Team:Aalto-Helsinki

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          <h1>Washington University<br>
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<h1>Aalto-Helsinki<br>
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<small>Bioworks</small></h1>
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              Engineering Ntrogen Fixation
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Figuring out how to combine business with science.
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            <a href="http://i-see-faces.deviantart.com/">Photo © Tanja Maria</a>
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<h2>Aalto-Helsinki Bioworks<br>
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<small>A Synthetic Biology Startup with a Three-Channel Gene Switch</small></h2>
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<h3>Project Description</h3>
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We have engineered a three-channel switch that is controlled with the intensity of blue light. By utilizing the mechanisms of the lambda repressor, we are able to switch between the expressions of three different genes with a short delay. This kind of mechanism provides a nearly real-time control over genes, which could provide advantages in variety of industrial bioprocesses.
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        <h2>Washington University in St. Louis<br>
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          <small>Engineering Nitrogen Fixation</small></h2>
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Inspired by the principles of open source software, we introduce an Open Source business model implemented around our switch. We want to encourage future companies to create Open Source based solutions and to empower customers to participate in the product development. Open Source model’s transparency as well as lower degree of protection raises trust and continuity and benefits larger community.
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We want to share our experiences and insights in biotech entrepreneurship and address the difficulties that students and newcomers may face in the early stages of building a synthetic biology startup.
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            <a href="http://youtu.be/tlc7MPY9SE8"><img src="https://static.igem.org/mediawiki/2014/7/79/Aaltohelsinki_pitc_capture.png" class="img-responsive smallerimg"></img></a>
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                Our pitch video on August 6th, Summer of Startups Demo Day.
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          <h3>Project Description</h3>
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            Some cyanobacteria fix nitrogen for nutritional needs, while most organisms can only acquire it from the food it consumes. Synthetic biology allows us to transfer this ability to fix nitrogen to a heterologous host that has many genetic tools, Escherichia coli, so that we can learn how to give single cell organisms, and eventually chloroplasts the ability to create their own nitrogen fertilizer.
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            Diazotrophic (organisms that fix nitrogen) cyanobacteria such Nostoc Punctiforme or Anabaena use heterocysts (specialized nitrogen fixing cells) to create a mini-anaerobic environment to aid nitrogen fixation. However, Cyanothece 51142, a non-heterocyst, fixes nitrogen in the same cell as photosynthesis by relying on a circadian metabolic process, when there is less oxygen byproduct from photosynthesis. This process is both fascinating and necessary since the key enzyme in nitrogen fixation, nitrogenase, is poisoned by oxygen. Our goal this summer is to engineer the regulation of the proteins necessary for nitrogen fixation so that they are highly repressed when activated by broad spectrum light (such as the sun), and are highly active when there is no light around, mimicking the cycle where photosynthesis occurs during the day and nitrogen fixation occurs at night.
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                Our pitch video.
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<h2>The Story of Aalto-Helsinki Bioworks</h2>
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              <h3>How does our project work?</h3>
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                Our team worked this summer on two projects towards a common purpose.
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We are Aalto-Helsinki Bioworks, the first-ever Finnish iGEM Team and one of the four teams in the new Entrepreneurship Track. Our <a href="https://2014.igem.org/Team:Aalto-Helsinki/Team">team</a> consists of nine students from Aalto University and the University of Helsinki and we are combining our interdisciplinary forces to develop something new and fascinating. We want to put Finland on the map of synthetic biology and improve undergraduate research opportunities in our universities.
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Richard and Caroline worked in the Pakrasi lab under Dr. Pakrasi, with Andrew Ng, Bert Berla, and Deng Liu as advisors on the getting nitrogen fixation working in E. coli.
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Benjamin and Jeffrey worked in the Moon lab under Dr. Moon, with Cheryl Immethun as an advisor, and created a repressor system to turn off transcription of a reporter protein in the light.
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We have <a href="https://2014.igem.org/Team:Aalto-Helsinki/Research">designed</a> a three-channel gene switch that would make it possible to control three user-defined genes with blue light intensity. We are using <a href="https://2014.igem.org/Team:Aalto-Helsinki/Research#yf1-title">YF1</a> as our light receptor protein and the signal is mediated to lambda repressor protein (CI) production via phosphorylation pathway. The concentration of the CI protein defines the gene that should be active at a time. The secret behind this function is our modified version of the <a href="https://2014.igem.org/Team:Aalto-Helsinki/Research#lambda-title">lambda repressor</a> mechanism.
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              <h3>What did we accomplish?</h3>
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              There are two key components of our project:
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We constructed a mathematical <a href="https://2014.igem.org/Team:Aalto-Helsinki/Modeling">model</a> that simulates the interactions of the molecules and function of the gene switch we designed. This revealed interesting phenomena in the dynamics of our system which helps us to better understand the capabilities and limitations of the gene switch. We also made an <a href="http://igem-qsf.github.io/SimCircus/WebUI/">interactive simulation</a> available to everybody to best illustrate how our idea actually works.
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              Richard and Caroline have been working in the Pakrasi lab, and have been using genes from cyanobacteria to get nitrogen fixation working in E. coli . They are testing nitrogen fixation by running acetylene reduction assays and designing experiments to test the optimal criteria (ie. E. coli strains, temperature, pH, nitrogen source) to get maximum results. For more info, visit the
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To control the amount of blue light on our cell cultures, we created the <a href="https://2014.igem.org/Team:Aalto-Helsinki/Research#ledrig-title">LED rig</a> device. This enabled us to perform diverse experiments in order to characterize our light response element. These <a href="https://2014.igem.org/Team:Aalto-Helsinki/Research#Results">results</a> show that our light response element is able to regulate the downstream gene expression precisely. In addition, the response time is in a ten-minute-scale, which enables constant and nearly real-time control over bacterial cultures. In addition, we hypothesize that this system is also applicable to bioreactors, which would enable higher level of control in industrial bioprocesses. However, our fully functional prototype is still under ongoing development.
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              <a href=""></a> nitrogenase tab.
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              <h3>Who will our project help?</h3>
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We have developed an open approach to <a href="https://2014.igem.org/Team:Aalto-Helsinki/Business">biotech business</a> inspired by the business models for open source software. Following the Open Source philosophy, we will distribute open Aalto-Helsinki Bioworks technologies for free to everybody - as long as they share the improvements made on the technology. Therefore, we empower our users to participate in product development. Our <a href="https://2014.igem.org/Team:Aalto-Helsinki/Business#canvas-title">business model</a> is based on hardware and wide range of services offered to our customers.
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              Our project is the first step of a much larger, much more complex endeavor. Nitrogen overabundance and nitrogen depletion are simultaneously big stumbling blocks in modern agriculture. The solution to both of these problems would be to endow plants themselves with the ability to fix nitrogen so that they could autonomously supply their own nitrogen for proteins, DNA, etc. We are taking the first step towards this ambitious goal by studying how the genes for nitrogen fixation from cyanobacteria work in different environments and constructing an artificial transcriptional system. We are currently working in E. coli because it is easy to engineer, but the next step would be to move into a cyanobacteria more closely related to chloroplasts. We hope that by making these initial steps that we may be helping to pave the way for future research that may put an end to world hunger.
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During the summer we participated in Aalto Entrepreneurship Society’s <a href="https://2014.igem.org/Team:Aalto-Helsinki/Business#Sos">Summer of Startups 2014</a> incubator programme to learn the essential entrepreneurial skills, such as pitching, investor relations, customer-driven development and <a href="https://2014.igem.org/Team:Aalto-Helsinki/Business#pitch-title">explaining</a> the science for general audience. See our Demo Day video for details.
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iGEM is an international experience and as the first Finnish team, we went to find advice and experience around the globe. We contributed to the iGEM community by building a <a href="https://2014.igem.org/Team:Aalto-Helsinki/Cooperation#Seekers">BioBrick Seeker</a> tool which makes it easy to find parts of your interest in the 2014 BioBrick distribution. This tool has been used by iGEM teams all over the world! We also did a lot of <a href="https://2014.igem.org/Team:Aalto-Helsinki/Cooperation#Interteam">cooperation</a>, including filling out surveys and having skype conversations and live meetings with current and previous iGEM teams from France, Colombia, Switzerland, USA and the Netherlands. We even made a <a href="http://www.youtube.com/embed/icPgP3OOVOQ?rel=0">video</a> together with ETH Zürich team to Colombia team’s challenge.
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We wanted to <a href="https://2014.igem.org/Team:Aalto-Helsinki/Outreach">raise awareness</a> about synthetic biology in Finland and also showcase researchers’ work to young people and undergraduate students. Therefore, we have been reaching out to general public, especially young people via <a href="https://2014.igem.org/Team:Aalto-Helsinki/Outreach#SoMe">social media</a>, including <a href="http://www.facebook.com/AaltoHelsinki">Facebook</a>, <a href="http://twitter.com/AaltoHelsinki">Twitter</a>, <a href="http://www.youtube.com/channel/UCEZliqjLu86CRpQlk57FfSw">Youtube</a>, <a href="http://www.flickr.com/photos/aaltohelsinki/">Flickr</a> and our own blog. We’ve shared stories, pictures, videos and experiences to our followers. In addition, we have been featured in radio interviews and articles on magazines and webzines. We also made a silly game: <a href="https://2014.igem.org/Team:Aalto-Helsinki/Flappycoli">Flappy Coli</a>. We have a public team webpage, <a href="http://2014.aaltohelsinki.com/">aaltohelsinki.com</a>, where you can find the latest stories of Aalto Helsinki also in the future. We lifted some of the highlights of this project on a <a href="https://2014.igem.org/Team:Aalto-Helsinki/Journal#Timeline">timeline</a>: the story of Aalto-Helsinki Bioworks is there for you to see!
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<h2 class="kakspaddingbot">Accomplishments</h2>
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<li>Best undergraduate wiki 2014</li>
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<li>Poster</li>
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<li>Presentation at the Giant Jamboree in Boston</li>
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<li>Background research, design and the creation of a <a href="https://2014.igem.org/Team:Aalto-Helsinki/Research">Three-Channel Gene Switch</a></li>
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<li>Submission of <a href="https://2014.igem.org/Team:Aalto-Helsinki/Research#Parts">three new BioBricks and two new primers to the Registry</a></li>
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<li>Creation of <a href="https://2014.igem.org/Team:Aalto-Helsinki/Business#Plan">an Open Source business model and a business plan</a> for Synthetic Biology Entrepreneurship</li>
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<li>Logo and brand design</li>
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<li><a href="http://youtu.be/tlc7MPY9SE8">Pitch</a> to an audience of 1000+ people</li>
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<li>Participation in the <a href="https://2014.igem.org/Team:Aalto-Helsinki/Business#Sos">Summer of Startups</a>, a startup incubator program</li>
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<li>Connecting with <a href="https://2014.igem.org/Team:Aalto-Helsinki/Outreach">investors and general public</a></li>
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<li>Received 45 000€ in <a href="https://2014.igem.org/Team:Aalto-Helsinki/Team#Sponsors">funding</a></li>
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<li>Drawing attention <a href="https://2014.igem.org/Team:Aalto-Helsinki/Outreach#Media">in the media</a></li>
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<li>BioBrick and Team <a href="https://2014.igem.org/Team:Aalto-Helsinki/Cooperation#Seekers">Seekers</a></li>
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<li>Collaboration with other <a href="https://2014.igem.org/Team:Aalto-Helsinki/Cooperation#Interteam">iGEM teams</a></li>
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<li>Participation in the <a href="https://2014.igem.org/Team:Aalto-Helsinki/Cooperation#Interlab">Measurement Interlab Study</a></li>
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<h2>Categories</h2>
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Our wiki has seven different categories in addition to this main page. On each of them you can just scroll through the content until you're finished reading. Everything about the subject can be found on one page, additional material is provided when possible and pages discussing similar topics are linked to each other. A submenu will also appear when you start scrolling through the other pages: see the top of the page as you advance in the wiki!
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<big><big><big>Team</big></big></big><br>
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We are a team of nine Finnish students and we've gotten amazing support during this project.
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<big><big><big>Business</big></big></big><br>
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We explored the possibilities of biotech and synthetic biology business.
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<big><big><big>Research</big></big></big><br>
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We engineered a three-channel switch that can be controlled with the intensity of blue light.
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<big><big><big>Modeling</big></big></big><br>
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We made mathematic models of the interactions behind our gene switch.
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<big><big><big>Cooperation</big></big></big><br>
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We got to know other iGEM teams and developed tools for everyone to use.
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<big><big><big>Outreach</big></big></big><br>
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We spread the word about iGEM and synthetic biology especially in Finland.
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<big><big><big>Journal</big></big></big><br>
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We documented the project well.
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<a href="http://i-see-faces.deviantart.com/">Photos © Tanja Maria</a>
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If you find yourself lost (or simply don't know where to start looking for what you'd want to find), <a href="https://static.igem.org/mediawiki/2014/7/73/Aalto_Helsinki_Wiki_Sitemap.png" target="_blank">here's a sitemap to help with the task</a>!
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Latest revision as of 02:07, 9 June 2015

Aalto-Helsinki
Bioworks

Figuring out how to combine business with science.

Scroll down to read more

Photo © Tanja Maria

Aalto-Helsinki Bioworks
A Synthetic Biology Startup with a Three-Channel Gene Switch

Project Description

We have engineered a three-channel switch that is controlled with the intensity of blue light. By utilizing the mechanisms of the lambda repressor, we are able to switch between the expressions of three different genes with a short delay. This kind of mechanism provides a nearly real-time control over genes, which could provide advantages in variety of industrial bioprocesses.

Inspired by the principles of open source software, we introduce an Open Source business model implemented around our switch. We want to encourage future companies to create Open Source based solutions and to empower customers to participate in the product development. Open Source model’s transparency as well as lower degree of protection raises trust and continuity and benefits larger community.

We want to share our experiences and insights in biotech entrepreneurship and address the difficulties that students and newcomers may face in the early stages of building a synthetic biology startup.

Our pitch video on August 6th, Summer of Startups Demo Day.

The Story of Aalto-Helsinki Bioworks

We are Aalto-Helsinki Bioworks, the first-ever Finnish iGEM Team and one of the four teams in the new Entrepreneurship Track. Our team consists of nine students from Aalto University and the University of Helsinki and we are combining our interdisciplinary forces to develop something new and fascinating. We want to put Finland on the map of synthetic biology and improve undergraduate research opportunities in our universities.

We have designed a three-channel gene switch that would make it possible to control three user-defined genes with blue light intensity. We are using YF1 as our light receptor protein and the signal is mediated to lambda repressor protein (CI) production via phosphorylation pathway. The concentration of the CI protein defines the gene that should be active at a time. The secret behind this function is our modified version of the lambda repressor mechanism.

We constructed a mathematical model that simulates the interactions of the molecules and function of the gene switch we designed. This revealed interesting phenomena in the dynamics of our system which helps us to better understand the capabilities and limitations of the gene switch. We also made an interactive simulation available to everybody to best illustrate how our idea actually works.

To control the amount of blue light on our cell cultures, we created the LED rig device. This enabled us to perform diverse experiments in order to characterize our light response element. These results show that our light response element is able to regulate the downstream gene expression precisely. In addition, the response time is in a ten-minute-scale, which enables constant and nearly real-time control over bacterial cultures. In addition, we hypothesize that this system is also applicable to bioreactors, which would enable higher level of control in industrial bioprocesses. However, our fully functional prototype is still under ongoing development.

We have developed an open approach to biotech business inspired by the business models for open source software. Following the Open Source philosophy, we will distribute open Aalto-Helsinki Bioworks technologies for free to everybody - as long as they share the improvements made on the technology. Therefore, we empower our users to participate in product development. Our business model is based on hardware and wide range of services offered to our customers.

During the summer we participated in Aalto Entrepreneurship Society’s Summer of Startups 2014 incubator programme to learn the essential entrepreneurial skills, such as pitching, investor relations, customer-driven development and explaining the science for general audience. See our Demo Day video for details.

iGEM is an international experience and as the first Finnish team, we went to find advice and experience around the globe. We contributed to the iGEM community by building a BioBrick Seeker tool which makes it easy to find parts of your interest in the 2014 BioBrick distribution. This tool has been used by iGEM teams all over the world! We also did a lot of cooperation, including filling out surveys and having skype conversations and live meetings with current and previous iGEM teams from France, Colombia, Switzerland, USA and the Netherlands. We even made a video together with ETH Zürich team to Colombia team’s challenge.

We wanted to raise awareness about synthetic biology in Finland and also showcase researchers’ work to young people and undergraduate students. Therefore, we have been reaching out to general public, especially young people via social media, including Facebook, Twitter, Youtube, Flickr and our own blog. We’ve shared stories, pictures, videos and experiences to our followers. In addition, we have been featured in radio interviews and articles on magazines and webzines. We also made a silly game: Flappy Coli. We have a public team webpage, aaltohelsinki.com, where you can find the latest stories of Aalto Helsinki also in the future. We lifted some of the highlights of this project on a timeline: the story of Aalto-Helsinki Bioworks is there for you to see!

Accomplishments

Categories

Our wiki has seven different categories in addition to this main page. On each of them you can just scroll through the content until you're finished reading. Everything about the subject can be found on one page, additional material is provided when possible and pages discussing similar topics are linked to each other. A submenu will also appear when you start scrolling through the other pages: see the top of the page as you advance in the wiki!

Team
We are a team of nine Finnish students and we've gotten amazing support during this project.

Business
We explored the possibilities of biotech and synthetic biology business.

Research
We engineered a three-channel switch that can be controlled with the intensity of blue light.

Modeling
We made mathematic models of the interactions behind our gene switch.

Cooperation
We got to know other iGEM teams and developed tools for everyone to use.

Outreach
We spread the word about iGEM and synthetic biology especially in Finland.

Journal
We documented the project well.

Photos © Tanja Maria

If you find yourself lost (or simply don't know where to start looking for what you'd want to find), here's a sitemap to help with the task!

Retrieved from "http://2014.igem.org/Team:Aalto-Helsinki"