Difference between revisions of "Team:UChile-OpenBio"

 
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             <!-- SI EXPORT END -->
 
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             <section>
 
             <section>
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                 <span class="titulo_seccion">Project</span>
 
                 <span class="titulo_seccion">Project</span>
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                 <img alt="Project overview" src="https://static.igem.org/mediawiki/2015/0/04/Description-overview.png" />
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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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                 <map name="overview">
 
                 <map name="overview">
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                     <area shape="circle" coords="120,178,101" alt="Overview" href="#background" />
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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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                     <area shape="circle" coords="79,400,80" alt="Specifics goals" href="#specific_goals" />
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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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                     <area shape="circle" coords="255,348,75" alt="Main goal" href="#main_goal" />
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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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                     <area shape="circle" coords="347,197,78" alt="Background" href="#background" />
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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="509,92,94" alt="Experiment" href="#" />
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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="404,460,87" alt="Lactate production and regulation system" href="#" />
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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="580,398,83" alt="Safety system" href="#" />
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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="708,239,85" alt="PLA production and exportation system" href="#" />
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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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                     <area shape="circle" coords="879,173,91" alt="Results" href="#" />
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                 </map>
 
                 </map>
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            </section>
 
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            <section id="background">
 
 
              
 
              
−
                 <span class="titulo_seccion" >Overview: Background</span>
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                <article>
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                    <div class="division">
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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>
 +
</section>
 +
<section id="background">
 +
<div class="division">
 +
<span class="titulo_seccion" >Overview: Background</span>  
 +
<article>                                        
 +
                        <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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                        <img id="bacteria_con_capa" class="bottom right" alt="OpenBio" src="https://static.igem.org/mediawiki/2015/6/6a/Uchile-Openbio_igem.jpeg" />
 
−
                       
 
−
                        <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. A sustainable initiative is to produce biodegradable plastics; however its synthesis process (chemical and biological) is complex and expensive.</p>
 
−
                            <p>The team UChile-OpenBio is designing two populations of Bacteria to achieve this: Escherichia coli to produce a biodegradable plastic called PLA (Polylactic acid) from easy to assimilate renewable resources.</p>
 
−
                            <p>In this way, the team would help fighting against pollution, contributing to a better world!</p>
 
−
                       
 
−
<img id="bacteria_con_capa" class="bottom right" alt="Super bacterias" src="https://static.igem.org/mediawiki/2015/9/94/Uchile-Openbio_hug.jpeg" />
 
 
                     </div>
 
                     </div>
 
                 </article>
 
                 </article>
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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>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>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 to regulate the quantity of produced proteins.</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>
 
                             <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">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>
 
                             <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 class="division">
 
                     <div class="division">
 
                         <div class="half">
 
                         <div class="half">
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                             <p>The team decided to used legos to explain the pla project due to diferent reasons.</p>
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                             <p>The team decided to used legos to explain the pla project due to different reasons.</p>
 
                         </div>
 
                         </div>
 
                     </div>
 
                     </div>
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             <section id="lego_description">
 
             <section id="lego_description">
 
                 <span class="titulo_seccion">Overview: Lego description</span>
 
                 <span class="titulo_seccion">Overview: Lego description</span>
 +
               
 +
 +
<img class="" alt="Simbologiía" src="https://static.igem.org/mediawiki/2015/f/f7/Uchile-Openbio_for_legos.jpeg" />
 +
 +
 +
 
                 <article>
 
                 <article>
 
                     <div class="division">
 
                     <div class="division">
 
                         <div class="half">
 
                         <div class="half">
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                             <h3>E. Coli 1 Poblation: “Lactadora”</h3>
+
                             <h3>E. Coli 1 Population: “Lactadora”</h3>
 
                             <img class="" alt="Lactadora" src="https://static.igem.org/mediawiki/2015/0/0b/Lego_description-bacteria_lego.png" />
 
                             <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 bacterias « Escherichia coli »: name and first name of the bacteria.<br>This population are responsible for lactate production.</p>
+
                             <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>
 
                         </div>
 
                         </div>
 
                         <div class="half last">
 
                         <div class="half last">
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                             <h3>E. Coli 2 Poblation: “PLAdora”</h3>
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                             <h3>E. Coli 2 Population: “PLAdora”</h3>
 
                             <img class="" alt="PLAdora" src="https://static.igem.org/mediawiki/2015/0/0b/Lego_description-bacteria_lego.png" />
 
                             <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>
 
                             <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>
 
                         </div>
 
                         <div class="one_third last">
 
                         <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 bacteria.</p>
+
                             <p>Finally, lactate can be obtained from glucose thanks to LDH, which gene we insert into the bacterium.</p>
 
                         </div>
 
                         </div>
 
                     </div>
 
                     </div>
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                     <div class="division">
 
                     <div class="division">
 
                         <div class="half">
 
                         <div class="half">
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                             <p>The lactate produced by the <span class="destacado">E.coli 1 Population</span> is secreted into the medium and enters in the bacterias of the E.coli 2 Population</p>
+
                             <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>
 
                         <div class="half last">
 
                         <div class="half last">
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                         </div>
 
                         </div>
 
                         <div class="one_third">
 
                         <div class="one_third">
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                             <p>PhaC1 gathers all the lactyl-CoA that are present in the cell and unites them together...</p>
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                             <p>PhaC1 gathers all the lactyl-CoA that are present in the cell and unites them together. . .</p>
 
                         </div>
 
                         </div>
 
                         <div class="one_third last">
 
                         <div class="one_third last">
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                 </article>
 
                 </article>
 
                 <article>
 
                 <article>
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                     <h3>Importan Modules of the process</h3>
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                     <h3>Important Modules of the process</h3>
 
                     <div class="division">
 
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                 <article>
 
                 <article>
 
                     <h3>Regulation of lactate production in E.coli 1</h3>  
 
                     <h3>Regulation of lactate production in E.coli 1</h3>  
−
                     <img class="" alt="Regulation E1" src="https://static.igem.org/mediawiki/2015/c/cb/Lego_description-regulation_E1.png" />
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                    <p>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.</p>
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                     <div class="division">
 
                     <div class="division">
 
                         <div class="two_third">
 
                         <div class="two_third">
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                            <img class="" alt="Regulation E1" src="https://static.igem.org/mediawiki/2015/9/92/Lego_description-ph_low.png" />
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                        <img class="" alt="Regulation E1" src="https://static.igem.org/mediawiki/2015/c/cb/Lego_description-regulation_E1.png" />  
 
                         </div>
 
                         </div>
 
                         <div class="one_third last">
 
                         <div class="one_third last">
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                             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.
+
                             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>
 
                     </div>
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                     <h3>Communication between E.coli 1 and E.coli 2</h3>  
 
                     <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" />
 
                     <img class="" alt="Regulation E1" src="https://static.igem.org/mediawiki/2015/a/af/Lego_description-communication.png" />
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                     <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 bacteria, being responsible for communication between E.coli 1 and 2.</p>
+
                     <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="division">
 
                         <div class="two_third">
 
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                 </article>
 
                 </article>
 
             </section>
 
             </section>
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            <section id="main_goal">
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                <span class="titulo_seccion">Overview: Main goal</span>
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                <article>
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                    <div class="division">
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−
                        <div class="half">
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                            <img class="" alt="Process" src="https://static.igem.org/mediawiki/2015/8/82/Main_goal-process.png" />
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                        </div>
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                        <div class="half last">
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                            <h2>Main goal</h2>
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−
                            <p>For the iGEM competition, the team aims to engineer a biological system, enabling it to degrade glucose in order to produce and export into the medium a biodegradable plastic called PLA.</p>
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−
                        </div>
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−
                    </div>
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                </article>
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                <article id="specific_goals">
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                    <div class="division">
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−
                        <div class="one_third">
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                            <h2>Goal 1</h2>
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                            <p>Designing and implementing a self-regulated lactate production system which will allow light green bacteria (Figure 1) to control the lactate production by pH-sensing: the higher lactate concentration, the lower the pH, which induces a negative control in the first population of E.coli, stopping the production of lactate and by the way, of PLA.</p>
+
−
                        </div>
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                        <div class="one_third">
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                            <h2>Goal 2</h2>
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                            <p>Designing and implementing a PLA production and exportation system which will allow blue bacteria to send the biological PLA outside the cells, into the medium. This way, the purification of the bioplastic would be easier.</p>
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−
                        </div>
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                        <div class="one_third last">
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                            <h2>Goal 3</h2>
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                            <p>Designing and implementing a safety system, which will consists in making arabinose-dependent the cell survival. If the medium contains arabinose, bacteria will grow up, but if bacteria escape from their medium, the cells will produce a toxin which will kill them. This way, we will ensure the safety of the persons working in the laboratory and of the environment.</p>
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                        </div>
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                    </div>
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                </article>
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            </section>
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     <footer>
 
     <footer>
 
         <h1>Our Sponsors</h1>
 
         <h1>Our Sponsors</h1>

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.

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