Difference between revisions of "Team:Oxford/Applied Design"

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<span id="header-lightbox-title">APPLIED DESIGN</span>
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<span id="header-lightbox-title">MEET THE TEAM</span>
 
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     <h1>Applied Design</h1>
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    <img class="img-responsive img-circle team-member-img alissa_open" src="https://static.igem.org/mediawiki/2017/1/13/T--oxford--team--alissa--circle.jpeg">
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    <span id="profile_caption"> Alissa Hummer </span>
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    <div class="subject-icon bioch"></div>
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<b>Alissa Hummer</b> (Biochemistry)<br/>
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<i>Co-leader<br/>
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She. cruzi</i><br/>
  
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    <h2>Introduction</h2>
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Alissa spends most of her iGEM days split between the wet lab, working with the engineers on mathematical modelling, and doing organizational things because she loves pretty much everything. Her experience in other labs prior to iGEM is invaluable to the team, because she knows all of the tips and tricks for efficient research. Outside of iGEM she enjoys playing football, being in nature, and reading.
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    iGEM encourages all teams to take their projects beyond the lab and to take a holistic approach to design. The question “What is our real world problem?” has been a key consideration from the beginning, and has guided our project throughout the summer.
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To  put our diagnostic device into context, we considered various aspects including safety, accessibility and socioeconomic factors in Latin America. Many design iterations were built upon over the course of the summer, influenced by discussions with experts from a range of disciplines, including blood coagulation, microfluidics and general diagnostic devices.</p>
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Having thoroughly examined and evaluated various design options, we propose a final design for our system which fulfills our criteria for a suitable diagnostic device.
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     <h2>Developing Our Design</h2>
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     <h3>Criteria for a suitable diagnostic device: considerations from the OpenPlant Forum</h3>
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    Our early design criteria was influenced by research into the challenges of designing new healthcare technologies in developing countries. Our research indicated that important considerations included the level of infrastructure present, the cost to the end-user and the amount of training required.
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    <img class="img-responsive img-circle team-member-img angela_open" src="https://static.igem.org/mediawiki/2017/a/a5/T--oxford--team--angela--circle.jpeg">
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    <span id="profile_caption"> Angela Hellyer </span>
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    <div class="subject-icon bioch"></div>
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  <p> In order to gain an insight into various aspects of synthetic biology, members of our team attended the OpenPlant Forum in Cambridge, UK. Dr Tempest van Schaik gave a talk titled ’Designing Diagnostics’, using her expertise in the development of bench-to-bedside healthcare technologies and importance of the end-user experience.</p>
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From her talk, 3 key points stood out to us:
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    <ol>
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<b>Angela Hellyer</b> (Biochemistry)<br/>
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        <li>Understand your analyte</li>
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<i>Wet Lab Co-ordinator &amp; Safety<br/>
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        <ol>
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G. weazli</i><br/>
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            <li>What is the context in which the kit will be understood?</li>
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            <li>How exactly does taking blood work? Will we transport the blood to a different place, or do a spot-test by the bedside?</li>
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        <li>Understand the users of the kit</li>
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        <ol>
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            <li>How will they be given the kit?</li>
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            <li>Will they want to use it?</li>
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            <li>Do they want it?</li>
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        <li>Understand the diagnosis procedure</li>
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        <ol>
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            <li>What problems are encountered from an end-user perspective?</li>
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            <li>Can we simulate a diagnostics procedure to discover any issues?</li>
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        </ol>
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    <p><br>
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    After discussing these findings as a team, we proposed a set of general criteria to guide our initial design brainstorming.
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    </p>
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Angela doesn’t really know how she ended up being in charge of safety, it kind of just happened when she wasn’t looking. Creator of the cake rota, she likes to keep things light, and provides some moral support for when things inevitably go wrong; only to be fixed promptly of course! Outside of iGEM she enjoys food and all things astro-, along with being Zoe F’s main Hogwarts buddy.
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    <h3>Our 4E’s Applied Design Framework</h3>
 
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    Applied design is an important component of most iGEM projects, and requires an integrated and holistic approach to ensure projects are considered from a ‘real-world’ perspective. Based on our findings from OpenPlant and research, the Oxford iGEM 2017 team came up with a framework for considering applied design - the 4 E’s (‘Effectiveness’, ‘Ease of use’, ‘Economics’ and ‘Environment &amp; Safety’).
 
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    This provides a structured method for applied design considerations, and we hope that this framework may prove useful for future iGEM teams.
 
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            <div class="four-e-box" style="background: rgb(190,15,52)">Effectiveness</div>
 
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            <ul>
 
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                <li>How long will it take to get a clear result?</li>
 
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                <li>How will we ensure the test it sensitive and specific?</li>
 
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                <li>How can we ensure it can be used at the bedside?</li>
 
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            <div class="four-e-box" style="background: rgb(72,145,220)">Ease of Use</div>
 
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            <ul>
 
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                <li>What equipment would be necessary to use it?</li>
 
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                <li>How can we present the result clearly?</li>
 
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                <li>What level of training would be required for the end-user?</li>
 
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            <div class="four-e-box" style="background: rgb(207,122,48)">Economics</div>
 
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            <ul>
 
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                <li>What materials will be used?</li>
 
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                <li>Will it be feasible to transport our device in large quantities?</li>
 
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                <li>How can we alter it to reduce the cost?</li>
 
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            <div class="four-e-box" style="background: rgb(170,179,0)">Environment &amp; Safety</div>
 
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                <li>Can we reduce risks associated with using GMOs in healthcare technologies?</li>
 
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                <li>How can we ensure our product is sustainable and environmentally friendly?</li>
 
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                <li>How will the end-user dispose of any used materials?</li>
 
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<center><h6>Figure 1: Four E's framework for Applied Design</h6></center>
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    <img class="img-responsive img-circle team-member-img arthur_open" src="https://static.igem.org/mediawiki/2017/f/f7/T--oxford--team--arthur--circle.jpeg">
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    <span id="profile_caption"> Arthur Norman </span>
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<b>Arthur Norman</b> (Biochemistry)<br/>
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<i>Co-leader<br/>
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T. freezi</i><br/>
  
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    <h3>Cell-free Systems</h3>
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Arthur has been dubbed ‘freezer boy’, and his super powers include being able to organise freezer boxes without them thawing and the ability to tidy away everyone else’s eppendorfs. Arthur spends his time split between working in the lab and coming up with novel ideas for the project. When outside the lab he plays tennis, runs, and drinks pimms, sometimes all three at the same time.
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    One of the first things we realised when planning our kit was that a cell based diagnostic would require a cold chain for transportation and maintenance of the culture once they had arrived in location and were being used for the kit. Whilst exploring the recent advantages in the synthetic biology literature we discovered a paper from Pardee at al. (2016), describing a method for freeze-drying cell lysate for use as a cell-free transcription-translation system. This was perfect, as there was no need for a cold chain, and the lysate could be produced cheaply and easily. At the open plant forum we received lots of ideas from talks by Jim Swartz and Keith Pardee. We discussed our project further with Keith Pardee, who gave us lots of practical advice on designing an optimal circuit for cell-free expression, influencing are decision to add pre-synthesised TetR to our kit rather than producing it in our kit, as we’d originally planned on doing.
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    </p>
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    <p>After further reading, including papers from Garamella et. al (2016), we improved the theoretical design of our kit by discovering that we could use linear DNA from a PCR reaction for our kit, rather than plasmid DNA therby almost eliminating the risk of environmental contamination, because bacteria will not take linear DNA up as easily as a plasmid.
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    <p>The final DNA-based part of the kit would be:</p>
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    <ul>
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        <li>Cell lysate, which can be mass-produced</li>
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        <li>PCR product ofr our circuitry thtat produces the TEV protease,</li>
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        <li>The TetR with the specific cleavage sequence that will be produced separately and added to the reaction.</li>
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    <p>These would all be freeze-dried in the well of our kit.</p>
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<p>During our research into cell-free, we noted a lack of information regarding its use in the field. This led us to produce a report on cell-free technology, which you can find below.<p>
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    <img class="img-responsive img-circle team-member-img chun_open" src="https://static.igem.org/mediawiki/2017/7/74/T--oxford--team--chun--circle.jpeg">
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    <span id="profile_caption"> Chun Ngai Au </span>
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<b>Chun Ngai Au</b> (Engineering)<br/>
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<i>Dry Lab Co-ordinator<br/>
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T. snoozi</i><br/>
  
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<p> <center> <a href="https://2017.igem.org/Team:Oxford/Cell_Free_Report"><img class="img-responsive" width="200px;" src="https://static.igem.org/mediawiki/2017/f/fc/Cell_free_report.png"></a></center></p>
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Chun likes creating colourful and cool looking graphs on Matlab, although he isn’t totally against putting on a lab coat and pipetting a couple of things every now and again. He put in a lot of work at the beginning of the project to catch up on the biochemistry, but is now as knowledgable as the rest of us. Outside of iGEM, he likes to play Ultimate, sleep, and eat spicy food - even his pizzas tend to have chillies on them.
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<p> <center><img class="img-responsive" width="1000px;" src="https://static.igem.org/mediawiki/2017/3/31/T--oxford--applied--design--fig3.jpg"></a><h6>Figure 2: A diagram showing the production process for cell-free technology</h6></center></p>
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     <h3>Initial Design Iterations</h3>
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     Our starting point involved the detection of cruzipain in a sample of blood, however we needed to design an output system and a method for reading the output. By applying our criteria to a cell-free diagnostic system, we were able to propose some early design options. We discussed these as a group, compared the relative merits of each, and decided which would be most suitable to carry on with.
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     <span id="profile_caption"> Helen Siyu Ren </span>
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<b>Helen Siyu Ren</b> (Engineering)<br/>
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<i>Dry Lab Co-ordinator<br/>
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Si. yuzi</i><br/>
  
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    <h4>Early Stage: Output Ideas</h4>
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As one of the few non-bio students, Helen is learning new things in the wet lab while spending the rest of time staring at her laptop doing wiki pages and trying to implement the complicated model that comes with all of our many parts. She is one of those people who really likes to sit on the floor, where her free time is spent reading, playing bridge, and eating delicious food she made earlier.
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<h6>Table 1: Pros and Cons of initial output ideas</h6>
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                    <th>Color Dye</th>
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                        <li>Many current spot tests use colour as an indicator</li>
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                        <li>Clear presentation of the result</li>
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                        <li>Possible to design bacteria to produce a clotting inhibitor</li>
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                        <li>Can perform test on blood sample without requiring preparation</li>
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                <th>Disadvantages</th>
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                        <li>Difficult to distinguish against the colour of blood</li>
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                        <li>Can't isolate plasma easily</li>
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                        <li>May be difficult to visualise clotting</li>
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                        <li>Result may be too subjective</li>
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    From our research we found that the ‘clot-buster’ drug streptokinase is naturally produced by bacteria inspiring us to use the properties of blood to our advantage: our output could interfere with the blood clotting system to produce a result.
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    With a coloured dye output, visualisation of the result would require the plasma to be isolated; this would increase the complexity and cost of the test.
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    Furthermore, a key goal for our applied design was to ensure it could be used in a scenario with minimal training and limited resources. Findings from the National Congenital Chagas Program in Bolivia (2004-2009) showed that follow-up after diagnosis was a major difficulty in controlling the disease; as such, an immediate bedside test would be most ideal. Isolation of plasma would require resources which may not be available at the bedside/in all healthcare settings.
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    Having reviewed these two options, we came to the conclusion that a system based around blood clotting as an output would be most suitable.
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+
  
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     <h4>Late Stage: Ideas to measure blood clotting output</h4>
+
     </div>
−
<h6>Table 2: Potential ideas for measuring output</h6>
+
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−
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+
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    <img class="img-responsive img-circle team-member-img jei_open" src="https://static.igem.org/mediawiki/2017/e/e6/T--oxford--team--jei--circle.jpeg">
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            <thead>
+
    <span id="profile_caption"> Jei Diwakar </span>
−
                <tr>
+
    <div class="subject-icon bioch"></div>
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                    <th>Blood Collection Tube</th>
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                    <th>Microfluidics</th>
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<img class="img-responsive img-circle" src="https://static.igem.org/mediawiki/2017/e/e6/T--oxford--team--jei--circle.jpeg">
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            </thead>
+
<b>Jei Diwakar</b> (Biochemistry)<br/>
−
            <tr>
+
<i>Wet Lab Co-ordinator &amp; Treasurer<br/>
−
                <th>Advantages</th>
+
T. schmoozi</i><br/>
−
                <td>
+
−
                    <ul>
+
−
                        <li>Equipment is easy to obtain</li>
+
−
                        <li>Relatively cheap</li>
+
−
                        <li>Would fit into current infrastructure</li>
+
−
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+
−
                </td>
+
−
                <td>
+
−
                    <ul>
+
−
                        <li>Provides a quantitative measure of coagulation</li>
+
−
                        <li>Decreases analysis time</li>
+
−
                        <li>Can use a smaller volume of blood (fingerprick)</li>
+
−
                    </ul>
+
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    </table>
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    <p></p>
+
−
    <ul>
+
−
        <li>Blood Collection Tube: Our research showed that most blood collection tubes are lined with anticoagulation factors, in order to prevent blood from clotting. This inspired us to produce a collection tube lined with our freeze-dried cell-free system.</li>
+
−
        <li>Microfluidics: Two papers published by Steckl et al. (Lab on a Chip 2014, Biomedical Microdevices 2017) inspired us to consider a new method to screen for blood coagulation. Steckkl and colleagues presented a cheap, point-of-care blood coagulation assay, which utilised microfluidics in a paper-based device.</li>
+
−
    </ul>
+
−
    <p></p>
+
−
    <p>
+
−
    Whilst simple, we decided that the blood collection tube method may not produce a clear result, which was an important consideration.
+
−
    </p>
+
  
−
    <h3>Blood-clotting System: Hirudin vs Bivalirudin</h3>
+
Jei’s role means that sending emails and adding SUM functions to Excel have become routine to him. He spends most of his time doing wet lab work, unless he is organising flights and hotels, then he is on the phone all day! Outside of the lab, Jei plays a lot of cricket for the Oxford University Cricket Club and also is a co-founder of the Oxford University Biotech Society.  
−
    <p>
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    Hirudin is a 65-amino acid peptide produced by leeches, and is used widely in the medical field as an anticoagulant. It is mass produced and purified using recombinant technology; initially hirudin was proposed as the output of our DNA/OMV systems, as recombinant hirudin expression in E. coli was shown to be efficient from the literature.
+
     <br/>
−
    </p>
+
−
    <p>
+
−
    Applying our 4E’s framework to our decision to use hirudin led us to explore cost-friendly alternatives. We came across bivalirudin, a congener of hirudin with a similar mechanism of action. However, importantly, bivalirudin is a smaller peptide at only 20-amino acids in length. As a result, our cost analysis showed that it would be cheaper to synthesise bivalirudin chemically than to produce hirudin recombinantly. This cost-difference provides a significant advantage in ensuring maximal availability of our kit.
+
−
     </p>
+
  
−
     <h3>Integrating Our Ideas Into A Design</h3>
+
     </div>
−
     <p>
+
    </div>
−
We began by sketching ideas on paper and sharing our thoughts during a group meeting. Following advice from Dr Tempest van Schaik, we produced a simple cardboard model of our design to view it from the end-user’s perspective. This guided some key changes for example our design originally included positive control and negative control indicators, but we realised that this created a bulky, complicated device requiring three blood samples, and would increase our costs.  
+
     <div class="col-sm-3">
 +
    <img class="img-responsive img-circle team-member-img john_open" src="https://static.igem.org/mediawiki/2017/6/69/T--oxford--team--john--circle.jpeg">
 +
    <span id="profile_caption"> John Myers </span>
 +
    <div class="subject-icon bioch"></div>
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        <!-- Add content to the popup -->
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<img class="img-responsive img-circle" src="https://static.igem.org/mediawiki/2017/6/69/T--oxford--team--john--circle.jpeg">
 +
<b>John Myers</b> (Biochemistry)<br/>
 +
<i>Secretary<br/>
 +
Oui. cruzi</i><br/>
  
−
Ultimately, we determined that by keeping the device as streamlined and inexpensive as possible, healthcare professionals using the kit could simply repeat the test for any inconclusive results.</p>
+
John keeps track of the team’s regular meetings and is enthusiastic about outreach. Often he can be found helping out in the lab, learning all of the protocols in detail. Outside of iGEM, he rows for his college, plays the violin, and cooks - very useful for the team’s weekly cake rota. He also introduced a large chunk of the team to Bridget Jones, for which we are all eternally grateful.
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    <br/>
  
−
<h2>Current Kit</h2>
+
    </div>
−
<p>Our current kit meets our criteria established from our 4E’s framework: it is effective, easy-to-use, economically viable and environmentally safe. A prototype version was designed using CAD software and 3D printed.</p>
+
    </div>
−
<br>
+
    <div class="col-sm-3">
−
<p> <center> <img class="img-responsive";" width="1000px" src="https://static.igem.org/mediawiki/2017/2/2c/T--oxford--kitlabelled.png"><h6>Figure 3: Annotated diagram of our kit</h6>
+
    <img class="img-responsive img-circle team-member-img kushal_open" src="https://static.igem.org/mediawiki/2017/e/ea/T--oxford--team--kushal--circle.jpeg">
−
</center></p>
+
    <span id="profile_caption"> Kushal Mansatta </span>
−
<br>
+
    <div class="subject-icon med"></div>
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<img class="img-responsive img-circle" src="https://static.igem.org/mediawiki/2017/e/ea/T--oxford--team--kushal--circle.jpeg">
 +
<b>Kushal Mansatta</b> (Medicine)<br/>
 +
<i>Wiki Co-ordinator &amp; Social Sec<br/>
 +
He. curezi</i><br/>
  
−
<h3>Using the kit<h3>
+
By day Kushal can usually be found browsing the wiki or reminding people to reference EVERYTHING they read; by night he makes sure everyone on the team has fun and eats well. His medical background has been invaluable for our diagnostic track. Outside of iGEM, he enjoys going to the gym and caring for patients at his job on a hospital ward.
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 +
    <br/>
  
−
<p> <center> <img class="img-responsive";" src="https://static.igem.org/mediawiki/2017/e/e8/T--oxford--applieddesignflowchart.png"><h6>Figure 4: Diagnostic Procedure Flowchart</h6>
+
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−
</center></p>
+
    </div>
 +
</div>
  
−
<h3>Review of our kit by healthcare professionals</h3>
+
<div class="row">
 +
    <div class="col-sm-3">
 +
    <img class="img-responsive img-circle team-member-img noah_open" src="https://static.igem.org/mediawiki/2017/1/12/T--oxford--team--noah--circle.jpeg">
 +
    <span id="profile_caption"> Noah Sprent </span>
 +
    <div class="subject-icon bioch"></div>
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        <!-- Add content to the popup -->
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    <div id="noah" class="popup_box">
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 +
<img class="img-responsive img-circle" src="https://static.igem.org/mediawiki/2017/1/12/T--oxford--team--noah--circle.jpeg">
 +
<b>Noah Sprent</b> (Biochemistry)<br/>
 +
<i>Co-leader<br/>
 +
No. shoezi</i><br/>
  
−
<p>We presented our prototype model to two healthcare professionals in order to re-evaluate our current kit. Recommendations gathered would be implemented into the future versions of our kit.</p>
+
Noah loves making agendas for meetings and reading about definitely-not-useless features on Benchling when he’s not keeping our lab beautifully clean. Although life outside of iGEM isn’t really life at all, Noah is a co-founder of the Oxford University Biotech Society, tries to do cool things with the Oxford University Gymnastics Club, and has confusing discussions with his philosopher housemates.
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 +
    <br/>
  
−
<h4>Mrs Sarah Dragonetti (Registered Nurse)</h4>
+
    </div>
 +
    </div>
 +
   
 +
    <div class="col-sm-3">
 +
    <img class="img-responsive img-circle team-member-img sumaera_open" src="https://static.igem.org/mediawiki/2017/2/2f/T--oxford--team--sumaera--circle.jpeg">
 +
    <span id="profile_caption"> Sumaera Rathore </span>
 +
    <div class="subject-icon bio"></div>
 +
        <!-- Add content to the popup -->
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    <div id="sumaera" class="popup_box">
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<img class="img-responsive img-circle" src="https://static.igem.org/mediawiki/2017/2/2f/T--oxford--team--sumaera--circle.jpeg">
 +
<b>Sumaera Rathore</b> (Biology)<br/>
 +
<i>iGEM Requirements Co-ordinator<br/>
 +
Tea. brewzi</i><br/>
  
−
Findings:
+
Sumaera puts the 'bio' into 'biochem' and is responsible for ensuring our project ticks all the boxes in the judging booklet so we can really impress the judges with all our hard work. She also knows a lot more about parasites than the rest of us. Outside of iGEM, Sumaera enjoys anything to do with plants, tea, and chocolate. In fact, she brightened up our iGEM desks with a collection of aloe plants!
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<ul>
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<li> Flat, rectangular pipette hole fits well
+
    <br/>
−
<li> Timestrip would be a useful tool during busy periods
+
−
<li> Good size and good shape - feels intuitive
+
−
<li> A window would allow you to see whether the pipette was emptied, preventing someone from accidentally drawing blood back up
+
−
<li> A red case would make it difficult to see the blood through the window, so white or translucent casing would be better
+
−
<li> Unclear on actual device when to click together the two components
+
−
<li> Unclear whether pipette should stay in kit or be taken out (and when)
+
−
</ul>
+
  
−
<h4>Dr Ben Riley (General Practice)</h4>
+
    </div>
 +
    </div>
 +
   
 +
    <div class="col-sm-3">
 +
    <img class="img-responsive img-circle team-member-img zoec_open" src="https://static.igem.org/mediawiki/2017/8/81/T--oxford--team--zoec--circle.jpeg">
 +
    <span id="profile_caption"> Zoë Catchpole </span>
 +
    <div class="subject-icon bioch"></div>
 +
        <!-- Add content to the popup -->
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    <div id="zoec" class="popup_box">
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    <button type="button" class="zoec_close close_button"><span class="glyphicon glyphicon-remove"></span></button>
 +
<img class="img-responsive img-circle" src="https://static.igem.org/mediawiki/2017/8/81/T--oxford--team--zoec--circle.jpeg">
 +
<b>Zoë Catchpole</b> (Biochemistry)<br/>
 +
<i>Outreach &amp; Human Practices<br/>
 +
Cant. choozi</i><br/>
  
−
Findings:
+
Zoe wants to show everyone that synbio is as cool as she thinks it is by designing ‘fun’ activities for outreach, and is key to co-ordinating all of our meetings with experts from across the globe. She is always keen to pitch in with the lab work too. Outside of iGEM she has grade 8 recorder, but unfortunately serenading our E. coli hasn’t yet helped our transformation efficiency!
−
<ul>
+
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−
<li> Kit is sealed so no worry about blood containment
+
    <br/>
−
<li> Ideal cost should be comparable to a one-use diabetes test strip (~£3)
+
−
<li> Size and shape is good for packaging and transport
+
−
<li> Distinctive shape will make it easy to identify
+
−
</ul>
+
−
These were very useful comments: they support some aspects of our current design, but also propose some changes which would further improve the end-user experience.
+
  
−
<h4>Overall recommendations:</h4>
+
    </div>
−
<ul>
+
    </div>
−
<li> Make the case transparent: prevents pipette errors but is more cost-effective than a window
+
   
−
<li> Make the key instructions as clear as possible, and include these within the kit
+
    <div class="col-sm-3">
−
<li> Evaluate the cost of the device (which we have presented below)
+
    <img class="img-responsive img-circle team-member-img zoef_open" src="https://static.igem.org/mediawiki/2017/e/eb/T--oxford--team--zoef--circle.jpeg" alt="" >
−
</ul>
+
    <span id="profile_caption"> Zoe Ford </span>
 +
    <div class="subject-icon bioch"></div>
 +
        <!-- Add content to the popup -->
 +
    <div id="zoef" class="popup_box">
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 +
<img class="img-responsive img-circle" src="https://static.igem.org/mediawiki/2017/e/eb/T--oxford--team--zoef--circle.jpeg">
 +
<b>Zoe Ford</b> (Biochemistry)<br/>
 +
<i>Wet Lab Co-ordinator &amp; Social Media<br/>
 +
'Wee'. cruzi</i><br/>
  
−
<h2>Integration of our kit into society</h2>
+
Zoe enjoys spending endless hours in the lab pipetting clear liquids from one tube into another. Along with being our Queen of SnapGene, they love taking pictures of everything and everyone to make the prettiest iGEM Instagram account in history. Outside of iGEM they referee quidditch, sing in choirs, and use a lot of their free time in the evenings cross-stitching everything - including our logo!
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<br>
+
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We consider integration of our device into existing healthcare systems and current infrastructure a key challenge, and therefore a fundamental aspect of our applied design considerations.
+
    <br/>
  
−
<h3>Dialogue with Juan Solano and Alfons Van Woerkom of The Global Fund</h3>
+
    </div>
 +
    </div>
 +
</div>
  
−
We contacted Juan Solano and Alfons Van Woerkom of The Global Fund, an international financing organisation which has worked to fund several large-scale projects in the fight against HIV/AIDS, TB and malaria. They introduced us to the concept of market and financial analyses, in order to outline opportunities for a new diagnostic to come to market and to optimise its implementation. We reviewed a set of key points:<br>
+
</div>
  
−
<ul>
+
<div class="container-fluid" id="supervisor-container">
−
<li> Existing diagnostics on the market
+
<div class="container">
−
<li> Information on the size of the market
+
−
<li> Regulatory framework of the country
+
−
<li> Well documented details of the unit cost
+
−
<li> Well documented details of the phases of production
+
−
<li> Delivery aspects (materials, transaction costs, depreciation)
+
−
</ul><br>
+
  
−
This will allow an optimal pricing strategy to be determined at the level of the product and its users. Furthermore, it provides recommendations to potential investors regarding the product’s investment feasibility.
+
<div class="row">
 +
    <div class="col-sm-12" id="supervisor-header">
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        <center><span>Supervisors</span></center>
 +
    </div>
 +
</div>
  
 +
<div class="row supervisor">
 +
    <div class="col-sm-3 supervisor-img">
 +
        <img class="img-responsive" src="https://static.igem.org/mediawiki/2017/0/01/T--oxford--team--george--circle.jpg">
 +
    </div>
 +
    <div class="col-sm-9 supervisor-description">
 +
    <b>Dr. George Wadhams</b><br />
 +
    <i>Oxford Department of Biochemistry</i><br /><br />
 +
    George's research interests lie in how bacteria sense and integrate environmental information. His group focuses on understanding in a quantitative manner how multiple, homologous pathways operate in individual cells and how the components of these pathways can be used to create synthetic pathways.<br />
 +
    George has been mentoring Oxford iGEM teams since they were founded in 2014.
 +
    </div>
 +
</div>
  
−
  <h3> Cost </h3>
 
−
    For costing of our kit we were aided by contact with David Sprent, an expert in International Supply Chain, and Juan Solano and Alfons Van Woerkom of the Global Fund. They helped us with costing, but also with the considerations that have to be taken into account when importing products into Latin America. We used Bolivia as a case study, and imagined what the situation would look like if the country were to adopt our kit wholesale, testing all 163,000 babies born every year. The kit would be manufactured in the UK and then transported to Bolivia, as according to <a href="https://2016.export.gov/industry/health/healthcareresourceguide/eg_main_092224.asp">Export.gov</a> as of 2014 there was no local production of pharmaceuticals.
 
−
    <h4> Materials </h4>
 
−
    <a href="#demo" class="btn btn-info" data-toggle="collapse"><center>Table of Costs<br>Click to expand</center>
 
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−
                  <th>Component</th>
 
−
                  <th>Cost Per Kit ($)</th>
 
−
                  <th>Source </th>
 
−
              </tr>
 
−
          </thead>
 
−
          <tr> <td> Bivalirudin </td> <td> 0.007 </td> <td> <a href="http://www.selleckchem.com/custom-peptide-synthesis.html">Cost (Selleckchem)</a> </br> (Modelling told us we needed 50uM) </td></tr>
 
−
          <tr> <td> Sodim Citrate </td> <td> 1.23^10-9 </td> <td><a href="https://www.researchgate.net/post/How_much_38_citrate_do_we_need_to_add_to_anticoagulate_blood_for_platelet_rich_plasma">Amount</a> </br>
 
−
            <a href="http://www.sigmaaldrich.com/catalog/product/aldrich/w302600?lang=en&region=GB">Cost (Sigma Aldrich) </a>
 
−
              </td></tr>
 
−
          <tr> <td> Calcium </td> <td> 0.00311 </td> <td><a href="http://onlinelibrary.wiley.com/doi/10.1046/j.1538-7836.2003.00075.x/full">Amount</a> </br>
 
−
            <a href="http://www.sigmaaldrich.com/catalog/product/aldrich/449709?lang=en&region=GB">Cost (Sigma Aldrich)</a>
 
−
              </td></tr>
 
−
          <tr> <td> Tissue Factor </td> <td> 8.78*10^-9 </td> <td><a href="http://onlinelibrary.wiley.com/doi/10.1046/j.1538-7836.2003.00075.x/full">Amount</a> </br>
 
−
            <a href="http://www.abcam.com/recombinant-human-tissue-factor-protein-ab119148.html">Cost (abcam)</a>
 
−
              </td></tr>
 
−
          <tr> <td> Capillary Tube </td> <td> 0.074 </td> <td> <a href="http://www.sigmaaldrich.com/catalog/product/aldrich/z611182?lang=en&region=GB">Cost (Sigma Aldrich)</a></td></tr>
 
−
          <tr> <td> Injection Molding of Kit </td> <td> 0.685 </td> <td> <a href="http://www.custompartnet.com/estimate/injection-molding/?units=1">Cost (CustomPartNet)</a></td></tr>
 
−
          <tr> <td> Cardboard Box (70x30x50mm) </td> <td> 0.1 </td> <td> <a href="https://www.abcpackaging.co.uk/">ABCPackaging</a></td></tr>
 
−
          <tr> <td> Microsafe Pipette </td> <td> 0.15 </td> <td> <a href="http://www.safe-tecinc.com/microsafe.htm">Cost (Safe-Tec)</a></td></tr>
 
−
          <tr> <td> Timestrip </td> <td> 0.11 </td> <td> <a href="http://timestrip.com/">Cost (Timestrip)</a></td></tr>
 
−
          <tr> <td> Printed Instructions </td> <td> 0.021 </td> <td> <a href="">?</a></td></tr>
 
−
          <tr> <td> TetR </td> <td> 8.25*10^-5 </td> <td> <a href="https://www.mybiosource.com/prods/Recombinant-Protein/Tetracycline-repressor-protein-class-B-from-transposon-Tn10/tetR/datasheet.php?products_id=1056262">Cost (MyBioSource)</a> </br> (Modelling told us we needed 100nM)</td></tr>
 
−
          <tr> <td> Cell Lysate for DNA Reaction </td> <td> 0.9 </td> <td> <a href="http://www.cell.com/cell/fulltext/S0092-8674(16)31246-6?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867416312466%3Fshowall%3Dtrue">Pardee et al. (2016)</a></td></tr>
 
−
          <tr> <td> DNAse 1 Inhibitor </td> <td> 0.007 </td> <td> <a href="http://www.molcells.org/journal/view.html?year=2005&volume=19&number=1&spage=54">Choi et al. (2005) </br> Cost was assumed same as bivalirudin</a></td></tr>
 
−
          <tr> <td> <b> Total Cost </B> </td> <td> <b> 2.06 </b> </td></tr>
 
−
        </tbody>
 
−
    </table>
 
−
  </div>
 
  
−
          <h4> Manufacturing Cost </h4>
+
<div class="row supervisor">
−
          <p> This was hard to estimate, given the unknowns in our kit, but we assumed we would ask a third-party to assemble the kit and this would lead to costs of around <b>$0.25</b> per/kit. </p>
+
    <div class="col-sm-3 supervisor-img">
 +
        <img class="img-responsive" src="https://static.igem.org/mediawiki/2017/f/fa/T--oxford--team--nick--circle.jpg">
 +
    </div>
 +
    <div class="col-sm-9 supervisor-description">
 +
    <b>Dr. Nicolas Delalez</b><br />
 +
    <i>Oxford Department of Engineering</i><br /><br />
 +
    Nick's research interests include synthetic biology and its biophysics of molecular machines.
 +
    <br />
 +
    Nick is the main person we go to when we are stuck on something in the lab. He can troubleshoot everything from a unsuccessful PCR to a contaminated plate of cells.
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          <h4> Transportation Costs </h4>
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          <p> We decided that with a minimum shelf life of around a year for our test it would be pertinent to send kits once a quarter to Bolivia, otherwise we risked them expiring before being used. With a 50x30x70mm box for our kit around 8,000 can fit on a europallet after taking into account further packaging for the pallet. This means we'd be sending 5 pallets/per quarter, and we estimated that this would cost around $12,000 per shipment to get from the factory in the UK to hospitals in Bolivia. This equates to around <b>$0.30</b> per kit. </p>  
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    <div class="col-sm-3 supervisor-img">
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        <img class="img-responsive" src="https://static.igem.org/mediawiki/2017/5/51/T--oxford--team--antonis--circle.jpg">
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    </div>
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    <div class="col-sm-9 supervisor-description">
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    <b>Prof. Antonis Papachristodoulou</b><br />
 +
    <i>Oxford Department of Engineering</i><br /><br />
 +
    Antonis' research interests include systems and synthetic biology, network systems, aerospace systems and flow control, and convex optimisation. Furthermore, he works on modern control theory, robust stability analysis and design, as well as nonlinear dynamical systems and Lyapunov stability.
 +
    </div>
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          <h4> Taxes </h4>
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          <p> Bolivia imposes a <a href"http://haiweb.org/wp-content/uploads/2015/08/Taxes-final-May2011a1.pdf"> <b>13%</b> </a> tax on pharmaceutical imports into the country.
+
    <div class="col-sm-3 supervisor-img">
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        <img class="img-responsive" src="https://static.igem.org/mediawiki/2017/2/23/T--oxford--team--harry--circle.jpg" width="500" height="500">
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    </div>
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    <div class="col-sm-9 supervisor-description">
 +
    <b>Harrison Steel</b><br />
 +
    <i>Oxford Department of Engineering</i><br /><br />
 +
    Harry is a PhD student whose research interests include control engineering and its application to Synthetic Biology, as well as mathematical tools for analysis of biological systems. Furthermore, he works on the design and development of new tools and hardware for use in Biological research.
 +
    </div>
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<div class="row supervisor">
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        <img class="img-responsive" src="https://static.igem.org/mediawiki/2017/8/8b/T--oxford--team--juditharmitage--circle.jpeg" width="500" height="500">
 +
    </div>
 +
    <div class="col-sm-9 supervisor-description">
 +
    <b>Prof. Judy Armitage</b><br />
 +
    <i>Oxford Department of Biochemistry</i><br /><br />
 +
Judy Armitage is interested in the dynamics of bacterial sensory transduction and the control of bacterial motility. In particular, her research group focuses on the communication between the sensory and adaptation mechanisms of the two pathways as a model for network sensory integration in general.
 +
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          <h4> <b>Total Cost</b> </h4>
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          <p>  Totalling up all these costs, and then adding 25%, as was suggested to us by those we contacted, brings the total cost of our kit to around <b>$3.90</b>, which is significantly less than the current other options on the market. </p>
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<h3>Dialogue with HeLEX</h3>
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<p> Consultation throughout with relevant stakeholders, including the Centre for Health, Law and Emerging Technologies (HeLEX) and Piers Millet, has brought some important difficulties to our attention. Key issues raised from our dialogue include: </p>
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<li> Dual-use technology in synthetic biology
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<li> Management of data gathered from our device
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<li> Transnational boundaries and international collaboration
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<p>You can read more about social, economic and political factors affecting our project on our <a href="https://2017.igem.org/Team:Oxford/HP/Silver">Silver Human Practices page</a> </p>
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<p>Whilst some of these issues (e.g. dual-use) may not immediately appear applicable to a diagnostic device, biosafety and biosecurity should be considered by any groups developing new technologies using synthetic biology. A component of our Education and Public Engagement activities therefore involved approaching some of these issues in order to foster a ‘culture of responsibility’ - <a href="https://2017.igem.org/Team:Oxford/Engagement">you can read more about our activities here</a>. </p>
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<p>We discussed how optimal integration of our device partly requires established guidelines to fill in gaps which may exist in current regulation. Using Bolivia as a case-study, we have produced a policy brief which summarises some of these findings, and proposes a flowchart showing our proposed optimal diagnostics strategy for Chagas disease.</p>
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<p> <center> <a href="https://2017.igem.org/Team:Oxford/Chagas_Public_Policy"><img class="img-responsive" width="200px;" src="https://static.igem.org/mediawiki/2017/9/98/T--oxford--chagas_disease--button.png"></a></center></p>
 
  
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<p> <center><img class="img-responsive" width="500px;" src="https://static.igem.org/mediawiki/2017/e/e6/Diagnostics_flowchart.png"></a><h6>Figure 5: A flowchart showing the optimal diagnostic strategy for congenital chagas disease using a rapid protease detecting kit.</h6></center></p>
 
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<p>One concern raised by our dialogue with HeLEX included the importance of public engagement in addressing the awareness of Chagas disease. A public health campaign rolled out in regions of Latin America with the implementation of our kit could circumvent future issues surrounding consent and knowledge of the risks associated with Chagas. Most importantly, this would need to be translated to local languages, including Spanish, to increase access of information to local stakeholders. To this end, we have produced a draft example of a public health poster which is concise and easy to read.</p>
 
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<p> <center><img class="img-responsive" width="250px;" src="https://static.igem.org/mediawiki/2017/6/69/Oxford_igem_public_health.png"></a><h6>Figure 6: A draft public health poster for Chagas disease, translated into Spanish</h6></center></p>
 
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<h2>Future Vision for our Kit</h2>
 
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<p>As our kit is modular, it will be able to be easily and cheaply adapted to diagnose different diseases; the cost of changing the disease is then only the input block, not also the output block. Our vision for the future is that a streamlined manufacturing process can be established which allows a rapid development of new diagnostic modules as people characterise specific proteases which are biomarkers for disease.<p>
 
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<p>References:
 
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Portable, On demand biomolecular manufacturing, Pardee
 
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The All E. coli TX-TL Toolbox 2.0: A platform for cell-free synthetic biology Garamella et al. </p>
 
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Revision as of 00:51, 2 November 2017


MEET THE TEAM
Alissa Hummer
Angela Hellyer
Arthur Norman
Chun Ngai Au
Helen Siyu Ren
Jei Diwakar
John Myers
Kushal Mansatta
Noah Sprent
Sumaera Rathore
Zoë Catchpole
Zoe Ford
Supervisors
Dr. George Wadhams
Oxford Department of Biochemistry

George's research interests lie in how bacteria sense and integrate environmental information. His group focuses on understanding in a quantitative manner how multiple, homologous pathways operate in individual cells and how the components of these pathways can be used to create synthetic pathways.
George has been mentoring Oxford iGEM teams since they were founded in 2014.
Dr. Nicolas Delalez
Oxford Department of Engineering

Nick's research interests include synthetic biology and its biophysics of molecular machines.
Nick is the main person we go to when we are stuck on something in the lab. He can troubleshoot everything from a unsuccessful PCR to a contaminated plate of cells.
Prof. Antonis Papachristodoulou
Oxford Department of Engineering

Antonis' research interests include systems and synthetic biology, network systems, aerospace systems and flow control, and convex optimisation. Furthermore, he works on modern control theory, robust stability analysis and design, as well as nonlinear dynamical systems and Lyapunov stability.
Harrison Steel
Oxford Department of Engineering

Harry is a PhD student whose research interests include control engineering and its application to Synthetic Biology, as well as mathematical tools for analysis of biological systems. Furthermore, he works on the design and development of new tools and hardware for use in Biological research.
Prof. Judy Armitage
Oxford Department of Biochemistry

Judy Armitage is interested in the dynamics of bacterial sensory transduction and the control of bacterial motility. In particular, her research group focuses on the communication between the sensory and adaptation mechanisms of the two pathways as a model for network sensory integration in general.