Cas9 & Cpf1 secretion
and activity
Difference between revisions of "Template:Team:Utrecht/MainBody"
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| − | As OUTCASST is a system with a very broad application, we wanted to find the most suitable end users and focus our design on their needs and restrictions. To achieve this goal, we have interviewed multiple professionals from different backgrounds. In these conversations, we tried to discover strengths and weaknesses of our system and design with regard to existing techniques and whether the OUTCASST system would be useful in the professions of the interviewed individuals. If not, we tried to figure out in what direction it might prove more useful or what aspects needed to be improved. In addition, we also discussed safety issues and technical aspects of our toolkit design. | + | As OUTCASST is a system with a very broad application, we wanted to find the most suitable end users and focus our design on their needs and restrictions. To achieve this goal, we have interviewed multiple professionals from different backgrounds. In these conversations, we tried to discover strengths and weaknesses of our system and design with regard to existing techniques and whether the OUTCASST system would be useful in the professions of the interviewed individuals. If not, we tried to figure out in what direction it might prove more useful or what aspects needed to be improved. In addition, we also discussed safety issues and technical aspects of our toolkit design, of which the outcomes were compiled on their own respective pages: <a onclick="return change_page('safety', 1)" href="safety">Safety</a> and <a onclick="return change_page('product-design', 1)" href="product-design">Design & Integration</a>. |
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In the short video below, we show a summary of the journey we made to get to our end users. Besides this summary, more elaborate descriptions of each interview can be found below. | In the short video below, we show a summary of the journey we made to get to our end users. Besides this summary, more elaborate descriptions of each interview can be found below. | ||
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<div><b>Utrecht University is a Dutch public university with over 50.000 students.</b> As our home university, they were our first sponsor. They have helped us generously with great financial support, meeting space, PR-facilities and the opportunity to use several labspaces on campus.</div> | <div><b>Utrecht University is a Dutch public university with over 50.000 students.</b> As our home university, they were our first sponsor. They have helped us generously with great financial support, meeting space, PR-facilities and the opportunity to use several labspaces on campus.</div> | ||
| + | <div><b>The Jong Alumni Netwerk (JAN) organizes activities and events to help support the careers of recent graduates by providing networking opportunities.</b> JAN agreed to financially support us to make this project possible.</div> | ||
<div><b>RIVM is the National Institute for Public Health and the Environment, which belongs to the Ministry of Health, Welfare and Sport of the Dutch government.</b> They offered a sponsorship to the Dutch iGEM teams based on an assignment titled ‘think before you do’, stimulating us to think about the societal implications that our project could have. We submitted a proposal and the RIVM offered us a €1500 grant to further our project.</div> | <div><b>RIVM is the National Institute for Public Health and the Environment, which belongs to the Ministry of Health, Welfare and Sport of the Dutch government.</b> They offered a sponsorship to the Dutch iGEM teams based on an assignment titled ‘think before you do’, stimulating us to think about the societal implications that our project could have. We submitted a proposal and the RIVM offered us a €1500 grant to further our project.</div> | ||
<div><b>DSM is a science-based company focusing on health, nutrition and materials to drive sustainable innovation.</b> DSM is active in many different markets, including medicine, energy and food, so developments in synthetic biology are of major interest to them. For our project, they sponsored us with €1000.</div> | <div><b>DSM is a science-based company focusing on health, nutrition and materials to drive sustainable innovation.</b> DSM is active in many different markets, including medicine, energy and food, so developments in synthetic biology are of major interest to them. For our project, they sponsored us with €1000.</div> | ||
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<div class="sponsors_slider" style="width: 100%;"> | <div class="sponsors_slider" style="width: 100%;"> | ||
<div style="width: 150px;"><img src="https://static.igem.org/mediawiki/2017/e/e0/Uu17logo.png"></div> | <div style="width: 150px;"><img src="https://static.igem.org/mediawiki/2017/e/e0/Uu17logo.png"></div> | ||
| + | <div style="width: 250px;"><img src="https://static.igem.org/mediawiki/2017/8/85/Uu-jongealumninetwerk.png"></div> | ||
<div style="width: 300px;"><img src="https://static.igem.org/mediawiki/2017/e/e6/Uurivm.png"></div> | <div style="width: 300px;"><img src="https://static.igem.org/mediawiki/2017/e/e6/Uurivm.png"></div> | ||
<div style="width: 250px;"><img src="https://static.igem.org/mediawiki/2017/5/5b/Uudsm.jpeg"></div> | <div style="width: 250px;"><img src="https://static.igem.org/mediawiki/2017/5/5b/Uudsm.jpeg"></div> | ||
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Medium of the cells was analysed on a western blot to compare extracellular protein expression. | Medium of the cells was analysed on a western blot to compare extracellular protein expression. | ||
This tells us whether Cas9 and Cpf1 are truly being secreted or if they just leak out of the cells. | This tells us whether Cas9 and Cpf1 are truly being secreted or if they just leak out of the cells. | ||
| − | The results of this validation can be found on the <a onclick="return change_page(' | + | The results of this validation can be found on the <a onclick="return change_page('basic_part', 1)" href="basic_part">Parts Page</a> and the experimental page on <a onclick="return change_page('secretion', 1)" href="secretion">secreted Cas9 and Cpf1</a>. |
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In return, for the Wageningen team, we did a blind validation of some of their biobricks. | In return, for the Wageningen team, we did a blind validation of some of their biobricks. | ||
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"model": "modeling-and-mathematics", | "model": "modeling-and-mathematics", | ||
"improve": "", | "improve": "", | ||
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"basic_part": "", | "basic_part": "", | ||
"composite_part": "", | "composite_part": "", | ||
Revision as of 18:13, 1 November 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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