Difference between revisions of "Team:UChile-OpenBio"

 
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{{UChile-OpenBio}}
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<!-- NO EXPORT START
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<h2> Welcome to iGEM 2015! </h2>
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<img src="https://static.igem.org/mediawiki/2015/thumb/f/fa/Team_UChile-OpenBio_banner.jpg/800px-Team_UChile-OpenBio_banner.jpg" />
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        <title>TODO supply a title</title>
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<p>Your team has been approved and you are ready to start the iGEM season! </p>
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        <meta charset="UTF-8">
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        <meta name="viewport" content="width=device-width, initial-scale=1.0">
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        <script src="//ajax.googleapis.com/ajax/libs/jquery/1.11.2/jquery.min.js"></script>
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        <link rel='stylesheet' id='teslawp-style-css'  href='./css/style.css' type='text/css' media='all' />
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        <link href='http://fonts.googleapis.com/css?family=Walter+Turncoat' rel='stylesheet' type='text/css'>
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    </head>
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    <body>
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        <header>
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            <img id="logo" alt="OpenBio Uchile PLA Project" src="https://static.igem.org/mediawiki/2015/b/b0/Cabecera.png" />
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            <nav id="menu">
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                <ul>
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                    <li><a href="https://2015.igem.org/Team:UChile-OpenBio">HOME</a></li>
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                    <li>
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                        <a href="https://2015.igem.org/Team:UChile-OpenBio/Description">PROJECT</a>
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                        <ul>
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                            <li><a href="https://2015.igem.org/Team:UChile-OpenBio/Description">PROJECT DESCRIPTION</a></li>
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                            <li><a href="https://2015.igem.org/Team:UChile-OpenBio/Experiments">EXPERIMENT AND PROTOCOLS</a></li>
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                            <li><a href="https://2015.igem.org/Team:UChile-OpenBio/Results">RESULTS</a></li>
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                        </ul>
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                    </li>
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                    <li><a href="https://2015.igem.org/Team:UChile-OpenBio/Parts">PARTS</a></li>
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                    <li><a href="https://2015.igem.org/Team:UChile-OpenBio/Notebook">NOTEBOOK</a></li>
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                    <li><a href="https://2015.igem.org/Team:UChile-OpenBio/Collaborations">COLLABORATION</a></li>
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                    <li><a href="https://2015.igem.org/Team:UChile-OpenBio/Practices">HUMAN PRACTICES</a></li>
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                    <li><a href="https://2015.igem.org/Team:UChile-OpenBio/Safety">SAFETY</a></li>
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                    <li><a href="https://2015.igem.org/Team:UChile-OpenBio/Modelling">MODELLING</a></li>
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                    <li><a href="https://2015.igem.org/Team:UChile-OpenBio/Team">TEAM</a></li>
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                </ul>
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            </nav>
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            </nav>
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        </header>
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            {{UChile-OpenBio}}
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            <section>
  
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<h4>Before you start: </h4>
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                <span class="titulo_seccion">Project</span>
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<p> Please read the following pages:</p>
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                <img alt="Project overview" src="https://static.igem.org/mediawiki/2015/d/d7/Uchile-Openbio_Home.png" usemap="#overview" />
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<ul>
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<li>  <a href="https://2015.igem.org/Requirements">Requirements page </a> </li>
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<li> <a href="https://2015.igem.org/Wiki_How-To">Wiki Requirements page</a></li>
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</ul>
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<div class="highlightBox">
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                <map name="overview">
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<h4> Styling your wiki </h4>
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                    <area shape="circle" coords="183,290,60" alt="Overview" href="https://2015.igem.org/Team:UChile-OpenBio/Description"/>
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<p>You may style this page as you like or you can simply leave the style as it is. You can easily keep the styling and edit the content of these default wiki pages with your project information and completely fulfill the requirement to document your project.</p>
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                    <area shape="circle" coords="620,150,60" alt="Overview" href="https://2015.igem.org/Team:UChile-OpenBio/Notebook"/>
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<p>While you may not win Best Wiki with this styling, your team is still eligible for all other awards. This default wiki meets the requirements, it improves navigability and ease of use for visitors, and you should not feel it is necessary to style beyond what has been provided.</p>  
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                    <area shape="circle" coords="700,450,60" alt="Overview" href="https://2015.igem.org/Team:UChile-OpenBio/Attributions"/>
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</div>
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                    <area shape="circle" coords="280,61,60" alt="Specifics goals" href="https://2015.igem.org/Team:UChile-OpenBio/Collaborations" />
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                    <area shape="circle" coords="100,350,60" alt="Specifics goals" href="https://2015.igem.org/Team:UChile-OpenBio/Practices" />
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                    <area shape="circle" coords="725,67,60" alt="Main goal" href="https://2015.igem.org/Team:UChile-OpenBio/Safety" />
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                    <area shape="circle" coords="485,67,60" alt="Background" href="https://2015.igem.org/Team:UChile-OpenBio/Modeling" />
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                    <area shape="circle" coords="485,407,60" alt="Experiment" href="https://2015.igem.org/Team:UChile-OpenBio/Team" />
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                </map>
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<img id="bacteria_con_capa" class="bottom right" alt="Super bacterias" src="https://static.igem.org/mediawiki/2015/9/94/Uchile-Openbio_hug.jpeg" /> <br></article><br>
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</section>
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<section id="background">
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<div class="division">
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<span class="titulo_seccion" >Overview: Background</span> 
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<article>                                       
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                        <p>Each year, 130 million tons of fossil plastics are produced in the world, which take 500-1000 years to degrade, and pollute the environment; 1,5 millions of marine animals were killed in 2014 and we will eventually kill us too (Figure 1, Project). A sustainable initiative is to produce biodegradable plastics; however its synthesis process (chemical and biological) is complex and expensive. The team UChile-OpenBio designed two populations of bacteria to achieve this: the  team will use Escherichia coli to produce a biodegradable plastic called PLA (Polylactic acid) from easy to assimilate renewable resources. The first population will convert glucose into lactate and will self-regulate its production by sensing the pH. The second population will polymerize lactate into PLA and will export it into the medium. In addition the team is planning to replace the glucose by Chilean brown macroalgae (kelp), a renewable resource to sustainably produce PLA. In this way, the team would help fighting against pollution, contributing to a better world! </p>
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<h4> Editing your wiki </h4>
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                    </div>
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<p>On this page you can document your project, introduce your team members, document your progress and share your iGEM experience with the rest of the world! </p>  
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                </article>
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<p> <a href="https://2015.igem.org/wiki/index.php?title=Team:UChile-OpenBio&action=edit"> Click here to edit this page! </a></p>
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                <article>
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<p>See tips on how to edit your wiki on the <a href="https://2015.igem.org/TemplatesforTeams_Code_Documentation">Template Documentation</a> page.</p>  
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                    <div class="division">
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                        <div class="half">
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                            <h1>General Concepts</h1>
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                            <p>A genetic module is constituted of 4 elements, called parts, that are DNA sequences which possess a specific function: the promotor, the RBS, the coding sequence and the terminator.</p>
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                            <p>The role of a genetic module is to produce certain quantity of a protein under some specific conditions. The fabrication process, from DNA to protein, consists in two steps: <span class="destacado">transcription</span> and <span class="destacado">translation</span>.</p>
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                            <p>If the DNA is a book of recipes, the transcription process consists in photocopying one page, in which are written the instructions for one specific food; and the translation process corresponds to the cooking phase, in which the "cooker" is the ribosome. The ribosome reads the instructions and at the same time builds the protein. This is called the <span class="destacado">Central Dogma of Biology</span>.</p>
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                        </div>
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                        <div class="half last">
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                            <img src="https://static.igem.org/mediawiki/2015/3/38/UChile_OpenBio_GeneralConcepts.png">
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                            <label> Scheme of the general concepts </label>
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                            <img src="https://static.igem.org/mediawiki/2015/d/d2/UChile_OpenBio_GeneralConcepts_Sev.png">
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                        </div>
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                    </div>
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                </article>
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                <article>
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                    <div class="division">
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                        <div class="half">
 +
                            <h1>General Concepts</h1>
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                            <p>The transcription can be regulated by different factors (repressors, pH, light, etc) which are detected by the <span class="destacado">promotor</span>. These signals induce or inhibit the activation of the module.</p>
 +
                            <p>If the module is activated then the transcription process begins, in which several copies of the message are made.</p>
 +
                            <p>The <span class="destacado">RBS</span> (Ribosomal Bonding Site) intervenes in the translation process: if it is strong, many proteins will be synthesised. If it is weak, few proteins will be synthetized. So the function of RBS is regulate the quantity of produced proteins.</p>
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                            <p>The <span class="destacado">coding sequence</span> is the message, the recipe that shall be translated to protein.</p>
 +
                            <p>The <span class="destacado">terminator</span> is a DNA sequence that puts an end to the transcription process.</p>
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                        </div>
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                        <div class="half last">
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                            <img class="" alt="Genetic module and parts in legos" src="https://static.igem.org/mediawiki/2015/f/f2/Description-genetic_module_parts_legos.png" />
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                            <img src="https://static.igem.org/mediawiki/2015/6/60/UChile_OpenBio_GeneralConcepts_Lucho.png">
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                        </div>
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                    </div>
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                </article>
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                <article>
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                    <h1>Why Legos are a friendly way to explain SB?</h1>
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                    <div class="division">
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                        <div class="half">
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                            <p>The team decided to used legos to explain the pla project due to different reasons.</p>
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                        </div>
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                    </div>
  
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                    <div class="division">
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                        <div class="one_third">
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                            <h2>First Reason</h2>
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                            <p>They make tangible microscopic things</p>
 +
                            <img src="https://static.igem.org/mediawiki/2015/7/7f/UChile_OpenBio_FirstReason.png" >
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                        </div>
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                        <div class="one_third">
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                            <h2>Second Reason</h2>
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                            <p>They allow a strong analogy with the DNA parts called « bio-bricks»</p>
 +
                            <p>They are standard and modular like a biobricks</p>
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                            <img src="https://static.igem.org/mediawiki/2015/9/9a/UChile_OpenBio_SecondReason.png">
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                            <p> <a href="https://www.flickr.com/photos/mknowles/47457221"> Source </a>
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                        </div>
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                        <div class="one_third last">
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                            <h2>Third Reason</h2>
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                            <p>Finally, they are a funny way to explain complex concepts... for the students...and the teachers!</p>
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                            <img src="https://static.igem.org/mediawiki/2015/e/ee/UChile_OpenBio_3rdReason.png" align=left>
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                            <img src="https://static.igem.org/mediawiki/2015/9/90/UChile_OpenBio_3rdReason_2.png" align=right >
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 +
                        </div>
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                    </div>
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                </article>
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            </section>
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            <section id="lego_description">
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                <span class="titulo_seccion">Overview: Lego description</span>
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<h4>Templates </h4>
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<img class="" alt="Simbologiía" src="https://static.igem.org/mediawiki/2015/f/f7/Uchile-Openbio_for_legos.jpeg" />
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<p> This year we have created templates for teams to use freely. More information on how to use and edit the templates can be found on the
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<a href="https://2015.igem.org/TemplatesforTeams_Code_Documentation">Template Documentation </a> page.</p>  
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<h4>Tips</h4>
 
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<p>This wiki will be your team’s first interaction with the rest of the world, so here are a few tips to help you get started: </p>
 
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<ul>
 
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<li>State your accomplishments! Tell people what you have achieved from the start. </li>
 
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<li>Be clear about what you are doing and how you plan to do this.</li>
 
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<li>You have a global audience! Consider the different backgrounds that your users come from.</li>
 
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<li>Make sure information is easy to find; nothing should be more than 3 clicks away.  </li>
 
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<li>Avoid using very small fonts and low contrast colors; information should be easy to read.  </li>
 
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<li>Start documenting your project as early as possible; don’t leave anything to the last minute before the Wiki Freeze. For a complete list of deadlines visit the <a href="https://2015.igem.org/Calendar_of_Events">iGEM 2015 calendar</a> </li>
 
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<li>Have lots of fun! </li>
 
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</ul>
 
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<h4>Inspiration</h4>
 
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<p> You can also view other team wikis for inspiration! Here are some examples:</p>
 
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<ul>
 
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<li> <a href="https://2014.igem.org/Team:SDU-Denmark/"> 2014 SDU Denmark </a> </li>
 
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<li> <a href="https://2014.igem.org/Team:Aalto-Helsinki">2014 Aalto-Helsinki</a> </li>
 
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<li> <a href="https://2014.igem.org/Team:LMU-Munich">2014 LMU-Munich</a> </li>
 
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<li> <a href="https://2014.igem.org/Team:Michigan"> 2014 Michigan</a></li>
 
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<li> <a href="https://2014.igem.org/Team:ITESM-Guadalajara">2014 ITESM-Guadalajara </a></li>
 
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<li> <a href="https://2014.igem.org/Team:SCU-China"> 2014 SCU-China </a></li>
 
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</ul>
 
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<h4> Uploading pictures and files </h4>
 
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<p> You can upload your pictures and files to the iGEM 2015 server. Remember to keep all your pictures and files within your team's namespace or at least include your team's name in the file name. <br />
 
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When you upload, set the "Destination Filename" to <code>Team:YourOfficialTeamName/NameOfFile.jpg</code>. (If you don't do this, someone else might upload a different file with the same "Destination Filename", and your file would be erased!)</p>
 
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<a href="https://2015.igem.org/Special:Upload">CLICK HERE TO UPLOAD FILES</a>
 
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</div></div> <!--These are the closing tags for div id="mainContainer" and div id="contentContainer". The corresponding opening tags appear in the template that is {{included}} at the top of this page.-->
 
  
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                <article>
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                    <div class="division">
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                        <div class="half">
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                            <h3>E. Coli 1 Population: “Lactadora”</h3>
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                            <img class="" alt="Lactadora" src="https://static.igem.org/mediawiki/2015/0/0b/Lego_description-bacteria_lego.png" />
 +
                            <p>In our project we used two bacteria « Escherichia coli »: name and first name of the bacteria.<br>This population are responsible for lactate production.</p>
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                        </div>
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                        <div class="half last">
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                            <h3>E. Coli 2 Population: “PLAdora”</h3>
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                            <img class="" alt="PLAdora" src="https://static.igem.org/mediawiki/2015/0/0b/Lego_description-bacteria_lego.png" />
 +
                            <p>« Escherichia coli »: name and first name of the bacteria. « 1 » y « 2 » only mean that these bacteria, in this process, are responsible for different functions (but they belong the same bacteria strain).<br>This population are responsible for process the lactate into PLA.</p>
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                        </div>
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                    </div>
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                </article>
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                <article>
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                    <div class="division">
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                        <div class="two_third">
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                            <img class="" alt="LDH" src="https://static.igem.org/mediawiki/2015/7/7f/Lego_description-LDH.png" />
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                        </div>
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                        <div class="one_third last">
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                            The « Lactate DeHydrogenase » (LDH) is responsible for lactate production.
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                        </div>
 +
                    </div>
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                    <img class="" alt="Scheme" src="https://static.igem.org/mediawiki/2015/6/64/Lego_description-esquema.png" />
 +
                    <div id="esquema_descripcion" class="division">
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                        <div class="one_third">
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                            <p>Transformation of glucose into pyruvate is a bacterial natural process, it doesn’t need human intervention.</p>
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                        </div>
 +
                        <div class="one_third">
 +
                            <p>LDH uses pyruvate and transforms it into lactate, the intermediate compound that allows PLA synthesis.</p>
 +
                        </div>
 +
                        <div class="one_third last">
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                            <p>Finally, lactate can be obtained from glucose thanks to LDH, which gene we insert into the bacterium.</p>
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                        </div>
 +
                    </div>
 +
                </article>
 +
                <article>
 +
                    <div class="division">
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                        <div class="two_third">
 +
                            <img class="" alt="Lactate" src="https://static.igem.org/mediawiki/2015/9/90/Lego_description-lactate.png" />
 +
                        </div>
 +
                        <div class="one_third last">
 +
                            According to last image, the module which produces LDH is indirectly responsible for lactate production, for it will be symbolized as if the LDH directly produced lactate.
 +
                        </div>
 +
                    </div>
 +
                    <img class="" alt="Lactate" src="https://static.igem.org/mediawiki/2015/b/b6/Lego_description-lactate_populations.png" />
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                    <div class="division">
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                        <div class="half">
 +
                            <p>The lactate produced by the <span class="destacado">E.coli 1 Population</span> is secreted into the medium and enters in the bacteria of the E.coli 2 Population</p>
 +
                        </div>
 +
                        <div class="half last">
 +
                            <p>Lactate enters into the <span class="destacado">E.coli 2 Population</span> to be processed into PLA by the presented module.</p>
 +
                        </div>
 +
                    </div>
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                </article>
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                <article>
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                    <div class="division">
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                        <div class="two_third">
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                            <img class="" alt="PhaC" src="https://static.igem.org/mediawiki/2015/3/3f/Lego_description-phac.png" />
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                        </div>
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                        <div class="one_third last">
 +
                            The lactate convertion into PLA is driven by two enzymes: « P-CoA-T »: Propionyl-CoA-Transferase « phaC1 »: PolyHydroxy Alkanoate –Class 1
 +
                        </div>
 +
                    </div>
 +
                    <img class="" alt="PLA" src="https://static.igem.org/mediawiki/2015/0/0d/Lego_description-lactato_pla.png" />
 +
                    <div id="esquema_descripcion" class="division">
 +
                        <div class="one_third">
 +
                            <p>The P-CoA-T unites lactate with a cofactor called « Coenzyme A », transforming lactate into « Lactyl-CoA ».</p>
 +
                        </div>
 +
                        <div class="one_third">
 +
                            <p>PhaC1 gathers all the lactyl-CoA that are present in the cell and unites them together. . .</p>
 +
                        </div>
 +
                        <div class="one_third last">
 +
                            <p>This reaction is called « polymerization ». The product of this polymerization is the PLA.</p>
 +
                        </div>
 +
                    </div>
 +
                </article>
 +
                <article>
 +
                    <img class="" alt="Lactate to PLA" src="https://static.igem.org/mediawiki/2015/3/38/Lego_description-sumpup_lactate_to_pla.png" />
 +
                    <div class="division">
 +
                        <div class="half">
 +
                            <p>To sum up, this module processes lactate to transform it into PLA.</p>
 +
                        </div>
 +
                        <div class="half last">
 +
                            <p>The produced PLA is processed by a second module, which produces a hybrid protein constituted of a first protein called phasyn and of a much smaller protein having affinity for PLA. The role of this hybrid protein is to make the cell know that PLA is ready for exportation.</p>
 +
                        </div>
 +
                    </div>
 +
                </article>
 +
                <article>
 +
                    <img class="" alt="PLA ready to export" src="https://static.igem.org/mediawiki/2015/f/f3/Lego_description-pla_export.png" />
 +
                    <p class="harto_margen">The hybrid protein sticks with PLA and the cell exports it into the extra-cellular medium, ready to be extracted and purified.</p>
 +
                </article>
 +
                <article>
 +
                    <h3>Important Modules of the process</h3>
 +
                    <div class="division">
 +
                        <div class="half">
 +
                            <h3>E.coli 1 Population</h3>
 +
                        </div>
 +
                        <div class="half last">
 +
                            <h3>E.coli 2 Population</h3>
 +
                        </div>
 +
                    </div>
 +
                    <img class="" alt="E1 E2 population" src="https://static.igem.org/mediawiki/2015/4/49/Lego_description-important_modules.png" />
 +
                    <div class="division">
 +
                        <div class="half">
 +
                            <div class="division">
 +
                                <div class="half centered">
 +
                                    Glucose transformation into lactate
 +
                                </div>
 +
                            </div>
 +
                        </div>
 +
                        <div class="half last">
 +
                            <div class="division">
 +
                                <div class="one_third centered">
 +
                                    Transformation of lactate into PLA
 +
                                </div>
 +
                                <div class="one_third centered">
 +
                                    PLA exportation
 +
                                </div>
 +
                            </div>   
 +
                        </div>
 +
                    </div>
 +
                </article>
 +
                <article>
 +
                    <h3>Regulation of lactate production in E.coli 1</h3>
 +
                   
 +
               
 +
                    <div class="division">
 +
                        <div class="two_third">
 +
                        <img class="" alt="Regulation E1" src="https://static.igem.org/mediawiki/2015/c/cb/Lego_description-regulation_E1.png" /> 
 +
                        </div>
 +
                        <div class="one_third last">
 +
                            When being outside the cells, lactate acidifies the medium, which is dangerous for the bacteria. That’s why a pH-sensing module has been built to detect pH levels and produce the TetR protein when the pH is lower than 5.5.
 +
                        </div>
 +
                    </div>
 +
                    <div class="division">
 +
                        <div class="two_third">
 +
                            <img class="" alt="Regulation E1" src="https://static.igem.org/mediawiki/2015/3/39/Lego_description-ph_increase.png" />
 +
                        </div>
 +
                        <div class="one_third last">
 +
                            TetR is a repressor of the lactate production module. It means, when pH becomes lower than 5.5, the lactate production is shut off by TetR. This shrinks the lactate concentration in the medium so that the pH increases again.
 +
                        </div>
 +
                    </div>
 +
                </article>
 +
                <article>
 +
                    <h3>Communication between E.coli 1 and E.coli 2</h3>
 +
                    <img class="" alt="Regulation E1" src="https://static.igem.org/mediawiki/2015/a/af/Lego_description-communication.png" />
 +
                    <p>In fact, the module that produces lactate not only produces it but is also responsible for the synthesis of a small molecule called HSL (HomoSeryl-Lactone) . This molecule is exported into the medium and is able to enter the second bacterium, being responsible for communication between E.coli 1 and 2.</p>
 +
                    <div class="division">
 +
                        <div class="two_third">
 +
                            <img class="" alt="Regulation E2" src="https://static.igem.org/mediawiki/2015/3/31/Lego_description-hsl.png" />
 +
                        </div>
 +
                        <div class="one_third last">
 +
                            Inside the E.coli 2 bacteria, is also inserted a module which produces a protein called LuxR.
 +
                        </div>
 +
                    </div>
 +
                    <div class="division">
 +
                        <div class="two_third">
 +
                            <img class="" alt="Regulation E2" src="https://static.igem.org/mediawiki/2015/3/33/Lego_description-luxr.png" />
 +
                        </div>
 +
                        <div class="one_third last">
 +
                            The concerted action of luxR with HSL activates the other modules of the E.coli 2 (logic door « AND »),
 +
                        </div>
 +
                    </div>
 +
                </article>
 +
                <article>
 +
                    <h3>Communication between E.coli 1 and E.coli 2</h3>
 +
                    <img class="" alt="Communication between" src="https://static.igem.org/mediawiki/2015/c/c8/Lego_description-between.png" />
 +
                    <p>The concerted action of LuxR with HSL activates the PLA production and makes possible its exportation. This activation is possible only if there is enough lactate in the medium (since it is the same module that produces lactate and HSL). This way, E.coli 1 leads the production, telling to E.coli 2 when the PLA synthesis can begin). That’s why it is said that HSL is a communication molecule.</p>
 +
                    <img class="" alt="Communication global" src="https://static.igem.org/mediawiki/2015/a/a0/Lego_description-global.png" />
 +
                    <p>The concerted action of LuxR with HSL activates the PLA production and makes possible its exportation. This activation is possible only if there is enough lactate in the medium (since it is the same module that produces lactate and HSL). This way, E.coli 1 leads the production, telling to E.coli 2 when the PLA synthesis can begin). That’s why it is said that HSL is a communication molecule.</p>
 +
                </article>
 +
            </section>
 +
 
 +
    <footer>
 +
        <h1>Our Sponsors</h1>
 +
        <img src="https://static.igem.org/mediawiki/2015/4/4f/Footer_sponsors.png" alt="UChile Sponsors" />
 +
    </footer>
 +
        </div> <!-- #contentContainer -->
 +
    </body>
 
</html>
 
</html>

Latest revision as of 15:54, 14 November 2015


TODO supply a title

Project Project overview Overview Overview Overview Specifics goals Specifics goals Main goal Background Experiment Super bacterias

Overview: Background

Each year, 130 million tons of fossil plastics are produced in the world, which take 500-1000 years to degrade, and pollute the environment; 1,5 millions of marine animals were killed in 2014 and we will eventually kill us too (Figure 1, Project). A sustainable initiative is to produce biodegradable plastics; however its synthesis process (chemical and biological) is complex and expensive. The team UChile-OpenBio designed two populations of bacteria to achieve this: the team will use Escherichia coli to produce a biodegradable plastic called PLA (Polylactic acid) from easy to assimilate renewable resources. The first population will convert glucose into lactate and will self-regulate its production by sensing the pH. The second population will polymerize lactate into PLA and will export it into the medium. In addition the team is planning to replace the glucose by Chilean brown macroalgae (kelp), a renewable resource to sustainably produce PLA. In this way, the team would help fighting against pollution, contributing to a better world!

General Concepts

A genetic module is constituted of 4 elements, called parts, that are DNA sequences which possess a specific function: the promotor, the RBS, the coding sequence and the terminator.

The role of a genetic module is to produce certain quantity of a protein under some specific conditions. The fabrication process, from DNA to protein, consists in two steps: transcription and translation.

If the DNA is a book of recipes, the transcription process consists in photocopying one page, in which are written the instructions for one specific food; and the translation process corresponds to the cooking phase, in which the "cooker" is the ribosome. The ribosome reads the instructions and at the same time builds the protein. This is called the Central Dogma of Biology.

General Concepts

The transcription can be regulated by different factors (repressors, pH, light, etc) which are detected by the promotor. These signals induce or inhibit the activation of the module.

If the module is activated then the transcription process begins, in which several copies of the message are made.

The RBS (Ribosomal Bonding Site) intervenes in the translation process: if it is strong, many proteins will be synthesised. If it is weak, few proteins will be synthetized. So the function of RBS is regulate the quantity of produced proteins.

The coding sequence is the message, the recipe that shall be translated to protein.

The terminator is a DNA sequence that puts an end to the transcription process.

Genetic module and parts in legos

Why Legos are a friendly way to explain SB?

The team decided to used legos to explain the pla project due to different reasons.

First Reason

They make tangible microscopic things

Second Reason

They allow a strong analogy with the DNA parts called « bio-bricks»

They are standard and modular like a biobricks

Source

Third Reason

Finally, they are a funny way to explain complex concepts... for the students...and the teachers!

Overview: Lego description Simbologiía

E. Coli 1 Population: “Lactadora”

Lactadora

In our project we used two bacteria « Escherichia coli »: name and first name of the bacteria.
This population are responsible for lactate production.

E. Coli 2 Population: “PLAdora”

PLAdora

« Escherichia coli »: name and first name of the bacteria. « 1 » y « 2 » only mean that these bacteria, in this process, are responsible for different functions (but they belong the same bacteria strain).
This population are responsible for process the lactate into PLA.

LDH
The « Lactate DeHydrogenase » (LDH) is responsible for lactate production.
Scheme

Transformation of glucose into pyruvate is a bacterial natural process, it doesn’t need human intervention.

LDH uses pyruvate and transforms it into lactate, the intermediate compound that allows PLA synthesis.

Finally, lactate can be obtained from glucose thanks to LDH, which gene we insert into the bacterium.

Lactate
According to last image, the module which produces LDH is indirectly responsible for lactate production, for it will be symbolized as if the LDH directly produced lactate.
Lactate

The lactate produced by the E.coli 1 Population is secreted into the medium and enters in the bacteria of the E.coli 2 Population

Lactate enters into the E.coli 2 Population to be processed into PLA by the presented module.

PhaC
The lactate convertion into PLA is driven by two enzymes: « P-CoA-T »: Propionyl-CoA-Transferase « phaC1 »: PolyHydroxy Alkanoate –Class 1
PLA

The P-CoA-T unites lactate with a cofactor called « Coenzyme A », transforming lactate into « Lactyl-CoA ».

PhaC1 gathers all the lactyl-CoA that are present in the cell and unites them together. . .

This reaction is called « polymerization ». The product of this polymerization is the PLA.

Lactate to PLA

To sum up, this module processes lactate to transform it into PLA.

The produced PLA is processed by a second module, which produces a hybrid protein constituted of a first protein called phasyn and of a much smaller protein having affinity for PLA. The role of this hybrid protein is to make the cell know that PLA is ready for exportation.

PLA ready to export

The hybrid protein sticks with PLA and the cell exports it into the extra-cellular medium, ready to be extracted and purified.

Important Modules of the process

E.coli 1 Population

E.coli 2 Population

E1 E2 population
Glucose transformation into lactate
Transformation of lactate into PLA
PLA exportation

Regulation of lactate production in E.coli 1

Regulation E1
When being outside the cells, lactate acidifies the medium, which is dangerous for the bacteria. That’s why a pH-sensing module has been built to detect pH levels and produce the TetR protein when the pH is lower than 5.5.
Regulation E1
TetR is a repressor of the lactate production module. It means, when pH becomes lower than 5.5, the lactate production is shut off by TetR. This shrinks the lactate concentration in the medium so that the pH increases again.

Communication between E.coli 1 and E.coli 2

Regulation E1

In fact, the module that produces lactate not only produces it but is also responsible for the synthesis of a small molecule called HSL (HomoSeryl-Lactone) . This molecule is exported into the medium and is able to enter the second bacterium, being responsible for communication between E.coli 1 and 2.

Regulation E2
Inside the E.coli 2 bacteria, is also inserted a module which produces a protein called LuxR.
Regulation E2
The concerted action of luxR with HSL activates the other modules of the E.coli 2 (logic door « AND »),

Communication between E.coli 1 and E.coli 2

Communication between

The concerted action of LuxR with HSL activates the PLA production and makes possible its exportation. This activation is possible only if there is enough lactate in the medium (since it is the same module that produces lactate and HSL). This way, E.coli 1 leads the production, telling to E.coli 2 when the PLA synthesis can begin). That’s why it is said that HSL is a communication molecule.

Communication global

The concerted action of LuxR with HSL activates the PLA production and makes possible its exportation. This activation is possible only if there is enough lactate in the medium (since it is the same module that produces lactate and HSL). This way, E.coli 1 leads the production, telling to E.coli 2 when the PLA synthesis can begin). That’s why it is said that HSL is a communication molecule.

Our Sponsors

UChile Sponsors