Difference between revisions of "Team:Valencia UPV/Practices"

 
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#banner{background-image: url("images/overlay.png"), url("https://static.igem.org/mediawiki/2015/f/f1/Valencia_upv_safety4.png");}
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#banner{background-image: url("images/overlay.png"), url("https://static.igem.org/mediawiki/2015/9/97/ValenciaUPVMain2.png");}
 
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<section id="banner">
 
<section id="banner">
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<h2 style="font-weight:bold">Polices and practices</h2>
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<h2>Policy and practices</h2>
 
<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">
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<li><a href="#scroll1" class="button">Minecraft</a></li>
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<li><a href="#scroll1" class="button">Overview</a></li>
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<li><a href="#scroll2" class="button">Safety</a></li>
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<li><a href="https://2015.igem.org/Team:Valencia_UPV/Practices/Minecraft" class="button">SynBiocraft</a></li>
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<li><a href="#scroll3" class="button">Collaboration</a></li>
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<li><a href="https://2015.igem.org/Team:Valencia_UPV/Practices/Safety" class="button">Safety</a></li>
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<li><a href="https://2015.igem.org/Team:Valencia_UPV/Collaborations" class="button">Collaboration</a></li>
 
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</ul>
 
</section>
 
</section>
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<section class="box">
 
<section class="box">
 
<header class="major">
 
<header class="major">
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<h2>Section 1<br />
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<h2>Overview<br />
 
</h2><hr>
 
</h2><hr>
 
</header>
 
</header>
 
 
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<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>
 
  
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<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>
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<p>Valencia-UPV team strongly believes that Synthetic Biology has the potential to change our world for good. To fulfil this potential, we as technologists should avoid repeating earlier technology mistakes, and very especially we should avoid developing a technology that ends up benefiting only a few.</p>
 +
 
 +
<p>In line with this, the Philosophy guiding the Valencia-UPV iGEM team considers Synthetic Biology as a technology that should be employed to the benefit of the Society in its broadest sense, and should be mainly directed to benefit those that need it most. In other words, we at the UPV-Team envision a <b>Synthetic for the People.</b> </p>
  
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<p>We also wanted to create our dream: SynBiocraft mod</p>
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<p>We also believe that the most efficient strategy to reach this aim is by narrowing the gap between the technology and the society. For this we need to increase the understanding of the technology, simplify procedures, develop open-source tools and instruments, and popularize its use. In other words, we envision a <b>Synthetic Biology</b> not only for the people, but also <b>by the People.</b></p>
  
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<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>Popularization of Synthetic Biology should not be at odds with safety. Broad use of the technology should walk along with a deep understanding of the risks/benefits balance of each project and should be always accompanied by the development and fulfilment of strict safety measures that ensure that each technical development brought to practice is <b>harmless</b> for the people and the environment. </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>
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<p>These are the three principles that inspired our Policy and Practices activities and indeed our project as a whole: Synthetic Biology for the people, by the people, and harmless by all means. </p>
  
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<p>We implemented:</p>
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<header class="major">
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<h3 style="text-align:left">Philosophy meets Practice<br />
 +
</h3>
 +
</header>
  
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<p>DNA blocks with the information of the FASTA files.</p>
 
  
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<img src=https://static.igem.org/mediawiki/2015/8/81/Valencia_UPV_PCDSTTU.png >
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<p>Early in our brainstorm meetings we were looking for a project that helped to improve the life conditions of the people, right now and in the near future. ….<b>and UPVteam created AladDNA.</b> Our eukaryotic decoder is first and above all projected as a portable factory of medicines; we engaged experts in our community (Farmamundi) to sort out which were the most needed medicines that could be produced with our system. See more on this in <a href="https://2015.igem.org/Team:Valencia_UPV/Collaborations">collaborations.</a></p>
  
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<details id="scrollsect1">
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<p>Our team also wanted to bring a new social dimension to our project, that is, the ability to explain it (and explain Synthetic Biology) in a completely unusual language. A language employed by more and more people in the world, especially by young people, those that we hope will be not only users but also developers of our technology: the language of the Computer Games...<b>and UPVteam created SynBioCraft.</b> Our Minecraft Mod is a virtual tool for building Synthetic Biology projects.  SynBioCraft has allowed us to interact with many young people using their same language. SynBioCraft is a virtual SynBio lab with the doors wide open to everyone with curiosity. See more on this in <a href="https://2015.igem.org/Team:Valencia_UPV/Practices/Minecraft">SynBioCraft.</a></p>
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<summary class="button fit">Promoters</summary>
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<div class="clsPadding">
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<p>
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<p>35s</p>
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<p>Etr8</p>
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<p>Finally, we investigated the risks associated to our AladDNA design and elaborated a set of technical recommendations aimed to minimize these risks, with special attention to detect and turn innocuous any unintended release of AladDNA components into the environment... <b>and UPVteam saw that it was safe.</b> Our risk analysis concluded that the risks associated with environmental release are low, and could be brought virtually to zero with the implementation of additional biotechnology measures. See more on <a href="https://2015.igem.org/Team:Valencia_UPV/Practices/Safety">Safety</a>
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</p>
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<ul class="actions" style="text-align:right">
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<li><a href="https://2015.igem.org/Team:Valencia_UPV/Practices/Minecraft" class="button alt">SynBiocraft</a></li>
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<li><a href="https://2015.igem.org/Team:Valencia_UPV/Practices/Safety" class="button alt">Safety</a></li>
 +
<li><a href="https://2015.igem.org/Team:Valencia_UPV/Collaborations" class="button alt">Collaborations</a></li>
  
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<p>Gal4</p>
 
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<p>LexA</p>
 
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<p>LacI</p>
 
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<p>BD1</p>
 
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<p>BD2</p>
 
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</p><br/>
 
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</div>
 
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</details>
 
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<details id="scrollsect1">
 
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<summary class="button fit">CDSs</summary>
 
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<div class="clsPadding">
 
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<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>
 
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<p>Amarillo</p>
 
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<p>Rojo</p>
 
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<p>Verde</p>
 
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</p><br/>
 
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</div>
 
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</details>
 
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<details id="scrollsect1">
 
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<summary class="button fit">Terminator</summary>
 
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<div class="clsPadding">
 
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<p><p>Tnos</p></p><br/>
 
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</div>
 
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</details>
 
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<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>
 
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<details id="scrollsect1">
 
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<summary class="button fit">TU</summary>
 
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<div class="clsPadding">
 
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<p>TU</p>
 
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<p>35s_EPIF_Tnos</p>
 
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<p>35s_Phy_Tnos</p>
 
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<p>35s_Gal4KDronpa_Tnos</p>
 
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<p>35s_Ndronpa_Tnos</p>
 
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<p>Etr8_LexPIF_Tnos</p>
 
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<p>Etr8_BD1KDronpa_Tnos</p>
 
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<p>Etr8_RecombinasaA_Tnos</p>
 
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<p>Gal4_LacPIF_Tnos</p>
 
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<p>Gal4_BD2Kdronpa_Tnos</p>
 
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<p>Gal4_RecombinasaB_Tnos</p>
 
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<p>LexA_azul_tnos</p>
 
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<p>BD1_Amarillo_Tnos</p>
 
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<p>LacI_Rojo_Tnos</p>
 
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<p>BD2_Verde_Tnos</p>
 
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<p>Stuffer fragment</p>
 
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</p><br/>
 
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</div>
 
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</details>
 
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<img src=https://static.igem.org/mediawiki/2015/0/0e/Valencia_UPV_ConstruccionBadDNA.png >
 
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<p>Bad DNA block</p>
 
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<p>Those transcription units can be joined in the different parts of our project</p>
 
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<details id="scrollsect1">
 
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<summary class="button fit">DNA Constructions:</summary>
 
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<img src=https://2015.igem.org/File:Valencia_UPV_Construccion.png>
 
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<div class="clsPadding">
 
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<p>
 
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<p>Toggle Rojo</p>
 
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<p>Toggle Azul</p>
 
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<p>Producto Toggle rojo 1</p>
 
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<p>Producto toggle rojo 2</p>
 
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<p>Producto Toggle Rojo</p>
 
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<p>Producto Toggle azul 1</p>
 
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<p>Producto Toggle azul 2</p>
 
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<p>Producto Toggle azul</p>
 
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<p>Pack Colores 1</p>
 
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<p>Pack colores 2</p>
 
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<p>Pack colores</p>
 
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<p>Circuito 1</p>
 
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<p>Circuito 2</p>
 
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<p>Circuito 3</p>
 
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<p>Circuito semifinal</p>
 
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<p>Circuito semifinal 2</p>
 
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<img src=https://static.igem.org/mediawiki/2015/4/42/Valencia_UPV_ConstruccionFinal.png>
 
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<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>
 
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</p><br/>
 
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</div>
 
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</details>
 
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<p>Lab machines implemented are:</p>
 
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<p>Electroporator at 1440 mW.</p>
 
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<p>This is the intensity needed in order to insert plasmids in <i><i>Agrobacterium</i> tumefaciens</i>.</p>
 
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<img src=https://static.igem.org/mediawiki/2015/0/06/Valencia_UPV_Electroporator.png >
 
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<p>BioBricks termocycler.</p>
 
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<p> Standard for iGEM DNA assembly. It allows binary joining in the DNA.</p>
 
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<img src=https://static.igem.org/mediawiki/2015/9/9b/Valencia_UPV_BioBricks.png >
 
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<p>Golden Gate termocycler.</p>
 
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<p> Standard for DNA assembly in plants. It allows joining promoter, CDS and terminator.</p>
 
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<img src=https://static.igem.org/mediawiki/2015/b/b1/Valencia_UPV_GoldenGate.png >
 
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<p>Golden Braid termocycler.</p>
 
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<p> Standard for DNA assembly in plants. It allows the union of transcription units and constructions. </p>
 
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<img src=https://static.igem.org/mediawiki/2015/b/ba/Valencia_UPV_GoldenBraid.png >
 
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<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>
 
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<img src=https://static.igem.org/mediawiki/2015/e/e4/Valencia_UPV_PlacasPetri.png >
 
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<img src=https://static.igem.org/mediawiki/2015/e/ea/Valencia_UPV_Flowers.png >
 
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<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>
 
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<p>Reaching the next level.</p>
 
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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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<br/>
 
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<header id="scrollsect1" class="major">
 
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<h3 style="text-align:left">Sub section 1<br />
 
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</h3>
 
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</header>
 
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<p>Hello world</p>
 
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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">
 
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<section class="box">
 
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<header id="scrollsect2" class="major">
 
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<h2>Safety<br />
 
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</h2><hr>
 
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</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.
 
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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:
 
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<ul>
 
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<li>Drugs production. (enlace)</li>
 
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<li>Circuit activation by light at different wavelength.</li>
 
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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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We want AladDNA to be a safe project for the environment and for people all over the world. (esto centrado y en cursiva)
 
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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.
 
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(Estos tres apartados aqui y al apretar el titulo llevan a el apartado correspondiente que se encuentra en la misma página, más abajo).
 
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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>Hello world</p>
 
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<br/>
 
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<header id="scrollsect2" class="major">
 
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<h3 style="text-align:left">Legal aspects<br />
 
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</h3>
 
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</header>
 
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<p>Hello world</p>
 
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<br/>
 
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<header id="scrollsect3" class="major">
 
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<h3 style="text-align:left">Solutions to have a safety AladDNA<br />
 
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</h3>
 
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</header>
 
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<p>Hello world</p>
 
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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>
 
 
</ul>
 
</ul>
 
 

Latest revision as of 17:23, 18 September 2015

Valencia UPV iGEM 2015

Overview

Valencia-UPV team strongly believes that Synthetic Biology has the potential to change our world for good. To fulfil this potential, we as technologists should avoid repeating earlier technology mistakes, and very especially we should avoid developing a technology that ends up benefiting only a few.

In line with this, the Philosophy guiding the Valencia-UPV iGEM team considers Synthetic Biology as a technology that should be employed to the benefit of the Society in its broadest sense, and should be mainly directed to benefit those that need it most. In other words, we at the UPV-Team envision a Synthetic for the People.

We also believe that the most efficient strategy to reach this aim is by narrowing the gap between the technology and the society. For this we need to increase the understanding of the technology, simplify procedures, develop open-source tools and instruments, and popularize its use. In other words, we envision a Synthetic Biology not only for the people, but also by the People.

Popularization of Synthetic Biology should not be at odds with safety. Broad use of the technology should walk along with a deep understanding of the risks/benefits balance of each project and should be always accompanied by the development and fulfilment of strict safety measures that ensure that each technical development brought to practice is harmless for the people and the environment.

These are the three principles that inspired our Policy and Practices activities and indeed our project as a whole: Synthetic Biology for the people, by the people, and harmless by all means.

Philosophy meets Practice

Early in our brainstorm meetings we were looking for a project that helped to improve the life conditions of the people, right now and in the near future. ….and UPVteam created AladDNA. Our eukaryotic decoder is first and above all projected as a portable factory of medicines; we engaged experts in our community (Farmamundi) to sort out which were the most needed medicines that could be produced with our system. See more on this in collaborations.

Our team also wanted to bring a new social dimension to our project, that is, the ability to explain it (and explain Synthetic Biology) in a completely unusual language. A language employed by more and more people in the world, especially by young people, those that we hope will be not only users but also developers of our technology: the language of the Computer Games...and UPVteam created SynBioCraft. Our Minecraft Mod is a virtual tool for building Synthetic Biology projects. SynBioCraft has allowed us to interact with many young people using their same language. SynBioCraft is a virtual SynBio lab with the doors wide open to everyone with curiosity. See more on this in SynBioCraft.

Finally, we investigated the risks associated to our AladDNA design and elaborated a set of technical recommendations aimed to minimize these risks, with special attention to detect and turn innocuous any unintended release of AladDNA components into the environment... and UPVteam saw that it was safe. Our risk analysis concluded that the risks associated with environmental release are low, and could be brought virtually to zero with the implementation of additional biotechnology measures. See more on Safety