Difference between revisions of "Team:Amsterdam"

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<html>   
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        <!-- Banner -->
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        <!--http://stackoverflow.com/questions/27800753/set-image-size-based-on-browser-size-->
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<section id="banner">
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<div class="full_image" style="background-image: ../images/banner.jpg">
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                <!--<div class="banner" style="background-image: ./images/banner.jpg">-->
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                    <header class="major">
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                    <h2>[Photo]Synthetic Bromance</h2>
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<p> Engineering microbial relationships for sustainable bioproduction</p>
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                    </header>
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</div>
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</section>
  
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        <section id="banner2">
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<div class="full_image" style="background-image: ../images/pollution.jpg">
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                    <header class="major">
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                    <h2>The Problem</h2>
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<p> The quest for sustainability</p>
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                    </header>
 +
                   
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                    <div class="container">
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<div class="row">
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<div class="4u">
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                    <section class="special box" style="background: rgba(0, 0, 0, 0.5)">
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<p align = "justify">
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                                                Our economy still depends largely on fossil resources. For decades, this has fueled the incredible progress of our world, but not without the massive cost of geopolitical instability and global warming - costs we’re now facing more than ever. With the current consequences of climate change visible around the world and global energy demands that are expected to double in 2050, the quest for clean, renewable energy is one of mankind’s most important modern challenges.
 +
                                </p>
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 +
                        <ul class="actions">
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<li><a href="project_overview.html#problem" class="button alt" style="color: #8A2E60">Learn More</a></li>
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</ul>
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</section>
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                        </div>
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                        </div>
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                    </div>
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</div>
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</section>
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        <section id="banner3">
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<div class="full_image" style="background-image: ../images/consortium_infographic.png">
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                    <h2>The Problem</h2>
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<p> The quest for sustainability</p>
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 +
 
 +
                    <div class="container">
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<div class="row">
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<div class="4u">
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                    <section class="special box" style="background: rgba(0, 0, 0, 0.5)">
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<p align = "justify">
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                                                Our economy still depends largely on fossil resources. For decades, this has fueled the incredible progress of our world, but not without the massive cost of geopolitical instability and global warming - costs we’re now facing more than ever. With the current consequences of climate change visible around the world and global energy demands that are expected to double in 2050, the quest for clean, renewable energy is one of mankind’s most important modern challenges.
 +
                                </p>
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 +
                        <ul class="actions">
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<li><a href="project_overview.html#problem" class="button alt" style="color: #8A2E60">Learn More</a></li>
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</ul>
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</section>
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                        </div>
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                    </div>-->
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</div>
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</section>
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 +
<!-- Solution -->
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<section id="solution" class="wrapper style2">
 +
<header class="major">
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<h2>Our solution</h2>
 +
<p >Combining the best of cyanobacterial sustainability and chemotroph productivity</p>
 +
</header>
 +
<div class="container">
 +
<div class="row">
 +
                       
 +
                       
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<div class="10u">
  
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<p align="justify">
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                            <section>
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Very recently, there’s been a small shift in the world of synthetic biology. Rather
+
                               
−
than focus on single organisms - the modus operandi of the biotech industry -
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<h3>Synthetic Consortium</h3>
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researchers are starting to recognize that synthetic ecosystems, consortia of
+
<p> the idea is simple: we engineer cyanobacteria to produce simple carbon compounds using CO2 and sunlight in ways that are genetically stable. These molecules are shared with a chemotroph like <i>E. coli</i>, which uses them to produce a desired end-product, like commodity chemicals, pharmaceuticals, or biofuels.</p>
−
multiple bacterial species, can be used for higher yields, robustness and more
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<!-- <ul class="actions">
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diverse purposes. Our goal is to tap into this potential by creating a self-sustaining
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<li><a href="#" class="button alt">Learn More</a></li>
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bio-factory of cyanobacteria - little fellows that need only CO<sub>2</sub> and light - and product-producing E. coli, the general workhorse of the synthetic biology world.</p>
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</ul>-->
 +
</section>
 +
                           
 +
                            <section class="special">
 +
<a href="#" class="image fit"><img src="images/consortium_infographic.png" alt="" /></a>
 +
                            </section>
 +
</div>
 +
<div class="10u">
 +
 +
                            <section> 
 +
<h3>The Goal</h3>
 +
<p>In our proof-of-principle consortium, <i>E. coli</i> produces isobutanol (an important biofuel) to highlight its sustainable production potential. But our engineered <i>Synechocystis</i> strains are essentially fully modular cyanobacterial production engines, and can be coupled to any biotechnological production process to remove dependencies on crops or petrochemicals and make it truly sustainable.
 +
</p>
 +
<!-- <ul class="actions">
 +
<li><a href="#" class="button alt">Learn More</a></li>
 +
</ul>-->
 +
</section>
 +
</div>
 +
</div>
 +
</div>
 +
</section>
  
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<p align="justify">
+
   
−
In short: the cyanobacteria will create sugars from CO<sub>2</sub> and sunlight, which it will
+
       
−
release and feed to E. coli as a result of our applied synthetic genetic circuits. E.
+
       
−
coli will then be engineered to use these sugars to create a product. In our
+
       
−
proof-of-concept bio-factory, this product will be fuel. This platform, however, can
+
        <!-- Results -->
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be expanded to produce any product E. coli can fabricate - medicine, plastics,
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<section id="results" class="wrapper style4">
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commodity chemicals - as long as it is fueled by the cyanobacteria that only needs
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<header class="major">
−
light and CO<sub>2</sub>.</p>
+
<h2>Results</h2>
 +
<p>How far did we get?</p>
 +
</header>
 +
<div class="container">
 +
<div class="row">                                                
 +
                        <div class="3u">
 +
                        <section>
 +
                              <h3><i>Synechocystis</i></h3>
 +
                            <a href="#" class="image fit"><img src="images/cuvettes.JPG" alt="" /></a>
 +
                            <p>We engineered various carbon producing pathways in Synechocystis and showed that the accumulation and sharing of carbon compounds can be used by E.coli to grow and make product. Moreover, we demonstrated the importance of genetic stability through evolutionary growth experiments that showed loss of productivity for strains with novel gene insertions and high fitness cost.</p>
 +
 +
                            </section>                 
 +
                        </div>
 +
                        <div class="3u">
 +
                        <section>
 +
                              <h3><i>e. coli</i></h3>
 +
                           
 +
                            <p>We designed and implemented a genetic safety switch based on E. coli sharing essential nutrients with an auxotrophic Synechocystis strain. We also built on [insert team] previous efforts and used their biobrick to engineer and demonstrate constitutive iso-1-butanol production of E. coli in co-culture, showing that our consortium can be effectively used for the sustainable production of biofuels.</p>
 +
<a href="#" class="image fit"><img src="images/E_coli_red_.JPG" alt="" /></a>
 +
                            </section>
 +
                       
 +
                       
 +
                        </div>
 +
                        <div class="3u">
 +
                        <section>
 +
                            <h3>Dry Lab</h3>
 +
             
 +
                            <p>Besides using simulations to guide our consortium design, we created software tools that can be used to design new synthetic consortia: <i>Sustainstability™</i> allows users to identify carbon compounds that can be engineered in a growth-coupled (stable) way, while <i>Auxotrophy Sniper™</i> identifies auxotrophies that can be engineered to increase bio-safety. Both of these tools are freely available <a href="https://2015.igem.org/Team:Amsterdam/Software">here</a>.</p>
 +
 +
                            <a href="#" class="image fit"><img src="images/randomcode.png" alt="" /></a>           
 +
                            </section>
 +
                       
 +
                       
 +
                        </div>
 +
                       
 +
                        <div class="3u">
 +
<section>
 +
<h3>Consortia</h3>
 +
                                <a href="#" class="image fit"><img src="images/MC_light.JPG" alt="" /></a>
 +
<p>We tested our proof-of-princple consortium using the carbon-sharing Synechocystis and bio-fuel producing E. coli and demonstrated mutual growth and product formation. We also developed a micro-droplet screening tool and demonstrated its effectiveness in identifying stable consortia consisting of carbon-sharing cyanobacteria and various chemotrops with biotechnological relevance.</p>
 +
 +
</section>
 +
 +
 +
                        </div>
 +
</div>
 +
</div>
 +
</section>
 +
       
 +
       
 +
              <!-- The team-->
 +
<section id="team" class="wrapper style5">
 +
<header class="major">
 +
<h2>The Team</h2>
 +
<p>Six students, trillions of microbes, one purpose</p>
 +
</header>
 +
<div class="container">
 +
<div class="row">
 +
<div class="6u">
 +
<section class="special">
 +
<a href="#" class="image fit"><img src="images/team_picture.jpg" alt="" /></a>
 +
<h3>Students</h3>
 +
<p>With a combined IQ that is manyfold larger than the sum of its parts, this lean mean student machine has willingly exhanged what could have been a summer of freedom and good weather for the most challenging scientific endeavor of their lives (in what is arguably the most rainy country in the known universe).</p>
 +
<ul class="actions">
 +
<li><a href="#" class="button alt">Meet us</a></li>
 +
</ul>
 +
</section>
 +
</div>
 +
<div class="6u">
 +
<section class="special">
 +
<a href="#" class="image fit"><img src="images/traffic_sign_scaled.png" alt="" /></a>
 +
<h3>Supervisors/Advisors</h3>
 +
<p>As in any learning process, working with mentors with laser eyes capable of piercing through a hazy cloud of results to distinguish the signal from the noise can mean the difference between succes and failure. Although our mentors could not shoot lasers out of their eyes, their guidance and advice along the way was invaluable.
 +
</p>
 +
<ul class="actions">
 +
<li><a href="#" class="button alt">Meet them</a></li>
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</ul>
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</section>
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</div>
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</div>
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</div>
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</section>
  
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<!-- Human practices -->
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        <section id="human_practices" class="wrapper style1">
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        <header class="major">
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<h2>Human practices</h2>
 +
<p>Applications and implications</p>
 +
</header>
 +
<div class="container">
 +
<div class="row">
 +
                        <div class="3u">
 +
                     
 +
                            <a href="http://www.synenergene.eu/information/igem-collaboration" class="image fit"><img src="images/synenergene.jpg" alt="" /></a>
 +
                              <h2>Synenergene</h2>
 +
                            <p>Synenergene is an organisation dedicated to fostering responsible research and innovation practices in synthetic biology. They selected a small group of iGEM teams from around the world to collaborate with, which included us. Our human practices efforts therefore revolved around our project with Synenergene.
 +
</p>
 +
                        </div>
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                        <div class="8u">
 +
                        <!--Application scenario BOX-->   
 +
                        <section>
 +
<h3 align="center">Application Scenarios</h3> 
 +
                            <div class="row">
 +
                           
 +
                                <div class="6u">
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                                <section>
 +
 +
                                    <a href="#" class="image fit"><img src="images/appl_scenario.jpg" alt=""/></a>
 +
                                    </section>
 +
                               
 +
                                </div>
 +
                                <div class="6u">
 +
                           
 +
<section>
 +
                                <p>With the help of experts, we wrote several application scenarios in which we conducted detailed investigations into potential real-world applications and their broader implications. These scenarios included companies and business plans that leverage the technology of synthetic consortia to create economic value.
 +
                                   
 +
                                </p>
 +
                                </section>
 +
                                </div>
 +
                            </div>
 +
                                </section>
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                <!--End Application Scenario BOX-->
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                            <section>
 +
<h3 align="center">Techno-moral Vignette</h3>
 +
                                    <div class="row">
 +
                           
 +
                                <div class="6u">
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                                <section>
 +
 +
                                    <a href="#" class="image fit"><img src="images/appl_scenario.jpg" alt=""/></a>
 +
                                    </section>
 +
                               
 +
                                </div>
 +
                                <div class="6u">
 +
                               
 +
<section>
 +
                                <p>Implementing synthetic biology to produce the things we need in a sustainable way sounds great, but comes with a unique set of repercussions. In a fictional newspaper from the year 2023, we explore potential reactions and consequences - both positive and negative - of the large-scale implementation of synthetic consortia in industrial biotech.
 +
                                </p>
 +
                                </section>
 +
                               
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Revision as of 17:37, 12 September 2015

iGEM Amsterdam 2015

iGEM Amsterdam 2015 

    
        
        
        
        
        
			

        
        
        
 
				

                    

                    
The Problem

					
 The quest for sustainability

                    

                    
                    

					

						

                    

								
								

                                                Our economy still depends largely on fossil resources. For decades, this has fueled the incredible progress of our world, but not without the massive cost of geopolitical instability and global warming - costs we’re now facing more than ever. With the current consequences of climate change visible around the world and global energy demands that are expected to double in 2050, the quest for clean, renewable energy is one of mankind’s most important modern challenges.

Our solution

Combining the best of cyanobacterial sustainability and chemotroph productivity

Synthetic Consortium

the idea is simple: we engineer cyanobacteria to produce simple carbon compounds using CO2 and sunlight in ways that are genetically stable. These molecules are shared with a chemotroph like E. coli, which uses them to produce a desired end-product, like commodity chemicals, pharmaceuticals, or biofuels.

The Goal

In our proof-of-principle consortium, E. coli produces isobutanol (an important biofuel) to highlight its sustainable production potential. But our engineered Synechocystis strains are essentially fully modular cyanobacterial production engines, and can be coupled to any biotechnological production process to remove dependencies on crops or petrochemicals and make it truly sustainable.

Results

How far did we get?

Synechocystis

We engineered various carbon producing pathways in Synechocystis and showed that the accumulation and sharing of carbon compounds can be used by E.coli to grow and make product. Moreover, we demonstrated the importance of genetic stability through evolutionary growth experiments that showed loss of productivity for strains with novel gene insertions and high fitness cost.

e. coli

We designed and implemented a genetic safety switch based on E. coli sharing essential nutrients with an auxotrophic Synechocystis strain. We also built on [insert team] previous efforts and used their biobrick to engineer and demonstrate constitutive iso-1-butanol production of E. coli in co-culture, showing that our consortium can be effectively used for the sustainable production of biofuels.

Dry Lab

Besides using simulations to guide our consortium design, we created software tools that can be used to design new synthetic consortia: Sustainstability™ allows users to identify carbon compounds that can be engineered in a growth-coupled (stable) way, while Auxotrophy Sniper™ identifies auxotrophies that can be engineered to increase bio-safety. Both of these tools are freely available here.

Consortia

We tested our proof-of-princple consortium using the carbon-sharing Synechocystis and bio-fuel producing E. coli and demonstrated mutual growth and product formation. We also developed a micro-droplet screening tool and demonstrated its effectiveness in identifying stable consortia consisting of carbon-sharing cyanobacteria and various chemotrops with biotechnological relevance.

The Team

Six students, trillions of microbes, one purpose

Students

With a combined IQ that is manyfold larger than the sum of its parts, this lean mean student machine has willingly exhanged what could have been a summer of freedom and good weather for the most challenging scientific endeavor of their lives (in what is arguably the most rainy country in the known universe).

Supervisors/Advisors

As in any learning process, working with mentors with laser eyes capable of piercing through a hazy cloud of results to distinguish the signal from the noise can mean the difference between succes and failure. Although our mentors could not shoot lasers out of their eyes, their guidance and advice along the way was invaluable.

Human practices

Applications and implications

Synenergene

Synenergene is an organisation dedicated to fostering responsible research and innovation practices in synthetic biology. They selected a small group of iGEM teams from around the world to collaborate with, which included us. Our human practices efforts therefore revolved around our project with Synenergene.

Application Scenarios

With the help of experts, we wrote several application scenarios in which we conducted detailed investigations into potential real-world applications and their broader implications. These scenarios included companies and business plans that leverage the technology of synthetic consortia to create economic value.

Techno-moral Vignette

Implementing synthetic biology to produce the things we need in a sustainable way sounds great, but comes with a unique set of repercussions. In a fictional newspaper from the year 2023, we explore potential reactions and consequences - both positive and negative - of the large-scale implementation of synthetic consortia in industrial biotech.