Difference between revisions of "Team:Madrid-OLM/Measurement"

 
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         <title>Titulo del apartado</title>
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         <title>Measurement </title>
 
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         <meta name="description" content="Measurement Award">
 
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                         <a href="#story" class="inner-link" data-title="1 apartado"></a>
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                         <a href="#optic" class="inner-link" data-title="The optics approach"></a>
 
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                         <a href="#ceremony" class="inner-link" data-title="2 apartado"></a>
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                         <a href="#electric" class="inner-link" data-title="The electrochemical approach"></a>
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                        <a href="#rsvp" class="inner-link" data-title="5 Apartado"></a>
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                             <h1 id="Teamtittle">Measurement </h1>
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                             <p class="lead">All along this year, we have been working in the problematic of how to measure almost any kind of protein with an automated device. We are willing to present our device to this award because we hope that you could see the potentiality of our system in the way in which we see it.</p>
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                             <h1 class="h1--large">
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                             <p class="lead">For solving this challenge we have developed two different measuring systems:</p>
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                                Titulo del apartado
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                                Alguna descripcion si queremos
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                                    Posible boton a alguna zona importante
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                            </a>
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                             <h2>Apartado 1</h2>
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                             <h2>The optics approach</h2>
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                             <p class="lead">
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                             <p class="lead">For our first approach, we have built, characterized and documented a microfluidic colorimeter, capable of measuring total protein concentration at 280 nm. We have designed all the parts included in the system:</p>
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                                 Cosas del apartado 1, se necesita meter mas divs seguramente
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                             </p>
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                            <ol class="ourlist">
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                                 <li class="nomargin"><p class="lead">A laser-cut structure.</p></li>
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                                <img  class="figureimage" alt="Image1" src="https://static.igem.org/mediawiki/2018/a/a6/T--Madrid-OLM--Device--FirstPrototype--Ensablaje1.png" style="width:70%;"/>
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                                <li class="nomargin"><p class="lead">A microfluidic chip which brings microliters of the sample to the measurement chamber. It handles two experiments at the same time.</p></li>
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                                <img  class="figureimage" alt="Image1" src="https://static.igem.org/mediawiki/2018/4/40/T--Madrid-OLM--Device--FirstPrototype--spectro.png" style="width:40%;"/>
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                                <li><p class="lead">An electronic PCBs capable of measure 4 microfluidics chambers at the same time.</p></li>
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                                <img  class="figureimage" alt="Image1" src="https://static.igem.org/mediawiki/2018/8/8f/T--Madrid-OLM--Device--FirstPrototype--electrmeasure.png" style="width:80%;"/>
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                                <li><p class="lead">A cassette, which carries the microfluidic chip inside it, surrounded by two methacrylate slides with the optic modules housing.</p></li>
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                                <img  class="figureimage" alt="Image1" src="https://static.igem.org/mediawiki/2018/9/99/T--Madrid-OLM--Device--FirstPrototype--caset.png" style="width:80%;"/>
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                                <li><p class="lead">We have also characterized the system with real protein concentrations (BSA), and modeled the system dependence under the change of different variables (time, the temperature of the led…):</p></li>
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                                <img  class="figureimage" alt="Image1" src="https://static.igem.org/mediawiki/2018/7/7c/T--Madrid-OLM--Device--FirstPrototype--graghoptics9.png" style="width:90%;"/>
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                             </ol>
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                            <p class="lead">If you want to know more about the system, check our First Prototype page:</p>
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                            <a class="btn btn--primary-2 btn--sm type--uppercase" href="https://2018.igem.org/Team:Madrid-OLM/FirstPrototype">
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                                <span class="btn__text">
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                                    First Prototype
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                                </span>
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             </section>
 
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            <!--MEETUPS-->
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                             <h2>Attendance to Meet Ups</h2>
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                             <h2>The electrochemical approach</h2>
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                             <p class="lead">The meets ups bring several advantages to the teams. It is one of the simplest ways to reach a greater number of people to whom you can explain your project. And therefore they allow you to know first-hand the projects of the rest of the teams so that you can consult and clarify doubts. These meetings also allow for more related and powerful collaborations thanks to knowing the rest of the teams in person. And last but not least, they allow you to practice exposing your project with a view to improving in the Giant Jamboree.</p>
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                             <p class="lead">We have realized that even if we accomplish a commercial Nanodrop sensibility, we are not going to measure accurately the concentration of our protein at the levels that we find in the environment. </p>
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                             <p class="lead">Our team attended two meet ups that took place in the month of August.</p>
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                             <p class="lead">So we have developed a completely new system, integrating aptamers for bringing the specificity of our target protein to our measures.</p>
 
                              
 
                              
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                             <div id="meetsups" class="tabs-container" data-content-align="center">
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                             <p class="lead">Before explaining the system and showing the results, we want to share with you our vision of why the aptamers are going to revolutionize the world of the organic measurements.</p>
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                                <ul class="tabs">
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                            <p class="lead">Aptamers are artificial engineered ADN (or ARN) strands capable of join specifically to almost any kind of molecule big enough for having epitopes. They are the alternative to antibodies which involve several improvements like the non-use of animals in their production, the more affordability or the more stability at higher temperatures.</p>
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                                    <li class="active">
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                            <a class="btn btn--primary-2 btn--sm type--uppercase" href="https://2018.igem.org/Team:Madrid-OLM/Aptamer">
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                                        <div class="tab__title">
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                                            <span class="h5">Marseille</span>
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                                            <h3>Mediterranean Meet Up (Marseille)</h3>
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                                            <img alt="Image1" src="https://static.igem.org/mediawiki/2018/9/9a/T--Madrid-OLM--Collaboration--Marseille--All.png" style="width:80%;"/>
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                                            <p class="lead">This meet up took place between Thursday 9 and Friday 10 August in the city of Marseille and was organized by the team of this city, the Aix-Marseille. In it, all the teams from the Mediterranean area were summoned, so they ended up attending both France and Spain. Francisco, Gonzalo and Ivan attended this meet up on behalf of the team.</p>
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                                            <p class="lead">The event began with a reception in which all teams had their first informal contact. Subsequently, a 5 minutes presentation of each of the projects was organized, summarizing the concept on which the proyect was based, the work carried out and the plans to complete it. After the exhibition, each team answered the questions that could have the jury and the rest of the teams.</p>
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                                            <img alt="Image2" src="https://static.igem.org/mediawiki/2018/4/49/T--Madrid-OLM--Collaboration--Marseille--Exp.png" style="width:70%;"/>
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                                            <p class="lead">Later they invited us to a joint meal. In the afternoon it was organized a sightseeing tour of the city, but due to inclement weather it had to be suspended, although we could enjoy a pleasant evening of board games and conversations with the rest of the teams. At night a meeting was also organized in a pub to end a day where we had met many new people.</p>
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                                            <p class="lead">The second (and last day) had two interesting activities. The first was the meetings with different experts from the university, which privately asked each team about controversial issues. To see if these issues had been taken into account and the possible solutions and consequences were debated.</p>
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                                            <img alt="Image3" src="https://static.igem.org/mediawiki/2018/2/22/T--Madrid-OLM--Collaboration--Marseille--Experts.png" style="width:70%;"/>
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                                            <p class="lead">To close the event, a poster presentation session was held, which was very enriching to know how to present our project in Boston..</p>
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                                            <p class="lead">One of the things that were achieved in this meet up was the agreement with the UPF-CRG-Barcelona group to organize an activity in their meet up. Activity that is explained in the following session (and that gave rise to a greater collaboration).</p>
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                                            <img alt="Image4" src="https://static.igem.org/mediawiki/2018/2/2b/T--Madrid-OLM--Collaboration--Marseille--Poster.png" style="width:70%;"/>
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                                            <span class="h5">Barcelona</span>
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                                            <h3>Spanish Meet Up (Barcelona)</h3>
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                                            <img alt="Image5" src="https://static.igem.org/mediawiki/2018/6/6d/T--Madrid-OLM--Collaboration--BCN--All.png" style="width:70%;"/>
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                                            <p class="lead">This meet up took place between Saturday 18 and Monday 20 August in the city of Barcelona and was organized by one of the two teams of this same city, the UPF-CRG-Barcelona. In it, all the teams from Spain were called, which all but the Valencia team attended. To this meet up they were representing the whole team: Laura, Iván and Francisco. The meet up took place in the Biomedical Research Park of Barcelona (PRBB), center where the host team operates and where they started with a welcome activity. This activity consisted of a game where each one of the assistants of each team presented themselves, so that the subsequent environment was much more relaxed.</p>
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                                            <p class="lead">The next activity was the one organized by our team. In this activity we proposed to carry out a collaborative guide in which each group would give the main ideas on how they have solved the main problems that have arisen in iGEM. The structure we proposed was followed. We collected these ideas and wrote a complete guide. We explain this collaboration in a later section of the collaborations. After this, some playful activities were carried out on the beach, including volleyball games. </p>
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                                            <img alt="Image6" src="https://static.igem.org/mediawiki/2018/5/5e/T--Madrid-OLM--Collaboration--BCN--Voley.png" style="width:65%;"/>
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                                            <p class="lead">During the morning of the second day, a more detailed presentation of each team's project was made. There was 30 minutes to expose each project in detail. This activity was very useful because the rest of the teams, besides getting to know the details of each project well, could intervene to give advice on how to make the presentations. Each team took a series of points in which they could be reinforced in the face of the presentation of the Giant Jamboree.</p>
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                                            <p class="lead">In the afternoon the time was taken to take a tour in the tourist center of the city and ended up having dinner with a picnic in the Parc Guell. A viewpoint that have views of the entire city at night.</p>
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                                            <img alt="Image7" src="https://static.igem.org/mediawiki/2018/7/78/T--Madrid-OLM--Collaboration--BCN--Tour.png" style="width:60%;"/>
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                                            <br/>
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                                            <p class="lead">During the morning of the last day, to close the meet up, we were able to attend to some enriching expert talks. They offered us their views on synthetic biology and they explained the works in which they are immersed today.</p>
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                                            <img alt="Image8" src="https://static.igem.org/mediawiki/2018/e/e3/T--Madrid-OLM--Collaboration--BCN--Bye.png" style="width:70%;"/>
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                            <a class="btn btn--primary-2 type--uppercase inner-link" href="#meetsups">
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                                     Back to Meet up Index
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                                     Aptamers
 
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                                 </span>
 
                             </a>
 
                             </a>
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                            <br/><br/>
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                            <p class="lead">Aptamers have a high potential to revolutionize the world of chemical measurements. The only reason why we did not find them in the previous iGEM years, is that there is not an easy, well documented and affordable system of discovery and measuring with them.</p>
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                            <p class="lead">This is what we have solved with the following results: </p>
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                            <ol class="ourlist">
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                                <li class="nomargin"><p class="lead">We have integrated the aptamers into a Cyclic Voltammetry measurement workflow. In this way, we have achieved quantification of 1.33 uM, integrating the gold standard of aptamers (the one for thrombin) in our system and measuring thrombin concentration.</p></li>
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                                <img  class="figureimage" alt="Image1" src="https://static.igem.org/mediawiki/2018/d/d8/T--Madrid-OLM--Aptamer--Electrode--T1.png" style="width:100%;"/>
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                                <li class="nomargin"><p class="lead">We have developed our final device: a complete system for measuring in an automated way any kind of protein concentration. It only has the requirement of developing an electrode for this protein.</p></li>
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                                <img  class="figureimage" alt="Image1" src="https://static.igem.org/mediawiki/2018/8/89/T--Madrid-OLM--Awards--device.png" style="width:40%;"/>
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                                <img  class="figureimage" alt="Image1" src="https://static.igem.org/mediawiki/2018/8/8f/T--Madrid-OLM--Device--FinalPrototype--Micro--circuit5.png" style="width:60%;"/>
 +
                                <br/>
 +
                                <a class="btn btn--primary-2 btn--sm type--uppercase" href="https://2018.igem.org/Team:Madrid-OLM/FinalPrototype">
 +
                                    <span class="btn__text">
 +
                                        Final Device
 +
                                    </span>
 +
                                </a>
 +
                                <br/><br/>
 +
                               
 +
                               
 +
                                <li><p class="lead">We have described a simple universal protocol for integrating any kind of aptamer in our electrodes. It cost less than 20€  so it is at hand for any future iGEM teams that want to work with aptamers.</p></li>
 +
                                <li><p class="lead">For the first time in iGEM, we have accomplished the first successful aptamer discovery method. We have also described a quantitative aptamer characterization method and a way to improve them computationally.</p></li>
 +
                                <a class="btn btn--primary-2 btn--sm type--uppercase" href="https://2018.igem.org/Team:Madrid-OLM/Aptamer">
 +
                                    <span class="btn__text">
 +
                                        Aptamers
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                                    </span>
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                                </a>
 +
                               
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 +
                            </ol>
 +
                            <p class="lead">With this methods we are not just bringing the aptamer measurement to iGEM, we bring a way in which future iGEMmers could integrate almost any kind of molecule to its measurements.</p>
 +
                            <p class="lead">Once this protocol has been described, we hope that we will see in the next years the aptamer’s registry page getting larger and larger.</p>
 +
 
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                            <h2>Organization of a Meet Up: Another European Meet Up</h2>
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                            <h5>Reason</h5>
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                            <p class="lead">After attending two meet ups we realized that these meetings are very enriching experiences in preparation for the Giant Jamboree. One of the main reasons for these meet ups is to get to know and know the project of other teams. Other reason is that its also serves to practice the presentations of the project and its results. And finally serve to open the network of contacts beyond the contest itself.</p>
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                            <p class="lead">We realized that the events to which more teams come are usually the first ones to be organized, and in these although if they serve to obtain collaborations, do not fulfill so much the function of practicing to present the results of your project due to at the beginning of the summer there are no results.</p>
+
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                            <p class="lead">This year the European meet up was on July 20. Date in which novice teams, without sufficient contacts do not yet know how to deal with these events and do not have the necessary funds to attend. And teams with more experience do not yet have conclusive results. With this context we proposed this ambitious project: Make another European meet up. We invited all the teams of the continent in mid-September. A date that was supposed to be the best for the organization of new teams and with the possibility of simulating the final event.</p>
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                            <h5>Event</h5>
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                            <p class="lead">The event was organized between September 14 and 16. Although this event was given as much publicity as possible and contact was made with all possible teams in Europe, attendance was low due to several factors:</p>
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                            <ul>
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                                <li>
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                                    <p class="lead"><b>- Spain is geographically at one end of Europe and travel is expensive.</b></p>     
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                                </li>
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                                <li>
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                                    <p class="lead"><b>- The teams were short of funds and were saving for the trip to Boston.</b></p>
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                                </li>
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                                <li>
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                                    <p class="lead"><b>- The event was announced at the beginning of September, many teams did not have room to maneuver in their organization to attend.</b></p>     
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                                </li>
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                            </ul>
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                            <br/>
+
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                            <p class="lead">Despite these inconveniences we had assistance from several participants of some teams (all of them came from within the Spanish territory thanks to the facilities for transport). Although there was an extensive program of activities, these had to be adjusted and reorganized so that the maximum number of attendees could enjoy them.</p>
+
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                            <h5>Activities</h5>
+
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                            <p class="lead">The event began on Friday the 14th in the afternoon with the main course. In it, after the reception of the attendees we gave way to a series of very interesting expert presentations. We were able to count on the attendance of the following personalities</p>
+
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                            <p class="lead"><u><b>Victor de Lorenzo</b></u></p>
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                            <p class="lead">He is one of the Spanish most relevant researchers in the Synthetic Biology field. He work in the National Biotechnology Center (CNB) a part of the Superior Council of Scientific Investigations (CSIC). His laboratory is specialized in solving environmental issues using genetically engineered Pseudomonas putida. He gave us an interesting talk about <i>"Synthetic Biology in the rescue of the planet Earth"</i>.</p>
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                            <img alt="Image5" src="https://static.igem.org/mediawiki/2018/e/ee/T--Madrid-OLM--Collaboration--Madrid--Conference1.png" style="width:70%;"/>
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                            <p class="lead"><u><b>Saul Ares</b></u></p>
+
−
                            <p class="lead">He is a researcher of the CNB too. His work is central in the mathematical modeling of Synthetic Biology systems. He has also collaborated with previous iGEM teams. His presentation talked about <i>"How do cyanobacteria count to ten"</i>.</p>
+
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                            <img alt="Image5" src="https://static.igem.org/mediawiki/2018/7/7e/T--Madrid-OLM--Collaboration--Madrid--Conference2.png" style="width:70%;"/>
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                            <p class="lead"><u><b>Krzysztof Wabnik</b></u></p>
+
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                            <p class="lead">He is a Young Investigator Researcher of the Center for Biotechnology and Plant Genomics (CBGP) at the Polytechnic University of Madrid (UPM). The group he is leading uses multilevel computer model simulations, synthetic biology experiments and microfluidics. The name of his presentation was: <i>"Combining computational and synthetic biology approaches to understand the dynamics of plant hormone signaling circuits"</i>.</p>
+
−
                            <img alt="Image5" src="https://static.igem.org/mediawiki/2018/2/2d/T--Madrid-OLM--Collaboration--Madrid--Conference3.png" style="width:70%;"/>
+
−
                           
+
−
                            <p class="lead">Despite these inconveniences we had assistance from several participants of some teams (all of them came from within the Spanish territory thanks to the facilities for transport). Although there was an extensive program of activities, these had to be adjusted and reorganized so that the maximum number of attendees could enjoy them.</p>
+
−
                            <img alt="Image5" src="https://static.igem.org/mediawiki/2018/4/4a/T--Madrid-OLM--Collaboration--Madrid--Conference4.png" style="width:70%;"/>
+
−
                            <p class="lead">After the talks a social event was held in which the attending teams could relax having dinner in the center of Madrid with one of the most typical activities here: go out for tapas.</p>
+
−
                            <p class="lead">The second day was inaugurated with a visit to the university to show the facilities where our team works and it was explained which procedures are used in each of the sections that were visited.</p>
+
−
                            <p class="lead">Subsequently, the presentations of the projects were made. A simulation of the presentation was carried out as it should be done in Boston, to learn how to take the time and try to correct the excesses or lack of time in each section that was exposed.</p>
+
−
                            <p class="lead">In the afternoon there was a tour around Madrid, where the most iconic places of the city were shown. And although there were activities scheduled for the next day, this was the activity that closed the meet up, since the attending teams had organized to return to their cities after this tour.</p>
+
−
                            <img alt="Image5" src="https://static.igem.org/mediawiki/2018/3/30/T--Madrid-OLM--Collaboration--Madrid--Tour.png" style="width:70%;"/>
+
−
                            <h5>Conclusion</h5>
+
−
                            <p class="lead">It was an event that few people could attend, due to the conditions explained above, but from which the attendees took much advantage. Holding such an event in September could be much more crowded if it was announced from the beginning of the summer and allowed the rest of the teams to organize around it. As it provides a series of very useful tools for the presentation of Boston.</p>
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Latest revision as of 02:45, 18 October 2018

Madrid-OLM

Measurement

Measurement

All along this year, we have been working in the problematic of how to measure almost any kind of protein with an automated device. We are willing to present our device to this award because we hope that you could see the potentiality of our system in the way in which we see it.

For solving this challenge we have developed two different measuring systems:

The optics approach

For our first approach, we have built, characterized and documented a microfluidic colorimeter, capable of measuring total protein concentration at 280 nm. We have designed all the parts included in the system:

  1. A laser-cut structure.

    2. Image1

  2. A microfluidic chip which brings microliters of the sample to the measurement chamber. It handles two experiments at the same time.

    3. Image1

  3. An electronic PCBs capable of measure 4 microfluidics chambers at the same time.

    4. Image1

  4. A cassette, which carries the microfluidic chip inside it, surrounded by two methacrylate slides with the optic modules housing.

    5. Image1

  5. We have also characterized the system with real protein concentrations (BSA), and modeled the system dependence under the change of different variables (time, the temperature of the led…):

    6. Image1

If you want to know more about the system, check our First Prototype page:

First Prototype

The electrochemical approach

We have realized that even if we accomplish a commercial Nanodrop sensibility, we are not going to measure accurately the concentration of our protein at the levels that we find in the environment.

So we have developed a completely new system, integrating aptamers for bringing the specificity of our target protein to our measures.

Before explaining the system and showing the results, we want to share with you our vision of why the aptamers are going to revolutionize the world of the organic measurements.

Aptamers are artificial engineered ADN (or ARN) strands capable of join specifically to almost any kind of molecule big enough for having epitopes. They are the alternative to antibodies which involve several improvements like the non-use of animals in their production, the more affordability or the more stability at higher temperatures.

Aptamers

Aptamers have a high potential to revolutionize the world of chemical measurements. The only reason why we did not find them in the previous iGEM years, is that there is not an easy, well documented and affordable system of discovery and measuring with them.

This is what we have solved with the following results:

  1. We have integrated the aptamers into a Cyclic Voltammetry measurement workflow. In this way, we have achieved quantification of 1.33 uM, integrating the gold standard of aptamers (the one for thrombin) in our system and measuring thrombin concentration.

    2. Image1

  2. We have developed our final device: a complete system for measuring in an automated way any kind of protein concentration. It only has the requirement of developing an electrode for this protein.

    3. Image1 Image1
    Final Device

  3. We have described a simple universal protocol for integrating any kind of aptamer in our electrodes. It cost less than 20€ so it is at hand for any future iGEM teams that want to work with aptamers.

  4. For the first time in iGEM, we have accomplished the first successful aptamer discovery method. We have also described a quantitative aptamer characterization method and a way to improve them computationally.

    5. Aptamers

With this methods we are not just bringing the aptamer measurement to iGEM, we bring a way in which future iGEMmers could integrate almost any kind of molecule to its measurements.

Once this protocol has been described, we hope that we will see in the next years the aptamer’s registry page getting larger and larger.