
| − | </p>
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| − | </div>
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| − | </div><!-- .row -->
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| | | | |
| − | <br> | + | <script> |
| − | <!-- image & text -->
| + | function openTab(evt, header) { |
| − | <div class="row">
| + | var i, tabcontent, tablinks; |
| − | <div class="col-md-6 col-box bg-gray-light">
| + | tabcontent = document.getElementsByClassName("tabcontent"); |
| − | <div class="page-header"> | + | for (i = 0; i < tabcontent.length; i++) { |
| − | <h3 class="page-head">Laura Karpauskaite</h3> | + | tabcontent[i].style.display = "none"; |
| − | </div>
| + | } |
| − | <p style="text-align:left">
| + | tablinks = document.getElementsByClassName("tablinks"); |
| − | Major: Biology<br>
| + | for (i = 0; i < tablinks.length; i++) { |
| − | Year: 2020 <br>
| + | tablinks[i].className = tablinks[i].className.replace(" active", ""); |
| − | Where are you from: Lithuania<br>
| + | } |
| − | Something interesting about yourself: Went to a 30km cross-country skiing marathon without knowing how to ski.<br>
| + | document.getElementById(header).style.display = "block"; |
| − | Why do you want to participate in iGEM? It seemed like a great opportunity to learn more about synthetic biology.
| + | evt.currentTarget.className += " active"; |
| − | </p>
| + | } |
| − | </div>
| + | |
| − | <div class="col-md-6 no-padding">
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| − | <img src="https://static.igem.org/mediawiki/2017/0/06/T--NYU_Abu_Dhabi--laura.jpg" class="img-responsive center-block" alt="">
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| + | |
| − | <h3 class="page-head">Muhammad Shehryar Hamid</h3> | + | |
| − | </div>
| + | |
| − | <p style="text-align:left">
| + | |
| − | Major: Civil Engineering (Biochemistry)<br>
| + | |
| − | Year: 2020 <br>
| + | |
| − | Where are you from: Pakistan <br>
| + | |
| − | Something interesting about yourself: I have lived at ten different houses, each for at least more than a year, throughout my life. <br>
| + | |
| − | Why do you want to participate in iGEM? To acknowledge myself with the meeting grounds of biology and engineering, and to learn how to integrate this knowledge in designing bioengineering systems.
| + | |
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| − | <h3 class="page-head">Pratik Maisuria</h3>
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| − | </div>
| + | |
| − | <p style="text-align:left">
| + | |
| − | Major: Mechanical Engineering<br>
| + | |
| − | Year: 2019<br>
| + | |
| − | Where are you from: Suva,Fiji <br>
| + | |
| − | Something interesting about yourself: Not many people can find Fiji on the map. <br>
| + | |
| − | Why do you want to participate in iGEM? YI get to work with machines and organisms, experimenting and creating a hybrid of life and automata.
| + | |
| − | </p>
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| − | <img src="https://static.igem.org/mediawiki/2017/f/f4/T--NYU_Abu_Dhabi--pratik.jpg" class="img-responsive center-block" alt="">
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| + | |
| − | <h3 class="page-head">Saad Sultan</h3> | + | |
| − | </div> | + | |
| − | <p style="text-align:left">
| + | |
| − | Major: Mechanical Engineering<br>
| + | |
| − | Year: 2019<br>
| + | |
| − | Where are you from: Faisalabad, Pakistan<br>
| + | |
| − | Something interesting about yourself: Snorkeled with Sharks, sea turtles and dolphins at three different reefs in the Maldives.<br>
| + | |
| − | Why do you want to participate in iGEM? I’ve always had a love for biology and, well, biology and engineering together just sound irresistible so I couldn’t hold myself back.
| + | |
| − | </p>
| + | |
| − | </div>
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| − | </div><!-- .row -->
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| − | <br>
| + | document.getElementById("defaultOpen").click(); |
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| − | <div class="col-md-6 col-box bg-gray-light"> | + | |
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| + | |
| − | <h3 class="page-head">Sampanna Bhattarai</h3>
| + | |
| − | </div>
| + | |
| − | <p style="text-align:left">
| + | |
| − | Major: Computer Engineering<br>
| + | |
| − | Year: 2020 <br>
| + | |
| − | Where are you from: Kathmandu, Nepal <br>
| + | |
| − | Something interesting about yourself: I haven’t seen snowfall yet (I’m from Nepal). <br>
| + | |
| − | Why do you want to participate in iGEM? The array of experiences required for iGEM, not only confined synthetic biology, instigated me to work on this project.
| + | |
| − | </p>
| + | |
| − | </div> | + | |
| − | <div class="col-md-6 no-padding">
| + | |
| − | <img src="https://static.igem.org/mediawiki/2017/9/9f/T--NYU_Abu_Dhabi--sampanna.jpg" class="img-responsive center-block" alt="">
| + | |
| − | </div>
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| − | </div>
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| − | </section>
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| | | | |
| − | <section id="humanpractices" class="page-activ"> | + | <!-- Footer --> |
| − | | + | <div class="footer"> |
| − | <div class="container-fluid"> | + | <div class = "container-fluid"> |
| − | <h2 align="center">The Road to Food Safety</h2> | + | <div class="row"> |
| − | <p class="geu">The aim of NYUAD iGEM team, E.CoLAMP, is to build a device that can test for the presence of Shiga toxin-producing Escherichia coli (STEC), to ensure that food safety is regulated and not compromised by food vendors. For improved prototyping and designing of this device, various food vendors were surveyed.</p> | + | <div class = "col-lg-4 footer-section"> |
| − | <p>During the summer of 2017, the NYUAD team for iGEM created the initial prototypes and the biological reactions for the device that would test for the presence of Shiga toxin-producing Escherichia coli (STEC). Since the prototypes had yet to go through further simplifications in terms of designs and device features, some members of the team took the time to conduct some surveys regarding food safety, and how it relates to our iGEM project. These surveys were conducted in Indonesia and Pakistan. This allowed for the engagement of international communities of food vendors. diversify the survey results, the surveys were conducted at various places, such as coffee shops, restaurants, and street food stalls. The conversations with food vendors provided some important information from potential consumers about their expectations for a useful device. With this information in mind, our team tailored the following prototyping stages accordingly.</p>
| + | <p class = " footer-text"> |
| − | <p>Since the purpose of our project is to ensure food safety, the vendors were initially asked about any practices that they undergo to ensure that the food they are selling to the general public is safe. Their responses were surprising, because there was little variation in their answers. A few clearly stated that they have never done anything to make sure that the food is safe. For such vendors, earning a living by making a profit was their only priority. Most other vendors that were surveyed claimed that they made some efforts to ensure that the food which they were selling was healthy and safe to eat. They did this by purchasing the raw meat and spices from trustworthy sources and by storing the ingredients in clean places. Some vendors mentioned that they tend to not prepare food beforehand, so that it would be fresh when served to customers. This showed that most of the food vendors, if not all, took responsibility in some way to ensure the safety of their food. However, none of them said “yes” when they were asked if they had heard about STEC before.</p> | + | NYU Abu Dhabi is a research university with a fully integrated liberal arts and science college. It draws students from around the world, and prepares them for the challenges and opportunities of our interconnected world. </ br> <a href="http://nyuad. nyu. edu/en/about. html">Read More</ a> |
| − | <p>Following this, they were told that STEC refers to the strains of bacteria that produce Shiga toxin, which can cause foodborne illnesses. The vendors were then asked if they would be interested in acquiring equipment to detect STEC in food samples, and 90% of the vendors replied in the affirmative, even if some showed initial hesitance. This paved way for the survey conductors to inquire what features should be present in the detection device. All of them wanted that the results provided by the device should be easy to visualize. Some also expressed that the device should be portable and easy to use. When asked about how long they would be willing to wait for the results, most vendors stated that any time less than two hours would be fine, as long as they did not have to constantly check the device during this time. This information was important, because the detection device was initially targeted to food vendors so that they could test for the safety of their food.</p> | + | </p> |
| − | <p>The vendors were then asked about the cost they would be willing to pay to purchase this equipment. Some vendors claimed that they would only pay up to $10 USD for the device, whereas others were willing to pay up to $100 USD. On average, those surveyed were willing to pay $60 USD for a STEC detection device. Most of the vendors were hesitant when they were asked if they would periodically acquire a kit of reagents in order to use this equipment, but on average, they were willing to pay $10 USD for such a kit if it was required. The NYUAD team, thus, took note to make the detection device as cost effective and affordable as possible.</p> | + | </div> |
| − | <p>In conclusion, the food vendors were asked for any suggestions regarding the device or the project. They mentioned that such a device should not be dangerous, and should be lightweight for easy use. They stressed again on the necessity of easily comprehensible results. They also mentioned that the device could be targeted to the initial manufacturers that are at the top of the food chain, and serve as the initial source of all food products. The vendors mentioned that the government should be involved in regulating food safety at every part of the food chain, and the provision of this STEC detection device should be subsidized by their governments. All surveyed agreed that safe food is the key to productive business and the creation of a healthy environment.</p>
| + | <div class = "col-lg-4 footer-section"> |
| − | <h1 align="center">Survey Data</h1>
| + | <p class = "footer-text"> |
| − | <img src="https://static.igem.org/mediawiki/2017/6/61/T--NYU_Abu_Dhabi--hp1.jpg">
| + | NYUAD Saadiyat Island </br> |
| − | <hr>
| + | Abu Dhabi, P.O. Box 129188, U.A.E </br> |
| − | <img src="https://static.igem.org/mediawiki/2017/6/6e/T--NYU_Abu_Dhabi--hp2.jpg">
| + | <a href="mailto:nyuad.igem@nyu.edu">Email</a> </br> |
| − | <hr>
| + | <a href="https://www.facebook.com/iGEMNYUAD/" target="_blank">Facebook</a> </br> |
| − | <img src=" https://static.igem.org/mediawiki/2017/5/52/T- -NYU_Abu_Dhabi--hp3.jpg" > | + | </p> |
| − | <hr>
| + | </div> |
| − | <img src="https://static.igem.org/mediawiki/2017/7/7a/T--NYU_Abu_Dhabi--hp4.jpg">
| + | <div class = "col-lg-4 footer-section"> |
| − | <hr>
| + | <img class = " footer- logo" src="https://static.igem.org/mediawiki/2017/7/ 71/ IDT. png" /> |
| − | <img src=" https://static.igem.org/mediawiki/2017/d/dc/T- -NYU_Abu_Dhabi--hp5.jpg" > | + | <img class = " footer- logo2" src="https://static.igem.org/mediawiki/2017/ 2/ 2d/T-- UrbanTundra_Edmonton-- igemlogo.jpg" /> |
| − | <hr>
| + | <img class = " footer- logo" src="https://static.igem.org/mediawiki/2017/ c/ c8/NYU_Abu_Dhabi. png" /> |
| − | <img src="https://static.igem.org/mediawiki/2017/8/83/T--NYU_Abu_Dhabi--hp6.jpg">
| + | |
| − | <hr>
| + | |
| − | <img src=" https://static.igem.org/mediawiki/2017/7/79/T- -NYU_Abu_Dhabi--hp7.jpg" > | + | |
| − | <hr>
| + | |
| − | <a href="https://static.igem.org/mediawiki/2017/b/ba/T--NYU_Abu_Dhabi--surveydata.zip">Survey Data.zip</a>
| + | |
| | | | |
| − | </div>
| + | </div> |
| − | </div>
| + | </div> |
| − | </section>
| + | </div> |
| | | | |
| − | | + | </body> |
| − | <section id="attributions">
| + | |
| − | <div class="content"> | + | |
| − | <div class="container-fluid">
| + | |
| − | <br><br>
| + | |
| − | <div class="page-bodyy"><p>We would like to thank the following individuals and departments for their help in making our project this year a success:</p></div>
| + | |
| − | <ol>
| + | |
| − | <li><b>Prof. Kourosh Salehi-Ashtiani, Prof. Yong-Ak Song, and Prof. Mazin Magzoub</b>, for leading our efforts and facilitating our research as principal investigators.</li>
| + | |
| − | <li><b>Ibrahim Chehade, Mona Kalmouni, and Ashley Isaac</b>, for being wonderful instructors in guiding us throughout the technical aspects of our project and the Interlab study.</li>
| + | |
| − | <li><b>Xi Wei</b>, for being a source of information and help in setting up our LAMP assay.</li>
| + | |
| − | <li><b>Nisala Saheed</b>, for designing the E. coLAMP logo.</li>
| + | |
| − | <li><b>Nouf Al-Hamly</b>, for reaching out to the UAE high school students and facilitating our synthetic biology workshop</li>
| + | |
| − | <li><b>Brighton College</b>, for attending our synthetic biology workshop enthusiastically</li>
| + | |
| − | <li><b>Joaquín Kunkel</b>, for designing the postcard for the Düsseldorf Koln collaboration</li>
| + | |
| − | </ol>
| + | |
| − | </div>
| + | |
| − | </div>
| + | |
| − | </section>
| + | |
| − | | + | |
| − | <section id="collaborations">
| + | |
| − | | + | |
| − | <img src="https://static.igem.org/mediawiki/2017/0/0c/T--NYU_Abu_Dhabi--postcardFront.jpg" height=800 width=1150 align="center">
| + | |
| − | <h3>Postcard collaboration with Team Düsseldorf Cologne, Germany. Participating teams created postcards depicting their project with a small description on the back. Pictured above is our team’s contribution, showing the LAMP reaction occurring against a background of the Abu Dhabi skyline. These postcards were then distributed to each of the participating teams to continue spreading the word about synthetic biology.</h3>
| + | |
| − | <br>
| + | |
| − | </section>
| + | |
| − | | + | |
| − | <section id="labnotebook">
| + | |
| − | <div class="content">
| + | |
| − | <div class="container-fluid">
| + | |
| − | <div class="row">
| + | |
| − | <div class="col-lg-10 col-lg-offset-1">
| + | |
| − | <br><br>
| + | |
| − | <div class="page-head">Development of a simple DNA extraction method</div>
| + | |
| − | <br>
| + | |
| − | <div class="page-bodyy"><p>In order to use Loop-mediated isothermal amplification (LAMP) as the basis of the detection method of our device, it is necessary to include a DNA extraction step to obtain the template DNA from a sample.</p>
| + | |
| − | <p>We explored the use of heat lysis with different buffers to obtain template DNA from DH5-alpha competent <i>Escherichia coli</i> previously transformed with pGLO plasmid (BioRad). This extraction method is simple and could potentially be incorporated as an automated step in our device.</p>
| + | |
| − | <p>We prepared three buffers with varying compositions, adjusting their pH to 8.0: </p>
| + | |
| − | <ul>
| + | |
| − | <li>Tris-HCl,</li>
| + | |
| − | <li>Tris-HCl + EDTA (TE)</li>
| + | |
| − | <li>Tris-HCl + EDTA + Triton-X 100 1% + Tween 20 0.5 percent</li>
| + | |
| − | </ul>
| + | |
| − | <p>We diluted the bacteria culture to an OD600 of 0.6. 20 µl of this solution was mixed with 40 µl of buffer and subjected to 95 °C heating for varying amounts of time ranging from zero to 20 min. Using a NanoDrop™ spectrophotometer (Thermo Scientific), the A260/A280 ratio was measured (Fig 1). According to the manufacturer, a ratio of 1.8 is generally accepted as pure DNA. However, the presence of other cell components present in the sample may alter the results. The trials were ran in duplicates.</p>
| + | |
| − | <figure>
| + | |
| − | <img src="https://static.igem.org/mediawiki/2017/7/71/T--NYU_Abu_Dhabi--htime.png" alt="my img"/>
| + | |
| − | <figcaption><i>Figure 1. Comparison of A260/280 absorbance ratio of three different buffers shows no apparent difference between heating time.</i></figcaption><br>
| + | |
| − | </figure>
| + | |
| − | <p>Due to the poor results of the buffer containing Triton-X 100 and Tween 20, we discarded this option. Since it is in the important for the user to waste as little time as possible during the food test, we decided to limit the DNA extraction step to 10 min maximum.</p>
| + | |
| − | <p>The presence of template DNA was corroborated through PCR targeting a sequence in the pGLO plasmid. The PCR products were ran in an agarose gel. We used DH5-Alpha <i>E. coli</i> transformed with BBa_J04450 (backbone: pSB1C3) as negative control and pGLO isolated using the MiniPrep kit (Qiagen) as positive control.</p>
| + | |
| − | <p>The performances of the Tris-HCl and TE buffers were compared by running PCRs with template obtained through heat lysis at 95 °C for 10 min (Fig 2).</p>
| + | |
| − | <figure>
| + | |
| − | <img src="https://static.igem.org/mediawiki/2017/f/f8/T--NYU_Abu_Dhabi--fig2.png" alt="my img"/>
| + | |
| − | <figcaption><i>Figure 2. Tris-HCL and TE buffer PCR products with controls. 1) 1 kb+ ladder. 2) Negative control. 3) Tris-HCI treatment. 4) TE treatment. 5) Positive control.</i></figcaption><br>
| + | |
| − | </figure>
| + | |
| − | <p>Since the Tris-HCl treatment did not yield template DNA, it was discarded as an option.</p>
| + | |
| − | <p>Next, we used the agarose gel as a semi-quantitative measure of the PCR output to observe the differences in extraction performance due to varying heating times (Figure 3). We observed that the 10 min treatment had a clearer band compared to the other times. We decided to keep 10 min as our final time for heat lysis.</p>
| + | |
| − | <figure>
| + | |
| − | <img src="https://static.igem.org/mediawiki/2017/d/d6/T--NYU_Abu_Dhabi--fig3.png" alt="my img"/>
| + | |
| − | <figcaption><i>Figure 3. TE buffer PCR products with different heating treatment times. 1) 1 kb+ ladder. 2) Positive control. 3) No-heating treatment. 4) 1 min heating treatment. 5) 5 min heating treatment. 6) 10 min heating treatment. 7) Negative control.</i></figcaption><br>
| + | |
| − | </figure>
| + | |
| − | <p>It is still necessary to test this protocol with the LAMP reaction, which requires reagents that were unavailable at the time of these trials.</p>
| + | |
| − | </div>
| + | |
| − | <div class="fancy">The Engineering Team</div>
| + | |
| − | | + | |
| − | <h3 class="page-head">Meeting 2:</h3>
| + | |
| − | <br>
| + | |
| − | <div class="page-bodyy"><p>The initial design that we looked into consisted of one tube with two or three compartments. Each compartment was to be adjusted with a heater, so that the first compartment is at 95 degrees, and the second at 65 degrees. The third compartment already contains the color assay reagents that would then be used to give a color output to show whether if the test was positive or negative for the presence of shiga toxin. However, the small size of the sample brought into consideration a few issues, such as:</p></div>
| + | |
| − | <ul>
| + | |
| − | <li>Evaporation of the sample</li>
| + | |
| − | <li>Excess dilution of the sample</li>
| + | |
| − | <li>Loss of sample as not all of it would pass on to the subsequent compartments</li>
| + | |
| − | <li>The fact that fluids rise as they are heated and this would prevent the horizontal or vertical flow of the fluid sample, as convection would always oppose the direction of preferred flow. </li>
| + | |
| − | </ul>
| + | |
| − | <div class="page-bodyy"><p>To resolve these issues, it was thought of to include a mechanical pressure system that would force the fluid sample into the direction of the subsequent compartments. A system of syringe was one of the methodologies that were thought of. Another method thought of was to use a capillary tube that would transport the fluid sample by a capillary force into the desired compartments. However, in using a capillary tube, the compartments themselves would be in the form of small separate tubes, all connected by capillary tubes that work on the basic principles of pressure.</p></div>
| + | |
| − | <h3 class="page-head">Meeting 3:</h3>
| + | |
| − | <br>
| + | |
| − | <div class="page-bodyy"><p>The previously thought of ideas were discussed more in the light of theoretical experimentation. Using a valve between the compartments was also researched upon, and suitable valve systems compatible with various tube systems were thought of. Some novel ideas for the device also came up. These included:</p></div>
| + | |
| − | <ol>
| + | |
| − | <li>Using straws or any similar polymer material for the transfer of sample from one compartment to another, so that the valves can easily be integrated into the design.</li>
| + | |
| − | <li>Using one heater device that can be automatically adjusted for the specific temperatures and the amount of time the heating device needs to be at that temperature. The tube would thus just have to be pushed a little so that at one time, the compartment that needs to be at the specific temperature is being heated.</li>
| + | |
| − | <li>Using a branching system of flow of the sample. This works in the way that a large sample is pushed out of the first compartment, and as the tube that carries this sample is branched into smaller tubes, these smaller tubes make the liquid flow with a greater speed. Some of these smaller tubes take the sample into a “waste” compartment, and the others take the sample to the second compartment, where the subsequent reactions occur. </li>
| + | |
| − | </ol>
| + | |
| − | <div class="page-bodyy"><p>Request for the materials needed for experimentation was sent out so that we may begin testing our theories. </p></div>
| + | |
| − | <h3 class="page-head">Meeting 4:</h3>
| + | |
| − | <br>
| + | |
| − | <div class="page-bodyy"><p>The 3D printed designs for the device, that were made as a result of the previous ideas and sketches, were assessed in terms of the microfluidic flow and the heating of the chambers.</p>
| + | |
| − | <p>The first 3D printed design works on the principle of applying physical pressure to push the fluid sample. It has four different compartments. The first compartment has the largest area, and this is where the sample is collected and heated at 95 degrees Celsius. The sample is then pushed forward. Among the next three compartments, two are waste compartments. This is where the excess sample is collected. And eventually, the last of the sample collects in the fourth chamber which is divided into partitions. This chamber is at 60 degrees Celsius, and this is where the lysis reaction takes place. </p>
| + | |
| − | <p>The second 3D printed design works on the principle of gravity. It is structured in a way that the sample would keep sliding down and then some of it will be collected as waste. The rest of it would overflow into the partitions where the lysis reaction will take place. The temperature for the initial sample chamber will be 95 degrees Celsius, and the temperature for the reaction where the lysis reaction takes place will be 60 degrees Celsius.</p>
| + | |
| − | <p>Moving on with these designs, the aspects of the device that need more research are:</p>
| + | |
| − | </div>
| + | |
| − | <ol>
| + | |
| − | <li><u>Inserting Valves</u>: Both the designs need to be fitted with valves to control the flow of the fluid from one chamber to another. The material of the valves, and their design that fits accurately in the device cartridges is what the experimentation and research needs to be focused on.</li>
| + | |
| − | <li><u>Inserting Heating Systems</u>Since two different chambers need to be at two different temperatures, appropriate heating systems need to be thought of. Currently, the ideas for heating are in the form of:</li>
| + | |
| − | </ol>
| + | |
| − | <ul>
| + | |
| − | <li>Using a water-bath or an oil-bath.</li>
| + | |
| − | <li>Using chemical hand warmers to generate the heat.</li>
| + | |
| − | <li>Asking a heater company to design heaters that can adjust to the device.</li>
| + | |
| − | </ul>
| + | |
| − | <br><br><br>
| + | |
| − | </div>
| + | |
| − | </div>
| + | |
| − | </div>
| + | |
| − | </div>
| + | |
| − | </section>
| + | |
| − | | + | |
| − | <section id="interlab">
| + | |
| − | <div class="content">
| + | |
| − | <div class="container-fluid">
| + | |
| − | <div class="row">
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| − | <div class="col-lg-10 col-lg-offset-1">
| + | |
| − | <br><br><br><br>
| + | |
| − | <h3 class="page-head">Introduction</h3>
| + | |
| − | <br>
| + | |
| − | <div class="page-bodyy"><p>The Fourth International InterLaboratory Measurement Study seeks to establish a reproducible plate reader-based GFP measurement protocol. Eight plasmids were transformed into competent DH5a E.coli cells and expressed for varying lengths of time. The optical density and fluorescence of each device was recorded over a 6 hour period. The major goal of this collective effort is to answer the following question: how close can the numbers be when fluorescence is measured all around the world?</p>
| + | |
| − | </div>
| + | |
| − | <h3 class="page-head">Materials and Methods</h3>
| + | |
| − | <div class="page-bodyy"><p>See our extraction method <a href="https://static.igem.org/mediawiki/2017/8/83/Extraction-method.docx">here.</a></p><p>In this Interlab study, the following 8 RBS devices were provided in the Kit Plate 7 in the 2017 Distribution Kit:</p></div>
| + | |
| − | <ul>
| + | |
| − | <li>Positive control</li>
| + | |
| − | <li>Negative control</li>
| + | |
| − | <li>Test Device 1: J23101.BCD2.E0040.B0015</li>
| + | |
| − | <li>Test Device 2: J23106.BCD2.E0040.B0015</li>
| + | |
| − | <li>Test Device 3: J23117.BCD2.E0040.B0015</li>
| + | |
| − | <li>Test Device 4: J23101+I13504</li>
| + | |
| − | <li>Test Device 5: J23106+I13504</li>
| + | |
| − | <li>Test Device 6: J23117+I13504</li>
| + | |
| − | </ul>
| + | |
| − | <div class="page-bodyy"><p>The transformation protocol was adapted from the iGEM protocol, which can be found <a href="http://parts.igem.org/Help:Protocols/Transformation"><u>here</u></a>
| + | |
| − | . All of the devices were transformed and cultured in LB (Luria Bertani) media containing 25 mg/mL chloramphenicol.<br>
| + | |
| − | The following adjustments were made to the protocol:</p></div>
| + | |
| − | <ul>
| + | |
| − | <li>2 uL DNA were added to 50 uL competent DH5a</li>
| + | |
| − | <li>The incubation times on ice before and after the heat shock were 20 minutes and 2 minutes, respectively.</li>
| + | |
| − | <li>The heat shock was performed for 90 seconds instead of 50 seconds.</li>
| + | |
| − | <li>800 uL SOC broth were added to each transformation.</li>
| + | |
| − | <li>Test Device 3: J23117.BCD2.E0040.B0015</li>
| + | |
| − | <li>After the one-hour shaking incubation, each transformation tube was centrifuged for 1 minute, 13,000 rpm. Afterwards, 700 uL supernatant were discarded and the pellet was resuspended with the remaining 100 uL before being plated onto LB agar plate.</li>
| + | |
| − | </ul>
| + | |
| − | <div class="page-bodyy"><p>On the next day, two colonies were picked from each plate and inoculated into two 5 mL cultures, yielding 16 cultures in total. The cultures were subsequently incubated at 37 ºC and 220 rpm for 18 hours.
| + | |
| − | Afterwards, the OD600 of the overnight cultures were measured using a spectrophotometer. The cultures were diluted to OD600 of 0.02 in 12 mL LB medium and subsequently incubated at 37 ºC and 220 rpm. At t = 0, 2, 4, and 6 hours, 500 uL sample from each culture was saved on ice, yielding 64 samples in the end. The dilution calculation can be found <a href="https://static.igem.org/mediawiki/2017/d/d2/NYU_Abu_Dhabi_2017_Interlab_Dilution_Calculation_Sheet.xlsx">here</a>. </p></div>
| + | |
| − | <div class="page-bodyy"><p>The 64 culture samples were transferred onto a clear, flat-bottomed 96-well plate according to the layout found <a href="https://static.igem.org/mediawiki/2017/8/85/InterLab_2017_Plate_Reader_Protocol.pdf"><u>here</u>.</a>
| + | |
| − | <br>The OD600 absorption and fluorescence spectroscopy were measured using Synergy H1 Hybrid Multi-Mode Microplate Reader. The machine was previously calibrated using LUDOX. A fluorescein standard curve was also obtained under the same settings that were used to measure the culture samples.</p></div>
| + | |
| − | <h3 class="page-head">Results</h3>
| + | |
| − | <div class="page-bodyy"><p>The results of the Interlab Study are tabulated <a href="https://static.igem.org/mediawiki/2017/5/51/T--NYU_Abu_Dhabi--results.xlsx"><u>here</u></a>.</p></div>
| + | |
| − | </div>
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| − | </div>
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