Difference between revisions of "Template:Groningen/Human Practices"

 
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<div class="igem_2018_team_content" style="background-color: white">
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<div class="col m1"></div>
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<div class="col s12 m10 l10">
  
            <h5>Integrated Human <br>Practices:</h5>
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<!-- HERE YOU CAN TYPE YOUR STUFF -->
            <ul>
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<div class="column">
                <li><a href="#intro-scroll">Introduction</a></li>
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                <li><a href="#timeline-scroll"></a>Project Timeline</li>
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                <li><a href="#integration-scroll">Integration in our project</a></li>
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            </ul>
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<img src="https://static.igem.org/mediawiki/2018/9/9a/T--Groningen--banner_HP.png" class="responsive-img">
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<p>To get a good overview, we invite you to have a look at our tree of thoughts. This tree catches ideas as new light in its leaves, and by making the right choices, it grew to a great height. Furthermore, we had great conversations on how to let our tree grow further after our iGEM journey has ended. We discussed how to scale up our product StyGreen, which safety procedures we have to keep in mind and how to eventually implement our product in society successfully. These insights plant a seed for a greener future. </p>
  
    <div class="igem_2018_team_column_wrapper">
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<ul class="collapsible popout" data-collapsible="expandable">
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<li id="timeline-scroll" class="scrollspy">
            <h1> Work in Progress </h1>        
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<div class="collapsible-header active">
        </div>
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Our Interactive Human Practices Tree
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<div class="collapsible-body">
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<div class="row">
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<div class="col s12">
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<p> Click on the icons in the timeline and find out all about the insights we gained from our stakeholders and how their input shaped our project. </p>
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</div>
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<div class="col m10 s12">
  
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<div id="HP-Timeline">
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<img src="https://static.igem.org/mediawiki/2018/3/35/T--Groningen--tree6.png" alt="" class="responsive-img">
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<a style="top: 3.05%; left: 42.96%;" class="modal-trigger tree_block" href="#footprint"></a>
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<a style="top: 6.23%; left: 67%;" class="modal-trigger tree_block" href="#katjeloos"></a>
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<a style="top: 4.6%; left: 74.1%;" class="modal-trigger tree_block" href="#karinree"></a>
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<a style="top: 8.15%; left: 12.1%;" class="modal-trigger tree_block" href="#knn"></a>
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<a style="top: 17.84%; left: 72.6%;" class="modal-trigger tree_block" href="#picchioni"></a>
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<a style="top: 20.80%; left: 78.9%;" class="modal-trigger tree_block" href="#fraaije"></a>
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<a style="top: 20.45%; left: 2.3%;" class="modal-trigger tree_block" href="#bordeaux"></a>
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<a style="top: 21.1%; left: 35.5%;" class="modal-trigger tree_block" href="#euvering"></a>
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<a style="top: 16.5%; left: 39.1%;" class="modal-trigger tree_block" href="#polman"></a>
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<a style="top: 31.05%; left: 10.4%;" class="modal-trigger tree_block" href="#driessen"></a>
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<a style="top: 32.63%; left: 64%;" class="modal-trigger tree_block" href="#rivm"></a>
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<a style="top: 47.63%; left: 65.8%;" class="modal-trigger tree_block" href="#evbiotech"></a>
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<a style="top: 48.7%; left: 41.9%;" class="modal-trigger tree_block" href="#scaffold"></a>
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<a style="top: 51.65%; left: 53.2%;" class="modal-trigger tree_block" href="#knockouts"></a>
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<a style="top: 53.3%; left: 24.1%;" class="modal-trigger tree_block" href="#sergey"></a>
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<a style="top: 59.65%; left: 62.9%;" class="modal-trigger tree_block" href="#stakeholderanalysis"></a>
  
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<a style="top: 75.6%; left: 16.2%;" class="modal-trigger tree_block" href="#photanol"></a>
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<a style="top: 75.8%; left: 32.6%;" class="modal-trigger tree_block" href="#zap"></a>
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<a style="top: 75.6%; left: 48.1%;" class="modal-trigger tree_block" href="#avantium"></a>
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<a style="top: 76.1%; left: 68%;" class="modal-trigger tree_block" href="#biobtx"></a>
  
                <h5>Integrated Human <br>Practices:</h5>
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<a style="top: 86.45%; left: 40.91%;" class="modal-trigger tree_block_big" href="#endproduct"></a>
                <ul>
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</div>
                    <li><a href="#intro-scroll">Introduction</a></li>
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<!-- HIER ALLE (POP-UP) MODALS-->
                    <li><a href="#timeline-scroll"></a>Project Timeline</li>
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                    <li><a href="#integration-scroll">Integration in our project</a></li>
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                </ul>
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<div id="fraaije" class="modal">
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<div class="modal-content">
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<h4>Prof. Dr. ir. M.W. Fraaije</h4>
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<p>
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We needed an assay to detect cellulase activity. Luckily, Prof. Fraaije could <a target="_blank" href="Human_Practices#fraaijeinterview">help us out</a>.                                                   
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</p>
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</div>
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<div id="polman" class="modal">
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<div class="modal-content">
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<h4>Prof. Dr. B. Poolman</h4>
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<p>
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We learned about the effects of styrene toxicity in production. Thus we reached out to <a target="_blank" href="Human_Practices#poolmaninterview">an expert</a> who helped us with finding a solution to overcome this limitation.
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</p>
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</div>
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<div id="footprint" class="modal">
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<div class="modal-content">
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<h4>Carbon footprint analysis</h4>
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<p>
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To investigate whether our technology is actually beneficial for the process towards a greener planet, and to what extent, we performed a  Carbon Footprint Analysis. In collaboration with Tjerk Douma we calculated the energy costs to create StyGreen compared to syrene. See <a target="_blank" href="Human_Practices#carbonfootprint">here</a> how we made this analysis.
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</p>
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</div>
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</div>
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<div id="katjeloos" class="modal">
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<div class="modal-content">
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<h4>Katja Loos</h4>
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<p>
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In the process of developing our project design, the decision on what our final product should become was essential. Katja Loos had an enormous influence in this phase, as she explained that biodegradable plastics are not as degradable as we imagine. See <a target="_blank" href="Human_Practices#katjaloosinterview">here</a> what she explained to us. 
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</p>
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</div>
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</div>
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<div id="karinree" class="modal">
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<div class="modal-content">
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<h4>Karin Ree</h4>
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<p>
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Karin Ree supports students that want to perform research outside their regular field. She provided us with connections and research papers on the feasibility of different bioplastics. See <a target="_blank" href="Human_Practices#karinreeinterview">here</a> how she aided us.
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</p>
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</div>
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</div>
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<div id="avantium" class="modal">
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<div class="modal-content">
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<h4>Avantium</h4>
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<p>
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To observe how cellulosic biomass is industrially processed with our own eyes, we drove to Delfzijl to visit the pilot plant of Avantium. We gained insights into upscaling, safety and the processing of cellulosic biomass. See <a target="_blank" href="Human_Practices#avantiuminterview">here</a> what this experience was like.
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</p>
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</div>
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</div>
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<div id="picchioni" class="modal">
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<div class="modal-content">
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<h4>Prof. dr. F. Picchioni</h4>
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<p>
 +
Professor Picchioni greatly influenced our project. He changed our concept of plastics completely, as we had more negative notions about plastics before this conversation than afterwards. You can find a summary of our interview <a target="_blank" href="Human_Practices#picchioniinterview">here</a>.
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</p>
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</div>
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</div>
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<div id="bordeaux" class="modal">
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<div class="modal-content">
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<h4>Collaboration Bordeaux</h4>
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<p>
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Together with the iGEM team of Bordeaux, we discussed the ethics concerning our product. Find more about our ethics collaboration<a target="_blank" href="Ethics">here</a>.
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</p>
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</div>
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</div>
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<div id="euvering" class="modal">
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<div class="modal-content">
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<h4>Gert-Jan Euverink</h4>
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<p>
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Gert-Jan Euverink was the supervisor of the winning 2012 iGEM team, and is also representative of the CADOS project on the use of cellulose in sewage water. Read more about what we discussed with him <a target="_blank" href="Human_Practices#gertjaneuverinkinterview">here</a>.
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</p>
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</div>
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</div>
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<div id="driessen" class="modal">
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<div class="modal-content">
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<h4>Prof. Dr. A.J.M. Driessen</h4>
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<p>
 +
Prof. Driessen helped us in the development of our genetic modification design. Interested? Read more about his input <a target="_blank" href="Human_Practices#driesseninterview">here</a>.
 +
</p>
 +
</div>
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</div>
 +
<div id="rivm" class="modal">
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<div class="modal-content">
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<h4>RIVM</h4>
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<p>
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During the work on our project, we found discussions about safety highly important. Together with the RIVM, we made sure that the safety was also implemented into our design. Would you like to know <a target="_blank" href="Human_Practices#safety">more</a> about this process?
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</p>
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</div>
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</div>
 +
<div id="evbiotech" class="modal">
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<div class="modal-content">
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<h4>EV Biotech</h4>
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<p>
 +
From the start, EV Biotech has been our intellectual partner, and helped us in many aspects of our (lab) work. See <a target="_blank" href="Human_Practices#evbiotechinterview">here</a> why we are very grateful for their support.
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</p>
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</div>
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</div>
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<div id="scaffold" class="modal">
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<div class="modal-content">
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<h4>Molecular Dynamics model</h4>
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<p>
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In our Molecular Dynamics modus, we demonstrated the function of the cellulose binding domain in our design. Visit <a target="_blank" href="Model/Molecular_Dynamics">this page</a> if you want to learn more.
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</p>
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</div>
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</div>
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<div id="knockouts" class="modal">
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<div class="modal-content">
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<h4>Flux Analysis Model</h4>
 +
<p>
 +
Our Flux Analysis Model enabled us to calculate how much styrene we theoretically could produce per kilo biomass. Additionally, we found potential interventions to enhance the production of styrene. Look <a target="_blank" href="Model/Flux_Based_Analysis">here</a> to see what we have learned.
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</p>
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</div>
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</div>
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<div id="sergey" class="modal">
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<div class="modal-content">
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<h4>Sergey (EV Bio)</h4>
 +
<p>
 +
During the TRIZ workshop, Sergey (EV Biotech) provided us with many helpful ideas, including on how we could engineer a continuous process instead of a batch based process. Read more <a target="_blank" href="Applied_Design#bioreactor">here</a> about what the results are.
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</p>
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</div>
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</div>
 +
<div id="stakeholderanalysis" class="modal">
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<div class="modal-content">
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<h4>Stakeholder Analysis</h4>
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<p>
 +
To investigate in which ways our technology would influence the world, we performed a Stakeholder Analysis. Do you want to <a target="_blank" href="Human_Practices#porterinterview">know more</a>?
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</p>
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</div>
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</div>
 +
<div id="photanol" class="modal">
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<div class="modal-content">
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<h4>Photanol</h4>
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<p>
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We visited Photanol for an inspiring look into their laboratory. We received information about the first steps of upscaling and accompanying challenges. For further information, you may <a target="_blank" href="Human_Practices#photanolinterview">click here</a> to see what we have learned.
 +
</p>
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</div>
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</div>
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<div id="zap" class="modal">
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<div class="modal-content">
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<h4>ZAP</h4>
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<p>
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What does it hold to make a pilot plant? What kind of permits are needed? The experts of ZAP patiently <a target="_blank" href="Human_Practices#zapinterview">explained</a>it to us.
 +
</p>
 +
</div>
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</div>
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<div id="knn" class="modal">
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<div class="modal-content">
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<h4>KNN</h4>
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<p>
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KNN is our main biomass supplier. KNN provided us with their product Recell and are curious to see how we will use their product as a feedstock to produce styrene. Find our first talk with them <a target="_blank" href="Human_Practices#knninterview">here</a>.
 +
</p>
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</div>
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</div>
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<div id="biobtx" class="modal">
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<div class="modal-content">
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<h4>BioBTX</h4>
 +
<p>
 +
BioBTX is a company which has similarities to us in some ways. They produce biobased aromatics, but in a chemical way. We discussed the differences between chemical and biological ways of styrene production <a target="_blank" href="Human_Practices#biobtxinterview">here</a>.
 +
</p>
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</div>
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</div>
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<div id="endproduct" class="modal">
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<div class="modal-content">
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<h4>Upscaling of our end-product</h4>
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<p>
 +
After realization of a proof-of-concept, several interested parties are willing to make investments. You can read more about our conversations <a target="_blank" href="Human_Practices#ludosinterview">here</a>.
 +
</p>
 +
</div>
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</div>
  
        <div class="column full_size">
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</div> <!-- END col m10 s12 -->
            <h1>Human Practices</h1>
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</div>
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</div>
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</div>
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</li>
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</ul>
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<div class="col m1"></div>        
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</div>
  
            <div id="HP-Timeline">
 
                <img src="https://static.igem.org/mediawiki/2017/a/ad/T--TUDelft--2017_IHP_TimelineV7.jpeg" alt="" class="responsive-img">
 
                <a style="top: 1.5%; left: 40%; height: 2%; width: 20%;" class="modal-trigger" href="#microbial-carrier"></a>
 
<a style="top: 56.5%; left: 61%; height: 1.5%; width: 31%;" class="modal-trigger" href="#beneluxmeetup"></a>
 
<a style="top: 3.7%; left: 8%; height: 1.7%; width: 33%;" class="modal-trigger" href="#shield"></a>
 
                <a style="top: 3.7%; left: 7%; height: 1.6%; width: 34%;" class="modal-trigger" href="#shield"></a>
 
                <a style="top: 5.5%; left: 70%; height: 3%; width: 20%;" class="modal-trigger" href="#rathenau"></a>
 
                <a style="top: 7.5%; left: 40%; height: 2%; width: 20%;" class="modal-trigger" href="#brainstorm"></a>
 
                <a style="top: 9%; left: 70%; height: 2%; width: 25%;" class="modal-trigger" href="#detection"></a>
 
                <a style="top: 11%; left: 10%; height: 3%; width: 25%;" class="modal-trigger" href="#storable"></a>
 
                <a style="top: 14%; left: 32%; height: 3%; width: 35%;" class="modal-trigger" href="#cellfree"></a>
 
                <a style="top: 14.7%; left: 65%; height: 3.5%; width: 27%;" class="modal-trigger" href="#ELSIB"></a>
 
                <a style="top: 17%; left: 0%; height: 3.5%; width: 45%;" class="modal-trigger" href="#synenergene"></a>
 
                <a style="top: 21.5%; left: 25%; height: 2%; width: 30%;" class="modal-trigger" href="#doctors"></a>
 
                <a style="top: 22.7%; left: 83%; height: 1.3%; width: 13%;" class="modal-trigger" href="#ster1"></a>
 
                <a style="top: 24.4%; left: 78%; height: 1.3%; width: 13%;" class="modal-trigger" href="#ster2"></a>
 
                <a style="top: 25.4%; left: 19%; height: 1.3%; width: 19%;" class="modal-trigger" href="#ster3"></a>
 
                <a style="top: 25.9%; left: 5%; height: 1.3%; width: 19%;" class="modal-trigger" href="#ster5"></a>
 
                <a style="top: 26.8%; left: 25%; height: 1.3%; width: 19%;" class="modal-trigger" href="#ster4"></a>
 
                <a style="top: 26.5%; left: 63%; height: 2.6%; width: 30%;" class="modal-trigger" href="#abres"></a>
 
                <a style="top: 30.8%; left: 58%; height: 3%; width: 30%;" class="modal-trigger" href="#GMO"></a>
 
                <a style="top: 32.4%; left: 4%; height: 3%; width: 30%;" class="modal-trigger" href="#tube"></a>
 
                <a style="top: 35.7%; left: 7%; height: 3%; width: 91%;" class="modal-trigger" href="#valuedesign"></a>
 
                <a style="top: 41.7%; left: 0%; height: 3%; width: 40%;" class="modal-trigger" href="https://2017.igem.org/Team:TUDelft/Design#vesicles"></a>
 
                <a style="top: 41.3%; left: 33%; height: 3%; width: 40%;" class="modal-trigger" href="https://2017.igem.org/Team:TUDelft/Design#cas13a"></a>
 
                <a style="top: 41.7%; left: 72%; height: 3%; width: 32%;" class="modal-trigger" href="https://2017.igem.org/Team:TUDelft/Design#TDP"></a>
 
                <a style="top: 48.3%; left: 63%; height: 2.3%; width: 24%;" class="modal-trigger" href="#mail"></a>
 
                <a style="top: 51.3%; left: 3%; height: 2%; width: 36%;" class="modal-trigger" href="#IKB"></a>
 
                <a style="top: 53.3%; left: 50%; height: 2.5%; width: 41%;" class="modal-trigger" href="#biotech"></a>
 
                <a style="top: 60.3%; left: 0%; height: 2.2%; width: 34%;" class="modal-trigger" href="#GD"></a>
 
                <a style="top: 59.3%; left: 41%; height: 1.8%; width: 21%;" class="modal-trigger" href="#vet1"></a>
 
                <a style="top: 60.5%; left: 65%; height: 1.8%; width: 21%;" class="modal-trigger" href="#vet2"></a>
 
                <a style="top: 63.9%; left: 56%; height: 4.5%; width: 39%;" class="modal-trigger" href="#farmer"></a>
 
                <a style="top: 66.2%; left: 0%; height: 3.9%; width: 38%;" class="modal-trigger" href="#RD"></a>
 
                <a style="top: 70.4%; left: 0%; height: 1.8%; width: 21%;" class="modal-trigger" href="#manager"></a>
 
                <a style="top: 71.9%; left: 45%; height: 3.8%; width: 58%;" class="modal-trigger" href="#BRC"></a>
 
                <a style="top: 77.5%; left: 6%; height: 1.8%; width: 37%;" class="modal-trigger" href="#IO"></a>
 
                <a style="top: 76.4%; left: 56%; height: 3.8%; width: 44%;" class="modal-trigger" href="#CEE"></a>
 
                <a style="top: 82%; left: 35%; height: 1.8%; width: 44%;" class="modal-trigger" href="#MD"></a>
 
                <a style="top: 84.5%; left: 0%; height: 1.6%; width: 53%;" class="modal-trigger" href="#parade"></a>
 
                <a style="top: 86%; left: 47%; height: 4.6%; width: 53%;" class="modal-trigger" href="#experts"></a>
 
                <a style="top: 90.4%; left: 4%; height: 3.8%; width: 89%;" class="modal-trigger" href="#validation"></a>
 
            </div>
 
            <div id="microbial-carrier" class="modal">
 
                <div class="modal-content">
 
                    <h4>Microbial Carrier</h4>
 
                    <h5>Insights</h5>
 
  
                    <ul class="skel browser-default">
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<!-- RIGHT BETWEEN THOSE TWO COMMENTS -->
                        <li>Not relevant - Which problem will it solve? How will it go to the pathogen in a pool of fishes where the current will be really strong? </li>
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</div>
                        <li>Not responsible - not safe due to the introduction of GMO in the open environment</li>
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<div class="col m1"></div>
                    </ul>
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                    <h5>Changes</h5>
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                    <ul class="skel browser-default">
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                        <li>Project change &amp; target/problem change to make it more relevant</li>
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                                Summary
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                                        <p style="text-align: justify">One of the industries that greatly contributes to the antibiotic resistance problem is the fish farming industry. To achieve high yields and profits, many farmers are now applying intensive farming methods which involves the misuse of antibiotic usage. Our first idea was to solve this problem by engineering a bacterium that can sense the pathogen and swim towards it. After arriving there, a neutralizing agent will either be released or produced and excreted on the spot. Antibiotic resistance shield The overuse of antibiotics has led to the development of antibiotic resistances. Although this problem has already been popping up in scientific and newspaper articles for over 30 years, its threat is one that can no longer be ignored. The US Department of Health and Human Services estimates that annually over 2 million illnesses and 23,000 deaths in the United States are caused by antibiotic resistance. Moreover, it is approximated that by 2050, 10 million people will die annually due to antibiotic resistance. The ‘antibiotic apocalypse’ needs to be prevented, so action should be taken now!</p>
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                                    </div>
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                                </div>
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                            </div>
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                        </li>
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                    </ul>
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                </div>
 
            </div>
 
<div id="beneluxmeetup" class="modal">
 
                    <div class="modal-content">
 
                        <h4>Benelux Meetup at Wageningen UR</h4>
 
                        <p>During the <a href="https://2017.igem.org/Team:Wageningen_UR/HP/Meetup" target="_blank">Benelux Meetup</a> we attend an extensive workshop.
 
                        </p>
 
                        <ul class="collapsible popout" data-collapsible="expandable">
 
                            <li>
 
                                <div class="collapsible-header">
 
                                    Citation Wageningen iGEM Team 2017
 
                                </div>
 
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                                        <div class="col s15">
 
  
                                            <blockquote>""The goal of the workshop was for each iGEM team to get out of their expert point of view and discover what the needs or problems would be for the end-user of their project. The teams were to find out: What would it mean to use the technology in practice? Three to six people of each iGEM team were coupled to a small group of another team. Next, one team got to shortly explain their project as 'developer'. The other team was to ask questions as 'end-user' about how the use of the technology and its influence on their lives or work. After 15 minutes, the roles were reversed. The experts and alumni iGEM teams were also invited to participate. </blockquote><cite>- Wageningen iGEM Team 2017</cite>
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                                        </div>
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 +
<div class="column">
 +
<h1>Introduction</h1>
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<p>For the StyGreen project, Human Practices was not a box that needed to be ticked. On the contrary, it was a tool to integrate our project into the real world. As production of plastics can be a sensitive subject, Human Practices was important from the very start of our project. </p>
  
                                    </div>
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<p>As Human Practices is not binary, but a continuous and constant process. Here provide a summary of the biggest influences on the design of our project. Additionally, many insights were gained by talking to our friends, family and complete strangers. One of the first questions was always: “why more plastics?”. We have discussed this with several experts and investigated the advantages and disadvantages of different plastics. We looked into both <a target="_blank" href="Human_Practices#katjaloosinterview">‘biodegradable’ plastics</a>, as well as non-biodegradable <a target="_blank" href="Human_Practices#avantiuminterview"></a> plastics. </p>
                                </div>
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                            </li>
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                        </ul>
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                    </div>
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                </div>
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            <div id="brainstorm" class="modal">
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<p>The starting point of our project was a look at the world as it is. We have marvelous technologies which make our lives better, things that were problems 100 years ago are forgotten and information can be shared faster than ever. However, there is also something terribly wrong with this world. Temperature is rising, animals go extinct: our advancement is at the cost of the planet.</p>
                <div class="modal-content">
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                    <h4>Brainstorming</h4>
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                    <p>As described before, combating the development of antibiotic resistances was a project we thought worth working on. Nevertheless, we did not consider the application in fish farms as a feasible option anymore. So, we went back to brainstorming. Here, we thought about a new potential application: fighting (the formation of) biofilms, for example in industrial pipelines and on boat hulls. Additionally, we came up with ideas to remove biofilms from food and plants (Agrobacterium). Nevertheless, all these ideas either had a much easier and well-implemented chemical alternative or they were very questionable with regards to safety (i.e. containment of the genetically modified organism) and effectivity. Luckily, we ran into new possibilities!
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                    </p>
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                </div>
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            </div>
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            <div id="rathenau" class="modal">
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                <div class="modal-content">
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                    <h4>Feedback Synergene/rathenau</h4>
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                    <div class="row">
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                        <div class="center-margin col s12 m10">
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                            <div class="col m4 s12">
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<p>We love all these advancements. We would lie if we say we did not, but we do want to solve the downside of our development. Therefore, we took a closer look at plastic. Plastic is a wonderful product and these days it is impossible to live without it. We looked into the production of plastic. Can we make clean plastic non-polluting plastic? And how do we use this plastic responsibly? On the Human Practices pages you'll found where our journey brought us; from schools to festivals; from start-ups to multinationals.  
                                <img class="responsive-img" src="https://static.igem.org/mediawiki/2017/7/71/T--TUDelft--Synenergene.png" alt="Synenergene">
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</p>
 +
</div>
  
                            </div>
 
  
                            <div class="col m6 s12">
 
                                <img class="responsive-img" src="https://static.igem.org/mediawiki/2017/f/f2/T--TUDelft--RathenauInstituut.png" alt="Rathenau">
 
  
                            </div>
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<div class="clear extra_space"></div>
                        </div>
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                    </div>
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                    <h5>Insights</h5>
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                    <ul class="skel browser-default">
 
                        <li>How to keep the GMO in a contained environment
 
                        </li>
 
                        <li>Think about worst case scenario, how to solve it</li>
 
                        <li>Kill switch when fish swallow the GMO</li>
 
                        <li>Way of how we sell our idea/ pitch presentation </li>
 
                        <li>Other methods of how to tackle this problem without the use of GMO
 
                        </li>
 
                        <li>Talk with stakeholders to really understand what the problem is or where the problem is
 
                        </li>
 
                        <li>Ask them what kind of solution is required</li>
 
                        <li>Relevance of using synthetic biology as a solution</li>
 
                    </ul>
 
                    <h5>Changes</h5>
 
                    <ul class="skel browser-default">
 
                        <li>Change project while using the same elements
 
                        </li>
 
                    </ul>
 
                    <br>
 
                    <ul class="collapsible popout" data-collapsible="expandable">
 
                        <li>
 
                            <div class="collapsible-header">
 
                                Summary
 
                            </div>
 
                            <div class="collapsible-body">
 
                                <div class="row center">
 
                                    <div class="col s15">
 
                                        <p>We were invited to the Synenergene event organised by Rathenau Institute. This event was to make iGEM teams realise the importance of performing a responsible research in their project. During the event we came into contact with several stakeholders and experts. </p>
 
                                    </div>
 
                                </div>
 
                            </div>
 
                        </li>
 
                    </ul>
 
                </div>
 
            </div>
 
  
            <div id="shield" class="modal">
 
                <div class="modal-content">
 
                    <h4>Antibiotic resistance shield</h4>
 
                    <p>The overuse of antibiotics has led to the development of antibiotic resistances. Although this problem has already been popping up in scientific and newspaper articles for over 30 years, its threat is one that can no longer be ignored. The US Department of Health and Human Services estimates that annually over 2 million illnesses and 23,000 deaths in the United States are caused by antibiotic resistance. Moreover, it is approximated that by 2050, 10 million people will die annually due to antibiotic resistance. The ‘antibiotic apocalypse’ needs to be prevented, so action should be taken now!
 
                    </p>
 
                </div>
 
            </div>
 
  
            <div id="detection" class="modal">
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<div class="column">
                <div class="modal-content">
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                    <h4>Antibiotic resistance detection with Cas13a</h4>
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                    <p>Up until now, we had been focussing on a plan with the protein Cas9. Nevertheless, this was not the optimal protein for what we wanted to achieve. Participating in iGEM, we caught up with the most recent achievements in the synthetic biology field, amongst which a very interesting paper about Cas13a by Gootenberg et al. Their paper indicated attomolar sensitivity in combination with rapid DNA or RNA detection, which would be perfect for detecting antibiotic resistance genes!
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                    </p>
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                </div>
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            </div>
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            <div id="storable" class="modal">
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                <div class="modal-content">
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                    <h4>Tardigrade proteins</h4>
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                    <p>Simultaneously, team members came up with a completely different idea, based on practical limitations in the lab instead of a societal problem: western blotting. In order to improve on this method, we would require proteins from tardigrades (also known as water bears). Tardigrades can survive under very extreme conditions, such as outer space. Their robustness is (partly) derived from the so-called tardigrade proteins, that protect cell(-structures) and proteins from dehydration and preserve protein activity after drying and rehydration. The western blotting idea was discarded because of practical limitations. Nevertheless, we saw the tardigrade proteins as a perfect opportunity to combine an antibiotic resistance detection system with microfluidics on paper, for which the drying of proteins would be necessary!
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                    </p>
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                </div>
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            </div>
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            <div id="cellfree" class="modal">
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                <div class="modal-content">
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                    <h4>Cas13a in vesicles</h4>
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                    <p>Now that we were thinking about using Cas13a in combination with paper microfluidics, we wanted a method to make it easier for us to dry the protein on the paper. Additionally, we wanted to do this in such a way that the final product would be cell-free. Inspiration for the solution came from other iGEM teams, who had previously tried to produce vesicles and transport green fluorescent protein in these vesicles. Vesiculation would indeed be a solution to our problem, so it was added as an integral part of our project.
+
                    </p>
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                </div>
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            </div>
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            <div id="ELSIB" class="modal">
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                <div class="modal-content">
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                    <h4>Ethical Legal and Social Issues in Biotechnology. </h4>
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                    <h5>Name</h5>
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                    <p>Dr. Lotte Asvled</p>
+
                    <h5>Function</h5>
+
                    <p>Assistant Professor Biotechnology and Society</p>
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                    <h5>Insights</h5>
+
                    <ul class="skel browser-default">
+
                        <li>Introduction to ethical, legal and social Issues in Biotechnology
+
                        </li>
+
                        <li>Importance of stakeholder mapping</li>
+
  
                    </ul>
+
<h1 id="carbonfootprint">Carbon footprint analysis</h1>
                    <h5>Changes</h5>
+
<h3>Producing styrene from organic waste</h3>
                    <ul class="skel browser-default">
+
<h4>The aim</h4>
                        <li>Validating project with stakeholders </li>
+
<p>We are facing a huge increase in global population: from the current world population of 7.6 billion to an expected 9.8 billion people in 2050 [<a target="_blank" href="https://www.un.org/development/desa/publications/world-population-prospects-the-2017-revision.html">1</a>]. This projected increase in global population leads to an increase in both food and energy consumption, which in turn in is associated with an increased emission of greenhouse gasses. Right now, we live in a plastic generation. The global production and consumption of plastics have been on the rise for over 50 years now, reaching a plastic consumption of 297.5 million tons by the end of 2015 [<a target="_blank" href="http://www.worldwatch.org/global-plastic-production-rises-recycling-lags-0">2</a>]. Plastic products from the petrochemical industry have a high carbon footprint (Boonniteewanich, Pitivut, Tongjoy, & Lapnonkawow, 2014). The combination of global population increase and a mass consumed non-eco-friendly product, in the form of petroleum-based plastics, could be disastrous. This is one of the reasons that the Groningen iGEM team’s project attempts to produce (bio)styrene, a building block for many plastics, from cellulose as an alternative to petroleum-based styrene. In this section we have carried out a partial Life Cycle Assessment (LCA) to identify the environmental impact of both petroleum-based styrene and bio-based styrene. The main purpose is to provide an insight in the environmental burden that is caused by the worldwide styrene industry in terms of carbon dioxide equivalent emissions (CO2-eq) and to showcase our greener alternative.</p>
                        <li>Towards a value sensitive design</li>
+
<p> For our LCA analysis we have used the Dutch Gross Energy Requirements values (GER) Values. These values are used for a ‘cradle to gate’ analysis and include all emissions that are needed to produce a certain product. These process emissions exclude any carbon flux from or to the atmosphere. In the case of a bio-based feedstock this is a complete analysis, because the carbon uptake is balanced with the emissions once the product is disposed of. For fossil fuel based styrene a value of 3,1 KG needs to be added to this  (Croezen & Lieshout, 2015) because these emission will lead to a net carbon emission. (see figure 1) (Croezen & Lieshout, 2015). A full LCA should also include other impact categories, however it is decided not to include these; we discovered the LCA analysis in a late phase of the project which forced us to simplify the analysis. </p>
                    </ul>
+
                    <br>
+
                    <ul class="collapsible popout" data-collapsible="expandable">
+
                        <li>
+
                            <div class="collapsible-header">
+
                                Summary
+
                            </div>
+
                            <div class="collapsible-body">
+
                                <div class="row center">
+
                                    <div class="col s15">
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                                        <p>We started this course by mapping all factors relevant for our design. We included every possible factor that could in some way be influenced by our technology. The next step was to identify the most important stakeholders and their values. We came up with many values, some were colliding. During this course we had to analyse potential stakeholders and we came up with a value sensitive design. However, we found out that we still had a broad range of stakeholders, leading to many values that had to be integrated. After this course, we really started steering our project towards a more relevant application. We decided that we needed to narrow our scope in order to integrate values into our design. We interacted with many more stakeholders and set up a new value sensitive design. This course was good practice and a good starting point after which the real stakeholder interactions began.</p>
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                                    </div>
+
                                </div>
+
                            </div>
+
                        </li>
+
                    </ul>
+
                </div>
+
            </div>
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            <div id="ster2" class="modal">
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                <div class="modal-content">
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                    <h4>Input farmer</h4>
+
                    <h5>Name</h5>
+
                    <p>Tjerkje Poppinga</p>
+
                    <h5>Function</h5>
+
                    <p>Tjerkje is studying higher professional education livestock farming. She helps her dad on his dairy farm.</p>
+
                    <h5>Insights</h5>
+
                    <ul class="skel browser-default">
+
                        <li>Udder infection (mastitis) is a long-standing disease at dairy farms.
+
                        </li>
+
                        <li>Farmers want a faster method to determine which antibiotics to use to treat mastitis if the default antibiotic does not work and if she can do the test herself she would like to, to save costs of the veterinarian.
+
                        </li>
+
  
                    </ul>
 
                    <h5>Changes</h5>
 
                    <ul class="skel browser-default">
 
                        <li>Meet the values fast and cheap
 
                        </li>
 
                        <li>Meet user-friendliness based on the farmer as potential user
 
                        </li>
 
                    </ul>
 
                    <br>
 
                    <ul class="collapsible popout" data-collapsible="expandable">
 
                        <li>
 
                            <div class="collapsible-header">
 
                                Summary
 
                            </div>
 
                            <div class="collapsible-body">
 
                                <div class="row center">
 
                                    <div class="col s15">
 
                                        <p>Tjerkje said the most common diseases on the farm are utter infection and claw disorders. The farmers treat udder infection (mastitis) themselves. For this they have antibiotics that they are allowed to inject in the cows. Most of the times this works, but sometimes it does not, then they have to call the veterinarian. They try to do most things by themselves to prevent high bills from the vet. With mastitis they then have to hand in milk for an antibiotic resistance test, this test takes 2-3 days until results come in on which antibiotics to use. Tjerkje wants a faster method and if she can do the test herself she would like to to save costs of the veterinarian.
 
                                        </p>
 
                                    </div>
 
                                </div>
 
                            </div>
 
                        </li>
 
                    </ul>
 
                </div>
 
            </div>
 
            <div id="ster3" class="modal">
 
                <div class="modal-content">
 
                    <h4>Input veterinarian</h4>
 
                    <h5>Name</h5>
 
                    <p>Gerbrich Bonekamp</p>
 
                    <h5>Function</h5>
 
                    <p>Student Bioveterinary Sciences</p>
 
                    <h5>Insights</h5>
 
                    <ul class="skel browser-default">
 
                        <li>The most common pathogens in livestock are <i>E. Coli</i>, <i>Salmonella</i>, <i>Streptococcus aureus</i>, <i>Staphylococcus agalactiae</i>
 
                        </li>
 
                        <li>Trade-off between reducing antibiotic resistance or animal health. Farmers are trying to reduce misuse of antibiotics, but if they wait to long with treatment the illness could become worse, resulting in reduced animal health.
 
  
                        </li>
+
<figure><img class="responsive-img" src="https://static.igem.org/mediawiki/2018/f/f9/T--Groningen--lcaexplain.jpg">
 +
<figcaption><i>Figure 1. Figure retrieved from: <a target="_blank" href="http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S1021-20192013000200001">http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S1021-20192013000200001</a></i></figcaption>
 +
</figure>
  
                    </ul>
 
                    <h5>Changes</h5>
 
                    <ul class="skel browser-default">
 
                        <li>Look into <i>Salmonella</i> </li>
 
                    </ul>
 
                    <br>
 
                    <ul class="collapsible popout" data-collapsible="expandable">
 
                        <li>
 
                            <div class="collapsible-header">
 
                                Summary
 
                            </div>
 
                            <div class="collapsible-body">
 
                                <div class="row center">
 
                                    <div class="col s15">
 
                                        <p>Gerbrich studies animal sciences. She told us that E. Coli, Salmonella, Streptococcus aureus and Staphylococcus agalactiae are the most common pathogens in livestock farming. Giving preventive antibiotics is not allowed anymore, the rules to prescribe antibiotics are quite strict in the Netherlands for the dairy sector. Every year the veterinarian composes a plan together with the farmer, for which antibiotics are allowed to use for which illnesses. When a farmer wants to deviate from this plan the veterinarian needs to have a written declaration. Every antibiotics used needs to be registered. A farmer can thus inject the antibiotics himself, the challenge is that while farmers are trying to reduce antibiotic usage, on the other hand, if they wait to long with treatment the illness could become worse, resulting in reduced animal health.
 
                                        </p>
 
                                        <p>We asked Gerbrich if there are possibilities to fight multi-resistant bacteria like the salmonella bacterium with antibiotics. She told us that there are still some antibiotics which are used only human. If the veterinarian decides it is necessary to use these, there can be an exception. It is however under strict supervision and noted down which veterinarian prescribes these antibiotics. If antibiotics can no longer be used because of stricter regulations, breeders should focus on health and robustness of the cow. Lower production of milk could also result in a healthier cow because the cow can put more energy in its own immune system. In order to bring the disease burden down, the environment and food for the cow should be adjusted accordingly. The stress on the animal should be minimized as stress has negative effects on the immune system of the cows. According to Gerbrich the solution to the antibiotic resistance problem is further reducing the use of antibiotics in all sectors of livestock farming. Besides this she thinks reducing the transport of animals can improve the situation as then the spreading of the resistant bacteria becomes less. When transport is necessary hygiene is of utter importance!
 
                                        </p>
 
                                    </div>
 
                                </div>
 
                            </div>
 
                        </li>
 
                    </ul>
 
                </div>
 
            </div>
 
            <div id="ster1" class="modal">
 
                <div class="modal-content">
 
                    <h4>Input farmer</h4>
 
                    <h5>Name</h5>
 
                    <p>Machiel Vries</p>
 
                    <h5>Function</h5>
 
                    <p>Cow farmer and breeder at Domela Holsteins</p>
 
                    <h5>Insights</h5>
 
                    <ul class="skel browser-default">
 
                        <li>There are plenty of different diseases that play a role in the dairy industry.
 
                        </li>
 
                        <li>Fast diagnosis is essential to minimize loss of cattle and productivity, since most illnesses cannot be prevented.
 
                        </li>
 
                        <li>While only sick cows are treated with antibiotics, more antibiotics are potentially used in the chicken and pig industry.
 
                        </li>
 
                        <li>Para-infectious diseases (spread through manure) are especially tricky.</li>
 
                        <li>The tool should neither be too complicated, nor take a lot of time.
 
                        </li>
 
  
                    </ul>
+
<h4>Analysis</h4>
                    <h5>Changes</h5>
+
<p>
                    <ul class="skel browser-default">
+
For our analysis, we compared the process of producing styrene from a bio-based feedstock to the process of producing styrene with petroleum as a feedstock. To define the cradle to gate emission of petroleum-based styrene we contacted two experts of the company CE Delft, the authors of a report stating the GER for industrial feedstock (Croezen & Lieshout, 2015). With their expert help, we were able to define the cradle to gate emission of petroleum-based styrene for our analysis, the value being: 7.8 CO2-eq per kilogram styrene.
                        <li>Research into the chicken and pig industry.
+
</p>
                        </li>
+
<p>
                        <li>Research into Bovine Virus <i>Diarrhoea</i>, a para-infectious disease.
+
Now we need to compare the GER of petroleum-based styrene with the GER of our StyGreen. In order to do this we need to define the GER of StyGreen. The first step in defining the amount of CO2-eq per kilogram StyGreen is: defining the feedstock. We explored many different <a target="_blank" href="Applied_Design#source">feedstock options</a>. After comparing many possibilities, we decided to use recycled toilet paper. The main reason for this choice was the sustainability aspect. Recycled toilet paper is not used for anything at this moment. Therefore, it could be argued that it does not hold monetary value or even a negative monetary value. This means that we can add value to the life-cycle of toilet paper. Another reason for choosing toilet paper, is that we do not want to compete with the food industry. It might be feasible to use sugar, or first generation resources to produce styrene, but this does not fit into our view of a better world.  
                        </li>
+
</p>
                    </ul>
+
<p>
                    <br>
+
The second step was to calculate the carbon footprint of recycled toilet paper. The carbon footprint of a feedstock in a certain phase of the Life-Cycle analysis is proportional to the monetary value the feedstock holds in that particular phase. Since the recycled toilet paper is derived from paper, we looked into the monetary value of recycled toilet paper in combination to the resource, paper. After this we looked at the price of the toilet paper, and compared to the price of wood. This way, we could make a parallel to the toilet paper CO2-eq. The cradle to grave carbon emission of paper is 0.9 CO2-eq per kg paper (Croezen & Lieshout, 2015; figure 2 gives a visual representation of the factors determining the carbon emission of paper feedstock).  
                    <ul class="collapsible popout" data-collapsible="expandable">
+
</p>
                        <li>
+
                            <div class="collapsible-header">
+
                                Summary
+
                            </div>
+
                            <div class="collapsible-body">
+
                                <div class="row center">
+
                                    <div class="col s15">
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                                        <p>As a farmer, Machiel aims to deliver qualitatively good cow milk as inexpensive as possible. In 2014 his company started to buy embryos to enhance the animal’s properties through breeding. These are strong races with health certificates.
+
                                        </p>
+
                                        <p>Machiel informed us about different diseases that play a role in the dairy industry, such as Infectious Bovine Rhinotracheitis (IBR; viral) and pneumonia. For some (like IBR), animals can be vaccinated. However, often this is not the case. So, the only thing that can be done to minimize the loss of cattle and productivity, is quick diagnosis of illnesses. Currently, a blood sample takes approximately half a week to be analysed.</p>
+
                                        <p>According to Machiel, no antibiotics are given to cows (in the Netherlands) unless they are sick. This is potentially different in the chicken and pig industry, which he suggested us to look into. Furthermore, he recommended research in para-infectious diseases, i.e. diseases spread via manure (e.g. Bovine Virus <i>Diarrhoea</i>).
+
                                        </p>
+
                                        <p>With regards to our tool, Machiel thinks this would be very useful. However, the tool should then neither be too complicated, nor take a lot of time, as farmers generally do not have much spare time.
+
                                        </p>
+
                                    </div>
+
                                </div>
+
                            </div>
+
                        </li>
+
                    </ul>
+
                </div>
+
            </div>
+
            <div id="synenergene" class="modal">
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                <div class="modal-content">
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                    <h4>iGEMMers guide to the future</h4>
+
                    <div class="row ">
+
                        <div class=" center-margin col m8 s12">
+
                            <img class="responsive-img" src="https://static.igem.org/mediawiki/2017/6/68/T--TUDelft--iGEMguide.jpeg" alt="Guide">
+
  
                        </div>
+
<figure><img class="responsive-img" src="https://static.igem.org/mediawiki/2018/5/52/T--Groningen--LCA.jpg">
                    </div>
+
<figcaption><i>Figure 2. Life cycle assessment of offset paper production (Silva et al., 2015). </a></i></figcaption>
                    <h5>Name</h5>
+
</figure>
                    <p>Zoe Robaey</p>
+
                    <h5>Function</h5>
+
                    <p>Researcher<br> Co-author iGEMer's Guide to the Future - SYNENERGENE/Rathenau Instituut
+
                    </p>
+
                    <h5>Insights</h5>
+
                    <ul class="skel browser-default">
+
                        <li>Many guidelines for Integrated Human practices
+
                        </li>
+
  
                    </ul>
+
<p>
                    <h5>Changes</h5>
+
The cost of paper is €150 per ton. Due to the fact that toilet paper recycling is still in its infancy, it was hard to define the representative price for this resource. However, after talking to several experts(<a target="_blank" href="Human_Practices#porter">as you see here</a>), we came to a price estimate of  €15 per ton. Since, toilet paper holds 10% of the monetary value of paper, we divided the CO2-eq by 10 as well, giving our recycled toilet paper feedstock a carbon footprint of 0.09 CO2-eq per kilogram.
                    <ul class="skel browser-default">
+
</p>
                        <li>Production of a video project explaining its value </li>
+
<figure>
                    </ul>
+
<table><tr><th>Feedstock</th><th>Price (€ per ton)</th><th>Conversion factor</th><th>Emissions (CO2 per kg)</th></tr><tr><td>Paper</td><td>150</td><td>90%</td><td>0.9</td></tr><tr><td>Recycled toilet paper</td><td>15</td><td>10%</td><td>0.09</td></tr></table>  
                    <br>
+
<figcaption><i>Table 1. The carbon emissions of our feedstock, recycled toilet paper.</i></figcaption>
                    <ul class="collapsible popout" data-collapsible="expandable">
+
</figure>
                        <li>
+
<p>Next we need to know how much energy (and therefore, how carbon emissions) is required to produce 1 kilogram of StyGreen. The energy requirement is based on the following formula (see table 2): </p>
                            <div class="collapsible-header">
+
                                Summary
+
                            </div>
+
                            <div class="collapsible-body">
+
                                <div class="row center">
+
                                    <div class="col s15">
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                                        <p>The iGEMmers guide to the future is a tool which helps iGEM teams to incorporate IHP in their project. On this website there are numerous methods on how to tackle several parts of the IHP, such as brainstorm mapping, stakeholder mapping and SWOT (risk analysis). Their goals is for us to do responsible innovation.</p>
+
                                    </div>
+
                                </div>
+
                            </div>
+
                        </li>
+
                    </ul>
+
                </div>
+
            </div>
+
  
            <div id="ster4" class="modal">
+
<img class="responsive-img" src="https://static.igem.org/mediawiki/2018/6/6e/T--Groningen--EnergyRequirementsFormula.png">
                <div class="modal-content">
+
                    <h4>KNMvD</h4>
+
                    <div class="row ">
+
                        <div class=" center-margin col m4 s12">
+
                            <img class="responsive-img" src="https://static.igem.org/mediawiki/2017/e/eb/T--TUDelft--KNMvD.png" alt="KNMvD">
+
  
                        </div>
+
<p>From the energy requirements we can now derive the process emissions in CO2 per kg StyGreen by means of the following formula (see table 2):</p>
                    </div>
+
                    <h5>Name</h5>
+
                    <p>Joost van Herten</p>
+
                    <h5>Function</h5>
+
                    <p>Senior Policy Advisor for Veterinary Affairs at the Royal Dutch Society for Veterinary Medicine (KNMvD). KNMvD is the professional organization for veterinary surgeons in the Netherlands. The KNMvD promotes the professional development considering veterinarians in the field of animal welfare, animal health, public health and food safety.
+
                    </p>
+
                    <h5>Insights</h5>
+
                    <ul class="skel browser-default">
+
                        <li>The use of formularies by veterinarians considering the bacterial infections and the antibiotic treatment per animal specie.
+
                        </li>
+
                        <li> Contact with veterinarian experts
+
                    </ul>
+
                    <h5>Changes</h5>
+
                    <ul class="skel browser-default">
+
                        <li>Integration of detection method in current treatment protocols
+
                        </li>
+
                        <li>Narrowing the detection method to one disease</li>
+
                    </ul>
+
                    <br>
+
                    <ul class="collapsible popout" data-collapsible="expandable">
+
                        <li>
+
                            <div class="collapsible-header">
+
                                Summary
+
                            </div>
+
                            <div class="collapsible-body">
+
                                <div class="row center">
+
                                    <div class="col s15">
+
                                        <p>The insights of the methods (<a href="http://wvab.knmvd.nl/formularia" target="_blank">formularies</a> and <a href="https://www.kwaliteitdiergeneeskunde.nl/kwaliteit/richtlijnen/algemeen-richtlijnen" target="_blank">guidelines</a>) veterinarians use, gave us insights in how our detection method could add value to the current regulations concerning antibiotic treatment. We found out that the treatment per animal disease is very specific, and that we had narrow our scope to one animal disease to add value. In the future, the detections methods could be slightly adapted with regards to a specific animal disease.
+
                                        </p>
+
                                    </div>
+
                                </div>
+
                            </div>
+
                        </li>
+
                    </ul>
+
                </div>
+
            </div>
+
            <div id="abres" class="modal">
+
                <div class="modal-content">
+
                    <h4>Input Microbial Resistance Expert</h4>
+
                    <h5>Name</h5>
+
                    <p>Mark van Passel</p>
+
                    <h5>Function</h5>
+
                    <p>Antiicrobial Resistance Expert</p>
+
                    <h5>Insights</h5>
+
                    <ul class="skel browser-default">
+
                        <li>Resistant bacteria are not necessarily the pathogen causing the infection
+
                        </li>
+
                        <li>Look into protocol of farmers and see where our project will shine</li>
+
  
                    </ul>
+
<img class="responsive-img" src="https://static.igem.org/mediawiki/2018/e/e8/T--Groningen--ProcessEmissionsFormula.png">
                    <h5>Changes</h5>
+
                    <ul class="skel browser-default">
+
                        <li>Narrowing our scope to 1 gene → blaZ
+
                        </li>
+
                        <li>on-site device
+
                        </li>
+
                    </ul>
+
                    <br>
+
                    <ul class="collapsible popout" data-collapsible="expandable">
+
                        <li>
+
                            <div class="collapsible-header">
+
                                Summary
+
                            </div>
+
                            <div class="collapsible-body">
+
                                <div class="row center">
+
                                    <div class="col s15">
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                                        <p>In the interview with Mark we discovered that detecting antibiotic resistance in bacteria is a rather challenging process. There are roughly 61.000 resistant genes and 24.000 genes are unique. Furthermore, even if it is found that the patient has antibiotic resistant genes it does not necessarily mean that this bacteria is the pathogen. In this interview, we realised that our final product of our project should be a device you can use on-site. Additionally, Mark mentioned several companies where they are developing techniques for the detection of antibiotic resistance. He also suggested to look what the farmers are doing now as a protocol when discovering that one of their cows got an infection. With this we could really state where the added values of our project lies. So, the detection device that we are making should be accurate of which antibiotics the farmer then needs to use.
+
                                        </p>
+
                                    </div>
+
                                </div>
+
                            </div>
+
                        </li>
+
                    </ul>
+
                </div>
+
            </div>
+
            <div id="GMO" class="modal">
+
                <div class="modal-content">
+
                    <h4>RIVM</h4>
+
                    <div class="row center">
+
                        <div class="center-margin col m6 s12">
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                            <img class="responsive-img" src=https://static.igem.org/mediawiki/2017/5/5f/T--TUDelft--RIVM.png alt="RIVM">
+
                        </div>
+
                    </div>
+
                    <h5>Name</h5>
+
                    <p>Cécile van der Vlugt</p>
+
                    <h5>Function</h5>
+
                    <p>Risk Assessor GMO, National Institute for Public Health and the Environment </p>
+
                    <h5>Insights</h5>
+
                    <ul class="skel browser-default">
+
                        <li>Involved institutes in The Netherlands and Europe to tackle antibiotic resistance </li>
+
                        <li>The political agenda on tackling antibiotic resistance</li>
+
                        <li>The overview of current developments to tackle antibiotic resistance</li>
+
                        <li>The need to decrease the overuse of current antibiotics
+
                        </li>
+
                        <li>The need to engage the public to implement our detection method not only in veterinary field, but also in society in the future
+
                        </li>
+
                        <li>The acceptance of the use of GMOs contained and in the environment
+
                        </li>
+
                    </ul>
+
                    <h5>Changes</h5>
+
                    <ul class="skel browser-default">
+
                        <li>The need to decrease inefficient antibiotic use to control resistance
+
                        </li>
+
                        <li>Development a new treatment strategy and frontline diagnostics
+
                        </li>
+
                        <li>A contained method detection method considering safety and public acceptance
+
                            <ol>
+
                                <li>From a paper chip to a tube
+
                                </li>
+
                                <li>Include safety as a value </li>
+
                            </ol>
+
                        </li>
+
                    </ul>
+
                    <br>
+
                    <ul class="collapsible popout" data-collapsible="expandable">
+
                        <li>
+
                            <div class="collapsible-header">
+
                                Summary
+
                            </div>
+
                            <div class="collapsible-body">
+
                                <div class="row center">
+
                                    <div class="col s15">
+
                                        <h5>Relevance</h5>
+
                                        <p>Korienke Smit and Cécile van der Vlugt gave insights on the political agenda concerning antibiotic resistance. This way, we were able to make an overview of the most important European and Dutch institutes and agencies. Besides new vaccines and new prevention strategies to tackle the infectious diseases, and besides the need for new antibiotics and new therapeutics, the increased use (including overuse and misuse) of the available antibiotics (ref. The Netherlands Center for One Health (NCOH)) should be stopped. The detection method could be used as frontline diagnostics and could be the key for new treatment strategies.</p>
+
                                        <h5>Safety and public acceptance
+
                                        </h5>
+
                                        <p>Besides designing in a relevant for the field, the acceptance of our detection method was considered. We aimed to design a detection method that could be broadly implemented to detect resistance on the spot. The public should be comfortable to use our method. Our idea was based on detection with GMOs with a kill-switch on a paper-chip. However, considering safety and public acceptance, we have chosen not to use GMOs in the environment, but only the products of the GMO. Taking into account the public opinion on GMOs and bacterial resistance, we aimed to design a product that looks as safe as possible to make the public comfortable when using our detection method.
+
                                        </p>
+
                                    </div>
+
                                </div>
+
                            </div>
+
                        </li>
+
                    </ul>
+
                </div>
+
            </div>
+
            <div id="tube" class="modal">
+
                <div class="modal-content">
+
                    <h4>RIVM</h4>
+
                    <div class="row center">
+
                        <div class="center-margin col m6 s12">
+
                            <img class="responsive-img" src=https://static.igem.org/mediawiki/2017/5/5f/T--TUDelft--RIVM.png alt="RIVM">
+
                        </div>
+
                    </div>
+
                    <h5>Name</h5>
+
                    <p>Korienke Smit</p>
+
                    <h5>Function</h5>
+
                    <p>Research assistant at National Institute for Public Health and the Environment (RIVM)
+
                    </p>
+
                    <h5>Insights</h5>
+
                    <ul class="skel browser-default">
+
                        <li>Involved institutes in The Netherlands and Europe to tackle antibiotic resistance </li>
+
                        <li>The political agenda on tackling antibiotic resistance</li>
+
                        <li>The overview of current developments to tackle antibiotic resistance</li>
+
                        <li>The need to decrease the overuse of current antibiotics
+
                        </li>
+
                        <li>The need to engage the public to implement our detection method not only in veterinary field, but also in society in the future
+
                        </li>
+
                        <li>The acceptance of the use of GMOs contained and in the environment
+
                        </li>
+
                    </ul>
+
                    <h5>Changes</h5>
+
                    <ul class="skel browser-default">
+
                        <li>The need to decrease inefficient antibiotic use to control resistance
+
                        </li>
+
                        <li>Development a new treatment strategy and frontline diagnostics
+
                        </li>
+
                        <li>A contained method detection method considering safety and public acceptance
+
                            <ol>
+
                                <li>From a paper chip to a tube
+
                                </li>
+
                                <li>Include safety as a value </li>
+
                            </ol>
+
                        </li>
+
                    </ul>
+
                    <br>
+
                    <ul class="collapsible popout" data-collapsible="expandable">
+
                        <li>
+
                            <div class="collapsible-header">
+
                                Summary
+
                            </div>
+
                            <div class="collapsible-body">
+
                                <div class="row center">
+
                                    <div class="col s15">
+
                                        <h5>Relevance</h5>
+
                                        <p>Korienke Smit and Cécile van der Vlugt gave insights on the political agenda concerning antibiotic resistance. This way, we were able to make an overview of the most important European and Dutch institutes and agencies. Besides new vaccines and new prevention strategies to tackle the infectious diseases, and besides the need for new antibiotics and new therapeutics, the increased use (including overuse and misuse) of the available antibiotics (ref. The Netherlands Center for One Health (NCOH)) should be stopped. The detection method could be used as frontline diagnostics and could be the key for new treatment strategies.</p>
+
                                        <h5>Safety and public acceptance
+
                                        </h5>
+
                                        <p>Besides designing in a relevant for the field, the acceptance of our detection method was considered. We aimed to design a detection method that could be broadly implemented to detect resistance on the spot. The public should be comfortable to use our method. Our idea was based on detection with GMOs with a kill-switch on a paper-chip. However, considering safety and public acceptance, we have chosen not to use GMOs in the environment, but only the products of the GMO. Taking into account the public opinion on GMOs and bacterial resistance, we aimed to design a product that looks as safe as possible to make the public comfortable when using our detection method.
+
                                        </p>
+
                                    </div>
+
                                </div>
+
                            </div>
+
                        </li>
+
                    </ul>
+
                </div>
+
            </div>
+
            <div id="valuedesign" class="modal">
+
                <div class="modal-content">
+
                    <h4>Value Sensitive Design with modules</h4>
+
                    <p>After mapping and interviewing different stakeholders, we were able to make a Value Sensitive Design of our project. In an extended report, we considered stakeholders values (including the values of iGEM) and translated these values to design requirements (figure hierarchical structure). We adapted our design and our project accordingly.</p>
+
                    <p>The reports of stakeholders mapping and the Value Sensitive Design can be found here:</p>
+
                    <a href=https://static.igem.org/mediawiki/2017/8/80/T--TUDelft--2017_ValueSensitiveDesign.pdf target="_blank">Report sensitive design</a><br>
+
                    <a href=https://static.igem.org/mediawiki/2017/5/59/T--TUDelft--2017_StakeholderAnalysis.pdf target="_blank">Stakeholder analysis</a>
+
                    <br><br>
+
                    <ul class="collapsible popout" data-collapsible="expandable">
+
                        <li>
+
                            <div class="collapsible-header">
+
                                Summary
+
                            </div>
+
                            <div class="collapsible-body">
+
                                <div class="row center">
+
                                    <div class="col s15">
+
                                        <p>
+
  
                                            On different levels, policy-, competition-, and user level, we investigated the values that our design had to meet. How we translated the values of the stakeholders to design requirements can be found in the figure about the Hierarchical Nature of Values (figure 1). Even though some norms were contradictory (as can be seen figure 2, summary values and norms) , we aimed to meet all the norms and values as good as possible.</p>
+
<p>This brings us the a process emissions of 1.229 CO2 per kg produced StyGreen. If our genetically engineered yeast had a 100% conversion rate, we would need 10 kilograms of recycled toilet paper to produce 1 kg of StyGreen (based on the theoretical maximum yield). Which would mean that the carbon footprint of our StyGreen would be 2.129 CO2-eq per kg. </p>
                                        <div class="row center">
+
                                            <div class="col s12">
+
                                                <img class="responsive-img" src="https://static.igem.org/mediawiki/2017/f/f3/T--TUDelft--piramid.png" alt="graph">
+
                                                <p><b>Figure. </b> Hierarchical nature of values filled in for our home detection kit. Michelfelder et al. (2013).</p>
+
                                            </div>
+
                                        </div>
+
  
                                        <div class="row center">
+
<figure>
                                            <div class="col s12">
+
<table><tr><th>Process assumptions</th><th></th></tr><tr><td>(a)Size of our bioreactor (in liters)</td><td>500</td></tr><tr><td>(b)Heating of water (per degree per 1000 liter/MJ)</td><td>4.19</td></tr><tr><td>(c) Temperature in bioreactor (in degrees Celsius)</td><td>30</td></tr><tr><td>(d) Ambient temperature (in degrees Celsius)</td><td>10</td></tr><tr><td>(e) Contribution exothermic reaction</td><td>10</td></tr><tr><td>(f) Heat loss (per 24 hour per degree in MJ)</td><td>0.03</td></tr><tr><td>(g) Calorific value of natural gas (m3)</td><td>32</td></tr><tr><td>(h) Natural gas (CO2/m3)</td><td>1.8</td></tr><tr><td>(i) Process time in bioreactor (in days)</td><td>3</td></tr><tr><td>(j) KG Styrene per bioreactor</td><td>1</td></tr><tr><td></td><td></td></tr><tr><td>Energy requirements (MJ)</td><td>21.85</td></tr><tr><td>Process emissions (CO2 per kg)</td><td>1.229</td></tr></table>
                                                <img class="responsive-img" src="https://static.igem.org/mediawiki/2017/f/fe/T--TUDelft--flowchart.png" alt="graph">
+
<figcaption><i>Table 2. The predicted process emissions of producing StyGreen in our bioreactor[<a target="_blank" href="http://www.joostdevree.nl/shtmls/warmtestroom.shtml ">3</a>] </i></figcaption>
                                                <p><b>Figure. </b> Figure. Summary of values and norms (based on concerns and potentials different actors see) in the design process. Model inspired by Investigating Ethical Issues in Engineering Design (van de Poel, 2001).
+
</figure>
                                                </p>
+
                                            </div>
+
                                        </div>
+
                                    </div>
+
                                </div>
+
                            </div>
+
                        </li>
+
                    </ul>
+
                </div>
+
            </div>
+
            <div id="mail" class="modal">
+
                <div class="modal-content">
+
                    <h4>Input Chicken Farmer</h4>
+
                    <h5>Name</h5>
+
                    <p>Sjouke Hoekstra</p>
+
                    <h5>Function</h5>
+
                    <p>Chicken farmer and poultry specialist at De Heus
+
                    </p>
+
                    <h5>Insights</h5>
+
                    <ul class="skel browser-default">
+
                        <li>In the poultry industry, <i>Salmonella</i> is a big problem.
+
                        </li>
+
                    </ul>
+
                    <h5>Changes</h5>
+
                    <ul class="skel browser-default">
+
                        <li>Look further into the <i>Salmonella</i> problem by contacting AVINED and the slaughterhouse/diagnostics centre.
+
                        </li>
+
                    </ul>
+
                    <br>
+
                    <ul class="collapsible popout" data-collapsible="expandable">
+
                        <li>
+
                            <div class="collapsible-header">
+
                                Summary
+
                            </div>
+
                            <div class="collapsible-body">
+
                                <div class="row center">
+
                                    <div class="col s15">
+
                                        <h5>Interview summary</h5>
+
                                        <p>Sjouke Hoekstra is a chicken farmer who has been battling salmonella for a long time. A new policy set up to tackle antibiotic resistance problems says that chickens that test positive for Salmonella have to be slaughtered immediately. In an attempt to prevent salmonella from spreading, Sjouke has spent a lot of money on different cleaning methods. However, the underlying, fundamental cause of the salmonella problem was never really looked into. Sjouke believes that his chickens were infected via their food, which is derived from the Yucca plant.
+
                                        </p>
+
  
                                        <p> Sjouke recommended us to dive deeper in the salmonella problem. For this purpose, he referred us to the company AVINED. Furthermore, we could contact the slaughterhouse, to which the diagnostics centre is connected.
+
<p>This is a lot better than 7.8 CO2-eq per kg for petroleum-based styrene. However, at this point in time our conversion are not yet 100%. For each kilo of styrene we produce, we need 263 kilograms of cellulose (recycled toilet paper) <a target="_blank" href="Model/Flux_Based_Analyses">right now</a>. This would result in 24.89 CO2-eq per kg, which is way worse than regular (petroleum-based) styrene. This partly due to the assumptions made in the flux model, which assumes that yeast needs have a net biomass gain at all times. While, that is not necessary in our bioreactor. Moreover, the first version of our yeast is just a proof of concept. There are still a lot of parts that can be optimized. Both in the yeast strain itself, in the form of knock-outs, and in the bioreactor, by reducing the process emissions. </p>
                                        </p>
+
                                    </div>
+
                                </div>
+
                            </div>
+
                        </li>
+
                    </ul>
+
                </div>
+
            </div>
+
            <div id="IKB" class="modal">
+
                <div class="modal-content">
+
                    <h4>AVINED</h4>
+
                    <div class="row center">
+
                        <div class="center-margin col m6 s12">
+
                            <img class="responsive-img" src="https://static.igem.org/mediawiki/2017/0/03/T--TUDelft--AVINED.jpeg" alt="pluimned">
+
                        </div>
+
                    </div>
+
                    <h5>Name</h5>
+
                    <p>Rik ter Loo</p>
+
                    <h5>Function</h5>
+
                    <p>Expert IKB Kip en Salmonella meat industry
+
  
                    </p>
 
                    <h5>Insights</h5>
 
                    <ul class="skel browser-default">
 
                        <li>Forbidden to treat salmonella in chickens with antibiotics
 
  
                        </li>
 
                        <li>No high need to make big investments in treatment of chickens</li>
 
                    </ul>
 
                    <h5>Changes</h5>
 
                    <ul class="skel browser-default">
 
                        <li>No focus on <i>Salmonella</i> and chickens
 
  
                        </li>
 
                    </ul>
 
                    <br>
 
                    <ul class="collapsible popout" data-collapsible="expandable">
 
                        <li>
 
                            <div class="collapsible-header">
 
                                Summary
 
                            </div>
 
                            <div class="collapsible-body">
 
                                <div class="row center">
 
                                    <div class="col s15">
 
  
                                        <p>Rik te Loo did not see any connection with the salmonella chicken challenges and the our detection method, because the treatment of <i>Salmonella</i> with antibiotics is currently forbidden. Antibiotic regulations considering chickens are currently.
 
                                        </p>
 
  
                                        <p> The IKB Kip certification scheme is a global chain quality system for the entire poultry meat sector. IKB Kip is a dynamic system that is constantly developing. IKB Kip’s scheme management lies with the PLUIMNED foundation. This allows all links involved in the production of IKB Kip poultry meat (from breeding to processing) to ensure production methods guarantees, for instance regarding the quality and safeguarding of the quality
 
  
                                        </p>
+
<h4>Conclusions</h4>
                                    </div>
+
<ol>
                                </div>
+
<li> Toilet paper waste is used as the primary raw material in the biorefinery to produce styrene. The reason for this it is not used for feeding humans. The other reason is we can add value to this product.</li>  
                            </div>
+
<li> Currently the process is not sustainable (based on flux model, with mass balance of 263 : 1) </li>
                        </li>
+
<li> We could still optimize our process a lot, so we should be able to decrease the mass balance by a lot. And starting from a mass balance of 33 : 1 we are cleaner than petroleum-based styrene </li>
                    </ul>
+
<li> We can also improve the process emissions, lower process emissions means our mass balance can be higher (at the moment the process emissions are more than 28% of the total emissions of petroleum-based styrene). </li>
                </div>
+
</ol>
            </div>
+
            <div id="vet1" class="modal">
+
                <div class="modal-content">
+
                    <h4>Input Veterinarian</h4>
+
  
                    <h5>Name</h5>
+
</div>
                    <p>Engeline van Duijkeren</p>
+
                    <h5>Function</h5>
+
                    <p>Veterinarian, works for RIVM, research on if antibiotic resistance is transferred from animal to human and via which ways.
+
  
  
                    </p>
 
                    <h5>Insights</h5>
 
                    <ul class="skel browser-default">
 
                        <li>Milk samples from cows that have mastitis but are not cured by certain antibiotics are not always sent to the lab for test, because it costs time and money (2-3 days). Sometimes farmers thus already administer other antibiotics not knowing if it might work.
 
  
                        </li>
 
                        <li>6 common pathogens causing mastitis</li>
 
                        <li>Taking a milk sample is the best sample for our tool.
 
                        </li>
 
                        <li>Extended-spectrum lactamases can break down a lot of types β-lactam antibiotics and thus can make a large group of antibiotics inactive.
 
                        </li>
 
                    </ul>
 
                    <h5>Changes</h5>
 
                    <ul class="skel browser-default">
 
                        <li>Focus on most common pathogens in mastitis</li>
 
                        <li>Focus on β-lactamases as these also have impact on humans</li>
 
                        <li>Focus on milk as milk is most accessible</li>
 
                    </ul>
 
                    <br>
 
                    <ul class="collapsible popout" data-collapsible="expandable">
 
                        <li>
 
                            <div class="collapsible-header">
 
                                Summary
 
                            </div>
 
                            <div class="collapsible-body">
 
                                <div class="row center">
 
                                    <div class="col s15">
 
  
                                        <p>Milk samples from cows that have mastitis but are not cured by certain antibiotics are not always sent to the lab for test, because it costs time and money (2-3 days). Sometimes farmers thus already register other antibiotics not knowing if it might work. When the milk sample goes to the lab, the untreated milk is plated on different agar plates. When colonies have grown, the microorganisms are often colored and examined through the microscope. Also, biochemical tests are done to see which compounds the bacteria can convert. When a cow has clinical mastitis (visible symptoms), it is most likely that one type of bacterium is the cause. There are 6 types of known, common pathogens for mastitis. Engeline tells us that farmers would like a on site test for which antibiotic can or can not be administered. She thinks that within several years whole genome sequencing will be the golden standard.</p>
 
  
                                        <p>We asked Engeline what is the most appropriate sample for detecting antibiotic resistance. She tells us that feces contains too many bacteria, blood is supposed to be sterile but is not common practice and thus economically not so attractive. Urine samples are often used with pet animals. Milk would be most suited as this is has little bacteria, only skin bacteria and the pathogens causing mastitis.
 
  
                                        </p>
 
  
                                        <p>Engeline also told us about extended-spectrum lactamases that can break down a lot of types β-lactam antibiotics and thus can make a large group of antibiotics inactive. A lot of β-lactamases can be passed on from animals to humans
 
  
                                        </p>
 
                                    </div>
 
                                </div>
 
                            </div>
 
                        </li>
 
                    </ul>
 
                </div>
 
            </div>
 
            <div id="ster4" class="modal">
 
                <div class="modal-content">
 
                    <h4>Input Bouwe Frank Gall
 
                    </h4>
 
  
                    <h5>Name</h5>
 
                    <p>Bouwe Frank Gall
 
                    </p>
 
                    <h5>Function</h5>
 
                    <p>Veterinarian (Dairy Cattle &amp; Horses) at Dierenartsencombinatie Gorredijk </p>
 
                    <h5>Insights</h5>
 
                    <ul class="skel browser-default">
 
                        <li>Mastitis (udder infection) is a challenging problem in the dairy industry
 
                        </li>
 
                        <li>The current diagnostics are not at all focused on detecting antibiotic resistances
 
                        </li>
 
  
                    </ul>
 
                    <h5>Changes</h5>
 
                    <ul class="skel browser-default">
 
                        <li>Contact Ynte Schukken (expert in mastitis at the Groningen University)
 
                        </li>
 
                        <li>Contact GD Animal Health
 
                        </li>
 
                    </ul>
 
                    <br>
 
                    <ul class="collapsible popout" data-collapsible="expandable">
 
                        <li>
 
                            <div class="collapsible-header">
 
                                Summary
 
                            </div>
 
                            <div class="collapsible-body">
 
                                <div class="row center">
 
                                    <div class="col s15">
 
                                        <h5>Interview summary</h5>
 
                                        <p>When asked about the most occurring/challenging bacterial infection in cattle, Bouwe Frank pointed us towards mastitis. This is in an infection of the udder. The problem with mastitis is that it can be caused by various bacteria. If you are interested in detecting antibiotic resistances in the case of mastitis, you will thus first have to establish which pathogen you are dealing with.
 
                                        </p>
 
  
                                        <p>How the current process goes, is that a sample of a sick animal is sent to the GD Animal Health. They cultivate the sample to see what bacteria causes the disease. Often, an educated guess considering the pathogen can be made. If the test is positive, the animal can get a suitable treatment. If not, the test is repeated under different conditions. These tests are not based on detecting antibiotic resistances, because this takes more time and money.
 
  
                                        </p>
 
  
                                        <p>Bouwe Frank referred us to the GD animal health to get a better insight in the current diagnostics process through the veterinarian laboratory. A valuable person to contact is Ynte Schukken, who is connected to the GD animal Health and professor at the Groningen University.
 
  
 +
<div class="clear"></div>
 +
<h1>Safety</h1>
 +
<div class="column">
 +
<p> Safety should be a cornerstone of every project, taken into account during every phase. For this reason the Dutch Governmental Institute for Public Health and Environment (RIVM) has challenged us to participate in their Safe-by-Design assignment. The goal of this assignment is to demonstrate how our team has taken safety into account throughout our project, in every aspect. Of particular importance is the human practices part, where our ideas get taken outside the lab and into the world surrounding us. Of special interest is the iterative process, where the direction of the project is adjusted based on input from stakeholders and experts in relevant fields, safety and ethical guidelines, and considerations regarding the upscaling of our project. We have had 2 Skype meetings with staff members of the RIVM, and using their tips and guidance we made some more adjustment. The final product, an infographical timeline describing the iterative process of our project, is pictured below.
 +
</p>
 +
</div>
 +
<div class="clear"></div>
 +
<div class="column">
 +
<img class="responsive-img" src="https://static.igem.org/mediawiki/2018/9/96/T--Groningen--RIVM_final_deliverable_infographic.png">
 +
</div>
 +
<div class="clear"></div>
  
                                        </p>
 
                                    </div>
 
                                </div>
 
                            </div>
 
                        </li>
 
                    </ul>
 
                </div>
 
            </div>
 
            <div id="vet2" class="modal">
 
                <div class="modal-content">
 
                    <h4>Input Vetenarian
 
                    </h4>
 
  
                    <h5>Name</h5>
 
                    <p>Maaike van den Berg
 
                    </p>
 
                    <h5>Function</h5>
 
                    <p>Veterinarian Van Stad tot Wad</p>
 
                    <h5>Insights</h5>
 
                    <ul class="skel browser-default">
 
                        <li>The integration of Formularies in our design
 
                        </li>
 
                        <li>The process from disease analysis to antibiotic prescription
 
  
                        </li>
+
<h1 id="porterinterview clear">Stakeholder Analysis</h1>
                        <li>The roles of the farmers, veterinarians and diagnostic centers in this process
+
<div class="clear extra_space" id="evbiotechinterview"></div>
                        </li>
+
                        <li>The requirements of first, second and third choice antibiotics
+
                        </li>
+
                        <li>Current diagnostic methods to determine pathogen sensitivity for antibiotics
+
                        </li>
+
                        <li>Pathogen sensitivity test by diagnostic center
+
                        </li>
+
                        <li>Relevance to narrow our scope to <i>Staphylococcus</i> or <i>E.Coli</i>
+
                        </li>
+
                    </ul>
+
                    <h5>Changes</h5>
+
                    <ul class="skel browser-default">
+
                        <li>Design detection method based on integration with formularies
+
  
                        </li>
+
<div class="column two_thirds_size">           
                        <li>Narrow scope to resistance in <i>Staphylococcus Aureus</i>
+
<h4> Porter Analysis</h4>
 +
<p>  
 +
To investigate our position and opportunities on the market, we performed a Five Forces analysis. Here, we looked at the strengths of our buyers and suppliers, substitutes for our product, competition and new entrants. The results indicate that we have a beneficial position in relation to our suppliers as there are multiple sources of cellulose. However, the buyers have a high switching cost, which is a potential threat to our technology. For new entrants, a large amount of prior knowledge is needed to enter the market, which is one of our strengths. The substitutes of our product are different kinds of plastics, but as the plastic market is large and specific, this is not a great threat.
 +
</p>
 +
</div>
 +
<div class="column third_size">
 +
<div class="clear extra_space"></div>
 +
<h4  style="text-align: center !important;font-style: italic !important;font-size: 1.6em !important;padding: 40px !important;background: #e2e2e2 !important;"> For buyers, production scale is very important </h4>
 +
</div>
 +
<div class="column"><img class="responsive-img" src="https://static.igem.org/mediawiki/2018/7/7b/T--Groningen--porter.png">
 +
</div>
  
                        </li>
 
                    </ul>
 
                    <br>
 
                    <ul class="collapsible popout" data-collapsible="expandable">
 
                        <li>
 
                            <div class="collapsible-header">
 
                                Summary
 
                            </div>
 
                            <div class="collapsible-body">
 
                                <div class="row center">
 
                                    <div class="col s15">
 
  
                                        <p>Maaike van den Berg showed told us about the current policies on antibiotics and how she as a veterinarian uses the formularies. Also, she gave us insights in her tasks as a veterinarian and how she prescribes antibiotics based on the results of the diagnostic center. Diagnostic centers do pathogen detection and determine the sensitivity for antibiotic resistance subsequently. In two to three days, the results include the pathogens sensitivity for all potential antibiotics. As we only could detect one kind of antibiotic resistance, we decided to scope our detection method on the most common mastitis pathogen, which is <i>Staphylococcus Aureus</i>.
+
<div class="clear extra_space" id="evbiotechinterview"></div>
                                        </p>
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<div class="line_divider"></div>
                                    </div>
+
<div class="clear_extra_space"></div>
                                </div>
+
<!----End sub part----->
                            </div>
+
                        </li>
+
                    </ul>
+
                </div>
+
            </div>
+
            <div id="GD" class="modal">
+
                <div class="modal-content">
+
                    <h4>Gezondheidsdienst voor Dieren - Healthcare for animals
+
                    </h4>
+
                    <div class="row center">
+
                        <div class="center-margin col m6 s12">
+
                            <img class="responsive-img" src="https://static.igem.org/mediawiki/2017/a/a1/T--TUDelft--GD.jpeg" alt="GD">
+
  
                        </div>
 
                    </div>
 
  
                    <h5>Insights</h5>
 
                    <ul class="skel browser-default">
 
                        <li>Annual report on monitoring pathogen sensitivity for antibiotics
 
  
                        </li>
+
<h1>Meetings with companies</h1>
                        <li>Trend: rapid decrease of pathogen sensitivity for penicillins
+
  
  
                        </li>
+
<div class="column two_thirds_size">           
                        <li>The roles of the farmers, veterinarians and diagnostic centers in this process</li>
+
<h4> EV Biotech </h4>
 +
<p>  
 +
The young, Groningen based biotech startup <a target="_blank" href="http://evbio.tech/">EV Biotech</a> offered to  collaborate with us in many aspects. Represented by Linda Dijkshoorn, Agnieszka Wegryzn and Sergey Lunev, EVBiotech was present at multiple meetings with our subgroups. Linda had fantastic tips about structure and organisation, and helped us to set up a SCRUM way of working. Agnieszka is an expert on modelling and helped a great deal with the flux balance analysis. Sergey helped us to set up the concept of a continuous bioreactor. Over the summer we had ten meetings to discuss our progress on the project. Next to technical help, we also profited greatly by gaining access to the big network of EV Biotech. As a special honor, we were invited to the official opening of the new EV Biotech office. Here we had the opportunity to pitch our project to several experienced business people.
 +
</p>
 +
<h4  style="text-align: center !important;font-style: italic !important;font-size: 1.6em !important;padding: 40px !important;background: #e2e2e2 !important;"> We also had a great deal of help accessing the big network of EV Biotech </h4>
 +
</div>
 +
<div class="column third_size">
 +
<div class="clear extra_space"></div>
 +
<img src="https://static.igem.org/mediawiki/2018/5/51/T--Groningen--evbiotech.png">
 +
<img src="https://static.igem.org/mediawiki/2018/4/42/T--Groningen--trizevbiotech.jpg">
 +
</div>
 +
<div class="clear extra_space" id="toymultinationalinterview"></div>
 +
<div class="line_divider"></div>
 +
<div class="clear_extra_space"></div>
 +
<!----End sub part----->
  
                    </ul>
+
<!-- Start sub part----->
                    <h5>Changes</h5>
+
<div class="column two_thirds_size">          
                    <ul class="skel browser-default">
+
<h4> Interviewing the Vice-President Materials of a Toy Multinational (16th October 2018)</h4>
                        <li>Scope on penicillin resistance of <i>Staphylococcus Aureus</i>
+
<p>Creating a bioplastic that is able to compete with conventional plastic means tapping into a market with unlimited potential. For example, 19 billion Lego elements are produced every year. This equals 2.16 million elements every hour, or 36.000 per minute. This premium toy-giant with an annual revenue of 4.8 billion USD (2017) is highly interested in swapping their current ABS feedstock to a more sustainable non-crude oil derived source. The Vice-President Materials of a Toy Multinational made time to sit down with us, despite a very full agenda. We discussed what drives companies when making transitioning decisions, what toy companies look for in materials and what to take into account throughout development.
                        </li>
+
</p>
                    </ul>
+
<p>While diving into the many applications of styrene, what most interested us was an application of styrene as raw material for a non-single use plastic. This was one of the drivers which pointed us towards Lego bricks: durable playing bricks for playful development. It turns out our visions align. During the course of our project, Lego has published various articles and press releases about their ambition to produce plant-based plastic playing bricks. The mentioned Vice-President Materials was happy to sit down with us to share views on the future of biobased plastics, as well as discussing some opportunities and limitations with regards to their production. Our discussion was highly insightful. Some highlights which will shape the future of our project:</p>
                    <br>
+
</div>
                    <ul class="collapsible popout" data-collapsible="expandable">
+
<div class="column third_size">
                        <li>
+
<div class="clear extra_space"></div>
                            <div class="collapsible-header">
+
<img src="https://static.igem.org/mediawiki/2018/4/49/T--Groningen--toys.jpg">
                                Summary
+
<h4  style="text-align: center !important;font-style: italic !important;font-size: 1.6em !important;padding: 40px !important;background: #e2e2e2 !important;"> Your choice for a 2G feedstock highly excites me  </h4>
                            </div>
+
</div>
                            <div class="collapsible-body">
+
                                <div class="row center">
+
                                    <div class="col s15">
+
  
                                        <p>After an elaborate conversation with the Lotte Roos from GD, she sent us the annual report on monitoring pathogen sensitivity. This way, we gained insights in the trends considering resistance of mastitis pathogens. The sensitivity for penicillins is rapidly decreasing or there was no sensitivity.
+
<div class="clear_extra_space"></div>
                                        </p>
+
                                    </div>
+
                                </div>
+
                            </div>
+
                        </li>
+
                    </ul>
+
                </div>
+
            </div>
+
            <div id="farmer" class="modal">
+
                <div class="modal-content">
+
                    <h4>Collaboration Dairy Farmer
+
                    </h4>
+
                    <h5>Name</h5>
+
                    <p>Paul Oosthoek
+
                    </p>
+
                    <h5>Function</h5>
+
                    <p>Paul Oosthoek is a dairy farmer at Oosthoek en Zn VOF. He explained about the protocols they use in cause of mastitis diagnosis.
+
                    </p>
+
                    <h5>Insights</h5>
+
                    <ul class="skel browser-default">
+
                        <li>Current methods to tackle disease and antibiotic resistance
+
                        </li>
+
                        <li>Early mastitis diagnosis
+
                        </li>
+
                        <li>Treatment protocols for mastitis </li>
+
                    </ul>
+
                    <h5>Changes</h5>
+
                    <ul class="skel browser-default">
+
                        <li>Collaboration with Paul (visited the farm several times)
+
                        </li>
+
                        <li>Using fresh milk samples from the farm </li>
+
                    </ul>
+
                    <br>
+
                    <ul class="collapsible popout" data-collapsible="expandable">
+
                        <li>
+
                            <div class="collapsible-header">
+
                                Summary
+
                            </div>
+
                            <div class="collapsible-body">
+
                                <div class="row center">
+
                                    <div class="col s15">
+
  
                                        <p>Paul elaborated on the mastitis problem by stating that cows can pass on the (potentially multiresistant bacteria) to their calves, further increasing the spread of antibiotics. Beyond the borders of the Netherlands, milk farmers have bigger challenges with antibiotic resistance. “Resistance transfer is a major challenge beyond the borders as antibiotic remainders can be found in food from cuttle.” In the Netherlands, this seems less of a problem, according to Paul. “We need to be sure that no antibiotics remain in the milk before we can sell the milk”.
+
<div class="column">
  
                                        </p>
+
<ol>
                                        <p>“Since two years we are breeding cows that are healthier and have more resistance against diseases. We treat mastitis with the antibiotic Ubrolexin in a late stage. In this stage the udder looks red and infected”. Paul is able to check himself whether or not the cow has mastitis in early stage. “If the cow has mastitis, the milk texture is different. In this early stage, Ice Mint, a treatment salve, can do the trick and cure the infection”. Paul told us about new techniques in the market, like the milk robots that detect the potential of mastitis. “Measurement on the milk conduction can predict whether or not a cow is infected with mastitis”. </p>
+
<li>From 1G to 2G feedstock: the Vice-President Materials is enthusiastic about our choice of a 2G feedstock: highlighting circularity, and also addressed a challenge we proposed, the loss of biomass to oxygen, stating that because our feedstock is 0-value this is not a problem!  Being a second generation feedstock, “sludge” (our toilet paper waste stream) does not compete with food supply. </li>
                                    </div>
+
<li>“Side effects” of transitioning to bio-based plastic: to guarantee trusted product characteristics for injection moulding playing bricks, every mould is tailored to the specific properties of the plastic used to inject the mould of the individual bricks. Transitioning for a multinational like this does not just mean searching for the right material. It means transforming the entire production process. Therefore, there is little room for errors when switching to a new composition. </li>
                                </div>
+
<li>Importance of constant feedstock: scale, constant (reliable) product with uniform properties: We were pointed towards an important bottleneck of bioplastics: going from start-up to scale up. In order to supply industrials, a reliable feedstock is necessary. Therefore, throughout developing StyGreen in the lab ample attention needs to be given to possible commercialization. Read about our dive into this on our <a target="_blank" href="Entrepeneurship"> Entrepeneurship</a> page.</li>
                            </div>
+
<li>Minimizing steps in the production process: Minimizing production process steps is appealing when producing plastics. Minimizing steps in the production process will contribute to the success of StyGreen, for example by minimizing energy consumption. This makes our product more competitive. </li>
                        </li>
+
<li>Who is responsible for this transition: to place our project in a societal context, we also had an insightful discussion on where the responsibility of the energy transition lies. </li>
                    </ul>
+
</ol>
                </div>
+
<p>
            </div>
+
According to the VP Materials we are operating at the right time. Speaking of an ever-increasing visible framework and the fact that we are currently operating in a more circular economy which will have large consequences.
            <div id="RD" class="modal">
+
</p>
                <div class="modal-content">
+
                    <h4>R&amp;D veterinary pharmaceutical products</h4>
+
                    <h5>Name</h5>
+
                    <p>Yvonne Verbeek and Bart Engelen</p>
+
                    <h5>Function</h5>
+
                    <p>Experts at R&amp;D veterinary pharmaceutical products
+
                    </p>
+
                    <h5>Insights</h5>
+
                    <ul class="skel browser-default">
+
                        <li>Current methods to detect resistance take too long when immediate treatment is needed
+
                            <ul>
+
                                <li>Antibiograms and sensitivity tests
+
                                </li>
+
                            </ul>
+
                        </li>
+
                        <li>Lab results are still needed to validate diagnosis and to monitor
+
                        </li>
+
                        <li>The use of milk robots</li>
+
                        <li>Need for argumentation to start with second choice antibiotics </li>
+
                        <li>Need for pathogen detection causing the disease</li>
+
                    </ul>
+
                    <h5>Changes</h5>
+
                    <ul class="skel browser-default">
+
                        <li>Look into pathogen detection</li>
+
                        <li>Look into developing a method for future milk robots (producer: <a href="https://www.lely.com/ie/www.lely.com/ie/the-barn/milking/astronaut-a4/roboticmilkingandgrazingopendays/" target="_blank">Lely</a>)</li>
+
                    </ul>
+
                    <br>
+
                    <ul class="collapsible popout" data-collapsible="expandable">
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                        <li>
+
                            <div class="collapsible-header">
+
                                Summary
+
                            </div>
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                            <div class="collapsible-body">
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                                    <div class="col s15">
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                                        <p>During this interview, we gained knowledge on current methods to identify pathogens and determine the sensitivity of these pathogens. These detailed methods will be necessary to follow trends and to validate current treatment and diagnosis. Furthermore, mastitis can be caused by different pathogens and it hard to identify which pathogen cause the disease and subsequently, identify which resistance genes this pathogen has. The milk robots are the new technologies in the field to detect and count cells in the cow's milk. The amount of cells (>25.000) is an indication for mastitis. </p>
+
<h4  style="text-align: center !important;font-style: italic !important;font-size: 1.6em !important;padding: 40px !important;background: #e2e2e2 !important;"> Optimizing scale and reliable production are of utmost importance when producing a successful bioplastic </h4>
                                    </div>
+
</div>
                                </div>
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<div class="clear extra_space" id="ludosinterview"></div>
                            </div>
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<div class="line_divider"></div>
                        </li>
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<div class="clear_extra_space"></div>
                    </ul>
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                </div>
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            </div>
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                <div class="modal-content">
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                    <h4>Sanbio meeting</h4>
+
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+
                    <h5>Name</h5>
+
                    <p>Maarten Jonkers</p>
+
                    <h5>Function</h5>
+
                    <p>Account Manager Life Science at Sanbio</p>
+
                    <h5>Insights</h5>
+
                    <ul class="skel browser-default">
+
                        <li>Current methods used for antibiotic detection</li>
+
                        <li>Most research is currently focused on real time PCR
+
                        </li>
+
                        <li>No demand for pathogen detection
+
                        </li>
+
                    </ul>
+
                    <h5>Changes</h5>
+
                    <ul class="skel browser-default">
+
                        <li>Collaboration with Sanbio</li>
+
                        <li>The use of the Milk DNA isolation kit to compare with boiling method</li>
+
                        <li>No focus on pathogen detection</li>
+
                    </ul>
+
                    <br>
+
                    <ul class="collapsible popout" data-collapsible="expandable">
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                        <li>
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                            <div class="collapsible-header">
+
                                Summary
+
                            </div>
+
                            <div class="collapsible-body">
+
                                <div class="row center">
+
                                    <div class="col s15">
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                                        <p>For antibiotic detection, most research is currently focused on real time PCR with specific probes that anneal to the antibiotic resistance genes. This method is comparable to our method, as specific primers are required per resistance. We decided to try out the Milk DNA Isolation Kit to be able to compare our boiling method with a commercially available isolation method.
 
                                        </p>
 
                                    </div>
 
                                </div>
 
                            </div>
 
                        </li>
 
                    </ul>
 
                </div>
 
            </div>
 
            <div id="BRC" class="modal">
 
                <div class="modal-content">
 
                    <h4>Collaboration Bioveterinary Research Center</h4>
 
                    <!-- image logo-->
 
                    <h5>Name</h5>
 
                    <p>prof. dr. Dik Mevius </p>
 
                    <h5>Function</h5>
 
                    <p>Senior researcher and agricultural researcher at Wageningen Bioveterinary Research, expertise: Bacteriology, Microbiology, veterinary studies, antibiotic resistance
 
                    </p>
 
                    <h5>Name</h5>
 
                    <p>dr. Fimme Jan van der Wal
 
                    </p>
 
                    <h5>Function</h5>
 
                    <p>Agricultural researcher at Wageningen Bioveterinary Research, expertises: animal illness, diagnostische techniques, infectious diseases
 
  
                    </p>
 
                    <h5>Insights</h5>
 
                    <ul class="skel browser-default">
 
                        <li>The gene blaZ is relevant in MRSA
 
                        </li>
 
                        <li>SSC-MEC, mecA is relevant for the multi resistance of MRSA beyond the scope of mastitis
 
  
                        </li>
+
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                        <li>Relevance of RNA detection to show expression
+
<div class="column two_thirds_size">          
                        </li>
+
<h4> Ludos Imaginem: George van den Nieuwenhuizen (19th September 2018)</h4>
                        <li>Challenge to do sample preparation with milk due to fats</li>
+
<p>
                        <li>Costs and speed of detection should stand out</li>
+
<a target="_blank" href="http://www.ludos.nl/">Ludos Imaginem</a> is a new company which creates toys with which you are able to create something out of your own imagination. Because they recently started, they are really interested in making their product as sustainable as possible. Ludos is willing to invest in us when we have the first results, and has shared the data about the styrene they need for their product. This way, we can optimize our StyGreen to the demand of the customer. We keep in contact with Ludos to update them on the developments in our process. Ludos is very interested in a biobased way to create plastics. They do not want to compete with the food industry, and therefore encourage our way of working with sludge.
                        <li>Key to success is simplicity and a result: yes or no</li>
+
</p>
                    </ul>
+
<h4  style="text-align: center !important;font-style: italic !important;font-size: 1.6em !important;padding: 40px !important;background: #e2e2e2 !important;"> "If you find a sustainable solution for current plastics, you will be bigger than Elon Musk" </h4>
                    <h5>Changes</h5>
+
</div>
                    <ul class="skel browser-default">
+
<div class="column third_size">
                        <li>Narrow scope to blaZ and mecA</li>
+
<div class="clear extra_space"></div>
                        <li>Collaboration with Wageningen Bioveterinary Research center
+
<img src="https://static.igem.org/mediawiki/2018/4/4d/T--Groningen--ludos.jpg">
                            <ul>
+
</div>
                                <li>Experiments with their isolates and validation
+
<div class="clear extra_space" id="knninterview"></div>
                                </li>
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<div class="line_divider"></div>
                            </ul>
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<div class="clear_extra_space"></div>
                        </li>
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                    </ul>
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                    <br>
+
                    <ul class="collapsible popout" data-collapsible="expandable">
+
                        <li>
+
                            <div class="collapsible-header">
+
                                Summary
+
                            </div>
+
                            <div class="collapsible-body">
+
                                <div class="row center">
+
                                    <div class="col s15">
+
  
                                        <p>Dik and Fimme do research on the development of diagnostic tools for pathogen resistance detection in the bioveterinary field. In S. aureus, blaZ is relevant when looking into the β-lactamases. Other β-lactamases are not relevant enough. BlaZ produces small-spectrum penicillinases. This means that benzylpenicillin, ampicillin and amoxicillin antibiotics, common first and second choice antibiotics that are empirically used by the farmer to treat mastitis, can not be used is blaZ is detected. Rapid detection of this gene could prevent the misuse of penicillins by the farmer and gives reason to directly prescribe other treatments. From the policy perspective, the presence of blaZ has a lot of impact.
+
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                                        </p>
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<div class="column third_size">
                                        <p>The mecA gene is also relevant to detect as this gene makes the pathogen resistant against all β-lactam antibiotics, leading to the well-known disease MRSA. The experts revealed insights for the key of success. Furthermore, they told us that farmers are able to work with tubes and pipettes. Farmers are willing to invest and follow a more challenging protocol if time for a good results.
+
<div class="clear extra_space"></div>
                                        </p>
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<img src="https://static.igem.org/mediawiki/2018/4/46/T--Groningen--knnlogo.jpg">
                                    </div>
+
<img src="https://static.igem.org/mediawiki/2018/4/48/T--Groningen--knn.jpg">
                                </div>
+
</div>
                            </div>
+
<div class="column two_thirds_size">           
                        </li>
+
<h4> KNN Cellulose: Yme Flapper (31st August 2018) </h4>
                    </ul>
+
<p>
                </div>
+
We visited <a target="_blank" href="https://www.knncellulose.nl/">KNN Cellulose</a>! After extensive research into possibilities of biomass, we found the company that produces Recell®. This is an innovative new product made from recycled toilet paper which consists of over 90% cellulose. KNN asked us whether there is a possibility to create styrene from their product. In this manner, we can really use waste streams to create StyGreen! The company develops biomass-derived chemicals and is looking for new innovative and sustainable ways of production. GMO technology fits this profile. KNN provided us with a sample of their product for our experiments and they are very interested in our results.  
            </div>
+
</p>
            <div id="CEE" class="modal">
+
<h4  style="text-align: center !important;font-style: italic !important;font-size: 1.6em !important;padding: 40px !important;background: #e2e2e2 !important;"> KNN provided us with a sample of their product </h4>
                <div class="modal-content">
+
</div>
                    <h4>Reflection with workshop</h4>
+
<div class="clear extra_space" id="nrkinterview"></div>
                    <div class="row center">
+
<div class="line_divider"></div>
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<div class="clear_extra_space"></div>
                            <img class="responsive-img" src="https://static.igem.org/mediawiki/2017/d/de/T--TUDelft--4TU.png" alt="4TU">
+
<!----End sub part----->
  
                        </div>
 
                    </div>
 
  
                    <h5>Insights</h5>
+
<div class="column two_thirds_size">           
                    <ul class="skel browser-default">
+
<h4> NRK: Martin van Dord (24th July 2018) </h4>
                        <li>Aspects that are still missing, like validation
+
<p>
                        </li>
+
<a href="http://www.nrk.nl/"> NRK </a> is the Dutch Federation of plastic and rubber converters, with 20 different sub associations and 400 member companies. We talked to <a href="https://www.linkedin.com/in/martin-van-dord-75268724/"> Martin van Dord</a>, innovation consultant at NRK and <a href="http://www.topsectorchemie.nl/"> Topsector Chemie</a>. According to the NRK facts and figures (2017) circa 2000 kilotonnes of plastics were used in 2017, of which circa 20 kilotonnes (1%) were bioplastics. The main problem associated with the use of bioplastics is the price, which can be up to twice as high as that of virgin plastics. In order to contribute to the goals of the Paris Agreement, the objective is to lift the market share of bioplastics to 15% in 2030. Mr. van Dord thought our project was very interesting, since we came up with a new way to produce bioplastics. However, he was wondering why we would focus so much on styrene. Why not create a new bioplastic with even better qualities? He also stated that the business case should be a part in the project in order to get a better insight in the potential of genetically manufactured or engineered bioplastics and the scale of economic feasible production facilities. NRK also published an article about us on their <a href="https://www.nrk.nl/nieuws/nieuws-detail?newsitemid=2907144192">website</a>
                        <li>To do’s to achieve a responsible and relevant synthetic biology design </li>
+
</p>
 +
<h4  style="text-align: center !important;font-style: italic !important;font-size: 1.6em !important;padding: 40px !important;background: #e2e2e2 !important;"> Only 1% of the plastic usage consists of bioplastics </h4>
 +
</div>
 +
<div class="column third_size">
 +
<div class="clear extra_space"></div>
 +
<img src="https://static.igem.org/mediawiki/2018/3/30/T--Groningen--nrk.jpg">
 +
</div>
 +
<div class="clear extra_space" id="bioclearinterview"></div>
 +
<div class="line_divider"></div>
 +
<div class="clear_extra_space"></div>
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<!----End sub part----->
  
                    </ul>
 
                    <h5>Changes</h5>
 
                    <ul class="skel browser-default">
 
                        <li>Achieve relevance by validating the design at the farm</li>
 
                        <li>Achieve responsibility by analyzing the risks when there is false positive or false negative</li>
 
                    </ul>
 
                    <br>
 
                    <ul class="collapsible popout" data-collapsible="expandable">
 
                        <li>
 
                            <div class="collapsible-header">
 
                                Reflection of the workshop
 
                            </div>
 
                            <div class="collapsible-body">
 
                                <div class="row center">
 
                                    <div class="col s15">
 
                                        <h5>Lists of responsible and relevant things in our project</h5>
 
                                        <p>Things that were considered as really responsible are listed below:</p>
 
                                        <ul class="skel browser-default">
 
                                            <li>Reliability (this is not yet know)
 
                                            </li>
 
                                            <li>GMO-free and safe
 
                                            </li>
 
                                            <li>Sensitive detection</li>
 
                                            <li>Contained</li>
 
                                            <li>The broad range of applications of TDPs</li>
 
                                        </ul>
 
  
                                        <p>Things that were considered as relevant are listed below:</p>
+
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                                        <ul class="skel browser-default">
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<div class="column two_thirds_size">          
                                            <li>Modules can be used separately and can be used for different purposes and broad applications: sustainable storability of TDPs
+
<h4> Bioclear Earth: Jeroen Tideman (27th July 2018) </h4>
                                            </li>
+
<p>
                                            <li>Tackling a real societal/local threat (ABR)</li>
+
We have been in touch with employees of <a target="_blank" href="https://bioclearearth.nl/">Bioclear Earth</a>, who gave us great suggestions on the financial aspects of our project. Because pure cellulose is more expensive than glucose, we needed to find a cellulose-rich waste stream which we could use in our process. They came up with the idea to use recycled toilet paper, which can not be used for other purposes due to its public perception. Subsequently, they explained to us how the market for enzymes works and also connected us with various people in the market. Additionally, they told us about various parties that are working on the conversion of cellulose into glucose. Lastly they gave us the suggestion to use glucose instead of cellulose for our project. However, we decided this was not feasible as we do not want to be competing with the the food industry.
                                            <li>Costs (are unclear)</li>
+
</p>
                                            <li>User Friendliness</li>
+
<h4  style="text-align: center !important;font-style: italic !important;font-size: 1.6em !important;padding: 40px !important;background: #e2e2e2 !important;"> Why don't you use toilet paper? </h4>
                                            <li>Biobrick can be used for broad application and we contribute to an integrated synbio engineering system</li>
+
</div>
                                        </ul>
+
<div class="column third_size">
                                        <h5>Reflection. What is beyond the scope of iGEM and what is things we still can include?</h5>
+
<div class="clear extra_space"></div>
                                        <p>Tackling a real problem</p>
+
<img src="https://static.igem.org/mediawiki/2018/5/52/T--Groningen--bioclear.jpg">
                                        <ul>
+
</div>
                                            <li>Beyond the scope of the project:
+
<div class="clear extra_space" id="avantiuminterview"></div>
                                                <ul class="skel browser-default">
+
<div class="line_divider"></div>
                                                    <li>The need is to identify which AB is relevant to use when facing a disease. Our tool gives insights in which ABs not to use. Although we think that our strategy will help to reduce the abuse of antibiotics, the question in the market is slidely different. Prototype tests should give insights whether are device is relevant enough to tackle current challenges.
+
<div class="clear_extra_space"></div>
                                                    </li>
+
<!----End sub part----->
                                                    <li>Point out which AB to use
+
                                                    </li>
+
                                                </ul>
+
                                            </li>
+
                                            <li>Sensitivity and reliability
+
                                                <ul>
+
                                                    <li>Things we can do:
+
                                                        <ul class="skel browser-default">
+
                                                            <li>What happens if there is a false positive or a false negative?
+
                                                                <ol>
+
                                                                    <li>Estimate the change to have a false positive or negative</li>
+
                                                                    <li>Make risks analysis: Contact TNO to talk about risks analysis</li>
+
                                                                </ol>
+
                                                            </li>
+
                                                        </ul>
+
                                                    </li>
+
                                                    <li>Beyond the scope of our project:
+
                                                        <ul>
+
                                                            <li>Being able to quantify detection</li>
+
                                                            <li>Make Cas13a able to detect mutated genes</li>
+
                                                        </ul>
+
                                                    </li>
+
                                                </ul>
+
                                            </li>
+
                                            <li>User Friendliness:
+
                                                <ul>
+
                                                    <li>Things we can do:
+
                                                        <ul>
+
                                                            <li>Contact farmer to check if we meet the friendliness requirements concerning farmers
+
                                                            </li>
+
                                                            <li>Contact industrial designer to think along with the final design</li>
+
                                                            <li>Make a decision tree so the farmer knows exactly what to do after obtaining the test results
+
                                                            </li>
+
                                                        </ul>
+
                                                    </li>
+
                                                    <li>Beyond the scope of the project:
+
                                                        <ul>
+
                                                            <li>Develop an easier RNA extraction (specialist should look into this): Adjusting the detection protein to detect the DNA directly instead of the RNA. This would take a step of reverse transcription out of the protocol and make the assay more direct instead of indirect.
+
                                                            </li>
+
                                                            <li>Develop a service “a traveling lab in a bus” that does this kind of ABR tests (Front end runner)
+
                                                            </li>
+
                                                        </ul>
+
                                                    </li>
+
                                                </ul>
+
                                            </li>
+
                                            <li>TDPs as sustainable storage solution:
+
                                                <ul>
+
                                                    <li>Beyond the scope of the project:
+
                                                        <ul>
+
                                                            <li>Talk to TDP experts about the possibilities</li>
+
                                                            <li>Talk to contextual experts to give insights on this sustainable solution</li>
+
                                                            <li>Make a risk analysis concerning worldwide TDP storage</li>
+
                                                        </ul>
+
                                                    </li>
+
                                                </ul>
+
                                            </li>
+
                                            <li>Costs savings:
+
                                                <ul>
+
                                                    <li>Beyond the scope of the project:
+
                                                        <ul>
+
                                                            <li>Look into cheaper materials</li>
+
                                                        </ul>
+
                                                    </li>
+
                                                </ul>
+
                                            </li>
+
                                            <li>What things need to be considered when bringing our prototype to the market:
+
                                                <ul>
+
                                                    <li>Next things to do: Brainstorm with TNO to gain insights and feedback
+
                                                    </li>
+
                                                </ul>
+
                                            </li>
+
                                        </ul><br>
+
                                        <h5>Conclusion</h5>
+
                                        <p>Concluding, we reflected our project with the different roles to make sure we did not miss anything. The workshop made us aware of the future challenge considering our project. Due to the reflection we gained insights in which things were beyond the scope of the project and we identified things we could still integrate in our project to make our project more relevant and responsible. Thinking from these four different perspectives was really effective. We were able to reflect the project on different levels, even though the team composition was balanced more towards the experts and system integrators. </p>
+
                                    </div>
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                                </div>
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                            </div>
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                        </li>
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                        <li>
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                            <div class="collapsible-header">
+
                                Summary
+
                            </div>
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                                        <p>The goal of the workshop had two sides. For iGEM, this workshop will be a design evaluation/reflection exercise. For the CEE it is important to receive feedback on the Engineering Roles; possibly determining more engineering roles and match specific skills with the roles.
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</div>
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<div class="column two_thirds_size">           
 +
<h4> Avantium: Ronny Pals (31st August 2018) </h4>
 +
<p>
 +
Rianne, Jens, Benno, Bram and team associate Tjerk Douma visited Chemical Park Delfzijl where we had a meeting with <a target="_blank" href="https://www.avantium.com/">Avantium</a>. Avantium is chemically breaking down wood chips to hemicellulose, glucose and lignin. Their technology allows them to break down cellulose with acid to glucose monomers in one reactor with high yields while recovering the acid. We are trying to do exactly the same, but enzymatically by employing our cellulosome. We agreed to test the suitability of Avantiums glucose for growth medium for our cells. Beyond that we learned a lot about the process of valorizing innovations in general. They gave us many insights regarding the financial and technical bottlenecks that stand between a promising idea and a large scale profitable industrial process. We were impressed by Avantiums technology as it is robust, works with almost any type of wood and requires only very little material preparation, especially in comparison to our enzymatic approach. An important take-away for us was that we have to consider the expenses and environmental implications of our cellulose pretreatment (grinding, autoclaving, phosphorylating) as well.
 +
</p>
 +
<h4  style="text-align: center !important;font-style: italic !important;font-size: 1.6em !important;padding: 40px !important;background: #e2e2e2 !important;"> It was an amazing experience to be in a real biomass pilot plant </h4>
 +
</div>
  
                                        </p>
+
<div class="clear extra_space" id="biobtxinterview"></div>
                                        <p>To conclude, we reflected on our project with the different roles to make sure we did not miss anything. The workshop made us aware of the future challenges considering our project. Due to the reflection we gained insights in which aspects were beyond the scope of the project and we identified aspects that we could still integrate in our project to make our project more relevant and responsible. Thinking from these four different perspectives was really effective. We were able to reflect on the project on different levels.
+
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<h4> BioBTX: Pieter Imhof (25th July 2018) </h4>
                            </div>
+
<p>
                        </li>
+
As suggested by the Science Shop, we got into contact with Pieter Imhof of <a target="_blank" href="https://www.biobtx.nl/">BioBTX</a>. This company produces chemical intermediates out of biomass, however they use a chemical process. They explained to us how they use pyrolysis and combine this with a catalytic conversion step. In this way they are able to reach aromatics yields of approximately 30-70%, with BTX (Benzene, Toluene, Xylene) yields ranging from 5-40%, with yields dependent on the feedstock and used process conditions.
                    </ul>
+
Regarding our project, Mr. Imhof thought that the process of turning glucose into styrene does not have high enough yields to be economically feasible. However, he thought that the conversion of cellulose to glucose in one reactor, combined with glucose to styrene conversion could be an interesting improvement. Additionally, he explained that CO2 is released at every chemical reaction step, the magnitude depending on reaction conditions. So, whereas our method would not be able to meet industrial needs, it would likely be greener than the chemical process of refining biomass, and significantly better than a fossil based process. These steps come together in the Life Cycle Analysis, which can be found on the wiki and in given references. Mr. Imhof explained to us that we should not go too deep into this and provided us with helpful references about their own research.
                </div>
+
</p>
            </div>
+
<h4  style="text-align: center !important;font-style: italic !important;font-size: 1.6em !important;padding: 40px !important;background: #e2e2e2 !important;"> The biological process is less feasible than the chemical, but probably more sustainable </h4>
            <div id="IO" class="modal">
+
</div>
                <div class="modal-content">
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<div class="column third_size">
                    <h4>Feedback Industrial Design Expert</h4>
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<div class="clear extra_space"></div>
                    <h5>Name</h5>
+
<img src="https://static.igem.org/mediawiki/2018/f/f5/T--Groningen--biobtxlogo.jpg">
                    <p>Bella Boven </p>
+
<img src="https://static.igem.org/mediawiki/2018/2/2c/T--Groningen--biobtxmeeting.jpg">
                    <h5>Function</h5>
+
                    <p>Graduated Industrial Design Engineer </p>
+
                    <h5>Insights</h5>
+
                    <ul class="skel browser-default">
+
                        <li>Not too small and not too precise
+
  
                        </li>
+
</div>
                        <li>Click system with different parts </li>
+
<div class="clear extra_space" id="photanolinterview"></div>
                        <li>clear difference between test and control </li>
+
<div class="line_divider"></div>
                        <li>Robust </li>
+
<div class="clear_extra_space"></div>
                        <li>Closed system</li>
+
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                    </ul>
+
  
                </div>
 
            </div>
 
            <div id="MD" class="modal">
 
                <div class="modal-content">
 
                    <h4>Medical Delta</h4>
 
                    <!--image logo -->
 
  
                    <p>The Medical Delta Café is an event that brings together innovators from the Life Sciences and Health &amp; Technology sectors. Doctors, researchers and entrepreneurs discuss and present opportunities for research cooperation and our product development. </p>
+
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<div class="column two_thirds_size">           
 +
<h4> Photanol: Wilmar van Grondelle (12th September 2018) </h4>
 +
<p>
 +
<a target="_blank" href="https://www.photanol.com">Photanol</a> is a platform renewable chemicals company that utilises proprietary engineered cyanobacteria to process carbon dioxide (CO2) and sunlight into valuable chemical products. They have performed a lot of research in the laboratory, and are scaling up now. They aim to demonstrate that their product works on an industrial scale, and Wilmar elaborated on the process from their concept to where they are now. The concept of Photanol started at university. Together with the university, they went to the University Holding, to get an initial investment. From this point on a biorefinery plan, business plan and LCA were made to attract more investors. He told us that it is important to have a good business plan and LCA when you look for investors, because these are the things that people will look at. Another good way to get income is using different subsidies. Photanol now has an industrial partner with whom they work together to scale their project up further. Wilmar adviced us to contact the GGO bureau and to keep close contact with them, as they know everything about safety and regulations. Especially in the phase where we are in now, it is good to contact them so we can put the safety into the design of our project. One example is that a GMO can never outcompete its wild-type. Besides that, there are two important permits you have to keep in mind; the GMO permit and the environment permit. These take in total about 6 months to get!
 +
</p>
 +
<h4  style="text-align: center !important;font-style: italic !important;font-size: 1.6em !important;padding: 40px !important;background: #e2e2e2 !important;"> It is important to have a good businessplan and LCA </h4>
 +
</div>
 +
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 +
<img src="https://static.igem.org/mediawiki/2018/4/4b/T--Groningen--photanol.png">
 +
<img src="https://static.igem.org/mediawiki/2018/0/0b/T--Groningen--riannephotanol.png">
  
                </div>
+
</div>
            </div>
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                    <h4>Dutch Biotechnology Conference</h4>
+
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                    <!--image logo -->
+
  
                    <p>iGEM TU Delft attended the Dutch Biotechnology Conference, organised by the Dutch Biotechnology Association (NBV). The NBV is an association for all professionals in the field of Applied Life Sciences, a valuable network with over 1000 members from different disciplines, from the business sector to education. We gained feedback on our project helping us to shape our project.</p>
 
                    <br>
 
  
                </div>
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<h4> Unipol </h4>
                <div class="modal-content">
+
<p>
                    <h4>Dutch Biotechnology Conference </h4>
+
Unipol is an European producer of EPS (expanded polystyrene, also known as styrofoam). They produce 90.000 tonnes of high quality EPS annually. Styrene is their main raw material. They are a member of EUMEPS, PlasticsEurope and OIK and are ISO 14001 certified. Unipol is interested in StyGreen, as styrene is their main raw material. Therefore, StyGreen would allow them to significantly increase the sustainability of their EPS production. We have presented our research to Unipol and they are highly interested and enthusiastic about our project. Hence we have acquired a substantial investment from them. Their financial investment as well as interest in our technology as a large industrial player is highly valuable to the entrepreneurial success of our project. We plan to continue our quest to produce biobased styrene in a scaled-up industrial setting.
                    <!--image logo -->
+
</p>
 +
<h4  style="text-align: center !important;font-style: italic !important;font-size: 1.6em !important;padding: 40px !important;background: #e2e2e2 !important;"> StyGreen would significantly increase the sustainability of our EPS production </h4>
 +
</div>
 +
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 +
<img src="https://static.igem.org/mediawiki/2018/thumb/f/f7/T--Groningen--unipol.png/1200px-T--Groningen--unipol.png">           
 +
</div>
 +
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                    <p>iGEM TU Delft attended the Dutch Biotechnology Conference, organised by the Dutch Biotechnology Association (NBV). The NBV is an association for all professionals in the field of Applied Life Sciences, a valuable network with over 1000 members from different disciplines, from the business sector to education. We gained feedback on our project helping us to shape our project.
 
                    </p>
 
  
                </div>
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<div class="column two_thirds_size">          
            <div id="parade" class="modal">
+
<h4> Fablab: Winand Slingenbergh </h4>
                <div class="modal-content">
+
<p>
                    <h4>Knowledge Parade: National Institute of Public Health and the Environment </h4>
+
As we aim to produce the plastic monomer styrene, making actual plastic products was an exciting idea. As the quantities of styrene we managed to produce are not large enough for industrial applications yet, we found an interesting partner in <a target="_blank" href="https://www.fablabgroningen.nl/">Fablab</a>, a 3D printing venture. Fablab is an open-source, global network that originated from an MIT course titled ‘How to make almost anything'. They have stayed true to this ideal and offer a wide variety of plastic and wood working techniques in their laboratories.
                    <!--image logo -->
+
3D printing with ABS plastic is possible, but it has some drawbacks, hence we decided to collaborate with Fablab Groningen without actually using StyGreen for 3D printing. We quickly realized that 3D printed biological structures can be of great educational value. Therefore, we made prints of the most important enzymes in our project: the cellulose binding domain, the endogluconase, the beta-glucosidase and the Phenylalanine Ammonia Lyase. We also printed some of their ligands and matched them size wise to showcase where the pocket with the active site in the enzyme is and which chemical alteration is happening.
 +
We also developed a kit of building blocks for styrene, butadiene, acrylnitril and divinylbenzene that can showcase the process of copolymerization through magnets. On top of that our mascot Styrene Steve was 3D printed multiple times and given as present to some of our sponsors as a nice gesture and to keep iGEM in people’s minds. All structures we designed with FabLab are open source and can be found on their website https://www.thingiverse.com/.
 +
</p>
 +
<h4  style="text-align: center !important;font-style: italic !important;font-size: 1.6em !important;padding: 40px !important;background: #e2e2e2 !important;"> We developed a kit of building blocks for ABS polymerization </h4>
 +
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<img src="https://static.igem.org/mediawiki/2018/b/bc/T--Groningen--fablab.jpg">
 +
<img src="https://static.igem.org/mediawiki/2018/7/7a/T--Groningen--fablabexample.jpg">
  
                    <p>During the knowledge parade, we met some farmers and doctors. Here, we gained more insights in the needs and the challenges in the field, like the demand for resistance detection for specific genes in the intensive care.
+
</div>
                    </p>
+
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            </div>
 
            <div id="doctors" class="modal">
 
                <div class="modal-content">
 
                    <h4>Doctors</h4>
 
                    <p>Investigating the needs in antibiotics field, we visited our general practitioners. They confirmed that there is a demand for diagnostic tools that reveal antibiotic resistance. Doctors seem to face challenges considering viral or bacterial infections, the identification of the pathogen causing the infection, resistance detection and the susceptibility to existing drugs.</p>
 
  
                </div>
+
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<img src="https://static.igem.org/mediawiki/2018/5/5e/T--Groningen--zap.jpg">
                    <h4>Feedback experts bioveterinary research</h4>
+
<img src="https://static.igem.org/mediawiki/2018/7/75/T--Groningen--zapBramJens.jpg">           
                    <p>Investigating the needs in antibiotics field, we visited our general practitioners. They confirmed that there is a demand for diagnostic tools that reveal antibiotic resistance. Doctors seem to face challenges considering viral or bacterial infections, the identification of the pathogen causing the infection, resistance detection and the susceptibility to existing drugs.
+
</div>
                        <br><br>See our <a href=https://2017.igem.org/Team:TUDelft/Applied_Design target="_blank">applied design page</a>.
+
<div class="column two_thirds_size">          
                    </p>
+
<h4> ZAP: Drs. R.J. van Linschoten (4th September 2018)</h4>
 +
<p>
 +
One of the first steps when considering upscaling of a process is finding a suitable location for a pilot plant. The province of Groningen is a strong agricultural and industrial area. Therefore, the province can support the conversion of waste streams from biomass into high-end products. <a target="_blank" href="http://www.zapgroningen.nl/en-gb/home">ZAP</a>, the Zernike Advanced Processing innovation cluster, is located on the Zernike campus, along with the University of Groningen, the Hanze University of Applied Sciences and a number of companies. This unique location offers a great opportunity to share and increase knowledge. ZAP offers a test environment for bio-based experiments in the northern region of the Netherlands, where they provide the facilities to set up a pilot plant. ZAP is interested in acting upon the need to lessen our reliance on fossil fuels. We met with drs. R.J. van Linschoten, director of the Zernike Advanced Processing and discussed the prerequisites for setting up a pilot plant.
 +
</p>
 +
<h4  style="text-align: center !important;font-style: italic !important;font-size: 1.6em !important;padding: 40px !important;background: #e2e2e2 !important;"> The province of Groningen supports the conversion of waste streams into high-end products </h4>
 +
</div>
  
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                    <h4>Validation with Dairy Farmer - Paul Oosthoek</h4>
+
                    <p>We also received feedback on how we can improve our device. Paul stated that it would be better if the test really showed which specific antibiotic should be used for treatment, instead of knowing which antibiotics should NOT be used. We completely agree with this statement; finding out which antibiotic to use is more effective in helping to solve the worldwide antibiotic resistance problem. Another piece of feedback was to use larger test tubes for the detection. Currently, we use 1.5 mL eppendorfs in which the detection is done. Paul recommended to perform the detection in larger tubes to increase the visibility and to be more user-friendly.
+
                        <br><br>See our <a href=https://2017.igem.org/Team:TUDelft/Applied_Design target="_blank">applied design page</a> and our <a href=https://2017.igem.org/Team:TUDelft/Demonstrate target="_blank">demonstrate page</a>.</p>
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<h4> NIOZ: Prof. Dr. Klaas Timmermans (27th August 2018)</h4>
 +
<p>
 +
At present, extensive research is carried out on the culturing of green algae. If green algae can be successfully cultured on the open sea, this provides a virtually unlimited source of cellulose. We arranged a skype meeting with Prof. dr. Klaas Timmermans, Senior scientist ecophysiology of seaweeds, head of Department Estuarine and Delta Systems (EDS) at  <a target="_blank" href="https://www.nioz.nl/en">NIOZ</a> and Honorary Professor at the University of Groningen. NIOZ is the Royal Dutch Institute for Sea Research, and is involved in research in the Netherlands as well as far beyond the Dutch border on topics such as biology, physics, chemistry and geography. We spoke with Prof. dr. Timmermans about our design and the potential usage of cellulose from green algae for our iGEM project. Currently, green algae are mainly cultured for their proteins and partly for their carbohydrate content. However, cellulose is a residual product at the moment, for which no suitable purpose has been found at NIOZ. In case we can show a proof-of-concept in our iGEM project, we could close the loop in green algae culturing, so all fractions are used. Prof. dr. Timmermans informed us  that there is still a long way to go before culturing green algae on the open sea is reality. On top of that, the separation of the different fractions (proteins, carbohydrates, etc.) proves to be difficult. All in all, the potential upside is enormous, once the research on culturing green algae has developed further. We are then able to tap into an infinite source of cellulose and use all fractions of the cultured green algae. A win-win situation.       
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</p>
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<h4  style="text-align: center !important;font-style: italic !important;font-size: 1.6em !important;padding: 40px !important;background: #e2e2e2 !important;"> NIOZ has not found a purpose for their cellulose yet </h4>
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<h4> RIVM </h4>
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The Dutch Governmental Institute for Public Health and Environment (<a target="_blank" href="https://www.rivm.nl/en/">RIVM</a>) wants to stimulate Dutch iGEM teams to consider the broader effects of their project on the world surrounding us. This includes investigating ethical, societal, and technical aspects concerning the project. They asked us to adhere to the Safe-by-Design concept, which states that safety should be an integral part of each project, to be considered during every phase and aspect from the early beginnings all the way to the end.
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The first meeting was with Korienke Smit, a policy advisor, and Niek Savelkoul, a trainee and member of the 2017 iGEM Wageningen team. This meeting took place on june 20th, 2018.
</div>
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During this meeting we discussed our initial ideas about how we are planning to implement the Safety-by-Design concept into our project. We got some valuable tips and input, especially about the upscaling of our process, which brings a whole set of new challenges with it, something we had not considered until then. We were planning to use antibiotics, which might be difficult to upscale safely regarding antibiotic resistance issues. Styrene is toxic, and having massive bioreactors filled with styrene-producing yeast strains could be a danger to public health. We were already considering to use CRISPR-Cas9 to remove the need for antibiotics, but these remarks contributed to our decision to make the switch. Another factor was our plan to run evolutionary experiments to improve yields. Korienke had suggestions for this as well, and suggested looking into the 2017 Heidelberg iGEM team, that came up with a clever way to accelerate evolution using quickly-mutating phages.
</li>
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At the end of the conversation we received some advice on how to pitch our idea: our main advantage is the reduction reliance on fossil fuels over traditional methods of styrene production, and the reduction of CO2 emissions.
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The second meeting was with Jaco Westra, a coordinator of synthetic biology, and an expert on safety and GMO regulations. This meeting took place on august 14th, 2018.
 +
We talked about our progress in the lab, which was going slower than expected at that time. Jaco was especially curious how progress on the Safe-by-Design assignment was progressing compared to the last meeting, and how we are integrating the associated principles into our project. We described the changes we had made, for example the consideration of using recycled toilet paper as cellulose source, or the plan to focus on toy makers as customers for our product. We discussed the best ways to market our product, and agreed that the focus should be on the reduction of CO2 emissions. Our plan is to do a Carbon Footprint Analysis to come to an exact figure, to make a better comparison. At the end of the conversation we also received advice on how to improve our infographic.
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<h4  style="text-align: center !important;font-style: italic !important;font-size: 1.6em !important;padding: 40px !important;background: #e2e2e2 !important;"> These remarks pushed us to make the switch </h4>
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<h3>Integration in our project </h3>
 
  
<p id="integration-scroll" class="scrollspy">There were several interactions with stakeholders that heavily impacted the direction of our design. Integrated Human Practices was extremely valuable in shaping our project. In response to dialogues with the public, risk assessors, and potential users, we changed our design from a GMO-based lab tool to a <i>safe</i> and <i>reliable</i> end product. Key points that we took from discussions with stakeholders were that the method needs to combine a <i>simplified sample preparation</i>, a <i>fast, easy readout</i> and the possibility for <i>on-site use</i>. We integrated all these in our project, by designing a cell-free method that can be stored for up to two weeks and produces a visible readout.
 
</p>
 
<p>We started by finding a relevant case in which our device could make a contribution. Through a conversation with a veterinarian, we were advised to narrow our scope to mastitis, an udder infection affecting dairy cows.
 
</p>
 
  
<blockquote>Every milk farmer faces mastitis, a challenging udder disease affecting dairy cows.<cite>Bouwe Gall Frank (veterinarian)</cite></blockquote>
 
  
<p>This infection is not easy to get rid of; udders are exposed to the open environment, making the infection a common re-occurrence. All dairy farmers we spoke to in the Netherlands have had to deal with mastitis. Farmers want to have fast administration of antibiotics when treating this disease, as time is of the essence. Our tool makes sure that fast treatment of mastitis can be done in a responsible way, without misusing antibiotics, thereby helping to prevent the evolution of antibiotic resistant bacteria. Looking to mastitis, we adapted our tool to detect relevant resistance genes in the common pathogen, Staphylococcus Aureus (SAU), causing this disease.
 
</p>
 
  
<blockquote>It is relevant to be able to detect SAU pathogens. As there is a huge difference in sensitivity for antibiotics considering MRSA, it would be added value to have a conclusive result on the sensitivity.<cite>Maaike van den Berg (veterinarian)</cite></blockquote>
+
<h1>Meetings with Experts</h1>
  
<p>
+
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After talking to experts with expertise in mastitis from the Wageningen Bioveterinary Research Center in Lelystad, we found that detecting the mecA and blaZ genes was the way to go.
+
</p>
+
  
<blockquote>MecA can be used to detect resistance against all β-lactam antibiotics.<cite>Fimme van der Wal (agricultural researcher)</cite></blockquote>
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<h4> Tjerk Douma (28th June 2018) </h4>
 +
<p>
 +
We sat down with Tjerk Douma, a Master student in Energy and Environmental Sciences. Tjerk explained the importance of a Life Cycle Analysis (LCA) and what factors are taken into account. We concluded that it may be interesting to look at the difference in the LCA of StyGreen and oil based Styrene. We agreed that Tjerk would help us with the LCA, and had regular meetings afterwards. This resulted in our <a target="_blank" href="Human_Practices#carbonfootprint">Carbon Footprint Analysis</a>
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</p>
 +
<h4  style="text-align: center !important;font-style: italic !important;font-size: 1.6em !important;padding: 40px !important;background: #e2e2e2 !important;"> We agreed that Tjerk would help us with the LCA </h4>
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<blockquote>Detection of blaZ is a conclusive result to exclude commonly used penicillin treatment.<cite>Dik Mevius (agricultural researcher)</cite></blockquote>
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<p>For further information about these genes check out our <a href="https://2017.igem.org/Team:TUDelft/Applied_Design" target="_blank">applied design</a> and <a href="https://2017.igem.org/Team:TUDelft/Demonstrate" target="_blank">demonstrate page</a>.
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<h4> Drs. Karin Ree (11th July 2018) </h4>
 +
<p>
 +
Drs. Karin Ree is a member of the Science Shop in Groningen. The Science Shop connects ambitious students to companies or academic research outside their field. As we were looking for connections to the bioplastic industry, Karin was able to give us great advice on who we should contact. She helped us to find contacts inside and outside of the university. Furthermore, she has sent us a various useful papers on the sustainability of bioplastics.  
 +
</p>
 +
<h4  style="text-align: center !important;font-style: italic !important;font-size: 1.6em !important;padding: 40px !important;background: #e2e2e2 !important;"> Karin was able to provide meaningful contacts </h4>
 +
</div>
  
<p>After defining our end-users and detection goal, we looked at how we could make our device as user-friendly as possible. From the start of our project, we wanted to integrate the use of tardigrade intrinsically disordered proteins (TDPs) which are able to maintain the functionality of other proteins upon desiccation. This fitted perfectly in our design with respect to our end-users, as our TDPs enable the transportation and storage of our detection tool at room temperature. Normally, protein function can be maintained when stored at -80 degrees celsius, something that is not always available at your local dairy farm! We also envisioned that this improved storage method will be advantageous for shipping our versatile RNA-detection tool for broader applications. For further information on our TDPs, check out our <a href="https://2017.igem.org/Team:TUDelft/Design#TDP" target="_blank">TDP design page</a>.
+
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+
  
<p>Adding to the storability, we realised that our tool needed to give a readout visible to the naked eye. At a farm, there are no fancy lasers or microscopes, so we had to get creative! We started by designing a microfluidics paper chip with GMOs with a kill switch to detect resistance genes, but gained crucial feedback on this.</p>
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<blockquote>Even <b>if</b> GMO kill switches were reliable, there is no public acceptance to use GMOs in the environment. <b>If</b> it will be accepted in the future, it will take years from now to legislate this principle. Innovation based on this gets stuck.<cite>Cecile van der Vlugt (Risk Assessor GMO)</cite></blockquote>
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<h4> Prof. Dr. Gert Jan Euverink (8th August 2018) </h4>
 +
<p>
 +
Gert Jan Euverink is the University of Groningen representative in the CaDOS project. Toilet paper in sewage material contains roughly 80% cellulose. In the CaDOS project, this cellulose material is used to drain water from the sludge, which improves the purification process. Furthermore, Euverink advises companies on the implementation of their technical ideas. His expertise has been helpful to previous iGEM teams, since he was a supervisor of the winning team of Groningen in 2012!
 +
</p>
 +
<h4  style="text-align: center !important;font-style: italic !important;font-size: 1.6em !important;padding: 40px !important;background: #e2e2e2 !important;"> In the CaDOS project, cellulose material is used to drain water from sludge </h4>
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<p>This led us to come up with a <b>new application: CINDY-Seq</b>. This method allows for a simple yes or no answer to the question: is the pathogen causing mastitis in my cow resistant to penicillins, or even all β-lactamases depending on the design of Cas13a, in a matter of hours, without the use of GMOs in the environment. For more information on how CINDY-Seq works, please visit our <a href="https://2017.igem.org/Team:TUDelft/Design#coacervation" target="_blank">coacervation design page</a>.</p>
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<p>Now that we completed the design of our detection tool, we needed to look at how we could make the sample preparation as simple as possible for a farmer, as farmers like to do most things themselves.</p>
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<h4> Prof. Dr. Katja Loos (5th July 2018) </h4>
 +
<p>
 +
Biodegradable plastics, like PLA, are technically biodegradable but only under controlled
 +
conditions. In nature they still take a long time to degrade on their own, only a bit faster than
 +
for example polystyrene. However, PLA being “biodegradable” sends a message that it is
 +
okay to throw it away anywhere because if its “biodegradability”, only adding to the problem.
 +
Just recently, the EU has moved to ban single use plastics. Therefore, what we should do is
 +
look into non-single use plastics. While polystyrene has numerous non-single use applications, the
 +
stigma of it being used as disposable packaging material is not easily erased. Some
 +
polymers that are nearly always single use include:</p>
 +
<ol>
 +
<li>Nylons</li>
 +
<li>Polyurethanes</li>
 +
<li>Polyamides</li>
 +
</ol>
 +
<h4  style="text-align: center !important;font-style: italic !important;font-size: 1.6em !important;padding: 40px !important;background: #e2e2e2 !important;"> PLA is only adding to the problem! </h4>
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<blockquote>We try to do most things by ourselves to prevent high bills from the veterinarian.<cite>Tjerkje Poppinga (dairy farmer)</cite></blockquote>
 
  
<p>In the case of mastitis, the pathogen is present in the milk of the infected cow. By hitting the books and optimising existing protocols, we came up with an easy method to prepare a fresh milk sample for the detection tool. To know more about which methods we came up with, look at our <a href="https://2017.igem.org/Team:TUDelft/Design#sampleprep" target="_blank">sample prep design page</a> where we describe this extensively.</p>
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<h3> Prof. Dr. Francesco Picchioni (3rd Oktober 2018) </h3>
 +
<p>
 +
We went to Francesco Picchioni, an expert in the field of polymers, to ask his view on styrene and our project design. Did he see the benefits, or would he think it was an unrealistic design? He explained to us that styrene is a very good material for various reasons. The first is its transparency, which is why it is easily colored with other chemicals. Styrene furthermore contains an aromatic ring and pi-pi stackings of these rings. This leads to the fact that styrene-based plastics have a high TG (Glass Transition Temperature). These connections are way stronger compared to the ester bonds in PET and PLA. No other plastics have these special characteristics, and therefore styrene is irreplaceable. Right now, styrene is not recycled to a high extent, as the price of newly produced styrene is lower. However, because styrene is a thermoplastic, it is easily recycled in case of a stronger market pull. Picchioni was suprised that biological styrene production was feasible. If a high yield can be engineered, this would be a major discovery and he would be very interested.
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</p>
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<h4  style="text-align: center !important;font-style: italic !important;font-size: 1.6em !important;padding: 40px !important;background: #e2e2e2 !important;"> "If you can make me a few kilo's, you can come back to me!" </h4>
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<p>Finally, our integrated human practices strategy helped us to think a step further about our design, regarding, for example, the costs involved in our device and what it should actually look like; what kind of ‘kit’ will it be and what will it contain? We also looked at the feasibility of our device in the context of whether or not farmers would actually be allowed to <i>use</i> such a device and what needs to be done considering legislation to make this possible.</p>
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<blockquote>Only veterinarians can prescribe or change antibiotic treatments.<cite>Engeline van Duijkeren (veterinarian)</cite></blockquote>
 
<p>Stakeholder interactions shaped our final design and made it feasible to transform our detection method into an application, resulting in a toolbox with which the farmers can perform the resistance test themselves on-site, instead of being dependent on slow lab processes. Simple, cheap and safe methods - for example the hand-powered centrifuge and boiling method during sample preparation, together with an optimized readout - make our device applicable for rapid frontline diagnostics. We developed our toolbox to detect the most relevant multiple antibiotic resistance genes, expanding the impact of our product to achieve better animal and human treatment strategies, see our <a href="https://2017.igem.org/Team:TUDelft/Applied_Design" target="_blank">applied design page</a> for more info!</p>
 
  
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<h4> Prof. Dr. A. J. M. Driessen </h4>
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In order to gain more insight into strain optimization, we met with professor Driessen, head of the molecular microbiology department at the University of Groningen. We discussed the best ways to implement and optimize our design. Driessen provided us with many helpful suggestions. For example, we went from the concept of two separate coexisting yeast strains (one cellulolytic, one producing styrene), to one yeast strain doing both processes simultaneously. Furthermore, we discussed metabolic engineering to gain higher yields, for example multiple knock-outs which we could implement. Finally, Driessen proposed to use the CRISPR-Cas9 technique to genomically integrate our genes of interest, instead of using several plasmids. Moreover, Driessen connected us to important contacts as well as providing us with additional laboratory space. </p>
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<h4  style="text-align: center !important;font-style: italic !important;font-size: 1.6em !important;padding: 40px !important;background: #e2e2e2 !important;"> His advice brought us from two seperate yeast strains to one yeast strain performing both processes.</h4>
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<h4> Prof. Dr. B. Poolman (1st June 2018)</h4>
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One of our team members visited professor Poolman of the Enzymology research group to discuss the possible effects of styrene toxicity in our design. During literature study we discovered the existence of styrene exporters and we wanted to discuss whether expression of such an exporter in <i>S. cerevisiae</i> would be beneficial for our design and styrene yield. Poolman pointed out that expressing prokaryotic proteins in eukaryotes is extremely difficult, but pointed towards the Pdr5 export protein and ABC transporters. Furthermore he suggested performing an evolution experiment in <i>S. cerevisiae</i> to decrease the sensitivity of our yeast towards styrene. </p>
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<h4  style="text-align: center !important;font-style: italic !important;font-size: 1.6em !important;padding: 40px !important;background: #e2e2e2 !important;"> An evolution experiment in S. cerevisae to decrease toxic effects from styrene  </h4>
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<h4> Shreyans Chordia (27th September 2018)</h4>
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Shreyans Chordia, a PhD student at the Biomolecular Chemistry & Catalysis group, works on styrene production in <i>E. coli</i> and provided us with an <i>E. coli</i> codon optimized version of the PAL2 gene. Shreyans has been able to produce styrene in <i>E. coli</i> at quite significant levels. He suggested the possibility of coculturing our cellulose degrading yeast strain with his styrene producing <i>E. coli</i> to convert cellulose to styrene in one bioreactor. He offered to help with the experimental setup and conducting the experiments. Furthermore, he got us in contact with Balin Fridrich, who works on the degradation of lignocellulose. </p>
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<h4  style="text-align: center !important;font-style: italic !important;font-size: 1.6em !important;padding: 40px !important;background: #e2e2e2 !important;"> Shreyans was able to produce styrene at quite significant levels </h4>
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<h4> Prof. Dr. Marco Fraaije (20th July 2018)</h4>
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Professor Marco Fraaije is an expert in the fields of biology, biochemistry, biotechnology and in particular enzyme engineering. His group published an extremely useful article for our project describing a fast and sensitive method for the detection of cellulase activity. We had a fruitful discussion about the assay described in the paper. One of the subjects that we discussed was the feasibility to detect cellulase activity with the assay while using our intact yeast cells instead of purified proteins. Finally, professor Fraaije provided us with the possibility for assistance, usage of the lab and supplied the materials required for the experiments.</p>
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Szymanski is an assistant professor, at the department of radiology and imaging, at the UMCG (University Medical Center Groningen). His fields of interests are molecular medical imaging and photopharmacology. Wiktor Szymanski was willing to help us optimize the protocol for the phosphorylation of cellulose at the 6th position. Furthermore, he was of great help performing the experiment and provided us with a lab and equipment for the experiment. The phosphorylation of cellulose was performed to increase the solubility of the polymer. The improved solubility resulted in an improved accessibility of the cellulosome complex towards the cellulose polymer. The cellulosome complex chops the cellulose polymer into glucose molecules. These glucose molecules are obtained by the yeast cells, as carbon source, and converted into styrene molecules.</p>
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<h4> Intellectual Property Office RUG (8th October 2018)</h4>
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To see if we could patent parts of our project, we contacted the IP center of the University of Groningen. We discussed three important subjects: inventorship, novelty and inventivity. The first subject we had to discuss was inventorship. Who contributed substantially to our project? Besides our team members, to what extent were the supervisors part of our idea? After consulting other iGEM teams, we decided that the patent should be shared with the supervisors. For the novelty of our project, it was important that the to be patented subject was not published already. We encountered problems with our own disclosure here due to our outreach and education activities. The most difficult part of a patent is the inventivity. Since we combine several methods of degrading cellulose together, this was an important option for patenting. Subsequently, we also had to think about the financial aspects of the patent. Would companies pay to use our technology? We discussed this factor with several investors and several companies that are highly interested in our product. </p>
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<p>Boonniteewanich, J., Pitivut, S., Tongjoy, S., & Lapnonkawow, S. (2014). Evaluation of Carbon Footprint of Bioplastic Straw compared to Petroleum based Straw Products. Energy Procedia, 56, 518–524. https://doi.org/10.1016/j.egypro.2014.07.187</p>
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<p>Croezen, H. J., & Lieshout, M. van. (2015). Handleiding CO2-waarden voor biobased grondstoffen volgens MJA3/MEE-methodiek. CE Delft, 73.</p>
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Latest revision as of 02:03, 18 October 2018

To get a good overview, we invite you to have a look at our tree of thoughts. This tree catches ideas as new light in its leaves, and by making the right choices, it grew to a great height. Furthermore, we had great conversations on how to let our tree grow further after our iGEM journey has ended. We discussed how to scale up our product StyGreen, which safety procedures we have to keep in mind and how to eventually implement our product in society successfully. These insights plant a seed for a greener future.

  • Our Interactive Human Practices Tree

    Click on the icons in the timeline and find out all about the insights we gained from our stakeholders and how their input shaped our project.

Introduction

For the StyGreen project, Human Practices was not a box that needed to be ticked. On the contrary, it was a tool to integrate our project into the real world. As production of plastics can be a sensitive subject, Human Practices was important from the very start of our project.

As Human Practices is not binary, but a continuous and constant process. Here provide a summary of the biggest influences on the design of our project. Additionally, many insights were gained by talking to our friends, family and complete strangers. One of the first questions was always: “why more plastics?”. We have discussed this with several experts and investigated the advantages and disadvantages of different plastics. We looked into both ‘biodegradable’ plastics, as well as non-biodegradable plastics.

The starting point of our project was a look at the world as it is. We have marvelous technologies which make our lives better, things that were problems 100 years ago are forgotten and information can be shared faster than ever. However, there is also something terribly wrong with this world. Temperature is rising, animals go extinct: our advancement is at the cost of the planet.

We love all these advancements. We would lie if we say we did not, but we do want to solve the downside of our development. Therefore, we took a closer look at plastic. Plastic is a wonderful product and these days it is impossible to live without it. We looked into the production of plastic. Can we make clean plastic non-polluting plastic? And how do we use this plastic responsibly? On the Human Practices pages you'll found where our journey brought us; from schools to festivals; from start-ups to multinationals.

Carbon footprint analysis

Producing styrene from organic waste

The aim

We are facing a huge increase in global population: from the current world population of 7.6 billion to an expected 9.8 billion people in 2050 [1]. This projected increase in global population leads to an increase in both food and energy consumption, which in turn in is associated with an increased emission of greenhouse gasses. Right now, we live in a plastic generation. The global production and consumption of plastics have been on the rise for over 50 years now, reaching a plastic consumption of 297.5 million tons by the end of 2015 [2]. Plastic products from the petrochemical industry have a high carbon footprint (Boonniteewanich, Pitivut, Tongjoy, & Lapnonkawow, 2014). The combination of global population increase and a mass consumed non-eco-friendly product, in the form of petroleum-based plastics, could be disastrous. This is one of the reasons that the Groningen iGEM team’s project attempts to produce (bio)styrene, a building block for many plastics, from cellulose as an alternative to petroleum-based styrene. In this section we have carried out a partial Life Cycle Assessment (LCA) to identify the environmental impact of both petroleum-based styrene and bio-based styrene. The main purpose is to provide an insight in the environmental burden that is caused by the worldwide styrene industry in terms of carbon dioxide equivalent emissions (CO2-eq) and to showcase our greener alternative.

For our LCA analysis we have used the Dutch Gross Energy Requirements values (GER) Values. These values are used for a ‘cradle to gate’ analysis and include all emissions that are needed to produce a certain product. These process emissions exclude any carbon flux from or to the atmosphere. In the case of a bio-based feedstock this is a complete analysis, because the carbon uptake is balanced with the emissions once the product is disposed of. For fossil fuel based styrene a value of 3,1 KG needs to be added to this (Croezen & Lieshout, 2015) because these emission will lead to a net carbon emission. (see figure 1) (Croezen & Lieshout, 2015). A full LCA should also include other impact categories, however it is decided not to include these; we discovered the LCA analysis in a late phase of the project which forced us to simplify the analysis.

Figure 1. Figure retrieved from: http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S1021-20192013000200001

Analysis

For our analysis, we compared the process of producing styrene from a bio-based feedstock to the process of producing styrene with petroleum as a feedstock. To define the cradle to gate emission of petroleum-based styrene we contacted two experts of the company CE Delft, the authors of a report stating the GER for industrial feedstock (Croezen & Lieshout, 2015). With their expert help, we were able to define the cradle to gate emission of petroleum-based styrene for our analysis, the value being: 7.8 CO2-eq per kilogram styrene.

Now we need to compare the GER of petroleum-based styrene with the GER of our StyGreen. In order to do this we need to define the GER of StyGreen. The first step in defining the amount of CO2-eq per kilogram StyGreen is: defining the feedstock. We explored many different feedstock options. After comparing many possibilities, we decided to use recycled toilet paper. The main reason for this choice was the sustainability aspect. Recycled toilet paper is not used for anything at this moment. Therefore, it could be argued that it does not hold monetary value or even a negative monetary value. This means that we can add value to the life-cycle of toilet paper. Another reason for choosing toilet paper, is that we do not want to compete with the food industry. It might be feasible to use sugar, or first generation resources to produce styrene, but this does not fit into our view of a better world.

The second step was to calculate the carbon footprint of recycled toilet paper. The carbon footprint of a feedstock in a certain phase of the Life-Cycle analysis is proportional to the monetary value the feedstock holds in that particular phase. Since the recycled toilet paper is derived from paper, we looked into the monetary value of recycled toilet paper in combination to the resource, paper. After this we looked at the price of the toilet paper, and compared to the price of wood. This way, we could make a parallel to the toilet paper CO2-eq. The cradle to grave carbon emission of paper is 0.9 CO2-eq per kg paper (Croezen & Lieshout, 2015; figure 2 gives a visual representation of the factors determining the carbon emission of paper feedstock).

Figure 2. Life cycle assessment of offset paper production (Silva et al., 2015).

The cost of paper is €150 per ton. Due to the fact that toilet paper recycling is still in its infancy, it was hard to define the representative price for this resource. However, after talking to several experts(as you see here), we came to a price estimate of €15 per ton. Since, toilet paper holds 10% of the monetary value of paper, we divided the CO2-eq by 10 as well, giving our recycled toilet paper feedstock a carbon footprint of 0.09 CO2-eq per kilogram.

FeedstockPrice (€ per ton)Conversion factorEmissions (CO2 per kg)
Paper15090%0.9
Recycled toilet paper1510%0.09
Table 1. The carbon emissions of our feedstock, recycled toilet paper.

Next we need to know how much energy (and therefore, how carbon emissions) is required to produce 1 kilogram of StyGreen. The energy requirement is based on the following formula (see table 2):

From the energy requirements we can now derive the process emissions in CO2 per kg StyGreen by means of the following formula (see table 2):

This brings us the a process emissions of 1.229 CO2 per kg produced StyGreen. If our genetically engineered yeast had a 100% conversion rate, we would need 10 kilograms of recycled toilet paper to produce 1 kg of StyGreen (based on the theoretical maximum yield). Which would mean that the carbon footprint of our StyGreen would be 2.129 CO2-eq per kg.

Process assumptions
(a)Size of our bioreactor (in liters)500
(b)Heating of water (per degree per 1000 liter/MJ)4.19
(c) Temperature in bioreactor (in degrees Celsius)30
(d) Ambient temperature (in degrees Celsius)10
(e) Contribution exothermic reaction10
(f) Heat loss (per 24 hour per degree in MJ)0.03
(g) Calorific value of natural gas (m3)32
(h) Natural gas (CO2/m3)1.8
(i) Process time in bioreactor (in days)3
(j) KG Styrene per bioreactor1
Energy requirements (MJ)21.85
Process emissions (CO2 per kg)1.229
Table 2. The predicted process emissions of producing StyGreen in our bioreactor[3]

This is a lot better than 7.8 CO2-eq per kg for petroleum-based styrene. However, at this point in time our conversion are not yet 100%. For each kilo of styrene we produce, we need 263 kilograms of cellulose (recycled toilet paper) right now. This would result in 24.89 CO2-eq per kg, which is way worse than regular (petroleum-based) styrene. This partly due to the assumptions made in the flux model, which assumes that yeast needs have a net biomass gain at all times. While, that is not necessary in our bioreactor. Moreover, the first version of our yeast is just a proof of concept. There are still a lot of parts that can be optimized. Both in the yeast strain itself, in the form of knock-outs, and in the bioreactor, by reducing the process emissions.

Conclusions

  1. Toilet paper waste is used as the primary raw material in the biorefinery to produce styrene. The reason for this it is not used for feeding humans. The other reason is we can add value to this product.
  2. Currently the process is not sustainable (based on flux model, with mass balance of 263 : 1)
  3. We could still optimize our process a lot, so we should be able to decrease the mass balance by a lot. And starting from a mass balance of 33 : 1 we are cleaner than petroleum-based styrene
  4. We can also improve the process emissions, lower process emissions means our mass balance can be higher (at the moment the process emissions are more than 28% of the total emissions of petroleum-based styrene).

Safety

Safety should be a cornerstone of every project, taken into account during every phase. For this reason the Dutch Governmental Institute for Public Health and Environment (RIVM) has challenged us to participate in their Safe-by-Design assignment. The goal of this assignment is to demonstrate how our team has taken safety into account throughout our project, in every aspect. Of particular importance is the human practices part, where our ideas get taken outside the lab and into the world surrounding us. Of special interest is the iterative process, where the direction of the project is adjusted based on input from stakeholders and experts in relevant fields, safety and ethical guidelines, and considerations regarding the upscaling of our project. We have had 2 Skype meetings with staff members of the RIVM, and using their tips and guidance we made some more adjustment. The final product, an infographical timeline describing the iterative process of our project, is pictured below.

Stakeholder Analysis

Porter Analysis

To investigate our position and opportunities on the market, we performed a Five Forces analysis. Here, we looked at the strengths of our buyers and suppliers, substitutes for our product, competition and new entrants. The results indicate that we have a beneficial position in relation to our suppliers as there are multiple sources of cellulose. However, the buyers have a high switching cost, which is a potential threat to our technology. For new entrants, a large amount of prior knowledge is needed to enter the market, which is one of our strengths. The substitutes of our product are different kinds of plastics, but as the plastic market is large and specific, this is not a great threat.

For buyers, production scale is very important

Meetings with companies

EV Biotech

The young, Groningen based biotech startup EV Biotech offered to collaborate with us in many aspects. Represented by Linda Dijkshoorn, Agnieszka Wegryzn and Sergey Lunev, EVBiotech was present at multiple meetings with our subgroups. Linda had fantastic tips about structure and organisation, and helped us to set up a SCRUM way of working. Agnieszka is an expert on modelling and helped a great deal with the flux balance analysis. Sergey helped us to set up the concept of a continuous bioreactor. Over the summer we had ten meetings to discuss our progress on the project. Next to technical help, we also profited greatly by gaining access to the big network of EV Biotech. As a special honor, we were invited to the official opening of the new EV Biotech office. Here we had the opportunity to pitch our project to several experienced business people.

We also had a great deal of help accessing the big network of EV Biotech

Interviewing the Vice-President Materials of a Toy Multinational (16th October 2018)

Creating a bioplastic that is able to compete with conventional plastic means tapping into a market with unlimited potential. For example, 19 billion Lego elements are produced every year. This equals 2.16 million elements every hour, or 36.000 per minute. This premium toy-giant with an annual revenue of 4.8 billion USD (2017) is highly interested in swapping their current ABS feedstock to a more sustainable non-crude oil derived source. The Vice-President Materials of a Toy Multinational made time to sit down with us, despite a very full agenda. We discussed what drives companies when making transitioning decisions, what toy companies look for in materials and what to take into account throughout development.

While diving into the many applications of styrene, what most interested us was an application of styrene as raw material for a non-single use plastic. This was one of the drivers which pointed us towards Lego bricks: durable playing bricks for playful development. It turns out our visions align. During the course of our project, Lego has published various articles and press releases about their ambition to produce plant-based plastic playing bricks. The mentioned Vice-President Materials was happy to sit down with us to share views on the future of biobased plastics, as well as discussing some opportunities and limitations with regards to their production. Our discussion was highly insightful. Some highlights which will shape the future of our project:

Your choice for a 2G feedstock highly excites me

  1. From 1G to 2G feedstock: the Vice-President Materials is enthusiastic about our choice of a 2G feedstock: highlighting circularity, and also addressed a challenge we proposed, the loss of biomass to oxygen, stating that because our feedstock is 0-value this is not a problem! Being a second generation feedstock, “sludge” (our toilet paper waste stream) does not compete with food supply.
  2. “Side effects” of transitioning to bio-based plastic: to guarantee trusted product characteristics for injection moulding playing bricks, every mould is tailored to the specific properties of the plastic used to inject the mould of the individual bricks. Transitioning for a multinational like this does not just mean searching for the right material. It means transforming the entire production process. Therefore, there is little room for errors when switching to a new composition.
  3. Importance of constant feedstock: scale, constant (reliable) product with uniform properties: We were pointed towards an important bottleneck of bioplastics: going from start-up to scale up. In order to supply industrials, a reliable feedstock is necessary. Therefore, throughout developing StyGreen in the lab ample attention needs to be given to possible commercialization. Read about our dive into this on our Entrepeneurship page.
  4. Minimizing steps in the production process: Minimizing production process steps is appealing when producing plastics. Minimizing steps in the production process will contribute to the success of StyGreen, for example by minimizing energy consumption. This makes our product more competitive.
  5. Who is responsible for this transition: to place our project in a societal context, we also had an insightful discussion on where the responsibility of the energy transition lies.

According to the VP Materials we are operating at the right time. Speaking of an ever-increasing visible framework and the fact that we are currently operating in a more circular economy which will have large consequences.

Optimizing scale and reliable production are of utmost importance when producing a successful bioplastic

Ludos Imaginem: George van den Nieuwenhuizen (19th September 2018)

Ludos Imaginem is a new company which creates toys with which you are able to create something out of your own imagination. Because they recently started, they are really interested in making their product as sustainable as possible. Ludos is willing to invest in us when we have the first results, and has shared the data about the styrene they need for their product. This way, we can optimize our StyGreen to the demand of the customer. We keep in contact with Ludos to update them on the developments in our process. Ludos is very interested in a biobased way to create plastics. They do not want to compete with the food industry, and therefore encourage our way of working with sludge.

"If you find a sustainable solution for current plastics, you will be bigger than Elon Musk"

KNN Cellulose: Yme Flapper (31st August 2018)

We visited KNN Cellulose! After extensive research into possibilities of biomass, we found the company that produces Recell®. This is an innovative new product made from recycled toilet paper which consists of over 90% cellulose. KNN asked us whether there is a possibility to create styrene from their product. In this manner, we can really use waste streams to create StyGreen! The company develops biomass-derived chemicals and is looking for new innovative and sustainable ways of production. GMO technology fits this profile. KNN provided us with a sample of their product for our experiments and they are very interested in our results.

KNN provided us with a sample of their product

NRK: Martin van Dord (24th July 2018)

NRK is the Dutch Federation of plastic and rubber converters, with 20 different sub associations and 400 member companies. We talked to Martin van Dord, innovation consultant at NRK and Topsector Chemie. According to the NRK facts and figures (2017) circa 2000 kilotonnes of plastics were used in 2017, of which circa 20 kilotonnes (1%) were bioplastics. The main problem associated with the use of bioplastics is the price, which can be up to twice as high as that of virgin plastics. In order to contribute to the goals of the Paris Agreement, the objective is to lift the market share of bioplastics to 15% in 2030. Mr. van Dord thought our project was very interesting, since we came up with a new way to produce bioplastics. However, he was wondering why we would focus so much on styrene. Why not create a new bioplastic with even better qualities? He also stated that the business case should be a part in the project in order to get a better insight in the potential of genetically manufactured or engineered bioplastics and the scale of economic feasible production facilities. NRK also published an article about us on their website

Only 1% of the plastic usage consists of bioplastics

Bioclear Earth: Jeroen Tideman (27th July 2018)

We have been in touch with employees of Bioclear Earth, who gave us great suggestions on the financial aspects of our project. Because pure cellulose is more expensive than glucose, we needed to find a cellulose-rich waste stream which we could use in our process. They came up with the idea to use recycled toilet paper, which can not be used for other purposes due to its public perception. Subsequently, they explained to us how the market for enzymes works and also connected us with various people in the market. Additionally, they told us about various parties that are working on the conversion of cellulose into glucose. Lastly they gave us the suggestion to use glucose instead of cellulose for our project. However, we decided this was not feasible as we do not want to be competing with the the food industry.

Why don't you use toilet paper?

Avantium: Ronny Pals (31st August 2018)

Rianne, Jens, Benno, Bram and team associate Tjerk Douma visited Chemical Park Delfzijl where we had a meeting with Avantium. Avantium is chemically breaking down wood chips to hemicellulose, glucose and lignin. Their technology allows them to break down cellulose with acid to glucose monomers in one reactor with high yields while recovering the acid. We are trying to do exactly the same, but enzymatically by employing our cellulosome. We agreed to test the suitability of Avantiums glucose for growth medium for our cells. Beyond that we learned a lot about the process of valorizing innovations in general. They gave us many insights regarding the financial and technical bottlenecks that stand between a promising idea and a large scale profitable industrial process. We were impressed by Avantiums technology as it is robust, works with almost any type of wood and requires only very little material preparation, especially in comparison to our enzymatic approach. An important take-away for us was that we have to consider the expenses and environmental implications of our cellulose pretreatment (grinding, autoclaving, phosphorylating) as well.

It was an amazing experience to be in a real biomass pilot plant

BioBTX: Pieter Imhof (25th July 2018)

As suggested by the Science Shop, we got into contact with Pieter Imhof of BioBTX. This company produces chemical intermediates out of biomass, however they use a chemical process. They explained to us how they use pyrolysis and combine this with a catalytic conversion step. In this way they are able to reach aromatics yields of approximately 30-70%, with BTX (Benzene, Toluene, Xylene) yields ranging from 5-40%, with yields dependent on the feedstock and used process conditions. Regarding our project, Mr. Imhof thought that the process of turning glucose into styrene does not have high enough yields to be economically feasible. However, he thought that the conversion of cellulose to glucose in one reactor, combined with glucose to styrene conversion could be an interesting improvement. Additionally, he explained that CO2 is released at every chemical reaction step, the magnitude depending on reaction conditions. So, whereas our method would not be able to meet industrial needs, it would likely be greener than the chemical process of refining biomass, and significantly better than a fossil based process. These steps come together in the Life Cycle Analysis, which can be found on the wiki and in given references. Mr. Imhof explained to us that we should not go too deep into this and provided us with helpful references about their own research.

The biological process is less feasible than the chemical, but probably more sustainable

Photanol: Wilmar van Grondelle (12th September 2018)

Photanol is a platform renewable chemicals company that utilises proprietary engineered cyanobacteria to process carbon dioxide (CO2) and sunlight into valuable chemical products. They have performed a lot of research in the laboratory, and are scaling up now. They aim to demonstrate that their product works on an industrial scale, and Wilmar elaborated on the process from their concept to where they are now. The concept of Photanol started at university. Together with the university, they went to the University Holding, to get an initial investment. From this point on a biorefinery plan, business plan and LCA were made to attract more investors. He told us that it is important to have a good business plan and LCA when you look for investors, because these are the things that people will look at. Another good way to get income is using different subsidies. Photanol now has an industrial partner with whom they work together to scale their project up further. Wilmar adviced us to contact the GGO bureau and to keep close contact with them, as they know everything about safety and regulations. Especially in the phase where we are in now, it is good to contact them so we can put the safety into the design of our project. One example is that a GMO can never outcompete its wild-type. Besides that, there are two important permits you have to keep in mind; the GMO permit and the environment permit. These take in total about 6 months to get!

It is important to have a good businessplan and LCA

Unipol

Unipol is an European producer of EPS (expanded polystyrene, also known as styrofoam). They produce 90.000 tonnes of high quality EPS annually. Styrene is their main raw material. They are a member of EUMEPS, PlasticsEurope and OIK and are ISO 14001 certified. Unipol is interested in StyGreen, as styrene is their main raw material. Therefore, StyGreen would allow them to significantly increase the sustainability of their EPS production. We have presented our research to Unipol and they are highly interested and enthusiastic about our project. Hence we have acquired a substantial investment from them. Their financial investment as well as interest in our technology as a large industrial player is highly valuable to the entrepreneurial success of our project. We plan to continue our quest to produce biobased styrene in a scaled-up industrial setting.

StyGreen would significantly increase the sustainability of our EPS production

Fablab: Winand Slingenbergh

As we aim to produce the plastic monomer styrene, making actual plastic products was an exciting idea. As the quantities of styrene we managed to produce are not large enough for industrial applications yet, we found an interesting partner in Fablab, a 3D printing venture. Fablab is an open-source, global network that originated from an MIT course titled ‘How to make almost anything'. They have stayed true to this ideal and offer a wide variety of plastic and wood working techniques in their laboratories. 3D printing with ABS plastic is possible, but it has some drawbacks, hence we decided to collaborate with Fablab Groningen without actually using StyGreen for 3D printing. We quickly realized that 3D printed biological structures can be of great educational value. Therefore, we made prints of the most important enzymes in our project: the cellulose binding domain, the endogluconase, the beta-glucosidase and the Phenylalanine Ammonia Lyase. We also printed some of their ligands and matched them size wise to showcase where the pocket with the active site in the enzyme is and which chemical alteration is happening. We also developed a kit of building blocks for styrene, butadiene, acrylnitril and divinylbenzene that can showcase the process of copolymerization through magnets. On top of that our mascot Styrene Steve was 3D printed multiple times and given as present to some of our sponsors as a nice gesture and to keep iGEM in people’s minds. All structures we designed with FabLab are open source and can be found on their website https://www.thingiverse.com/.

We developed a kit of building blocks for ABS polymerization

ZAP: Drs. R.J. van Linschoten (4th September 2018)

One of the first steps when considering upscaling of a process is finding a suitable location for a pilot plant. The province of Groningen is a strong agricultural and industrial area. Therefore, the province can support the conversion of waste streams from biomass into high-end products. ZAP, the Zernike Advanced Processing innovation cluster, is located on the Zernike campus, along with the University of Groningen, the Hanze University of Applied Sciences and a number of companies. This unique location offers a great opportunity to share and increase knowledge. ZAP offers a test environment for bio-based experiments in the northern region of the Netherlands, where they provide the facilities to set up a pilot plant. ZAP is interested in acting upon the need to lessen our reliance on fossil fuels. We met with drs. R.J. van Linschoten, director of the Zernike Advanced Processing and discussed the prerequisites for setting up a pilot plant.

The province of Groningen supports the conversion of waste streams into high-end products

NIOZ: Prof. Dr. Klaas Timmermans (27th August 2018)

At present, extensive research is carried out on the culturing of green algae. If green algae can be successfully cultured on the open sea, this provides a virtually unlimited source of cellulose. We arranged a skype meeting with Prof. dr. Klaas Timmermans, Senior scientist ecophysiology of seaweeds, head of Department Estuarine and Delta Systems (EDS) at NIOZ and Honorary Professor at the University of Groningen. NIOZ is the Royal Dutch Institute for Sea Research, and is involved in research in the Netherlands as well as far beyond the Dutch border on topics such as biology, physics, chemistry and geography. We spoke with Prof. dr. Timmermans about our design and the potential usage of cellulose from green algae for our iGEM project. Currently, green algae are mainly cultured for their proteins and partly for their carbohydrate content. However, cellulose is a residual product at the moment, for which no suitable purpose has been found at NIOZ. In case we can show a proof-of-concept in our iGEM project, we could close the loop in green algae culturing, so all fractions are used. Prof. dr. Timmermans informed us that there is still a long way to go before culturing green algae on the open sea is reality. On top of that, the separation of the different fractions (proteins, carbohydrates, etc.) proves to be difficult. All in all, the potential upside is enormous, once the research on culturing green algae has developed further. We are then able to tap into an infinite source of cellulose and use all fractions of the cultured green algae. A win-win situation.

NIOZ has not found a purpose for their cellulose yet

RIVM

The Dutch Governmental Institute for Public Health and Environment (RIVM) wants to stimulate Dutch iGEM teams to consider the broader effects of their project on the world surrounding us. This includes investigating ethical, societal, and technical aspects concerning the project. They asked us to adhere to the Safe-by-Design concept, which states that safety should be an integral part of each project, to be considered during every phase and aspect from the early beginnings all the way to the end.

The first meeting was with Korienke Smit, a policy advisor, and Niek Savelkoul, a trainee and member of the 2017 iGEM Wageningen team. This meeting took place on june 20th, 2018. During this meeting we discussed our initial ideas about how we are planning to implement the Safety-by-Design concept into our project. We got some valuable tips and input, especially about the upscaling of our process, which brings a whole set of new challenges with it, something we had not considered until then. We were planning to use antibiotics, which might be difficult to upscale safely regarding antibiotic resistance issues. Styrene is toxic, and having massive bioreactors filled with styrene-producing yeast strains could be a danger to public health. We were already considering to use CRISPR-Cas9 to remove the need for antibiotics, but these remarks contributed to our decision to make the switch. Another factor was our plan to run evolutionary experiments to improve yields. Korienke had suggestions for this as well, and suggested looking into the 2017 Heidelberg iGEM team, that came up with a clever way to accelerate evolution using quickly-mutating phages. At the end of the conversation we received some advice on how to pitch our idea: our main advantage is the reduction reliance on fossil fuels over traditional methods of styrene production, and the reduction of CO2 emissions.

The second meeting was with Jaco Westra, a coordinator of synthetic biology, and an expert on safety and GMO regulations. This meeting took place on august 14th, 2018. We talked about our progress in the lab, which was going slower than expected at that time. Jaco was especially curious how progress on the Safe-by-Design assignment was progressing compared to the last meeting, and how we are integrating the associated principles into our project. We described the changes we had made, for example the consideration of using recycled toilet paper as cellulose source, or the plan to focus on toy makers as customers for our product. We discussed the best ways to market our product, and agreed that the focus should be on the reduction of CO2 emissions. Our plan is to do a Carbon Footprint Analysis to come to an exact figure, to make a better comparison. At the end of the conversation we also received advice on how to improve our infographic.

These remarks pushed us to make the switch

Meetings with Experts

Tjerk Douma (28th June 2018)

We sat down with Tjerk Douma, a Master student in Energy and Environmental Sciences. Tjerk explained the importance of a Life Cycle Analysis (LCA) and what factors are taken into account. We concluded that it may be interesting to look at the difference in the LCA of StyGreen and oil based Styrene. We agreed that Tjerk would help us with the LCA, and had regular meetings afterwards. This resulted in our Carbon Footprint Analysis

We agreed that Tjerk would help us with the LCA

Drs. Karin Ree (11th July 2018)

Drs. Karin Ree is a member of the Science Shop in Groningen. The Science Shop connects ambitious students to companies or academic research outside their field. As we were looking for connections to the bioplastic industry, Karin was able to give us great advice on who we should contact. She helped us to find contacts inside and outside of the university. Furthermore, she has sent us a various useful papers on the sustainability of bioplastics.

Karin was able to provide meaningful contacts

Prof. Dr. Gert Jan Euverink (8th August 2018)

Gert Jan Euverink is the University of Groningen representative in the CaDOS project. Toilet paper in sewage material contains roughly 80% cellulose. In the CaDOS project, this cellulose material is used to drain water from the sludge, which improves the purification process. Furthermore, Euverink advises companies on the implementation of their technical ideas. His expertise has been helpful to previous iGEM teams, since he was a supervisor of the winning team of Groningen in 2012!

In the CaDOS project, cellulose material is used to drain water from sludge

Prof. Dr. Katja Loos (5th July 2018)

Biodegradable plastics, like PLA, are technically biodegradable but only under controlled conditions. In nature they still take a long time to degrade on their own, only a bit faster than for example polystyrene. However, PLA being “biodegradable” sends a message that it is okay to throw it away anywhere because if its “biodegradability”, only adding to the problem. Just recently, the EU has moved to ban single use plastics. Therefore, what we should do is look into non-single use plastics. While polystyrene has numerous non-single use applications, the stigma of it being used as disposable packaging material is not easily erased. Some polymers that are nearly always single use include:

  1. Nylons
  2. Polyurethanes
  3. Polyamides

PLA is only adding to the problem!

Prof. Dr. Francesco Picchioni (3rd Oktober 2018)

We went to Francesco Picchioni, an expert in the field of polymers, to ask his view on styrene and our project design. Did he see the benefits, or would he think it was an unrealistic design? He explained to us that styrene is a very good material for various reasons. The first is its transparency, which is why it is easily colored with other chemicals. Styrene furthermore contains an aromatic ring and pi-pi stackings of these rings. This leads to the fact that styrene-based plastics have a high TG (Glass Transition Temperature). These connections are way stronger compared to the ester bonds in PET and PLA. No other plastics have these special characteristics, and therefore styrene is irreplaceable. Right now, styrene is not recycled to a high extent, as the price of newly produced styrene is lower. However, because styrene is a thermoplastic, it is easily recycled in case of a stronger market pull. Picchioni was suprised that biological styrene production was feasible. If a high yield can be engineered, this would be a major discovery and he would be very interested.

"If you can make me a few kilo's, you can come back to me!"

Prof. Dr. A. J. M. Driessen

In order to gain more insight into strain optimization, we met with professor Driessen, head of the molecular microbiology department at the University of Groningen. We discussed the best ways to implement and optimize our design. Driessen provided us with many helpful suggestions. For example, we went from the concept of two separate coexisting yeast strains (one cellulolytic, one producing styrene), to one yeast strain doing both processes simultaneously. Furthermore, we discussed metabolic engineering to gain higher yields, for example multiple knock-outs which we could implement. Finally, Driessen proposed to use the CRISPR-Cas9 technique to genomically integrate our genes of interest, instead of using several plasmids. Moreover, Driessen connected us to important contacts as well as providing us with additional laboratory space.

His advice brought us from two seperate yeast strains to one yeast strain performing both processes.

Prof. Dr. B. Poolman (1st June 2018)

One of our team members visited professor Poolman of the Enzymology research group to discuss the possible effects of styrene toxicity in our design. During literature study we discovered the existence of styrene exporters and we wanted to discuss whether expression of such an exporter in S. cerevisiae would be beneficial for our design and styrene yield. Poolman pointed out that expressing prokaryotic proteins in eukaryotes is extremely difficult, but pointed towards the Pdr5 export protein and ABC transporters. Furthermore he suggested performing an evolution experiment in S. cerevisiae to decrease the sensitivity of our yeast towards styrene.

An evolution experiment in S. cerevisae to decrease toxic effects from styrene

Shreyans Chordia (27th September 2018)

Shreyans Chordia, a PhD student at the Biomolecular Chemistry & Catalysis group, works on styrene production in E. coli and provided us with an E. coli codon optimized version of the PAL2 gene. Shreyans has been able to produce styrene in E. coli at quite significant levels. He suggested the possibility of coculturing our cellulose degrading yeast strain with his styrene producing E. coli to convert cellulose to styrene in one bioreactor. He offered to help with the experimental setup and conducting the experiments. Furthermore, he got us in contact with Balin Fridrich, who works on the degradation of lignocellulose.

Shreyans was able to produce styrene at quite significant levels

Prof. Dr. Marco Fraaije (20th July 2018)

Professor Marco Fraaije is an expert in the fields of biology, biochemistry, biotechnology and in particular enzyme engineering. His group published an extremely useful article for our project describing a fast and sensitive method for the detection of cellulase activity. We had a fruitful discussion about the assay described in the paper. One of the subjects that we discussed was the feasibility to detect cellulase activity with the assay while using our intact yeast cells instead of purified proteins. Finally, professor Fraaije provided us with the possibility for assistance, usage of the lab and supplied the materials required for the experiments.

How to detect cellulase activity?

Dr. W.C. Szymanski (27th September 2018)

Szymanski is an assistant professor, at the department of radiology and imaging, at the UMCG (University Medical Center Groningen). His fields of interests are molecular medical imaging and photopharmacology. Wiktor Szymanski was willing to help us optimize the protocol for the phosphorylation of cellulose at the 6th position. Furthermore, he was of great help performing the experiment and provided us with a lab and equipment for the experiment. The phosphorylation of cellulose was performed to increase the solubility of the polymer. The improved solubility resulted in an improved accessibility of the cellulosome complex towards the cellulose polymer. The cellulosome complex chops the cellulose polymer into glucose molecules. These glucose molecules are obtained by the yeast cells, as carbon source, and converted into styrene molecules.

Szymanski helped us to optimize the phosphorylation of cellulose

Intellectual Property Office RUG (8th October 2018)

To see if we could patent parts of our project, we contacted the IP center of the University of Groningen. We discussed three important subjects: inventorship, novelty and inventivity. The first subject we had to discuss was inventorship. Who contributed substantially to our project? Besides our team members, to what extent were the supervisors part of our idea? After consulting other iGEM teams, we decided that the patent should be shared with the supervisors. For the novelty of our project, it was important that the to be patented subject was not published already. We encountered problems with our own disclosure here due to our outreach and education activities. The most difficult part of a patent is the inventivity. Since we combine several methods of degrading cellulose together, this was an important option for patenting. Subsequently, we also had to think about the financial aspects of the patent. Would companies pay to use our technology? We discussed this factor with several investors and several companies that are highly interested in our product.

References

Boonniteewanich, J., Pitivut, S., Tongjoy, S., & Lapnonkawow, S. (2014). Evaluation of Carbon Footprint of Bioplastic Straw compared to Petroleum based Straw Products. Energy Procedia, 56, 518–524. https://doi.org/10.1016/j.egypro.2014.07.187

Croezen, H. J., & Lieshout, M. van. (2015). Handleiding CO2-waarden voor biobased grondstoffen volgens MJA3/MEE-methodiek. CE Delft, 73.