Cas9 & Cpf1 secretion
and activity
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<div class="page-heading">OUTCASST Safety information</div> | <div class="page-heading">OUTCASST Safety information</div> | ||
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Since safety is a very important aspect in synthetic biology, we collaborated with the RIVM (the National Institute for Public Health and Environment of the Netherlands). They encouraged us to think about safety before we act. We came to the conclusion that safety has different meanings for different stakeholders. Here we describe the most important points for these stakeholders. Besides safety, we’ve also thought about the societal impact of our tool and the possible ethical issues involved. The information we gathered was summarized in an infographic, which we used to talk to the general public about synthetic biology and safety at an event organized by the RIVM. | Since safety is a very important aspect in synthetic biology, we collaborated with the RIVM (the National Institute for Public Health and Environment of the Netherlands). They encouraged us to think about safety before we act. We came to the conclusion that safety has different meanings for different stakeholders. Here we describe the most important points for these stakeholders. Besides safety, we’ve also thought about the societal impact of our tool and the possible ethical issues involved. The information we gathered was summarized in an infographic, which we used to talk to the general public about synthetic biology and safety at an event organized by the RIVM. | ||
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<b>User Safety</b><br><br> | <b>User Safety</b><br><br> | ||
| − | Since we are going to use OUTCASST for the diagnosis of Chagas disease, our users will be caregivers and medical professionals in rural areas. Safety of our device is of great importance to them. During the interviews to find suitable end users (see the end-users section), we also discussed the safety of HEK293T cells to detect specific DNA regions. All interviewees were unanimous that these cell lines would not be a problem regarding safety issues and that potential risks would lie with the samples applied to the device. Since we are going to use blood from people that are potentially infected with parasites, it is important to point out the risk of contamination of the caregiver or other people. This risk is, however, no different from that of other simple diagnostic procedures. | + | Since we are going to use OUTCASST for the diagnosis of Chagas disease, our users will be caregivers and medical professionals in rural areas. |
| + | Safety of our device is of great importance to them. During the interviews to find suitable end users (<a onclick="return change_page('stakeholders', 1)" href="stakeholders">see the end-users section</a>), we also discussed the safety of HEK293T cells to detect specific DNA regions. All interviewees were unanimous that these cell lines would not be a problem regarding safety issues and that potential risks would lie with the samples applied to the device. Since we are going to use blood from people that are potentially infected with parasites, it is important to point out the risk of contamination of the caregiver or other people. This risk is, however, no different from that of other simple diagnostic procedures. | ||
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Since the HEK293T cells are too fragile to use in the device, we opt to use air-dried cells from the anhydrobiotic insect, <i>Polypedilum vanderplanki</i>. To make the use of these cells as safe as possible, the design of our tool is going to be a closed system, wherein everything is present and only the blood sample will be applied. There will also be several mechanisms and kill-switches incorporated in the detecting cells. This way, the cells are physically separated from both the user and patients and this minimizes the chance of survival of these cells outside of the system. | Since the HEK293T cells are too fragile to use in the device, we opt to use air-dried cells from the anhydrobiotic insect, <i>Polypedilum vanderplanki</i>. To make the use of these cells as safe as possible, the design of our tool is going to be a closed system, wherein everything is present and only the blood sample will be applied. There will also be several mechanisms and kill-switches incorporated in the detecting cells. This way, the cells are physically separated from both the user and patients and this minimizes the chance of survival of these cells outside of the system. | ||
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We want to take this information into account to design the target DNA. There are two possibilities from which we can choose. The first option would be to permit certain mutations in the target DNA, to prevent getting a false negative result in some cases. The second option would be to use a very conserved domain as target DNA and don’t allow any mismatches. From our perspective, we think the second option would be more suitable, since the specificity in our system is a very valuable aspect of the design. We have chosen to use the satellite DNA, which is present in the <i>T. cruzi</i> parasite as a 195 base pair repeat with about 100,000 copies (Aldert Bart, Academical Medical Center Amsterdam: Clinical molecular parasitologist). | We want to take this information into account to design the target DNA. There are two possibilities from which we can choose. The first option would be to permit certain mutations in the target DNA, to prevent getting a false negative result in some cases. The second option would be to use a very conserved domain as target DNA and don’t allow any mismatches. From our perspective, we think the second option would be more suitable, since the specificity in our system is a very valuable aspect of the design. We have chosen to use the satellite DNA, which is present in the <i>T. cruzi</i> parasite as a 195 base pair repeat with about 100,000 copies (Aldert Bart, Academical Medical Center Amsterdam: Clinical molecular parasitologist). | ||
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Revision as of 21:50, 31 October 2017
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Comparison of endonuclease activity for Cas9 and Cpf1 that has been produced in, and excreted by, HEK293 cells.
MESA two-component system replication
Details on the MESA two-component system, explanation of its relation to our design and the results of its reproduction.
OUTCASST system production
Detailed explanation of the OUTCASST mechanism, experimental progress and technical prospects.
Modeling and
mathematics
mathematics
Ordinary differential equations, cellular automaton and an object based model for optimal linker-length estimation.
InterLab study participation
Results and details of our measurements for the iGEM 2017 InterLab Study.
Stakeholders & opinions
Interviews and dialogues with stakeholders, potential users, third parties and experts relating to pathogen detection or DNA-based diagnostics.
Risks & safety-issues
Implications and design considerations relating to safety in the usage and implementation of OUTCASST as a diagnostics tool.
Design & integration
OUTCASST toolkit and product design with factors such as bio-safety and user-friendliness taken into account.
Outreach
Videos we made for the dutch public, together with 'de Kennis van Nu'.
Meet our team
About us, our interests and roles in the team and our supervisors.
Sponsors
A listing of our sponsors, how they assisted us and our gratitude for their assistance.
Collaborations
Read about our exchanges with other iGEM teams and government agencies.
Achievements
A short description of all that we have achieved during our participation in the iGEM.
Attributions
A thank-you for everyone that assited us, both in and outside the lab.
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