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

 
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<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;
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<img src="https://static.igem.org/mediawiki/2019/a/ae/T--DTU-Denmark--hpheader1.svg" alt="Fungi around the World and the DTU Biobuilders" style="margin-top:75px;max-width:80%;margin-right:auto; margin-left:auto;display: block;
 
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<div class="team-heading"><h2>Human Practices</h2></div>
 
<div class="team-heading"><h2>Human Practices</h2></div>
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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>
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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). </p>
  
 
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<p>Our human practices section consists of several different parts.<br>
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During the creation of the project, we contacted a lot of people to get their help and feedback. To read more about this, see our <a href="#HPiHP">integrated human practices section</a>.<br>
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Another important part of our project is <a href="#HPaccessibility">accessibility</a>, as we believe that science should be available for everyone.<br>
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Additionally, we wanted to make iGEM a more integrated part of the Danish society. We, therefore, grouped up with the two other Danish teams to form the <a href="#HPDanishiGEM">DanishiGEM</a>.<br>
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iGEM is not only a competition in synthetic biology but it also inspires people to make the world a better place. Our project reflects several of the UN sustainable development <a href="#HPgoals">goals</a>.<br>
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<h2>Regarding the organism</h2>
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<h2>Human Practices</h2>
  
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<p>Filamentous fungi form the base of our project, and as mentioned in the <a target="_blank" href="https://2019.igem.org/Team:DTU-Denmark/Description">project description</a>, they are important producers in the biotechnological industry.
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As mentioned in the <a target="_blank" href="https://2019.igem.org/Team:DTU-Denmark/Description">project description</a>, filamentous fungi are important producers of proteins and biological compounds in industry. Although they are very important, filamentous fungi are heavily underrepresented in the iGEM competition. We think this is very unfortunate, and therefore we developed the tools to fill this gap.<br>
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We have chosen to work with <i>Aspergillus niger</i> as it is an important production organism, and the tools required to genetically engineer the organism already exist. The specific strain we are working with, ATCC1015 [1], is classified as Biosafety Level 1, indicating that it is safe to use and handle in the lab. In addition to this declaration, we have performed a safety check-in, as spore-forming fungi are not directly on the <a target="_blank" href="https://2019.igem.org/Safety/White_List">whitelist</a>. <br>
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At DTU we are specialists in using filamentous fungi as a chassis in synthetic biology and we have shared this knowledge on this wiki. Our efforts include:
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<i>Aspergillus</i> spores are airborne and cannot only contaminate other samples but additionally cause aspergillosis. Therefore, anytime we worked with <i>Aspergillus</i> we worked in a biosafety cabinet which was cleaned thoroughly with ethanol before and after work.
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<ul>
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<li>A <a href="https://2019.igem.org/Team:DTU-Denmark/Part_Collection
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" target="_blank">promoter library</a>
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</li>
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<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K3046029" target="_blank">Auxotrophic selection marker for <i>Aspergillus</i> spp.</a></li>
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<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K3046032" target="_blank">Homology</a> <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K3046033" target="_blank">regions</a> for genomic integration in <i>Aspergillus niger</i></li>
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<li>Protocols for <a href="#Shakeflaskcultivation" target="_blank">growing</a>, <a href="#protoplast" target="_blank">protoplasting</a>, and <a href="#AspergillusTransformation" target="_blank">transforming filamentous fungi.</a></li>
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<li>Notes on growing filamentous fungi in larger equipment like <a href="#Biolector" target="_blank">Biolector</a>, <a href="#Shakeflaskcultivation" target="_blank">shake flasks</a>, and <a href="#Bioreactorcultivation" target="_blank">bioreactors</a>. </li>
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<h2>Fermentation safety</h2>
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<p>During the project, we will be using bioreactors to verify our promoters. This introduces new challenges in safely handling our organism and the larger equipment.
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The production of spores by <i>Aspergillus niger</i> and many other filamentous fungi is dependent on external conditions of the fermentation. That is why, during our work with  fermentation, only members who had received training in bioreactors participated in the experiment.
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These team members wore safety goggles, gloves, and lab coats whenever entering the fermentation platform and made sure that qualified personnel were on-site for help and advice if needed.  
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<h2>Integrated Human Practices</h2>
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<p>This page is only the non-integrated part of our human practices page. <a href="https://2019.igem.org/Team:DTU-Denmark/Integrated_Human_Practices" target="_blank">Click here to get to the integrated human practices page</a>.  
  
  
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<h2>Accessibility</h2>
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Inspired by the lack of accessibility of fungal parts, the team decided to strive towards making the entire project take a LEAP towards accessibility.
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In addition to making our library and software available to others, we wanted to make science and synthetic biology more accessible to the public by attending events and talking about synthetic biology.<br>
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Even our wiki is designed to be accessible to everyone. This is why we translated our front page and description into several different languages and furthermore followed multiple best practices for accessibility for blind people and the visually impaired, including the one from Dansk Blindesamfund’s (Danish Society of Blind People). Their TIBS guide to accessibility for blind people and the visually impaired, can be found <a href="https://blind.dk/udgivelser/tibs-tilgaengelighed-blinde-svagsynede" target="_blank">here</a>, (accessed: 18. October 2019).
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With this in mind, we added specific descriptions for all images on the wiki in order for reading software to be able to tell what is on the pictures.
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<h2 id="HPDanishiGEM">Danish iGEM Network</h2>
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<p>Inspired by a presentation by <a target="_blank" href="https://2019.igem.org/Team:Stockholm">iGEM Stockholm</a> at the Nordic iGEM conference, we have worked with <a target="_blank" href="https://2019.igem.org/Team:UCopenhagen">UCopenhagen</a> and <a target="_blank" href="https://2019.igem.org/Team:SDU-Denmark">SDU-Denmark</a> to start a network between the danish iGEM teams as well. The ultimate goal with the Danish iGEM Network is to improve the efforts of danish iGEM teams in the iGEM competition.
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We expect this network to take many forms but mainly as a platform for collaborations between danish iGEM teams, enabling a greater ability for teams to coordinate for big events like the Folkemøde (People’s meeting), where prominent politicians, scientists, and companies celebrate the Danish community and democracy. In 2019, the SDU team was present at the People’s meeting and saw great opportunities in talking about GMOs to the public as the audience was engaged and interested.
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In the future, we also want to use the Danish iGEM Network to establish more iGEM teams in Denmark as there are currently three universities offering biotechnology/molecular biology degrees but do not have iGEM teams (AAU, AU, and RUC).
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<h2>UN sustainable development</h2>
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<p style="font-size:1.2em">We have also looked at how our project will influence the world as a whole and how we can use it to make it a better place. One could think that the creation of a library of promoters may not have a big influence, but our library can certainly have a great impact in many different ways. In determining how our project can make the world a better place, we looked to the The UN Sustainable Development Goals (SDGs).
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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.
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<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>
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<h2>Primary goals</h2>
 
<h2>Primary goals</h2>
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<p><a target="_blank" href="https://sustainabledevelopment.un.org/sdg8">Goal 8: Decent work and economic growth</a>
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<p>Goal 8: Decent work and economic growth.
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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>
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This goal focuses on economic development, measured by the growth of GDP, education, and financial institutions. We specifically focus on goal 8.2, in that we can improve the economic productivity of fermentation by using our promoter library to conduct metabolic engineering in an important production organism, <i>Aspergillus niger</i>. Furthermore, as our research is accessible, it invites others to build upon a solid biotechnological foundation and spearhead new innovation in ever-increasing markets.  
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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.  
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<a target="_blank" href="https://sustainabledevelopment.un.org/sdg9">Goal 9: Industry, innovation and infrastructure</a>
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Goal 9: Industry, innovation, and infrastructure.
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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>
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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.  
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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.  
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Goal 9.4 revolves around the addition of value without a large increase in CO<sub>2</sub> output and the use of our promoter library, as well as other biotechnological tools, allows for tighter control over the production of many important products where resource efficiency is a key aspect.
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<br>
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In addition to this, we are also working towards goal 9.5 by contributing 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.  
  
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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>
 
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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.
 
  
 
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<a target="_blank" href="https://sustainabledevelopment.un.org/sdg12">Goal 12: Responsible consumption and production</a>
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Goal 12: Responsible consumption and production.
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This development goal is centered around the minimization of waste products and material use in addition to increasing recycling.  
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This development goal is centered around the minimization of waste products and material used in addition to increasing recycling.  
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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."
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We are specifically focusing on goal 12.2 and 12.5 through the improvement of fermentation resource efficiency by offering tighter control over the metabolism of the filamentous fungus used. Furthermore, our promoter library enables others to develop more efficient ways of using waste products in industrial fermentations by giving them the basic tools needed for more advanced biotechnological research.
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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.
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<a target="_blank" href="https://sustainabledevelopment.un.org/sdg15">Goal 15: Life on land</a>
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Goal 15: Life on land.
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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.
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This development goal focuses on the protection, restoration, and sustainable management of terrestrial resources and we are focusing on a subsection of 15.6, concerning itself with the sharing of genetic resources and the ease of access to these. By publishing our findings on our wiki, we make sure that everyone has equal access to our methods and results.
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<a target="_blank" href="https://sustainabledevelopment.un.org/sdg17">Goal 17: Partnerships for the goals</a>
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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.
 
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.
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<h2>Secondary goals</h2>
 
<h2>Secondary goals</h2>
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<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>
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<p>The secondary goals are not directly affected by our project, but our promoter library can be used by others to improve the world in amazing ways.<br><br>
  
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<a target="_blank" href="https://sustainabledevelopment.un.org/sdg3">Goal 3: Good health and well-being</a>
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Goal 3: Good health and well-being.
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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>
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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. This includes both industrial products and biopharmaceuticals which are in high demand everywhere in the world.[3]
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Goal 7: Affordable and clean energy.
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The addition to new and improved tools in biotechnology our promoters could be used to improve the production of biofuels which are essential in the sustainable development of the energy production of the future.
  
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<a target="_blank" href="https://sustainabledevelopment.un.org/sdg7">Goal 7: Affordable and clean energy</a>
 
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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.
 
 
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<a target="_blank" href="https://sustainabledevelopment.un.org/sdg14">Goal 14: Life below water</a>
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Goal 14: Life below water.
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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.  
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The marine environment is highly susceptible to the pollution of heavy industry. Biotechnology offers multiple ways to minimize this pollution by e.g. shifting traditional chemical processes towards production in biological organisms. The use of genetic engineering allows for production to reach the highest yields possible and this project has the potential to influence many more aspects of the world as we learn to harness the innate potential of the biological resources available to us.  
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(1) <a target="_blank" href="https://www.genengnews.com/insights/key-trends-in-2018-in-the-biopharmaceutical-market/"> retrieved 7/8 2019</a></p>
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(1) Hunt, D. M: Color Blindness, Brenner's Encyclopedia of Genetics: Second Edition, 2013 pp. 94-96<br>
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(2) <a target="_blank" href="https://www.genengnews.com/insights/key-trends-in-2018-in-the-biopharmaceutical-market/"> https://www.genengnews.com/insights/key-trends-in-2018-in-the-biopharmaceutical-market/</a>, (Retrieved 07/08 2019)<br>
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Latest revision as of 21:45, 13 December 2019

Fungi around the World and the DTU Biobuilders

Human Practices

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).

Our human practices section consists of several different parts.
During the creation of the project, we contacted a lot of people to get their help and feedback. To read more about this, see our integrated human practices section.
Another important part of our project is accessibility, as we believe that science should be available for everyone.
Additionally, we wanted to make iGEM a more integrated part of the Danish society. We, therefore, grouped up with the two other Danish teams to form the DanishiGEM.
iGEM is not only a competition in synthetic biology but it also inspires people to make the world a better place. Our project reflects several of the UN sustainable development goals.

Human Practices

As mentioned in the project description, filamentous fungi are important producers of proteins and biological compounds in industry. Although they are very important, filamentous fungi are heavily underrepresented in the iGEM competition. We think this is very unfortunate, and therefore we developed the tools to fill this gap.
At DTU we are specialists in using filamentous fungi as a chassis in synthetic biology and we have shared this knowledge on this wiki. Our efforts include:

Integrated Human Practices

This page is only the non-integrated part of our human practices page. Click here to get to the integrated human practices page.

Accessibility

Inspired by the lack of accessibility of fungal parts, the team decided to strive towards making the entire project take a LEAP towards accessibility. In addition to making our library and software available to others, we wanted to make science and synthetic biology more accessible to the public by attending events and talking about synthetic biology.
Even our wiki is designed to be accessible to everyone. This is why we translated our front page and description into several different languages and furthermore followed multiple best practices for accessibility for blind people and the visually impaired, including the one from Dansk Blindesamfund’s (Danish Society of Blind People). Their TIBS guide to accessibility for blind people and the visually impaired, can be found here, (accessed: 18. October 2019). With this in mind, we added specific descriptions for all images on the wiki in order for reading software to be able to tell what is on the pictures.

Danish iGEM Network

Inspired by a presentation by iGEM Stockholm at the Nordic iGEM conference, we have worked with UCopenhagen and SDU-Denmark to start a network between the danish iGEM teams as well. The ultimate goal with the Danish iGEM Network is to improve the efforts of danish iGEM teams in the iGEM competition. We expect this network to take many forms but mainly as a platform for collaborations between danish iGEM teams, enabling a greater ability for teams to coordinate for big events like the Folkemøde (People’s meeting), where prominent politicians, scientists, and companies celebrate the Danish community and democracy. In 2019, the SDU team was present at the People’s meeting and saw great opportunities in talking about GMOs to the public as the audience was engaged and interested. In the future, we also want to use the Danish iGEM Network to establish more iGEM teams in Denmark as there are currently three universities offering biotechnology/molecular biology degrees but do not have iGEM teams (AAU, AU, and RUC).

UN sustainable development

We have also looked at how our project will influence the world as a whole and how we can use it to make it a better place. One could think that the creation of a library of promoters may not have a big influence, but our library can certainly have a great impact in many different ways. In determining how our project can make the world a better place, we looked to the The UN Sustainable Development Goals (SDGs). 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.

Primary goals

Goal 8: Decent work and economic growth. This goal focuses on economic development, measured by the growth of GDP, education, and financial institutions. We specifically focus on goal 8.2, in that we can improve the economic productivity of fermentation by using our promoter library to conduct metabolic engineering in an important production organism, Aspergillus niger. Furthermore, as our research is accessible, it invites others to build upon a solid biotechnological foundation and spearhead new innovation in ever-increasing markets.

Goal 9: Industry, innovation, and infrastructure. 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. Goal 9.4 revolves around the addition of value without a large increase in CO2 output and the use of our promoter library, as well as other biotechnological tools, allows for tighter control over the production of many important products where resource efficiency is a key aspect.
In addition to this, we are also working towards goal 9.5 by contributing 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.

Goal 12: Responsible consumption and production. This development goal is centered around the minimization of waste products and material used in addition to increasing recycling. We are specifically focusing on goal 12.2 and 12.5 through the improvement of fermentation resource efficiency by offering tighter control over the metabolism of the filamentous fungus used. Furthermore, our promoter library enables others to develop more efficient ways of using waste products in industrial fermentations by giving them the basic tools needed for more advanced biotechnological research.

Goal 15: Life on land. This development goal focuses on the protection, restoration, and sustainable management of terrestrial resources and we are focusing on a subsection of 15.6, concerning itself with the sharing of genetic resources and the ease of access to these. By publishing our findings on our wiki, we make sure that everyone has equal access to our methods and results.

Goal 17: Partnerships for the goals. 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.

Secondary goals

The secondary goals are not directly affected by our project, but our promoter library can be used by others to improve the world in amazing ways.

Goal 3: Good health and well-being. 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. This includes both industrial products and biopharmaceuticals which are in high demand everywhere in the world.[3]

Goal 7: Affordable and clean energy. The addition to new and improved tools in biotechnology our promoters could be used to improve the production of biofuels which are essential in the sustainable development of the energy production of the future.

Goal 14: Life below water. The marine environment is highly susceptible to the pollution of heavy industry. Biotechnology offers multiple ways to minimize this pollution by e.g. shifting traditional chemical processes towards production in biological organisms. The use of genetic engineering allows for production to reach the highest yields possible and this project has the potential to influence many more aspects of the world as we learn to harness the innate potential of the biological resources available to us.



(1) Hunt, D. M: Color Blindness, Brenner's Encyclopedia of Genetics: Second Edition, 2013 pp. 94-96
(2) https://www.genengnews.com/insights/key-trends-in-2018-in-the-biopharmaceutical-market/, (Retrieved 07/08 2019)

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