Difference between revisions of "Team:DTU-Denmark/Integrated Human Practices"

(Created page with "{{DTU-Denmark}} {{DTU-Denmark/mainCSS}} {{DTU-Denmark/carouselCSS}} <html> <img class="effect" id="effect2" src="https://static.igem.org/mediawiki/2019/e/ea/T--DTU-Denmark--back...")
 
 
(41 intermediate revisions by 4 users not shown)
Line 2: Line 2:
 
{{DTU-Denmark/mainCSS}}
 
{{DTU-Denmark/mainCSS}}
 
{{DTU-Denmark/carouselCSS}}
 
{{DTU-Denmark/carouselCSS}}
<html>
+
<html lang="en">
 +
  <head>
 +
    <!-- Required meta tags -->
 +
    <meta charset="utf-8">
 +
    <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no, user-scalable=0">
 +
 
 +
 
 +
  <link rel="stylesheet" type="text/css" href="Template:DTU-Denmark/fontCSS?action=raw&ctype=text/css">
 +
 
 +
 
 +
 
 +
  </head>
 +
  <body>
 +
 
  
  
Line 23: Line 36:
 
 
  
<div class=" topimg pull-right sm-no-float col-md-8 ">
+
<div class=" topimg pull-right sm-no-float col-md-7 ">
 
 
  
  
<img src="https://static.igem.org/mediawiki/2019/4/41/T--DTU-Denmark--hpheader.svg" title="As science affects the world, the world affects science. This page describes what this project is going to bring to the world, and what we have learned and used from others" style="margin-top:75px;max-width:70%;margin-right:auto; margin-left:auto;display: block;
+
<img src="https://static.igem.org/mediawiki/2019/4/41/T--DTU-Denmark--hpheader.svg" alt="As science affects the world, the world affects science. This page describes what this project is going to bring to the world, and what we have learned and used from others" style="margin-top:75px;max-width:70%;margin-right:auto; margin-left:auto;display: block;
 
     height:auto;z-index:5;">
 
     height:auto;z-index:5;">
  
Line 34: Line 47:
 
 
 
        
 
        
     
+
 
       <div class="pull-left col-md-4 sm-text-center com-sm-12 ">
+
       <div class="pull-left col-md-5 sm-text-center com-sm-12 ">
 
<div class="team-heading"><h2>Integrated Human Practices</h2></div>
 
<div class="team-heading"><h2>Integrated Human Practices</h2></div>
<div class="team-overview">
+
<div class="team-overview" style="font-size: .9em;">
 
 
 
<p>
 
<p>
  
  
The creation of a library of promoters may not be very applicable in the everyday life of most people, but the library can certainly have a great impact on many people’s lives as well as contributing to several of UN's Sustainable Development Goals (SDGs). </a></p>
+
From the very beginning of our project, our team shared a common goal – we wanted to create something meaningful. To this end, we have been in contact with important stakeholders and their advice has shaped our approach, and the project's direction.
 +
</p>
  
 
</div>
 
</div>
Line 71: Line 85:
  
  
<div class="row flex-center sm-no-flex interlabspace">
+
<div class="row flex-center sm-no-flex" style="margin-bottom:25px;">
 +
 
 +
 +
 
 +
 
 +
 
 +
<div class="sm-no-float col-md-10 col-xs-12">
 +
 
 +
<p>Despite their relative anonymity, filamentous fungi are responsible for most of the industrially produced enzymes and are therefore exceptionally important to a lot of people’s everyday lives. <br>
 +
Project LEAP was founded in response to the acute lack of publicly available resources for synthetic biology work within filamentous fungi, and therefore aimed to expand the synthetic biology toolbox for these organisms. <br>
 +
Originally, the project aspired to create synthetic promoter libraries for filamentous fungi, yeast, and moss – but following valuable discussions with several companies and scientists, the team decided to develop a software that would enable the creation of promoters for any organism, and attempted to test the function of said software in Aspergilli.
 +
 
 +
 
 +
</p>
 +
 
 +
 
 +
  </div>
 +
 
  
<div class=" sm-no-float col-md-4 bbmobile col-sm-12">
 
  
<div class="container_rowhp">
 
    <div class="layer1hp">
 
        <span> <img class="active hp1img" src="https://static.igem.org/mediawiki/2019/0/0a/T--DTU-Denmark--hpgoal8.gif"></span>
 
    </div>
 
    <div class="layer2hp">
 
      <img class="statichp hp1img" src="https://static.igem.org/mediawiki/2019/6/6c/T--DTU-Denmark--hpgoal8png.png">
 
    </div>
 
 
</div>
 
</div>
<div class="container_rowhp">
+
 
    <div class="layer1hp">
+
 
        <span> <img class="active hp1img" src="https://static.igem.org/mediawiki/2019/d/d5/T--DTU-Denmark--hpgoal09.gif"></span>
+
 
    </div>
+
 
    <div class="layer2hp">
+
 
      <img class="statichp hp1img" src="https://static.igem.org/mediawiki/2019/1/19/T--DTU-Denmark--hpgoal09png.png">
+
 
    </div>
+
 
 +
<div class="row flex-center sm-no-flex">
 +
 
 +
<div class=" sm-no-float col-md-12 col-sm-12">
 +
 
 +
 
 +
<figure>
 +
<img src="https://static.igem.org/mediawiki/2019/1/15/T--DTU-Denmark--iHPmainfigurebigdone.png" alt="Our stakeholder analysis led us to talk to 3 different companies: Zymergen, Novozymes, and Bolt Threads. We also talked to 3 fungal experts: Peter Richard (VTT, Finland), Jens Christian Frisvad (DTU, Denmark) and Jakob Blæsbjerg (DTU, Denmark). Additionally, we addressed the public by attending Science EXPO in Copenhagen, two biotechnology camps for high school students, and teaching synthetic biology in two high schools.
 +
" style="width:100%;    max-width: 650px;
 +
    margin-right: auto;
 +
    margin-left: auto;
 +
    display: flex;">
 +
  <figcaption>Fig. 1: Overview of the process for integrated human practices throughout the project.</figcaption>
 +
</figure>
 +
 
 +
 
 
</div>
 
</div>
<div class="container_rowhp">
 
    <div class="layer1hp">
 
        <span> <img class="active hp1img" src="https://static.igem.org/mediawiki/2019/e/ef/T--DTU-Denmark--hpgoal12.gif"></span>
 
    </div>
 
    <div class="layer2hp">
 
      <img class="statichp hp1img" src="https://static.igem.org/mediawiki/2019/8/83/T--DTU-Denmark--hpgoal12png.png">
 
    </div>
 
</div>
 
<div class="container_rowhp">
 
    <div class="layer1hp">
 
        <span> <img class="active hp1img" src="https://static.igem.org/mediawiki/2019/9/93/T--DTU-Denmark--hpgoal015.gif"></span>
 
    </div>
 
    <div class="layer2hp">
 
      <img class="statichp hp1img" src="https://static.igem.org/mediawiki/2019/2/20/T--DTU-Denmark--hpgoal015png.png">
 
    </div>
 
</div>
 
<div class="container_rowhp">
 
    <div class="layer1hp">
 
        <span> <img class="active hp1img" src="https://static.igem.org/mediawiki/2019/5/58/T--DTU-Denmark--hpgoal017.gif"></span>
 
    </div>
 
    <div class="layer2hp">
 
      <img class="statichp hp1img" src="https://static.igem.org/mediawiki/2019/3/31/T--DTU-Denmark--hpgoal017png.png">
 
    </div>
 
 
</div>
 
</div>
 +
 +
 +
 +
 +
 +
 +
 +
<div class="row flex-center sm-no-flex interlabspace">
 +
 +
<div class=" sm-no-float col-md-4 bbmobile col-sm-12">
 +
 +
<figure>
 +
<img src="https://static.igem.org/mediawiki/2019/2/22/T--DTU-Denmark--iHPstakeholder1.svg" alt="The stakeholder analysis shows a square with four sections, which divides stakeholder’s into four categories: high interest and high power, high interest and low power, low interest, and high power, and low interest and low power.
 +
" style="width:100%;    padding-top: 30%;">
 +
  <figcaption>Fig. 2: Stakeholder analysis</figcaption>
 +
</figure>
  
 
</div>
 
</div>
Line 120: Line 151:
  
 
<div class="sm-no-float col-md-8">
 
<div class="sm-no-float col-md-8">
<p>We have identified 5 main goals that our project contributes to. We call these our primary SDGs. Following this, we have further 3 goals that are affected by our efforts in the primary goals.</p>
+
<h2>Stakeholder Analysis
 +
</h2>
 +
<p>
  
<h2>Primary goals</h2>
+
In March, the team looked into the impact the project could have on different stakeholders, and therefore made a stakeholder analysis, as shown in figure 2.
<p><a target="_blank" href="https://sustainabledevelopment.un.org/sdg8">Goal 8: Decent work and economic growth</a>
+
This goal focuses on the economic development, measured by the growth of GDP, education and financial institutions. We specifically focus on goal 8.2: "Achieve higher levels of economic productivity through diversification, technological upgrading and innovation, including through a focus on high-value added and labour-intensive sectors"<br>
+
Here we can improve the economic productivity of fermentations by using our promoter library to conduct metabolic engineering in an important production organism, <i>Aspergillus niger</i>. Furthermore, as our research is open-source, it invites others to build upon a solid biotechnological foundation and spearhead new innovation in ever-increasing markets.  
+
<br><br>
+
  
<a target="_blank" href="https://sustainabledevelopment.un.org/sdg9">Goal 9: Industry, innovation and infrastructure</a>
+
This stakeholder analysis reveals that companies such as Novozymes, Zymergen, and Bolt Threads are among the most important to our project, both in interest and power. This means that their opinions should be managed closely. Additionally, researchers such as Jens Frisvad (DTU, Denmark), Jakob Blæsbjerg (DTU, Denmark), and Peter Richard (VTT, Finland) could benefit from our project, making them important stakeholders. Although other iGEM teams do not have a lot of power, their interest could nevertheless be great and they should, therefore, be well informed.  
This goal is focused on the development of sustainable industry and infrastructure, especially in developing countries. In this regard, our project has a lot to offer. <br>
+
The public and the DTU BlueDot program will most likely not take much interest in the project as a promoter library can be a very technical concept and not immediately usable by non-specialists. However, as DTU BlueDot is a big sponsor of the team, they are important to keep satisfied.
Goal 9.4 revolves around the addition of value without a large increase in CO2 output. The goal states: "... upgrade infrastructure and retrofit industries to make them sustainable, with increased resource-use efficiency and greater adoption of clean and environmentally sound technologies and industrial processes…". The use of our promoter library, and other biotechnological tools, allows for tighter control over the production of many important products, where resource efficiency is a key aspect.  
+
  
<br><br>
 
In addition to this, we are also working towards goal 9.5 to "...Enhance scientific research, upgrade the technological capabilities of industrial sectors in all countries…" and "...encourage innovation…". <br>
 
Here we contribute to the ability of other scientists to efficiently conduct research in filamentous fungi and by providing the foundation for others to build novel and innovative solutions in their community using filamentous fungi.
 
  
 
<br><br>
 
<br><br>
 
+
Based on the stakeholder analysis, we decided to contact three different biotech companies; Novozymes, Zymergen, and Bolt Threads as they all work with genetically modified filamentous fungi. We asked them how our project could influence their work, and for suggestions regarding the experiments.
<a target="_blank" href="https://sustainabledevelopment.un.org/sdg12">Goal 12: Responsible consumption and production</a>
+
This development goal is centered around the minimization of waste products and material use in addition to increasing recycling.
+
We are specifically focusing on goal 12.2 and 12.5 that works to achieve "...efficient use of natural resources." and "...substantially reduce waste generation through prevention, reduction, recycling and reuse."
+
We are contributing to this by improving the resource efficiency of fermentation of fermentation by offering tighter control over the metabolism of the filamentous fungi used. Furthermore, our promoter library opens the opportunity for others to develop more efficient ways of using waste products in industrial fermentation by giving them the basic tools needed for more advanced biotechnological research.
+
 
<br><br>
 
<br><br>
 +
We also reached out to several scientists, including Jakob Blæsbjerg from DTU and Peter Richard from VTT (Technical Research Centre) in Finland. They provided us with protocols and advice on how to grow the fungi, and how to ensure we acquired reproducible and comparable results.
 +
<br><br>
 +
Even though the public is neither very powerful nor particularly interested in the project, at least according to our stakeholder analysis, we nevertheless decided to contact high schools in order to talk to young people about synthetic biology, our project and what good we believe it can do in the world. We also partook in several events: The annual UNF (Ungdommens Naturvidenskabelige Forening) Biotech Camp; Science Expo, a large science fair in Copenhagen; and the annual Biotech Academy Camp in order to increase their knowledge and interest in a topic like synthetic biology. This is described further on <a target="_blank" href="https://2019.igem.org/Team:DTU-Denmark/Public_Engagement">Education and Engagement</a>.
  
<a target="_blank" href="https://sustainabledevelopment.un.org/sdg15">Goal 15: Life on land</a>
 
This development goal focuses on the protection, restoration, and sustainable management of terrestrial resources. We are focusing on a subsection of 15.6, that concerns itself with the sharing of genetic resources and the ease of access to these these. We are doing this by publishing everything as open-source so everyone has equal access to our methods and results.
 
 
<br><br>
 
<br><br>
<a target="_blank" href="https://sustainabledevelopment.un.org/sdg17">Goal 17: Partnerships for the goals</a>
 
The partnerships for the completion of the sustainable development goals are important for the realization of these most important tasks of our generation. With our participation in the iGEM competition, we are doing our part in achieving goal 17.6, 17.7, and 17.8, collectively known as the technology goals.
 
 
  
  
Line 158: Line 177:
 
   </div>
 
   </div>
  
<div class=" sm-no-float col-md-4 bbmobileshow col-sm-12 ">
+
<div class=" sm-no-float col-md-4 bbmobileshow col-sm-8 " style="padding:25px;">
 +
 
 +
<figure>
 +
<img src="https://static.igem.org/mediawiki/2019/2/22/T--DTU-Denmark--iHPstakeholder1.svg" alt="The stakeholder analysis shows a square with four sections, which divides stakeholder’s into four categories: high interest and high power, high interest and low power, low interest, and high power, and low interest and low power.
 +
" style="width:100%">
 +
  <figcaption>Fig. 2: Stakeholder analysis</figcaption>
 +
</figure>
 +
 
  
<div class="container_rowhp">
 
    <div class="layer1hp">
 
        <span> <img class="active hp1img" src="https://static.igem.org/mediawiki/2019/0/0a/T--DTU-Denmark--hpgoal8.gif"></span>
 
    </div>
 
    <div class="layer2hp">
 
      <img class="statichp hp1img" src="https://static.igem.org/mediawiki/2019/6/6c/T--DTU-Denmark--hpgoal8png.png">
 
    </div>
 
</div>
 
<div class="container_rowhp">
 
    <div class="layer1hp">
 
        <span> <img class="active hp1img" src="https://static.igem.org/mediawiki/2019/d/d5/T--DTU-Denmark--hpgoal09.gif"></span>
 
    </div>
 
    <div class="layer2hp">
 
      <img class="statichp hp1img" src="https://static.igem.org/mediawiki/2019/1/19/T--DTU-Denmark--hpgoal09png.png">
 
    </div>
 
</div>
 
<div class="container_rowhp">
 
    <div class="layer1hp">
 
        <span> <img class="active hp1img" src="https://static.igem.org/mediawiki/2019/e/ef/T--DTU-Denmark--hpgoal12.gif"></span>
 
    </div>
 
    <div class="layer2hp">
 
      <img class="statichp hp1img" src="https://static.igem.org/mediawiki/2019/8/83/T--DTU-Denmark--hpgoal12png.png">
 
    </div>
 
</div>
 
<div class="container_rowhp">
 
    <div class="layer1hp">
 
        <span> <img class="active hp1img" src="https://static.igem.org/mediawiki/2019/9/93/T--DTU-Denmark--hpgoal015.gif"></span>
 
    </div>
 
    <div class="layer2hp">
 
      <img class="statichp hp1img" src="https://static.igem.org/mediawiki/2019/2/20/T--DTU-Denmark--hpgoal015png.png">
 
    </div>
 
</div>
 
<div class="container_rowhp">
 
    <div class="layer1hp">
 
        <span> <img class="active hp1img" src="https://static.igem.org/mediawiki/2019/5/58/T--DTU-Denmark--hpgoal017.gif"></span>
 
    </div>
 
    <div class="layer2hp">
 
      <img class="statichp hp1img" src="https://static.igem.org/mediawiki/2019/3/31/T--DTU-Denmark--hpgoal017png.png">
 
    </div>
 
</div>
 
 
</div>
 
</div>
  
 
</div>
 
</div>
 +
 +
 +
  
 
<div class="row flex-center sm-no-flex">
 
<div class="row flex-center sm-no-flex">
  
 
 
      <div class="sm-no-float col-md-8" style="margin-left:25px">
 
  
  
  
<h2>Secondary goals</h2>
+
<div class="sm-no-float col-md-8 col-xs-12">
<p>The secondary goals are not directly affected by our projects, but the promoter library can be used by others to improve the world in amazing ways.<br><br>
+
  
<a target="_blank" href="https://sustainabledevelopment.un.org/sdg3">Goal 3: Good health and well-being</a>
+
<h2>Click on the different bubbles to read more about what we learned from each stakeholder.</h2>
The introduction of tighter metabolic control in the use of filamentous fungi could allow for higher production, which in turn would hopefully translate into lower prices and wider distribution of important products. Included in this is both industrial products andbiopharmaceuticals, which are highly needed everywhere in the world.[1]<br><br>
+
  
<a target="_blank" href="https://sustainabledevelopment.un.org/sdg7">Goal 7: Affordable and clean energy</a>
 
The addition to new and improved tools in biotechnology our promoters could be used to improveme biofuels, which offer a good alternative to fossil fuels.Biofuels are essential in the sustainable development of the energy production of the future.
 
<br><br>
 
  
<a target="_blank" href="https://sustainabledevelopment.un.org/sdg14">Goal 14: Life below water</a>
 
The marine environment is susceptible to the pollution of heavy industry. Biotechnology offers multiple ways to minimize this pollution. One of these is by shifting traditional chemical processes towards production in biological organisms. A classic example of this is the production of citric acid, which is hugely important in many industries. When first produced, it was gathered from citrus fruits, but it soon became more efficient to produce it in filamentous fungi, more specifically <i>Aspergillus niger</i>. The next step in this evolution of increased production is to optimize the fungal strains to produce as much citric acid as possible. Conventional methods can only achieve a certain level of production. The use of genetic engineering allows for production to reach the highest yields possible. This is just one example, many more exist and their number will only grow when we learn to harness the innate potential of the biological resources available to us.
 
  
  
  
 +
<!-- Image Map Generated by http://www.image-map.net/ -->
 +
<img style="padding:15px;margin: 0 auto;  max-width: 100%; height: auto;" src="https://static.igem.org/mediawiki/2019/4/42/T--DTU-Denmark--newiHPMainThingy.png"  border="0" width="800" height="944" orgWidth="800" orgHeight="944" alt="Interactive figure of what we learned from our stakeholders: Bolt Threads, Jens Frisvad, Jakob Blæsbjerg, Zymergen, Peter Richards, and Novozymes" usemap="#integratedhpfig3">
  
 +
<map name="integratedhpfig3">
 +
    <area target="" alt="Zymergen" title="Zymergen" href="#zymergen" coords="327,772,105" shape="circle">
 +
    <area target="" alt="Zymergen" title="Zymergen" href="#zymergen" coords="344,504,43" shape="circle">
 +
    <area target="" alt="Peter Richards" title="Peter Richards" href="#peterR" coords="115,582,106" shape="circle">
 +
    <area target="" alt="Peter Richards" title="Peter Richards" href="#peterR" coords="296,450,39" shape="circle">
 +
    <area target="" alt="Novozymes" title="Novozymes" href="#novo" coords="100,303,107" shape="circle">
 +
    <area target="" alt="Novozymes" title="Novozymes" href="#novo" coords="371,402,48" shape="circle">
 +
    <area target="" alt="Bolt Threads" title="Bolt Threads" href="#boltt" coords="304,316,43" shape="circle">
 +
    <area target="" alt="Bolt Threads" title="Bolt Threads" href="#boltt" coords="286,104,105" shape="circle">
 +
    <area target="" alt="Jens Frisvad" title="Jens Frisvad" href="#jensf" coords="562,132,107" shape="circle">
 +
    <area target="" alt="Jens Frisvad" title="Jens Frisvad" href="#jensf" coords="407,329,39" shape="circle">
 +
    <area target="" alt="Jakob Blæsbjerg" title="Jakob Blæsbjerg" href="#jakobb" coords="482,395,50" shape="circle">
 +
    <area target="" alt="Jakob Blæsbjerg" title="Jakob Blæsbjerg" href="#jakobb" coords="696,364,104" shape="circle">
 +
</map>
 +
 +
 +
 +
<div id="zymergen" class="overlay" style="z-index: 18;">
 +
<div class="popup">
 +
<h2>Zymergen</h2>
 +
<a class="close" href="#figure3">&times;</a>
 +
<div class="content">
 +
<p>Kenneth Bruno and Grayson Wawrzyn from Zymergen visited DTU in May 2019. On this occasion, we met with them and discussed our project.
 +
As Zymergen works with i.a. filamentous fungi and know what other biotechnology companies look for in promoters, they were able to provide us with a lot of valuable advice on how to approach our project.
 +
Among other things, they advised us to use the <i>Aspergillus niger</i> strain ATCC 1015 since this strain is commonly used in industry and contains an auxotrophic selection marker. <br>
 +
Zymergen specialises in genetically engineering a broad range of non-standard hosts, and this directed us to open the software to be able to parse any given organism genome. Additionally, Zymergen is in the business of gene expression regulation/control, and a stable promoter ladder is therefore vital to their setup. Accordingly, we directed our experimental setup to also test the scalability of our synthetic promoters.
 +
Additionally, we learned that the industry is interested in scarless assemblies between the promoter region and the start codon, as well as promoters that are active in the stationary phase. We took all of this into consideration when designing the software to create the promoters and when assembling the plasmids.</p>
 +
</div>
 +
</div>
 +
</div>
 +
 +
 +
<div id="peterR" class="overlay" style="z-index: 18;">
 +
<div class="popup">
 +
<h2>Peter Richard</h2>
 +
<a class="close" href="#figure3">&times;</a>
 +
<div class="content">
 +
<p>We talked to Peter Richard, a principal scientist at VTT in Finland. He is an expert in using synthetic biology with regards to <i>Aspergillus</i> spp. and provided feedback on our approach, in addition to advice on making our results as applicable as possible. He advised us to grow the fungi under comparable conditions, i.e. that we should keep things such as growth phase, temperature, media, and reporter gene consistent and in mind when testing the promoters. We implemented this throughout the project, most notably in the characterization phase where a standardized media was used. RFP was used as a reporter and the growth was measured over time, enabling evaluation of the promoters during both the lag phase, exponential phase, stationary phase, and eventually the death phase.
 +
 +
Furthermore, he recommended keeping the plasmid copy number in mind while running the experiments as this would enable us to correlate gene expression to each promoter. We, therefore, decided to integrate the constructs in the <i>Aspergillus</i> genome, but unfortunately, we did not have time to test our promoters further in this construct, as described in the <a target="_blank" href="https://2019.igem.org/Team:DTU-Denmark/Results/">results</a>.
 
</p>
 
</p>
 +
</div>
 +
</div>
 +
</div>
  
  
 +
 +
<div id="novo" class="overlay" style="z-index: 18;">
 +
<div class="popup">
 +
<h2>Novozymes</h2>
 +
<a class="close" href="#figure3">&times;</a>
 +
<div class="content">
 +
<p>
 +
In June, the team visited the Novozymes facilities in Lyngby to learn about their approach to working with filamentious fungi in the industry. Apart from a guided tour around the facilities, the team also had an inspiring talk with Mikako Sasa, Science Manager and fungi specialist, where we discussed different fungal species and their potential applications.
 +
<br><br>
 +
From this initial meeting, we learned that promoters are valuable assets for a company such as Novozymes, and that our promoters would be even more valuable if they were consistent across different scales and conditions. This allows the user to worry less about the implementation of the promoters and enables them to focus on optimizing pathways and fermentation conditions.
 +
<br><br>
 +
In August, we came back and talked with Mary Ann Stringer and Kirk Matthew Schnorr, both scientists at Novozymes. Here, we learned more about what Novozymes looks for in a desirable promoter. As they are in the business of producing enzymes, they are usually looking for strong promoters, however, ideally they would want a promoter that was inactive in the exponential phase and highly active in the stationary phase. This would limit the stress on the organism while growing and building biomass, and maintain the high production rates when the amount of biomass is sufficiently large. This is consistent with what we had previously heard from Zymergen, and we decided to prioritize promoters that fulfilled these criteria.
 +
<br><br>
 +
At this meeting, we also learned about their concept of “Tank Years”. This refers to the number of times a tank can be run in a year and takes into consideration cleaning, sterilization, inoculating, running, and extraction of the product. Novozymes is interested in producing as much as possible, as quickly as possible, and this means that the production time in the tanks should be minimal, the cleaning easy, and the enzyme titers maximized. <br>
 +
We have taken this into account when designing our bioreactor experiments, where a conscious effort was taken to minimize downtime between runs.
 +
</p>
 +
</div>
 +
</div>
 
</div>
 
</div>
  
  
  
<div class=" sm-no-float col-md-4 col-sm-12">
+
<div id="boltt" class="overlay" style="z-index: 18;">
 +
<div class="popup">
 +
<h2>Bolt Threads</h2>
 +
<a class="close" href="#figure3">&times;</a>
 +
<div class="content">
 +
<p>We have been in contact with the bio-materials company Bolt Threads which among other things work with filamentous fungi. We were in contact with Edyta Szewczyk, senior scientist at Bolt Threads, who gave us a lot of feedback and ideas. Especially three key points were emphasized: Filamentous fungi takes a long time to grow, which means we need to plan ahead; good reporter systems are essential for detecting transformants and expression, and; targeted genomic integration is a good solution to control for copy-number and genomic context.
  
<div class="container_rowhp">
+
We have tackled these point by, 1) transforming our fungi as soon as possible, 2) using fluorescence (both GFP and RFP) to measure the expression, and 3) testing genomic integration methods which can be seen on  <a target="_blank" href="https://2019.igem.org/Team:DTU-Denmark/Design">Design</a> page.
    <div class="layer1hp">
+
</p>
        <span> <img class="active hp1img" src="https://static.igem.org/mediawiki/2019/8/8a/T--DTU-Denmark--hpgoal03.gif"></span>
+
</div>
    </div>
+
</div>
    <div class="layer2hp">
+
      <img class="statichp hp1img" src="https://static.igem.org/mediawiki/2019/2/2c/T--DTU-Denmark--hpgoal03png.png">
+
    </div>
+
 
</div>
 
</div>
<div class="container_rowhp">
+
 
    <div class="layer1hp">
+
 
        <span> <img class="active hp1img" src="https://static.igem.org/mediawiki/2019/c/cc/T--DTU-Denmark--hpgoal007.gif"></span>
+
 
    </div>
+
<div id="jensf" class="overlay" style="z-index: 18;">
    <div class="layer2hp">
+
<div class="popup">
      <img class="statichp hp1img" src="https://static.igem.org/mediawiki/2019/b/b1/T--DTU-Denmark--hpgoal007png.png">
+
<h2>Jens Frisvad</h2>
    </div>
+
<a class="close" href="#figure3">&times;</a>
</div>
+
<div class="content">
<div class="container_rowhp">
+
<p>
    <div class="layer1hp">
+
We reached out to one of the leading research scientists in filamentous fungi, Jens Christian Frisvad.
        <span> <img class="active hp1img" src="https://static.igem.org/mediawiki/2019/6/67/T--DTU-Denmark--hpgoal14.gif"></span>
+
Among other things, he told us to look at a several different fungal species, and not only the standard ones, as these might be able to expand the range of products that are possible to produce industrially. By basing our software on genomes from many different <i>Aspergillus</i> spp. our promoters are ideally applicable in several different species. Additionally, our software allows for the application of any list of genomes and the creation of promoters for any given species, enabling the creation of promoter libraries for non-standard organisms.
    </div>
+
</p>
    <div class="layer2hp">
+
</div>
      <img class="statichp hp1img" src="https://static.igem.org/mediawiki/2019/3/38/T--DTU-Denmark--hpgoal14png.png">
+
</div>
    </div>
+
 
</div>
 
</div>
  
 +
 +
 +
<div id="jakobb" class="overlay" style="z-index: 18;">
 +
<div class="popup">
 +
<h2>Jakob Blæsbjerg</h2>
 +
<a class="close" href="#figure3">&times;</a>
 +
<div class="content">
 +
<p>
 +
Following the discussion with Zymergen, we decided to contact Jakob Blæsbjerg Hoof, associate professor at the Department of Biotechnology and Biomedicine. He told us that using a fluorescence marker was the easiest approach to select for transformants, and that we should add a secretion tag to the fluorescent protein in order to prevent accumulation inside the cell. This was later backed up by Bolt Threads.
 +
Additionally, Blæsbjerg provided us with the ATCC 1015 <i>Aspergillus niger</i> strain, in addition to a protease-deficient variation (<i>prtT</i> KO), which were used in the experiment as well as protocols for protoplasting and transformation.
 +
</p>
 +
</div>
 +
</div>
 
</div>
 
</div>
  
  </div>
 
  
 +
 +
 +
 +
</p>
 +
 +
 +
</div>
 +
 +
</div>
  
 
<div class="column full_size" >
 
<div class="column full_size" >
  
 
<p style="color:#000; font-size:14px;"><br><br>
 
<p style="color:#000; font-size:14px;"><br><br>
(1) <a target="_blank" href="https://www.genengnews.com/insights/key-trends-in-2018-in-the-biopharmaceutical-market/"> retrieved 7/8 2019</a></p>
+
</p>
  
 
   </div>
 
   </div>
Line 336: Line 402:
 
          
 
          
 
     </footer>
 
     </footer>
<img src="https://static.igem.org/mediawiki/2019/9/91/T--DTU-Denmark--biggrants.svg" title="The logos of our three biggest supporters, DTU Blue Dot, Novo Nordisk fonden and Otto Mønsted fonden" alt="The logos of our three biggest supporters, DTU Blue Dot, Novo Nordisk fonden and Otto Mønsted fonden" style="margin: 20px;max-width:50%;margin-right:auto; margin-left:auto;display: block;
+
<img class="footergrants" src="https://static.igem.org/mediawiki/2019/9/91/T--DTU-Denmark--biggrants.svg" title="The logos of our three biggest supporters, DTU Blue Dot, Novo Nordisk fonden and Otto Mønsted fonden" alt="The logos of our three biggest supporters, DTU Blue Dot, Novo Nordisk fonden and Otto Mønsted fonden">
    height:auto;z-index:5;">
+
<img class="footersponsors" src="https://static.igem.org/mediawiki/2019/d/d9/T--DTU-Denmark--sponsorsfooter.svg" title="The logos of all of our sponsors, DTU, BioNordica, Eurofins Genomics, Qiagen, NEB New England biolabs, IDT Integrated DNA technologies and Twist bioscience" alt="The logos of all of our sponsors, DTU, BioNordica, Eurofins Genomics, Qiagen, NEB New England biolabs, IDT Integrated DNA technologies and Twist bioscience">
<img src="https://static.igem.org/mediawiki/2019/d/d9/T--DTU-Denmark--sponsorsfooter.svg" title="The logos of all of our sponsors, DTU, BioNordica, Eurofins Genomics, Qiagen, NEB New England biolabs, IDT Integrated DNA technologies and Twist bioscience" alt="The logos of all of our sponsors, DTU, BioNordica, Eurofins Genomics, Qiagen, NEB New England biolabs, IDT Integrated DNA technologies and Twist bioscience" style="margin: 20px;max-width:100%;margin-right:auto; margin-left:auto;display: block;
+
    height:auto;z-index:5;">
+
 
</div></div>
 
</div></div>
  
 +
<script src="/Template:DTU-Denmark/mapresizer?action=raw&ctype=text/javascript"></script>
 +
<script>
 +
    imageMapResize();
 +
 +
 +
$(document).keydown(function(event) {
 +
  if (event.keyCode == 27) {
 +
    window.location.href='#figure3';
 +
  }
 +
});
 +
 +
</script>
  
  
  
 
</html>
 
</html>

Latest revision as of 02:27, 22 October 2019

As science affects the world, the world affects science. This page describes what this project is going to bring to the world, and what we have learned and used from others

Integrated Human Practices

From the very beginning of our project, our team shared a common goal – we wanted to create something meaningful. To this end, we have been in contact with important stakeholders and their advice has shaped our approach, and the project's direction.

Despite their relative anonymity, filamentous fungi are responsible for most of the industrially produced enzymes and are therefore exceptionally important to a lot of people’s everyday lives.
Project LEAP was founded in response to the acute lack of publicly available resources for synthetic biology work within filamentous fungi, and therefore aimed to expand the synthetic biology toolbox for these organisms.
Originally, the project aspired to create synthetic promoter libraries for filamentous fungi, yeast, and moss – but following valuable discussions with several companies and scientists, the team decided to develop a software that would enable the creation of promoters for any organism, and attempted to test the function of said software in Aspergilli.

Our stakeholder analysis led us to talk to 3 different companies: Zymergen, Novozymes, and Bolt Threads. We also talked to 3 fungal experts: Peter Richard (VTT, Finland), Jens Christian Frisvad (DTU, Denmark) and Jakob Blæsbjerg (DTU, Denmark). Additionally, we addressed the public by attending Science EXPO in Copenhagen, two biotechnology camps for high school students, and teaching synthetic biology in two high schools.
Fig. 1: Overview of the process for integrated human practices throughout the project.
The stakeholder analysis shows a square with four sections, which divides stakeholder’s into four categories: high interest and high power, high interest and low power, low interest, and high power, and low interest and low power.
Fig. 2: Stakeholder analysis

Stakeholder Analysis

In March, the team looked into the impact the project could have on different stakeholders, and therefore made a stakeholder analysis, as shown in figure 2. This stakeholder analysis reveals that companies such as Novozymes, Zymergen, and Bolt Threads are among the most important to our project, both in interest and power. This means that their opinions should be managed closely. Additionally, researchers such as Jens Frisvad (DTU, Denmark), Jakob Blæsbjerg (DTU, Denmark), and Peter Richard (VTT, Finland) could benefit from our project, making them important stakeholders. Although other iGEM teams do not have a lot of power, their interest could nevertheless be great and they should, therefore, be well informed. The public and the DTU BlueDot program will most likely not take much interest in the project as a promoter library can be a very technical concept and not immediately usable by non-specialists. However, as DTU BlueDot is a big sponsor of the team, they are important to keep satisfied.

Based on the stakeholder analysis, we decided to contact three different biotech companies; Novozymes, Zymergen, and Bolt Threads as they all work with genetically modified filamentous fungi. We asked them how our project could influence their work, and for suggestions regarding the experiments.

We also reached out to several scientists, including Jakob Blæsbjerg from DTU and Peter Richard from VTT (Technical Research Centre) in Finland. They provided us with protocols and advice on how to grow the fungi, and how to ensure we acquired reproducible and comparable results.

Even though the public is neither very powerful nor particularly interested in the project, at least according to our stakeholder analysis, we nevertheless decided to contact high schools in order to talk to young people about synthetic biology, our project and what good we believe it can do in the world. We also partook in several events: The annual UNF (Ungdommens Naturvidenskabelige Forening) Biotech Camp; Science Expo, a large science fair in Copenhagen; and the annual Biotech Academy Camp in order to increase their knowledge and interest in a topic like synthetic biology. This is described further on Education and Engagement.

The stakeholder analysis shows a square with four sections, which divides stakeholder’s into four categories: high interest and high power, high interest and low power, low interest, and high power, and low interest and low power.
Fig. 2: Stakeholder analysis

Click on the different bubbles to read more about what we learned from each stakeholder.

Interactive figure of what we learned from our stakeholders: Bolt Threads, Jens Frisvad, Jakob Blæsbjerg, Zymergen, Peter Richards, and Novozymes Zymergen Zymergen Peter Richards Peter Richards Novozymes Novozymes Bolt Threads Bolt Threads Jens Frisvad Jens Frisvad Jakob Blæsbjerg Jakob Blæsbjerg



The logos of our three biggest supporters, DTU Blue Dot, Novo Nordisk fonden and Otto Mønsted fonden The logos of all of our sponsors, DTU, BioNordica, Eurofins Genomics, Qiagen, NEB New England biolabs, IDT Integrated DNA technologies and Twist bioscience