Difference between revisions of "Template:Team:TU Eindhoven/Practices HTML"

 
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<span class="tekst1BI">Dig Deeper</span><br />
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Meet the stakeholders who helped us develop our application scenarios.
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See who've helped us over the course of the summer.</span>
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Policy and Practices plays a central role within the iGEM competition. In the Policy and Practices aspect of our project, we considered what impact COMBs could have on the world. Therefore, we have identified <span class="tekst1B">three possible application scenarios</span>. For each of our scenarios, we have reached out to stakeholders to find out which bars there are within the application scenarios and <span class="tekst1B">how our COMBs could play a role in clearing these bars</span>. Rather than just identifying the challenges we should still overcome, we have set first steps by <span class="tekst1B">calling policy officers' attention to the problems at hand</span>.<br />
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Policy and Practices is also about <span class="tekst1B">outreach and inclusion</span>. Therefore, we have not only talked to policy officers and stakeholders, but also to <span class="tekst1B">students and lay people</span>. We showed them the amazing promise of synthetic biology as well as the risks associated with synthetic biology, but also made an effort to <span class="tekst1B">involve them in a discussion on SynBio</span>. An overview of our Policy & Practices activities is shown below:
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We have developed Clickable Outer Membrane Biosensors as a universal membrane sensor platform for biosensors. Our dream is that <span class="tekst1B">any chassis</span> may be functionalized with COMBs. This chassis should then be able to <span class="tekst1B">detect virtually any biomarker</span> and translate detection of this biomarker into <span class="tekst1B">any desired response</span>. To obtain such a system, it is of the utmost importance that the system is inherently modular. The modularity of our system is reached through rational choices for the recognition element, the scaffold and the signaling components for our COMBs.
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<h3>The recognition elements - Aptamers</h3><br />
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<h3>Application Scenarios</h3><br />
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Molecular recognition is central to biosensing <a name="reft1" href="#ref1" class="textanchor">[1]</a>. The moieties responsible for molecular recognition are better known as recognition elements. Recognition elements frequently used in biosensors are <span class="tekst1B">aptamers</span>. These aptamers are small oligonucleotides which fold spontaneously into intricate <span class="tekst1B">three-dimensional structures</span>. These structures <span class="tekst1B">fit perfectly</span> into a wide range of disease markers, with affinities reaching into the low nanomolar range. Through modifications, these aptamers can be attached post-translationally to our proteins, resulting in a truly modular membrane sensor platform. Read more on aptamers: <a name="jump1a" href="#jump1b"><img src="https://static.igem.org/mediawiki/2015/5/5d/TU_Eindhoven_Jump_Button.png"/></a>
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COMBs are inherently modular and the use of aptamers allows for the detection of a virtually all disease markers. To give an overview of the possibilities our COMBs offer, we sketch three application scenarios. The first application scenario concerns the zoonosis Q Fever, of which a large outbreak was reported in the Netherlands in 2007. The second application concerns the use of COMBs within the gastrointestinal tract. The third application scenario is aimed at countering pesticide overuse. Read more on our application scenarios here:
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Aptamers are folded oligo- nucleotides (orange) which perfectly fit into biomarkers (purple).<br/>
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We sketch three application scenario's: use of COMBs within the intestines, to prevent Q Fever and to reduce use of pesticides.
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<h3>The scaffold - Outer Membrane Proteins</h3><br />
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Outer membrane proteins form an essential component for Gram-negative bacteria, providing the bacteria with protection against a harsh environment <a name="reft2" href="#ref2" class="textanchor">[2]</a>. <span class="tekst1B">More than six outer membrane protein families</span> have been discovered, which all share a beta barrel secondary structure. Thanks to this structure, the proteins feature <span class="tekst1B">loops protruding from the bacterial outer membrane</span>, and <span class="tekst1B">intracellular C-termini</span>. This enables clicking of aptamers to the membrane proteins and fusing signaling components to the outer membrane proteins intracellularly, making outer membrane proteins the perfect scaffold for COMBs. Read more on outer membrane proteins: <a name="jump2a" href="#jump2b"><img src="https://static.igem.org/mediawiki/2015/5/5d/TU_Eindhoven_Jump_Button.png"/></a>
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To identify which challenges are yet to be overcome within the application scenarios we envisioned, we have reached out to many stakeholders. These stakeholders include scientists, policymakers, doctors, journalists and professors. Many of the problems we sketch in each of the application scenarios are the fruits of these talks. Moreover, the particular implementation of our device within each of the application scenarios stems from talks with these stalkholders. A short overview of the conversations we had with these stakeholders is shown here: <a href="https://2015.igem.org/Team:TU_Eindhoven/Policy_Practices/Stakeholders"><img src="https://static.igem.org/mediawiki/2015/5/5d/TU_Eindhoven_Jump_Button.png"/></a>
 
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OMPs can feature as a scaffold as aptamers can be clicked on the protruding loops & signaling components fused intracellularly.
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To identify challenges which COMBs can overcome, we have reached out to many stakeholders, including jour- nalists, doctors, policymakers, scientists, and professors.
 
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Molecular recognition in our device Fis translated into close proximity of two membrane proteins. The signaling components used for COMBs translate a close proximity into a response. Signaling components which do exactly this are <span class="tekst1B">split luciferases & fluorescent and bioluminescent proteins</span>, through Resonance Energy Transfer. In the future, TEV Proteases may be used to translate a proximity into the release of the transcription factor, coupling COMBs recognition to the vast amount of cellular responses bacteria have available. Read more our signaling components: <a name="jump3a" href="#jump3b"><img src="https://static.igem.org/mediawiki/2015/5/5d/TU_Eindhoven_Jump_Button.png"/></a>
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The National Institute for Public Health and Environment (RIVM) and the Rathenau Institute organized a convention on synthetic biology for representatives from the government, scientific institutions, enterprise & NGO's. Titled "Industrial Biotechnology: exclusive supplier for biobased products", the convention was aimed at envisioning the impact and future role of synthetic biology. During this convention, we pitched our COMBs to show the attendees which great promises synthetic biology hold. We also sounded the alarm to report that intellectual property rights have limited development of new aptamers.
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COMBs signaling components translate a close proximity into a measurable signal. Here shown is BRET.<br/>
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The RIVM and Rathenau Institute organized a SynBio convention where we could pitch our project.<br/>
 
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We contacted Bureau GGO, the institution responsible for the use of GMOs within the Netherlands, to obtain the regulations to which future use of our COMBs will be subject. To make the notion of COMBs more tangible, we presented our application scenarios to Bureau GGO and inquired about applicable regulations. Not only did we learn about regulations through Bureau GGO, but we also managed to establish contact between Bureau GGO with the Centre of Health Protection.
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Latest revision as of 10:33, 21 November 2015





Policy & Practices



Policy and Practices plays a central role within the iGEM competition. In the Policy and Practices aspect of our project, we considered what impact COMBs could have on the world. Therefore, we have identified three possible application scenarios. For each of our scenarios, we have reached out to stakeholders to find out which bars there are within the application scenarios and how our COMBs could play a role in clearing these bars. Rather than just identifying the challenges we should still overcome, we have set first steps by calling policy officers' attention to the problems at hand.
Policy and Practices is also about outreach and inclusion. Therefore, we have not only talked to policy officers and stakeholders, but also to students and lay people. We showed them the amazing promise of synthetic biology as well as the risks associated with synthetic biology, but also made an effort to involve them in a discussion on SynBio. An overview of our Policy & Practices activities is shown below:

Application Scenarios


COMBs are inherently modular and the use of aptamers allows for the detection of a virtually all disease markers. To give an overview of the possibilities our COMBs offer, we sketch three application scenarios. The first application scenario concerns the zoonosis Q Fever, of which a large outbreak was reported in the Netherlands in 2007. The second application concerns the use of COMBs within the gastrointestinal tract. The third application scenario is aimed at countering pesticide overuse. Read more on our application scenarios here:
We sketch three application scenario's: use of COMBs within the intestines, to prevent Q Fever and to reduce use of pesticides.


Stakeholders


To identify which challenges are yet to be overcome within the application scenarios we envisioned, we have reached out to many stakeholders. These stakeholders include scientists, policymakers, doctors, journalists and professors. Many of the problems we sketch in each of the application scenarios are the fruits of these talks. Moreover, the particular implementation of our device within each of the application scenarios stems from talks with these stalkholders. A short overview of the conversations we had with these stakeholders is shown here:
To identify challenges which COMBs can overcome, we have reached out to many stakeholders, including jour- nalists, doctors, policymakers, scientists, and professors.


SynBio convention


The National Institute for Public Health and Environment (RIVM) and the Rathenau Institute organized a convention on synthetic biology for representatives from the government, scientific institutions, enterprise & NGO's. Titled "Industrial Biotechnology: exclusive supplier for biobased products", the convention was aimed at envisioning the impact and future role of synthetic biology. During this convention, we pitched our COMBs to show the attendees which great promises synthetic biology hold. We also sounded the alarm to report that intellectual property rights have limited development of new aptamers.
The RIVM and Rathenau Institute organized a SynBio convention where we could pitch our project.


Outreach


At the start of the summer, we reached out to future students to inform them about synthetic biology and the iGEM competition. Near the end of the summer, we also hosted an open convention at the TU Eindhoven where we were joined by all sorts of people unfamiliar with synthetic biology. Visitors included optometrists, teachers, physiotherapists and civil servants. During these conventions, we shortly pitched our project and some case studies based on which we held ethical discussions with the attendees. For more information, check here:
We presented attendees to our open floor with cases based on which ethical discussions where held.


Regulations


We contacted Bureau GGO, the institution responsible for the use of GMOs within the Netherlands, to obtain the regulations to which future use of our COMBs will be subject. To make the notion of COMBs more tangible, we presented our application scenarios to Bureau GGO and inquired about applicable regulations. Not only did we learn about regulations through Bureau GGO, but we also managed to establish contact between Bureau GGO with the Centre of Health Protection.
The RIVM and Rathenau Institute organized a SynBio convention where we could pitch our project.