Difference between revisions of "Team:UNebraska-Lincoln/Integrated Practices 1"

 
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<a href="https://2016.igem.org/Team:UNebraska-Lincoln/human_practices">Human Practices</a>
 
<a href="https://2016.igem.org/Team:UNebraska-Lincoln/human_practices">Human Practices</a>
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                                                        <a href="https://2016.igem.org/Team:UNebraska-Lincoln/Integrated_Practices">Integrated Practices</a>
 
<a href="https://2016.igem.org/Team:UNebraska-Lincoln/collaboration">Collaboration</a>
 
<a href="https://2016.igem.org/Team:UNebraska-Lincoln/collaboration">Collaboration</a>
 
<a href="https://2016.igem.org/Team:UNebraska-Lincoln/industry">Industry</a>
 
<a href="https://2016.igem.org/Team:UNebraska-Lincoln/industry">Industry</a>
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<h2 class="major">Human Practices Project Integration</h2>
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<h2><font color="white"><strong><br>How Human Practices were Integrated into our Project:<br></strong></font></h2>
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<p><font color="white">Since the inception of the project, we aimed to provide a scientifically feasible and practically safe solution to managing the nitrogen cycle. One that can be applied to the natural environment.  We designed and installed a novel kill-switch that leads to the death of our machine once the concentration of nitrate is reduced below the safety level. Over the summer, we met with scientists from local biotech companies and fellow iGEMers to discuss both the scientific and safety aspects our project design.  Based on the feedback, we became more mindful of safety and began to integrate an interdisciplinary tool to our project. We developed safety cases, a method that is currently used to gauge the safety of critical software systems to simulate the end-results of releasing our engineered microorganisms into the environment. </p></font>
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<p><font color="white"><span style="font-weight: 400;">Our human practices efforts directly contributed to our awareness of biosafety. We discussed our project and safety concerns with scientists from biotech companies including Monsanto, Li-Cor, and Nature Tech. The feedback we received from them was valuable and helped us to modify and improve our existing ideas. Because the end goal of our project is to create a system that will be introduced into a marine environment, scientists from Nature Tech raised the concern of bacterial conjugation and suggested incorporating the genes into the chromosomal DNA. This would mitigate the concerns with bacterial conjugation compared to the use of plasmids. Our project is only a proof of concept and actually incorporating our reductase genes into the chromosomal DNA is out of the scope of our project, but it was still valuable insight and became a part of our safety case considerations.</span></p>
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<p><font color="white"><span style="font-weight: 400;">Over the summer, our team attended the Heartland iGEM Regional Meetup where we participated in a Building with Biology public forum on engineering Mosquitos to fight malaria and cohosted a BioBuilders workshop to educate students and the community. Through these outreach events, we were able to hold meaningful conversations with members of the general public about their perception of genetically modified organisms. It became very clear to us that biosafety and bioethics are some of the public’s main concerns regarding the use of transgenic organisms. </span></p>
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<p><font color="white"></p></font>
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<p><font color="white">
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<p><font color="white"><span style="font-weight: 400;">Our meetings with local companies and our interactions at the regional meetup inspired us to make safety one of the centerpieces of our project. The safety case we developed is a unique example the integration of safety concerns our human practice efforts illuminated. We hosted our own Building with Biology Public event at a local museum where we educated public on synthetic biology as a whole and emphasized the safety measures that are currently used in synthetic biology. Developing a relationship with the public and building safety cases played a large role in our project. <br><br></span></p>
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These aspects of our project served the dual benefit of improving our design by forcing us to think critically about the mechanisms and environment of our project and allowing us to connect with and respond to the public in order to educate them and respond to their concerns.</font></p>
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<h2><font color="white"><strong>How did safety discussions influence our design?<br></strong></h2>
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<p><font color="white"><span style="font-weight: 400;">Through human practices and safety discussions, our team realized the importance of designing the kill switch mechanism that regulates our own system. The introduction of nitrate reducing E. coli into waterways could have unintended environmental impacts and the kill switch mechanism mitigates this risk by ensuring that the cells will not be able to reproduce indefinitely.</span></p>
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<p><font color="white"><span style="font-weight: 400;">The strain of E. coli  we used as our chassis cannot synthetize serine, an amino acid it needs to survive. We decided to use this strain of bacteria for several reasons:</span></p>
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<ul>
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<li style="font-weight: 400;"><span style="font-weight: 400;">All organisms require serine for survival</span></li>
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<li style="font-weight: 400;"><span style="font-weight: 400;">Natural marine environments lack the concentration of serine that our chassis requires for survival</span></li>
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<li style="font-weight: 400;"><span style="font-weight: 400;">Many other kill switches induce death through synthesis of toxins</span></li>
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<li style="font-weight: 400;"><span style="font-weight: 400;">If other bacteria uptake our kill switch through bacterial conjugation, they will synthesize more serine in the presence of nitrates, and consequences will be minimal (serine is already synthesized in wild type bacteria)</span></li>
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<br>
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<p><font color="white">The plasmid we used to complement this strain only allows the bacteria to synthesize serine if the nitrate concentration is sufficient. This means that when the bacteria are no longer needed (because they have sufficiently reduced the concentration of nitrate) they will no longer be able to survive.</font></p>
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</ul>
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<p><font color="white"><span style="font-weight: 400;">More details of our kill switch design can be found </span><strong><a href="https://2016.igem.org/Team:UNebraska-Lincoln/Composite_Part">here.<a></strong></p>
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<a href="https://2016.igem.org/Team:UNebraska-Lincoln/Integrated_Practices" style="top: 10%; left: 10%; width: 10%; height: 80%;">
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  <a href="https://2016.igem.org/Team:UNebraska-Lincoln/Integrated_Practices_1" style="top: 10%; left: 20%; width: 10%; height: 80%;">
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  <a href="https://2016.igem.org/Team:UNebraska-Lincoln/Integrated_Practices_2" style="top: 10%; left: 30%; width: 10%; height: 80%;">
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<a href="https://2016.igem.org/Team:UNebraska-Lincoln/Integrated_Practices_3" style="top: 10%; left: 40%; width: 10%; height: 80%;">
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  <a href="https://2016.igem.org/Team:UNebraska-Lincoln/Integrated_Practices_4" style="top: 10%; left: 50%; width: 10%; height: 80%;">
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  <a href="https://2016.igem.org/Team:UNebraska-Lincoln/Integrated_Practices_6" style="top: 10%; left: 70%; width: 10%; height: 80%;">
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  <a href="https://2016.igem.org/Team:UNebraska-Lincoln/Integrated_Practices_7" style="top: 10%; left: 80%; width: 10%; height: 80%;"></a>
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<img src="https://static.igem.org/mediawiki/2016/b/bd/T--UNebraska-Lincoln--IHP2.png" align="middle" style="width:100%; height:auto; transform: scale(0.8)" alt="image"/>
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<a href="https://2016.igem.org/Team:UNebraska-Lincoln/Integrated_Practices" style="top: 10%; left: 10%; width: 10%; height: 80%;">
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  <a href="https://2016.igem.org/Team:UNebraska-Lincoln/Integrated_Practices_1" style="top: 10%; left: 20%; width: 10%; height: 80%;">
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  <a href="https://2016.igem.org/Team:UNebraska-Lincoln/Integrated_Practices_2" style="top: 10%; left: 30%; width: 10%; height: 80%;">
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<a href="https://2016.igem.org/Team:UNebraska-Lincoln/Integrated_Practices_3" style="top: 10%; left: 40%; width: 10%; height: 80%;">
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  <a href="https://2016.igem.org/Team:UNebraska-Lincoln/Integrated_Practices_4" style="top: 10%; left: 50%; width: 10%; height: 80%;">
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  <a href="https://2016.igem.org/Team:UNebraska-Lincoln/Integrated_Practices_5" style="top:10%; left: 60%; width: 10%; height: 80%;">
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  <a href="https://2016.igem.org/Team:UNebraska-Lincoln/Integrated_Practices_6" style="top: 10%; left: 70%; width: 10%; height: 80%;">
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  <a href="https://2016.igem.org/Team:UNebraska-Lincoln/Integrated_Practices_7" style="top: 10%; left: 80%; width: 10%; height: 80%;"></a>
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Latest revision as of 02:32, 20 October 2016

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How Human Practices were Integrated into our Project:

Our human practices efforts directly contributed to our awareness of biosafety. We discussed our project and safety concerns with scientists from biotech companies including Monsanto, Li-Cor, and Nature Tech. The feedback we received from them was valuable and helped us to modify and improve our existing ideas. Because the end goal of our project is to create a system that will be introduced into a marine environment, scientists from Nature Tech raised the concern of bacterial conjugation and suggested incorporating the genes into the chromosomal DNA. This would mitigate the concerns with bacterial conjugation compared to the use of plasmids. Our project is only a proof of concept and actually incorporating our reductase genes into the chromosomal DNA is out of the scope of our project, but it was still valuable insight and became a part of our safety case considerations.

Over the summer, our team attended the Heartland iGEM Regional Meetup where we participated in a Building with Biology public forum on engineering Mosquitos to fight malaria and cohosted a BioBuilders workshop to educate students and the community. Through these outreach events, we were able to hold meaningful conversations with members of the general public about their perception of genetically modified organisms. It became very clear to us that biosafety and bioethics are some of the public’s main concerns regarding the use of transgenic organisms.

Our meetings with local companies and our interactions at the regional meetup inspired us to make safety one of the centerpieces of our project. The safety case we developed is a unique example the integration of safety concerns our human practice efforts illuminated. We hosted our own Building with Biology Public event at a local museum where we educated public on synthetic biology as a whole and emphasized the safety measures that are currently used in synthetic biology. Developing a relationship with the public and building safety cases played a large role in our project.

How did safety discussions influence our design?

Through human practices and safety discussions, our team realized the importance of designing the kill switch mechanism that regulates our own system. The introduction of nitrate reducing E. coli into waterways could have unintended environmental impacts and the kill switch mechanism mitigates this risk by ensuring that the cells will not be able to reproduce indefinitely.

The strain of E. coli we used as our chassis cannot synthetize serine, an amino acid it needs to survive. We decided to use this strain of bacteria for several reasons:

  • All organisms require serine for survival
  • Natural marine environments lack the concentration of serine that our chassis requires for survival
  • Many other kill switches induce death through synthesis of toxins
  • If other bacteria uptake our kill switch through bacterial conjugation, they will synthesize more serine in the presence of nitrates, and consequences will be minimal (serine is already synthesized in wild type bacteria)

    • The plasmid we used to complement this strain only allows the bacteria to synthesize serine if the nitrate concentration is sufficient. This means that when the bacteria are no longer needed (because they have sufficiently reduced the concentration of nitrate) they will no longer be able to survive.

More details of our kill switch design can be found here.

image
image