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| − | | + | STIR Protocol |
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| − | <h1> Project Description </h1>
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| − | <p> Our project idea is to develop a biosensor to detect the presence of the bacteria <i>Campylobacter</i>. This sensor will utilise the rare sugar xylulose, which is found in the polysaccharide capsule of campylobacter and is released when the bacteria is run through an acidic solution. By exploiting the mannitol operon that is present in the bacteria <i>Pseudomonas fluorescens</i> and expressing this in our chassis organism, <i>Escherichia Coli</i>, we will produce a biosensor that will express the reporter molecule Green Fluorescent Protein (GFP) when xylulose interacts with the repressor molecule of the mannitol operon. Additional sub-projects will include; investigating the quorum sensing mechanisms in <i>campylobacter</i> to increase the specificity of our sensor, developing hardware to produce a functioning biosensor and investigating the legal and ethical issues associated with our project.</p>
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| − | <p>The mannitol operon contains a promoter, Pe, which is regulated by xylulose, sorbitol and mannitol. The operon typically regulates the expression of genes required for mannitol consumption. By hijacking this xylulose regulated promoter we hope to develop a construct capable of activating GFP in the presence of xylulose. A schematic of the construct is shown in the diagram opposite. To provide increased specificity to our biosensor, we are aiming to detect autoinducer-2, a quorum sensing molecule released by <i>campylobacter</i>. We aim to insert the LsrA promotor followed by YFP into a plasmid which turns on when autoinducer-2 is present. For our proof of concept, we need to work with xylulose. However, xylulose is rare and, as such, is expensive. Therefore, we will synthesise xylulose by utilising a metabolic step in the bacterial pentose pathway. The enzyme Xylose Isomerase can be purified from E. coli, and used to convert the inexpensive sugar xylose in to xylulose.</p>
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| − | <p>For the engineering part of the project, we are aiming to build a functional biosensor that will be able to prove our construct. We will use technologies such as microfluidics and ultrafiltration to produce a sensor that will use our modified E.coli to give a visual indication of the presence of campylobacter. In terms of human practices, we will be adopting a double approach; one that focuses on the legal and political issues concerning EU legislation, which will affect our ability to manufacture a biosensor outside a properly licensed laboratory; and one on ethical issues concerning the impact that food safety has on human health. This second approach will mainly aim to raise awareness among the public on preventative measures in order to avoid campylobacter poisoning.</p>
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| + | ==Overview== |
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| − | <p>Tell us about your project, describe what moves you and why this is something important for your team.</p>
| + | This year, as part of our silver medal criteria, we decided to implement the STIR protocol into our project, which helped us to have a better understanding of how our work is going to affect several socio-political scenarios, and how these realms have affected our project. |
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| | + | In order to better implement the <b>Socio-Technical Integration Research (STIR) protocol </b> <ref>Arizona State University. (2016). Socio-Technical Integration Research (STIR). Available: https://cns.asu.edu/research/stir. Last accessed 19th Aug 2017</ref>, we contacted the STIR associate in the UK, Dr Paul Everest, in order to have a better overview of the processes that characterise the protocol. Even though we had previously read and examined the videos and reports that describe the protocol, we thought it would be valuable to have a human approach with someone who was directly involved in the implementation of STIR. Dr Everest accepted to speak to us and explained the typical features that distinguish the STIR protocol. |
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| − | <h5>What should this page contain?</h5>
| + | Dr Everest explained that STIR is entirely based on the idea of a collaboration between social and natural science. In order to achieve this, a joint effort was needed from both the social and the natural world, which could be created with the use of targeted questions that identified connections between the scientific project and how it could have had an impact on the rest of the world. |
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| − | <li> A clear and concise description of your project.</li>
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| − | <li>A detailed explanation of why your team chose to work on this particular project.</li>
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| − | <li>References and sources to document your research.</li>
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| − | <li>Use illustrations and other visual resources to explain your project.</li>
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| − | </ul>
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| | + | What was most interesting about the conversation with Dr Everest is that we realised that we were, almost unknowingly, already implementing the STIR protocol. Clearly the conversation with Dr Everest helped us refine the implementation and ask more structured questions, however we have been trying to create a bond between social and natural world since the very beginning of our project. Our team included members from a social science background as well as natural scientists, and this diversity has helped us to create a multi-dimensional approach that has benefitted the purpose of the project. |
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| + | In order to implement the STIR protocol in its full potential, we have also reviewed previous implementations of the protocol from previous iGEM teams and noticed how its implementations was mainly tied to the creation of the project idea. Teams in the past have engaged in the approach proposed by the protocol and used it to come up with an idea that complied with the STIR structure and was well-thought in terms of social aspects of the project. However, once a project idea was conceived, several teams have abandoned the STIR protocol structured approach to focus on a closer analysis of the socio-ethical aspects of the project. |
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| + | This, also according to Dr Everest, might cause the STIR protocol to lose its focus, since it is specifically characterised by a defined structure that should ideally be followed at every stage of the process. For this reason, not only did we implement the STIR protocol when choosing our project idea; but we also continued to adopt the same approach throughout the entire duration of the project. |
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| − | <h5>Advice on writing your Project Description</h5>
| + | We believe that the protocol, alongside other social analyses and reflections throughout our project, have helped us to achieve a project that has taken into full consideration several social, political, and economic aspects that will have an impact on our work, and also changed the way our project was conceived since its very inception. We considered the three main variables of the STIR protocol for both creating a project idea, but more importantly, for developing it. |
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| + | The variables we considered for integration were |
| − | We encourage you to put up a lot of information and content on your wiki, but we also encourage you to include summaries as much as possible. If you think of the sections in your project description as the sections in a publication, you should try to be consist, accurate and unambiguous in your achievements.
| + | *Learning and exploring societal dimensions of laboratory technical work |
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| + | *Capacity to anticipate societal dimensions |
| | + | *Bringing in alternative perspectives such as social and public values; ethical concerns; and stakeholder considerations. |
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| − | Judges like to read your wiki and know exactly what you have achieved. This is how you should think about these sections; from the point of view of the judge evaluating you at the end of the year.
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| + | For additional information on how we have implemented each of the mentioned variables please have a look at our gold medal criteria for human practices. |
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| − | | + | ==References== |
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| + | <small><references/></small> |
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| − | <h5>References</h5>
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| − | <p>iGEM teams are encouraged to record references you use during the course of your research. They should be posted somewhere on your wiki so that judges and other visitors can see how you thought about your project and what works inspired you.</p>
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| − | <h5>Inspiration</h5>
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| − | <p>See how other teams have described and presented their projects: </p>
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| − | <li><a href="https://2016.igem.org/Team:Imperial_College/Description">2016 Imperial College</a></li>
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| − | <li><a href="https://2016.igem.org/Team:Wageningen_UR/Description">2016 Wageningen UR</a></li> | + | |
| − | <li><a href="https://2014.igem.org/Team:UC_Davis/Project_Overview"> 2014 UC Davis</a></li> | + | |
| − | <li><a href="https://2014.igem.org/Team:SYSU-Software/Overview">2014 SYSU Software</a></li>
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Overview
This year, as part of our silver medal criteria, we decided to implement the STIR protocol into our project, which helped us to have a better understanding of how our work is going to affect several socio-political scenarios, and how these realms have affected our project.
In order to better implement the Socio-Technical Integration Research (STIR) protocol [1], we contacted the STIR associate in the UK, Dr Paul Everest, in order to have a better overview of the processes that characterise the protocol. Even though we had previously read and examined the videos and reports that describe the protocol, we thought it would be valuable to have a human approach with someone who was directly involved in the implementation of STIR. Dr Everest accepted to speak to us and explained the typical features that distinguish the STIR protocol.
Dr Everest explained that STIR is entirely based on the idea of a collaboration between social and natural science. In order to achieve this, a joint effort was needed from both the social and the natural world, which could be created with the use of targeted questions that identified connections between the scientific project and how it could have had an impact on the rest of the world.
What was most interesting about the conversation with Dr Everest is that we realised that we were, almost unknowingly, already implementing the STIR protocol. Clearly the conversation with Dr Everest helped us refine the implementation and ask more structured questions, however we have been trying to create a bond between social and natural world since the very beginning of our project. Our team included members from a social science background as well as natural scientists, and this diversity has helped us to create a multi-dimensional approach that has benefitted the purpose of the project.
In order to implement the STIR protocol in its full potential, we have also reviewed previous implementations of the protocol from previous iGEM teams and noticed how its implementations was mainly tied to the creation of the project idea. Teams in the past have engaged in the approach proposed by the protocol and used it to come up with an idea that complied with the STIR structure and was well-thought in terms of social aspects of the project. However, once a project idea was conceived, several teams have abandoned the STIR protocol structured approach to focus on a closer analysis of the socio-ethical aspects of the project.
This, also according to Dr Everest, might cause the STIR protocol to lose its focus, since it is specifically characterised by a defined structure that should ideally be followed at every stage of the process. For this reason, not only did we implement the STIR protocol when choosing our project idea; but we also continued to adopt the same approach throughout the entire duration of the project.
We believe that the protocol, alongside other social analyses and reflections throughout our project, have helped us to achieve a project that has taken into full consideration several social, political, and economic aspects that will have an impact on our work, and also changed the way our project was conceived since its very inception. We considered the three main variables of the STIR protocol for both creating a project idea, but more importantly, for developing it.
The variables we considered for integration were
- Learning and exploring societal dimensions of laboratory technical work
- Capacity to anticipate societal dimensions
- Bringing in alternative perspectives such as social and public values; ethical concerns; and stakeholder considerations.
For additional information on how we have implemented each of the mentioned variables please have a look at our gold medal criteria for human practices.
References
- ↑ Arizona State University. (2016). Socio-Technical Integration Research (STIR). Available: https://cns.asu.edu/research/stir. Last accessed 19th Aug 2017
