Team:Warwick/Human/Changes

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             <li> <a href = "/Team:Warwick/Interlab"> INTERLAB </a> </li>
             <li> <a href = "/Team:Warwick/Interlab"> INTERLAB </a> </li>
             <li> <a href = "/Team:Warwick/Attributions"> ATTRIBUTIONS </a> </li>
             <li> <a href = "/Team:Warwick/Attributions"> ATTRIBUTIONS </a> </li>
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             <li> <a href = "/Team:Warwick/Judging"> JUDGING </a> </li>
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h1>Project Specific Changes</h1><br><br>
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<h1>Project Specific Changes</h1> <br> </br>  
<p>As part of the project we looked to spread synthetic biology throughout the community. We approached this feat through several different avenues.</p>
<p>As part of the project we looked to spread synthetic biology throughout the community. We approached this feat through several different avenues.</p>
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<br> </br>
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Our project came into fruition after extensive debate and discussion, the idea of introducing a mechanism by which RNA can be propagated is both conceptually and theoretically appealing. Using our replicon system to target production of a siRNA directed against a target (DPP-IV) shows just one of many applications that our system holds.  
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<p>Our project came into fruition after extensive debate and discussion, the idea of introducing a mechanism by which RNA can be propagated is both conceptually and theoretically appealing. Using our replicon system to target production of a siRNA directed against a target (DPP-IV) shows just one of many applications that our system holds.  
Initially, it was not so straight forward when considering additional elements that we might require – for safety of the system was not on our minds. However, after due deliberation we decided to embark and ask questions and most importantly, seek answers.  
Initially, it was not so straight forward when considering additional elements that we might require – for safety of the system was not on our minds. However, after due deliberation we decided to embark and ask questions and most importantly, seek answers.  
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We started small and simple, with the obvious question on how people perceive our system?  
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We started small and simple, with the obvious question on how people perceive our system? </p>
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<p>We decided to conduct a Q + A session, in which academics, students and the wider public were in attendance. Whilst lots of interesting questions were raised, we collectively became stuck when faced with the following question: </p>
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<br> <p> <b>What have you done to ensure your system is safe?</b>  <br>
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We decided to conduct a Q + A session, in which academics, students and the wider public were in attendance.  
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Having reflected on this question, we realized that we failed to consider how our system would be safe - as one of the main applications of our system was to help treat Diabetes, we had to re-think and go back to the drawing board. We came up with two ideas which we feel will greatly improve the safety, but also the efficiency of our system </p>
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<br> <p> <ins>Aptazyme </ins>
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<br><br>
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<br> We decided to use a theophylline induced aptazyme, this essentially acts as a kill-switch if our system becomes unstable - it is possible to cleave our siRNA transcript and prevent our system from functioning. A general descriptor for the Aptazyme is below:
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What have you done to ensure your therapy is practical and safe?
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This specific question made us reconsider the design of our system; essentially we were initially going to create a replicon system that had no control on itself. We scratched our heads and came up with various different ways in which we could control our system, but at the same <br><br><br><br>
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<br> An aptazyme is an RNA based switch that operates by ribozyme-mediated cleavage of RNA. This part derives from Hartig et al., 2002 and requires the addition of theophylline to induce hammerhead ribozyme activation and cleavage, as depicted in Figure 1a. The part sequence is modified to contain a stop codon at the end, as an RBS is present. </p>  
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Lucie also spent some time in the lab, observing what lab work at undergraduate level looks like and the differences it bears to school. [Insert about what she did in lab]<br><br>We felt that this was a very beneficial way of approaching the issue of synthetic biology as there is currently talk about introducing topics within the GCSE and A-Level syllabi. We felt that by providing hands on experience we have given Lucie a “boost” in this respect, but also allowed her to open her options to perhaps continuing study within the field at university. By providing pathways such as this, it also allows the student to gain valuable experience to help with university applications within scientific fields and it was regretful that we could not have offered this opportunity to more students. [insert something Lucie said about how awesome we are and analyse in context]</p>
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<img style="width:70%;" align="middle" src="https://static.igem.org/mediawiki/2014/b/b5/Aptazyme.png " width="500" height="400"></center><br>
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<p><b>Raising awareness amongst students</b><br>
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<br> <p> <ins>MS2 </ins><br>In addition, we introduced another safety device, essentially this would rate limit the level of RNA dependent RNA polymerase (RdRp) production. Our design of RNA dependent RNA polymerase essentially incorporated an MS2 bacteriophage coat protein, linked via a P2A linker protein. A general descriptor for the part we used is below:
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MS2 bacteriophage coat protein part derives from Fussenegger et al., 2012. The MS2 coat protein binds a specific stem-loop structure, referred to as the MS2 box. This acts as a silencing mechanism of RNA through translational repression (Ni et al., 1995). The full sequence found in Fussenegger et al., 2012 has been retained, as previous analysis has indicated alteration of MS2 coat protein reduces cooperative protein-RNA binding (Uhlenbeck et al., 1995). MS2 is also frequently used in biochemical purification of RNA-protein complexes and is combined with GFP to detect RNA in living cells. <br> </p>  
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  <img class = "floatLeft" src="https://static.igem.org/mediawiki/2014/0/0f/Warwick_2014-09-08_16.49.29.jpg" width="360" height="228">
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  We also looked to create awareness amongst our peers. Although university students, we felt that most were not in fact alert to this new and emerging field of synthetic biology, and upon speaking with students through lecture shout-outs and social media. We discovered this was indeed true. As a result, we will be establishing a brand new society at the university, SynBioWarwick. <br><br>The aim of our society would be to promote synthetic biology amongst students but also across the local community by holding several types of events. These would range from obtaining guest speakers to speak on the subject to current PhD students giving talks on the subject of their dissertations. We would also look to increase knowledge about iGEM. We would very much like to share the experience with others, and as we were the first Warwick team, we would like to provide advice to the subsequent teams who will follow. To this end, we aim to hold talks about our project, to gauge interest, but also hold seminars and workshop classes to teach students the relevant skills prior to actually beginning their project in the summer. These would include classes on: practical lab work skills (such as: mini-prepping, loading gel, etc.) to modelling (such as: constructing systems of equations, looking through literature to find suitable parameters, etc.). <br><br>
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<img style="width:70%;" align="middle" src="https://static.igem.org/mediawiki/2014/6/64/Ms2.png" width="500" height="350"></center><br>
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We felt that by taking a two-pronged approach to this by first doing our “market research”, and then deciding to set up a society was a much better line to take. It allowed us to make an informed decision about whether it would be worth setting up a society, and also if we decided we would (as we did) it gives us support in our application by seeing so many people interested within the field. This also will line us up to help the wider local community because it is common for guest speaker talks to be aimed at the general public as well as at students. By doing this and establishing links, we will be able to hold said events with regularity, and thereby be able to increase public knowledge within a field little is currently known about.</p>
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<p><b>Survey</b><br>
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<br> <p> In the end, we were glad to have used and created two new parts for the iGEM registry - these parts ensure that any system similar to ours can be controlled. Check out the parts pages for more information on both the Aptazyme and the MS2 protein. We were very happy with the responses that we received when giving a SynBioCDT for new and upcoming PhD students - with the general consensus that our system looked both promising and safe. </br> </p>  
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<img class = "floatRight" src="https://static.igem.org/mediawiki/2014/a/a2/Warwick_Delivery.PNG" width="280" height="220">Our survey allowed us to explore questions pertaining to our project as well as to synthetic biology as a whole. Due to use of an online third party survey constructor, we were able to send the survey far and wide. We spread the survey through social media, through email amongst the university, to other iGEM teams and also across the world through strategically placed contacts the team had. <br><br>
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We will not talk much about the survey here as there is a whole section dedicated to the results obtained from it, however it was a very worthwhile exercise and I would encourage all iGEM teams to undertake a survey as part of their Policy & Practices, as it allows for the understanding and observation of responses from a wide collective. Moreover, with strategic questioning, there is a lot to gain and perhaps from an iGEM perspective even collaboration because we began talks with M.I.T. regarding delivery mechanisms for their project as a result of our survey.<br><br>For a full look at the responses we received, please see <a href = "https://static.igem.org/mediawiki/2014/9/93/Warwick_SurveySummary_10122014.xls"> here</a>.</p><br>
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<p><b>Reddit</b><br>We asked the IGEM subreddit "How comfortable would you be with modified bacteria or viruses being injected into you?" We had several interesting responses from members of other IGEM teams, which you can read <a href="http://www.reddit.com/r/iGEM/comments/2gun5r/how_comfortable_would_you_be_with_modified/">here</a>. Reddit user <a href="http://www.reddit.com/user/204027288">204027288</a> made a good point that made our team think about how mutations could be dangerous in our system, a problem that we hadn't thought about before.</p><p> Despite the detailed responses, the lack of responses was indicative of how the IGEM community on Reddit is still relatively new and developing. We hope that the subreddit can become more popular in the future, and act as a good space for the IGEM community to spread to.</p>
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Latest revision as of 02:19, 18 October 2014

Project Specific Changes



As part of the project we looked to spread synthetic biology throughout the community. We approached this feat through several different avenues.



Our project came into fruition after extensive debate and discussion, the idea of introducing a mechanism by which RNA can be propagated is both conceptually and theoretically appealing. Using our replicon system to target production of a siRNA directed against a target (DPP-IV) shows just one of many applications that our system holds. Initially, it was not so straight forward when considering additional elements that we might require – for safety of the system was not on our minds. However, after due deliberation we decided to embark and ask questions and most importantly, seek answers. We started small and simple, with the obvious question on how people perceive our system?

We decided to conduct a Q + A session, in which academics, students and the wider public were in attendance. Whilst lots of interesting questions were raised, we collectively became stuck when faced with the following question:


What have you done to ensure your system is safe?
Having reflected on this question, we realized that we failed to consider how our system would be safe - as one of the main applications of our system was to help treat Diabetes, we had to re-think and go back to the drawing board. We came up with two ideas which we feel will greatly improve the safety, but also the efficiency of our system


Aptazyme
We decided to use a theophylline induced aptazyme, this essentially acts as a kill-switch if our system becomes unstable - it is possible to cleave our siRNA transcript and prevent our system from functioning. A general descriptor for the Aptazyme is below:
An aptazyme is an RNA based switch that operates by ribozyme-mediated cleavage of RNA. This part derives from Hartig et al., 2002 and requires the addition of theophylline to induce hammerhead ribozyme activation and cleavage, as depicted in Figure 1a. The part sequence is modified to contain a stop codon at the end, as an RBS is present.



MS2
In addition, we introduced another safety device, essentially this would rate limit the level of RNA dependent RNA polymerase (RdRp) production. Our design of RNA dependent RNA polymerase essentially incorporated an MS2 bacteriophage coat protein, linked via a P2A linker protein. A general descriptor for the part we used is below: MS2 bacteriophage coat protein part derives from Fussenegger et al., 2012. The MS2 coat protein binds a specific stem-loop structure, referred to as the MS2 box. This acts as a silencing mechanism of RNA through translational repression (Ni et al., 1995). The full sequence found in Fussenegger et al., 2012 has been retained, as previous analysis has indicated alteration of MS2 coat protein reduces cooperative protein-RNA binding (Uhlenbeck et al., 1995). MS2 is also frequently used in biochemical purification of RNA-protein complexes and is combined with GFP to detect RNA in living cells.



In the end, we were glad to have used and created two new parts for the iGEM registry - these parts ensure that any system similar to ours can be controlled. Check out the parts pages for more information on both the Aptazyme and the MS2 protein. We were very happy with the responses that we received when giving a SynBioCDT for new and upcoming PhD students - with the general consensus that our system looked both promising and safe.