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| Line 13: |
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| | <p> How AladDNA affects the world, and how the world affects AladDNA</p> | | <p> How AladDNA affects the world, and how the world affects AladDNA</p> |
| | <ul class="actions"> | | <ul class="actions"> |
| − | <li><a href="#scroll1" class="button">Minecraft</a></li> | + | <li><a href="#scroll1" class="button">Overview</a></li> |
| − | <li><a href="#scroll2" class="button">Safety</a></li> | + | <li><a href="https://2015.igem.org/Team:Valencia_UPV/Practices/Minecraft" class="button">SynBiocraft</a></li> |
| − | <li><a href="#scroll3" class="button">Collaboration</a></li> | + | <li><a href="https://2015.igem.org/Team:Valencia_UPV/Practices/Safety" class="button">Safety</a></li> |
| | + | <li><a href="https://2015.igem.org/Team:Valencia_UPV/Collaborations" class="button">Collaboration</a></li> |
| | </ul> | | </ul> |
| | </section> | | </section> |
| Line 26: |
Line 27: |
| | <section class="box"> | | <section class="box"> |
| | <header class="major"> | | <header class="major"> |
| − | <h2>Minecraft<br /> | + | <h2>Overview<br /> |
| | </h2><hr> | | </h2><hr> |
| | </header> | | </header> |
| | | | |
| − | <p>The idea of Minecraft is simple. Create your own constructions using blocks by moving them from one site to another in a 3D virtual world.</p>
| |
| − |
| |
| − | <p>This idea has catch more than 34 million players that are moving around, manipulating their space in order to build everything that comes out from their imagination.</p>
| |
| − |
| |
| − | <p>We also wanted to create our dream: SynBiocraft mod</p>
| |
| − |
| |
| − | <p>From an engineering point of view, Minecraft is just a huge 3D matrix where every cell can contain a lot of information. With a little knowledge of java language, the blocks inside the game can be modified; more kinds of blocks can be created, and the most important, more different traits can be implemented to those blocks. This allowed us to implement Synthetic Biology inside the game.</p>
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| − |
| |
| − | <p>DNA pieces, machines, DNA ligation, Petri dishes… this powerful tool provides all possibilities to recreate the practices that can be done in a lab without spending material and without having to wait days in order to carry the experiment out. In fact, ligations always occur, no mistakes, no one opens your termocycler while the ligation is being carried out and plasmid insertions are always done correctly, there are always white colonies.</p>
| |
| − |
| |
| − | <p>We implemented:</p>
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| − |
| |
| − | <p>DNA blocks with the information of the FASTA files.</p>
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| − |
| |
| − | <div style="text-align:center"><img src=https://static.igem.org/mediawiki/2015/8/81/Valencia_UPV_PCDSTTU.png ></div>
| |
| − |
| |
| − | <details>
| |
| − | <summary class="button fit">Promoters</summary>
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| − | <div class="clsPadding">
| |
| − | <p>
| |
| − | <p>35s</p>
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| − |
| |
| − | <p>Etr8</p>
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| − |
| |
| − | <p>Gal4</p>
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| − |
| |
| − | <p>LexA</p>
| |
| − |
| |
| − | <p>LacI</p>
| |
| − |
| |
| − | <p>BD1</p>
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| − |
| |
| − | <p>BD2</p>
| |
| − |
| |
| − | </p><br/>
| |
| − | </div>
| |
| − | </details>
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| − |
| |
| − | <details>
| |
| − | <summary class="button fit">CDSs</summary>
| |
| − | <div class="clsPadding">
| |
| − | <p>
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| − | <p>EPIF</p>
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| − |
| |
| − | <p>Phy</p>
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| − |
| |
| − | <p>Gal4Kdronpa</p>
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| − |
| |
| − | <p>Ndronpa</p>
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| − |
| |
| − | <p>LexAPIF</p>
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| − |
| |
| − | <p>BD1Kdronpa</p>
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| − |
| |
| − | <p>Recombinasa A</p>
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| − |
| |
| − | <p>LACIPIF</p>
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| − |
| |
| − | <p>BD2KDronpa</p>
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| − |
| |
| − | <p>Recombinasa B</p>
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| − |
| |
| − | <p>Azul</p>
| |
| − |
| |
| − | <p>Amarillo</p>
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| − |
| |
| − | <p>Rojo</p>
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| − |
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| − | <p>Verde</p>
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| − |
| |
| − | </p><br/>
| |
| − | </div>
| |
| − | </details>
| |
| − |
| |
| − | <details>
| |
| − | <summary class="button fit">Terminator</summary>
| |
| − | <div class="clsPadding">
| |
| − | <p><p>Tnos</p></p><br/>
| |
| − | </div>
| |
| − | </details>
| |
| − |
| |
| − | <p>That can be joined in Transcription units (if the construction makes no sense they are transformed in a “BAD DNA block”). For the creation of the TU, it is needed the usage of a termocycler</p>
| |
| − |
| |
| − | <details>
| |
| − | <summary class="button fit">TU</summary>
| |
| − | <div class="clsPadding">
| |
| − |
| |
| − | <p>35s_EPIF_Tnos</p>
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| − |
| |
| − | <p>35s_Phy_Tnos</p>
| |
| − |
| |
| − | <p>35s_Gal4KDronpa_Tnos</p>
| |
| − |
| |
| − | <p>35s_Ndronpa_Tnos</p>
| |
| − |
| |
| − | <p>Etr8_LexPIF_Tnos</p>
| |
| − |
| |
| − | <p>Etr8_BD1KDronpa_Tnos</p>
| |
| − |
| |
| − | <p>Etr8_RecombinasaA_Tnos</p>
| |
| − |
| |
| − | <p>Gal4_LacPIF_Tnos</p>
| |
| − |
| |
| − | <p>Gal4_BD2Kdronpa_Tnos</p>
| |
| − |
| |
| − | <p>Gal4_RecombinasaB_Tnos</p>
| |
| − |
| |
| − | <p>LexA_azul_tnos</p>
| |
| − |
| |
| − | <p>BD1_Amarillo_Tnos</p>
| |
| − |
| |
| − | <p>LacI_Rojo_Tnos</p>
| |
| − |
| |
| − | <p>BD2_Verde_Tnos</p>
| |
| − |
| |
| − | <p>Stuffer fragment</p>
| |
| − | </p><br/>
| |
| − |
| |
| − | </div>
| |
| − | </details>
| |
| − |
| |
| − | <p style="text-align:center;font-weight:bold">Bad DNA block</b></p>
| |
| − | <div style="text-align:center"><img src=https://static.igem.org/mediawiki/2015/0/0e/Valencia_UPV_ConstruccionBadDNA.png ></div>
| |
| − |
| |
| − | <p>Those transcription units can be joined in the different parts of our project</p>
| |
| − |
| |
| − | <details>
| |
| − | <summary class="button fit">DNA Constructions:</summary>
| |
| − | <div style="text-align:center"><img src=https://static.igem.org/mediawiki/2015/5/50/Valencia_UPV_Construccion.png></div>
| |
| − | <div class="clsPadding">
| |
| − |
| |
| − | <p>Toggle Rojo</p>
| |
| − |
| |
| − | <p>Toggle Azul</p>
| |
| − |
| |
| − | <p>Producto Toggle rojo 1</p>
| |
| − |
| |
| − | <p>Producto toggle rojo 2</p>
| |
| − |
| |
| − | <p>Producto Toggle Rojo</p>
| |
| − |
| |
| − | <p>Producto Toggle azul 1</p>
| |
| − |
| |
| − | <p>Producto Toggle azul 2</p>
| |
| − |
| |
| − | <p>Producto Toggle azul</p>
| |
| − |
| |
| − | <p>Pack Colores 1</p>
| |
| − |
| |
| − | <p>Pack colores 2</p>
| |
| − |
| |
| − | <p>Pack colores</p>
| |
| − |
| |
| − | <p>Circuito 1</p>
| |
| − |
| |
| − | <p>Circuito 2</p>
| |
| − |
| |
| − | <p>Circuito 3</p>
| |
| − |
| |
| − | <p>Circuito semifinal</p>
| |
| − |
| |
| − | <p>Circuito semifinal 2</p>
| |
| − |
| |
| − | <div style="text-align:center"><img src=https://static.igem.org/mediawiki/2015/4/42/Valencia_UPV_ConstruccionFinal.png></div>
| |
| − |
| |
| − | <p>Circuito Final Final: This is our final circuit, needs to be electroporated and cell cultured in a Petri dish in order to infiltrate it into a plant.</p>
| |
| − |
| |
| − | </p><br/>
| |
| − | </div>
| |
| − | </details>
| |
| | | | |
| − | <p>Lab machines implemented are:</p> | + | <ul class="actions" style="text-align:right"> |
| − |
| + | <li><a href="https://2015.igem.org/Team:Valencia_UPV/Practices/Minecraft" class="button alt">SynBiocraft</a></li> |
| − | <details>
| + | <li><a href="https://2015.igem.org/Team:Valencia_UPV/Practices/Safety" class="button alt">Safety</a></li> |
| − | <summary class="button fit">Electroporator at 1440 mW</summary>
| + | <li><a href="https://2015.igem.org/Team:Valencia_UPV/Collaborations" class="button alt">Collaborations</a></li> |
| − | <div class="clsPadding">
| + | |
| − | <p>This is the intensity needed in order to insert plasmids in <i><i>Agrobacterium</i> tumefaciens</i>.</p>
| + | |
| − | <img src=https://static.igem.org/mediawiki/2015/0/06/Valencia_UPV_Electroporator.png >
| + | |
| − | </div>
| + | |
| − | </details>
| + | |
| − |
| + | |
| − | <details>
| + | |
| − | <summary class="button fit">BioBricks termocycler</summary>
| + | |
| − | <div class="clsPadding">
| + | |
| − | <p> Standard for iGEM DNA assembly. It allows binary joining in the DNA.</p>
| + | |
| − | <img src=https://static.igem.org/mediawiki/2015/9/9b/Valencia_UPV_BioBricks.png >
| + | |
| − | </div>
| + | |
| − | </details>
| + | |
| − |
| + | |
| − | <details>
| + | |
| − | <summary class="button fit">Golden Gate termocycler</summary>
| + | |
| − | <div class="clsPadding">
| + | |
| − | <p> Standard for DNA assembly in plants. It allows joining promoter, CDS and terminator.</p>
| + | |
| − | <img src=https://static.igem.org/mediawiki/2015/b/b1/Valencia_UPV_GoldenGate.png >
| + | |
| − | </div>
| + | |
| − | </details>
| + | |
| | | | |
| − | <details>
| |
| − | <summary class="button fit">Golden Braid termocycler</summary>
| |
| − | <div class="clsPadding">
| |
| − | <p> Standard for DNA assembly in plants. It allows the union of transcription units and constructions. </p>
| |
| − | <img src=https://static.igem.org/mediawiki/2015/b/ba/Valencia_UPV_GoldenBraid.png >
| |
| − | </div>
| |
| − | </details>
| |
| − |
| |
| − | <details>
| |
| − | <summary class="button fit">Petri dishes</summary>
| |
| − | <div class="clsPadding">
| |
| − | <p> And do not forget the Petri dishes! If you have done it correctly and the piece of DNA is electroporated, you will obtain white colonies that can be taken with a syringe and inserted into one of our plants in order to create a light sensitive GMO. By using our light sticks, it will change to one color or another. </p>
| |
| − | <img src=https://static.igem.org/mediawiki/2015/e/e4/Valencia_UPV_PlacasPetri.png >
| |
| − | </div>
| |
| − | </details>
| |
| − |
| |
| − | <div style="text-align:center"><img style="width: 35em;" src=https://static.igem.org/mediawiki/2015/e/ea/Valencia_UPV_Flowers.png ></div>
| |
| − |
| |
| − | <p>And it does not stop there!</p>
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| − |
| |
| − | <p>We have also implemented Cholerae in Minecraft, and the only method to obtain the vaccine is by creating the green flower. </p>
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| − |
| |
| − | <p>Will you survive this new challenge?</p>
| |
| − |
| |
| − | <header class="major">
| |
| − | <h3 style="text-align:left">Reaching the next level<br />
| |
| − | </h3>
| |
| − | </header>
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| − |
| |
| − | <p>Implementing our project inside the game has not been easy, but it has taught us that Minecraft is more powerful than we expected. So, why should we stop there?</p>
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| − |
| |
| − | <p>By using a DNA database and BioBricks assembly method, we have reached the next level, we have recreated a represilator that was created by Elowitz & Liebler in 2000 and also the SEXY Plant project (Valencia_UPV 2014). But this can be expanded to all BioBricks database. We expect that, in the future, you will be able to replicate all the projects that have already been done in iGEM competition.</p>
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| − |
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| − | <br/>
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| − |
| |
| − | </section>
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| − | </div>
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| − | </div>
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| − |
| |
| − | <div id="scroll2" class="row" style="font-size:initial">
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| − | <div class="12u">
| |
| − | <section class="box">
| |
| − | <header id="scrollsect2" class="major">
| |
| − | <h2>Safety<br />
| |
| − | </h2><hr>
| |
| − | </header>
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| − |
| |
| − | <p>The safety of a project is always a very important part to take into account, especially if the project involves living organisms*. For that reason in our project we have taken all the safety precautions while working in the lab. Things like working on sterile conditions, using gloves or disposing waste in the corresponding container were the bases of our diary work lab, obviously.</p>
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| − |
| |
| − | <p>But with our project, AladDNA, we thought to make a step further and think about the safety of our circuit chassis, our genetically modify plant. We had to make a real effort in this due to that the special characteristics that our plant has:</p>
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| − |
| |
| − | <ul><li><a href="https://2015.igem.org/Team:Valencia_UPV/Components#scroll4">Drugs production.</a></li>
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| − |
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| − | <li>Circuit activation by light at different wavelength.</li>
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| − |
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| − | <li>Functionality of both things named before in a germinated seed. </li>
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| − |
| |
| − | </ul>
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| − |
| |
| − | <p>To afford all the questions that appeared during the realization of the project we decided to talk to some experts in the area. Also we make some research in the field of legality of transgenic modify organisms and the regulation of the plant growing and production. To see in more detail click the buttons bellow.</p>
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| − | <ul class="actions" style="text-align:center">
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| − | <li><a href="#scrollsect1" class="button alt">Expertise</a></li>
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| − | <li><a href="#scrollsect3" class="button alt">Solutions to have a safety AladDNA</a></li>
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| − | <li><a href="#scrollsect2" class="button alt">Legal aspects</a></li>
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| − |
| |
| − | </ul>
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| − |
| |
| − |
| |
| − | </p>
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| − | <br/>
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| − |
| |
| − | <header id="scrollsect1" class="major">
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| − | <h3 style="text-align:left">Expertise<br />
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| − | </h3>
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| − | </header>
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| − |
| |
| − | <p><p>Having other people opinion is always a good thing so we talk with two different experts, Carmelo López that guides us in the general legislation of a GMO and Jose Miguel Mullet (pendiente)…</p>
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| − |
| |
| − | <p>First we talk to Carmelo López del Rincón, titular professor of the Biotechnology Department at the UPV. He imparts courses related to plants production and genetically modified food as well as courses of the GMO legislation.</p>
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| − |
| |
| − | <p>He showed us the general legislation that a transgenic plant has to accomplish in Spain, Europe and internationally to be accepted and commercialized.</p>
| |
| − |
| |
| − | <p>As it is said before, there are three levels of legislation that our transgenic plant will have to accomplish. The first one is the estate level, the second one is the EU although both are closely related and finally the international level that is ruled by the Cartagena treaty (enlace al doc). In the legal aspect part this is widely explain.</p>
| |
| − |
| |
| − | <p>Also we talked about possible measures that will improve and facilitate the introduction into the environment of our plant. The most highlight option was to locate our circuit into the chloroplasts. Chloroplasts will avoid that the production go out the cell and so secrete it into the environment. But main problems were found, for example the insertion of the DNA will have to be in a 100% effectiveness. Other issue that we found is that in seeds the chloroplasts are immature because they do not receive light and so they will not be working normally.</p>
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| − |
| |
| − | <p>Finally we discard this option. </p>
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| − |
| |
| − | <p>(Lo que se haya hablado con mullet)</p></p>
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| − |
| |
| − | <br/>
| |
| − |
| |
| − | <header id="scrollsect2" class="major">
| |
| − | <h3 style="text-align:left">Legal aspects<br />
| |
| − | </h3>
| |
| − | </header>
| |
| − |
| |
| − | <p><p>In this submenu we are going to amplify the information obtained by the interview with Carmelo. So, we are going to talk with more detail about the specific laws in Spain, Europe and internationally. (gift de Obama “it’s the law”)</p>
| |
| − |
| |
| − | <p>Something to point out is that after researching and reading some documents we can observed that the main idea is the same. The law wants to protect people and the environment avoiding any incident cause by a GMO. We as a group human beings and citizens, want that anyone or anything can be injure so for that we decided invest time to know how to prevent any kind of problem that may or may not occur with our genetically modify plant.</p>
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| − |
| |
| − | <p>Let’s begin with the Spanish law about GMO. It is controlled by the Ministerio de Agricultura, Alimentación y Medio Ambiente. It is in charge of controlling the commercialization and voluntary liberation of the GMO in the environment in case that this organism produce medicines for human and veterinary use, as it is in our case (Chapter2, article3 from law 9/2003, de 25 April). Also the ministry collaborate and exchange information with the European Union that have an important role making the decisions.</p>
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| − |
| |
| − | <p>One thing to keep in mind is that our project will be evaluated step by step so is very important to fill correctly all the attaches needed. This are the general data asked in the </p>
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| − |
| |
| − | <p>The competency of the EU is</p>
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| − |
| |
| − | <p>The protocol of Cartagena is…</p></p>
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| − | <br/>
| |
| − |
| |
| − | <header id="scrollsect3" class="major">
| |
| − | <h3 style="text-align:left">Solutions to have a safety AladDNA<br />
| |
| − | </h3>
| |
| − | </header>
| |
| − |
| |
| − | <p><p>After researching about all the conditions to handle and distribute our plant finally we come up with some conclusions to make AladDNA a very very safety project.</p>
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| − |
| |
| − | <p>First of all, our seedlings will germinate into a recipient, “the magic lamp” (enlace a magic lamp), a handling device that has been designed exclusively to put up with the growing seeds. The lamp will give to the seedlings the right light pulses controlling the optimal conditions to make a regular production of the drugs. </p>
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| − |
| |
| − | <p>It is made taking into account all the details for instance the electronic part is isolated form the growing section. The system to close the device is hermetic so the seeds can go out until their need to be consumed. More info here.</p>
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| − |
| |
| − | <p>(foto de la lamapara por la mitad y con un germinado)</p>
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| − |
| |
| − | <p>Furthermore, we thought about the idea of growing our plant in a greenhouse to produce more drugs doses to supply a small village in a remote place in the world, for instance. This is also possible! With the respective bureaucracy and a close and hermetic greenhouse authorized for that kind of activity (quiza alguna palabra mas tecnica), it just will be necessary the seeds, the leds, a bit of water and… magic! The production made by a live organism avoids the big expenses on money that will suppose create in a difficult access place an industry to produce unlimited drugs.</p>
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| − |
| |
| − | <p>The information is reduced to its minimal expression and the infrastructure is just a small seed!</p>
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| − |
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| − | <p>If our chassis stay inside a controlled device and there is no intentionally liberation into the environment, there will be no problem at all. But, what happened if someone accidentally drop a seed into the wild… DISASTER! </p>
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| − |
| |
| − | <p>
| |
| − | <p><div style="text-align: center;"><img width=600em src="https://static.igem.org/mediawiki/2015/a/a4/Valencia_upv_carasorpresa.png" ></div> </p>
| |
| − | <p><div style="text-align: center;"><img width=600em src="https://static.igem.org/mediawiki/2015/2/29/Valencia_upv_bombasemilla.png" ></div> </p>
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| − |
| |
| − | <p>No, it is just a joke! AladDNA will pass for sure the controls of a transgenic plant. Moreover we think in a method of regulation in case that something happen. We can make our seed WHAT? (necesito un metodo que 1.evite que la semilla germine y por tanto que no se produzcca ningun medicamento O 2.que apenas germine se muera)(creo que acabaría de rematar toda la idea del safety)</p>
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| − |
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| − | <p>The especial “what ever” regulator allow AladDNA to be also safe in case accidentally liberation.</p>
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| − |
| |
| − |
| |
| − |
| |
| − | <p>Ok, now after reading all this restrictions that we make to our plant you might think, why all this restrictions to their plant? Well that is a good question.</p>
| |
| − |
| |
| − | <p>AladDNA was thought as a perfect way to reduce to the minimum all the information needed for the production of drugs or any other substance but with a social propose: provide an easy, self-made, and cheap way to get closer the products need in specific situations.</p>
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| − |
| |
| − | <p>Our aim is that no matter where you are, in a lost mountain, in a catastrophic area, in the middle of the desert or in the middle of the city in rush hour or even far away in the space, you can cover in a short period of time your necessity.</p>
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| − |
| |
| − |
| |
| − |
| |
| − | <p>The characteristic that AladDNA is for all users leads to the following point. As our project is think as a biopharmaceutical resource, pointing out that the circuit can have any final biological production, we will need to study in a future al the drugs produced. This is even more complicated, it is easy to explain, just watch the graphic and the numbers in it… Xmillion dollars!?</p>
| |
| − | </p>
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| − |
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| − | <ul class="actions" style="text-align:right">
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| − | <li><a href="scroll1" class="button alt">Back to Minecraft</a></li>
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| − | <li><a href="scroll3" class="button alt">Collaborations</a></li>
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