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

 
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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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<h2 id="title">Introduction</h2>
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<p>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.</p><br>
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<p>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><br>
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<p>Having thoroughly examined and evaluated various design options, we propose a final design for our system which fulfils our criteria for a suitable diagnostic device.</p><br>
  
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<h2>What diagnostics for Chagas disease currently exist?</h2>
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<img class="img-responsive img-circle" src="https://static.igem.org/mediawiki/2017/1/13/T--oxford--team--alissa--circle.jpeg">
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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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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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<p>Diagnosis of Chagas disease is difficult, as the disease is mostly asymptomatic in the acute phase and for the majority of the chronic phase.</p><br>
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<p>We spoke to Dr Carol Lole Harris, who advised us on the practical and social considerations involved in the application of our diagnostic in Latin America, based on her experience working in Paraguay. We discussed the current tests available for Chagas and Carol emphasised that a spot test would be by far the best option for a multitude of reasons.</p><br>
  
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<p>Following further reading, we created a table of our findings to highlight the lack of a rapid and feasible diagnostic for congenital Chagas disease. </p><br>
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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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<b>Angela Hellyer</b> (Biochemistry)<br/>
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<i>Wet Lab Co-ordinator &amp; Safety<br/>
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G. weazli</i><br/>
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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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<h6>Table 1: Main diagnostic methods currently used to diagnose Chagas disease</h6>
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     <thead>
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      <tr>
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     <span id="profile_caption"> Arthur Norman </span>
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        <th>Test</th>
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        <th>How it works</th>
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        <th>Benefits</th>
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        <th>Limitations</th>
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        <th>Suitable for newborns</th>
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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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      <tr>
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        <td>Whole parasite microscopy</td>
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        <td>
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        <ul>
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        <li>Preparation of Giesma blood smears</li>
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        <li>Visualised using light microscopy</li>
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        </ul>
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         </td>
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        <td>
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        <ul>
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        <li>Established method</li>
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        <li>Carried out by already trained professionals</li>
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        <td>
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        <ul>
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        <li>Not suitable for the when there is little <em>T. cruzi</em> in the blood</li>
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        <li>Not always possible to differentiate between <em>T. cruzi</em> from <em>T. rangeli</em>, which does not cause disease in humans.</li>
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        </td>
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        <td>Yes</td>
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      </tr>
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    <td>Polymerase Chain Reaction (PCR)</td>
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    <td>
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    <ul>
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    <li>Molecular detection of <em>T. cruzi</em> DNA is performed using a combination of three real-time PCR assays.</li>
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    <li>Acceptable specimen types are EDTA blood, heart biopsy tissue or cerebrospinal fluid.</li>
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    </ul>
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    </td>
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    <td>
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    <ul>
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    <li>Allows high sensitivity in the acute phase</li>
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    <li>Allows the presence of <em>T.cruzi</em> to be accurately distinguished from <em>T. rangeli</em></li>
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    <li>Allows direct detection of infection and easy interpretation of results</li>
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    </ul>
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    </td>
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    <td>
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    <ul>
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    <li>High variation in accuracy and lack of international quality controls</li>
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    <li>High cost and complexity means it is not practical to use in a clinical practice</li>
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    <li>Further validation is needed to prove whether PCR is suitable to diagnose the  chronic phase of Chagas</li>
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    </ul>
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    </td>
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    <td>Yes</td>
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      </tr>
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      <tr>
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      <td>Serological tests</td>
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      <td>
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      <ul>
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      <li>Detection of antibodies against <em>T. cruzi</em></li>
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      <li>Includes techniques such as indirect fluorescent antibody (IFA) test, a commercial enzyme immunoassay (EIA) and immunochromatographic tests</li>
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      </ul>
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      </td>
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      <td>
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      <ul>
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      <li>Can be used for acute phase and chronic phase</li>
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      <li>High specificity and sensitivity</li>
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      <li>Commercialised and approved for use by WHO</li>
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      <li>Low-cost formats are available</li>
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      </ul>
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      <td>
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      <ul>
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      <li>Cross reactivity can occur with diseases, such as leishmaniasis and schistosomiasis </li>
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      <li>Performance of these tests is lower than reported by their manufacturer, especially against specific strains of <em>T. cruzi</em></li>
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      <li>Not suitable for immunocompromised patients and newborns</li>
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      </ul>
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      </td>
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      <td>No</td>
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  </tr>
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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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<p>We also spoke to Professor Dias Borges Lalwani is professor of epidemiology at the Faculty of pharmaceutical sciences at UFAM, whose contact details were forwarded to us by the AQA Amazonas team. We were fortunate enough to be able to arrange a Skype meeting with Jaila, which helped us contextualise the problem of Chagas highlighting the difficulty of seeking diagnosis given non-specific early disease symptoms. </p><br>
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<h2>Why congenital Chagas disease?</h2>
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<p>We spoke to Dr Alonso-Vega of the University of San Simón, Cochabamba who ran the National Congenital Chagas Disease Programme in Bolivia from 2004-2009, and is an expert in congenital Chagas. Dr Alonso-Vega’s Chagas Disease Program recommended the need for a new congenital diagnostic. She gave us specific guidance for implementation of our diagnostic device in Bolivia and confirmed the suitability of our congenital test in Bolivian hospitals, where most deliveries occur.</p><br>
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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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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>We first contacted Professor Yves Carlier early on in our project to gain more information about the pathology of congenital Chagas disease. Professor Carlier is a researcher in infectious diseases and clinical immunology at the Université Libre de Bruxelles. He re-emphasised the need for a diagnostic for neonates, strengthening our resolve to focus on congenital Chagas disease. He also informed us about the benefits of diagnosing Chagas disease in neonates, such as that treatment with benznidazole cures around 100% of babies if given before one year of age but not later in life.</p><br>
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<p>We also learnt that Chagas treatment for under 15’s is free, giving us confidence that our diagnostic would be accessible and impactful in containing Chagas if provided in a hospital setting. Our discussion with her further emphasised the requirement for a rapid point of care test that would allow treatment of infected newborns to begin before they left the hospital.</p><br>
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<h2>How did we develop our design?</h2>
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<p>Based on our findings from the OpenPlant conference, we established a set of criteria for our applied design - the 4 E’s (‘Effectiveness’, ‘Ease of use’, ‘Economics’ and ‘Environment & Safety’).</p><br>
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    <img class="img-responsive img-circle team-member-img helen_open" src="https://static.igem.org/mediawiki/2017/7/7c/T--oxford--team--helen--circle.jpeg">
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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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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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<p>Prototyping involved extensive consideration of various design iterations. We progressed from paper to cardboard to 3D printing - at each stage of this process, we were able to iron out flaws in our design and to incorporate new features from our evaluations.
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<p><a href = "https://2017.igem.org/Team:Oxford/Applied_Design_Developing">Read more here.</a></p>
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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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    <span id="profile_caption"> Jei Diwakar </span>
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<b>Jei Diwakar</b> (Biochemistry)<br/>
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<i>Wet Lab Co-ordinator &amp; Treasurer<br/>
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T. schmoozi</i><br/>
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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.
 
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<h2>What is our solution?</h2>
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    <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">
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    <span id="profile_caption"> John Myers </span>
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<b>John Myers</b> (Biochemistry)<br/>
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<i>Secretary<br/>
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Oui. cruzi</i><br/>
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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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<p>Our current kit meets our criteria established from our 4E’s framework: it is effective, easy-to-use, economically viable and environmentally safe. Furthermore, it incorporates many of the recommendations provided to us by the experts we contacted. Our solution is a rapid, point-of-care diagnostic for congenital Chagas disease which can easily be used by any healthcare professional.</p><br>
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<p>Following extensive design and development, we produced a 3D prototype version of our kit. We spoke to Tim Ring, the vice president of safe-tec sales and marketing who generously sent us MICROSAFE® pipette samples so we could test the compatibility of these with our kit design. These pipettes are advantageous for blood collection and allowed us to test our applied design more rigorously.</p><br>
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    <span id="profile_caption"> Kushal Mansatta </span>
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<b>Kushal Mansatta</b> (Medicine)<br/>
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<i>Wiki Co-ordinator &amp; Social Sec<br/>
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He. curezi</i><br/>
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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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<p> Our 3D prototype design was refined by the healthcare professionals we contacted for evalutation. The insights from Sarah Dragonetti (Registered Nurse) and Dr. Ben Riley (General Practice doctor) were hugely useful in assessing and refining the practicality of our diagnostic kit, consequently improving our applied design.</p>
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<p><a href = "https://2017.igem.org/Team:Oxford/Applied_Design_Solution">Read more here.</a></p>
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    <span id="profile_caption"> Noah Sprent </span>
 
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<b>Noah Sprent</b> (Biochemistry)<br/>
 
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<i>Co-leader<br/>
 
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No. shoezi</i><br/>
 
  
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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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<h2>How will we implement our design?</h2>
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    <span id="profile_caption"> Sumaera Rathore </span>
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<b>Sumaera Rathore</b> (Biology)<br/>
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<i>iGEM Requirements Co-ordinator<br/>
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Tea. brewzi</i><br/>
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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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<p>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.</p><br>
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<p>We received invaluable advice from David Sprent, an expert in International Supply Chain, and Juan Solano and Alfons Van Woerkom, representatives of the Global Fund who advised us on evaluating costs of manufacture, transport and taxation of a kit for end use by the Bolivian healthcare system. </p><br>  
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    <span id="profile_caption"> Zoë Catchpole </span>
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<b>Zoë Catchpole</b> (Biochemistry)<br/>
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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!
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<p>We consulted with HeLEX, (Centre for Health, Law and Emerging Technologies) and with InSIS (Institute for Science, Innovation and Society). InSIS researches and informs key contemporary and emerging issues and processes of social, scientific, and technological change. The insights from both HeLEX and InSIS were highly useful in evaluating the ethical and social issues related to our project, and heavily influenced our applied design.</p></br>
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<p>Professor Keith Pardee has worked on cell-free technologies, and he informed us how cell-free systems could solve a lot of issues around safety and cost.</p><br>
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    <span id="profile_caption"> Zoe Ford </span>
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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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<p>Dr Piers Millett is a Senior Research Fellow at the Future of Humanity Institute, and he introduced us to the concept of platform technologies and how this could be applied to our project. This provides a good way of fast tracking future developments because the platform will already have met regulatory approval, therefore allowing the device to be more rapidly adapted for other diseases.</p><br>
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<p><a href = "https://2017.igem.org/Team:Oxford/Applied_Design_Implementation">Read more here.</a></p>
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<p>Carlier, Y. and Truyens, C. 2017 Maternal-fetal transmission of Trypanosoma cruzi. Second Edition, American Trypanosomiasis Chagas Disease: One Hundred Years of Research: Second Edition. Second Edition. Elsevier Inc. doi: 10.1016/B978-0-12-801029-7.00024-1.</p>
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<p>Cencig, S. et al. 2012 ‘Evaluation of benznidazole treatment combined with nifurtimox, posaconazole or AmBisome?? in mice infected with Trypanosoma cruzi strains’, International Journal of Antimicrobial Agents. Elsevier B.V., 40(6), pp. 527–532. doi: 10.1016/j.ijantimicag.2012.08.002.</p>
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    <b>Dr. George Wadhams</b><br />
 
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Latest revision as of 14:49, 15 December 2017


APPLIED DESIGN

Introduction

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.


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.


Having thoroughly examined and evaluated various design options, we propose a final design for our system which fulfils our criteria for a suitable diagnostic device.


What diagnostics for Chagas disease currently exist?

Diagnosis of Chagas disease is difficult, as the disease is mostly asymptomatic in the acute phase and for the majority of the chronic phase.


We spoke to Dr Carol Lole Harris, who advised us on the practical and social considerations involved in the application of our diagnostic in Latin America, based on her experience working in Paraguay. We discussed the current tests available for Chagas and Carol emphasised that a spot test would be by far the best option for a multitude of reasons.


Following further reading, we created a table of our findings to highlight the lack of a rapid and feasible diagnostic for congenital Chagas disease.


Table 1: Main diagnostic methods currently used to diagnose Chagas disease
Test How it works Benefits Limitations Suitable for newborns
Whole parasite microscopy
  • Preparation of Giesma blood smears
  • Visualised using light microscopy
  • Established method
  • Carried out by already trained professionals
  • Not suitable for the when there is little T. cruzi in the blood
  • Not always possible to differentiate between T. cruzi from T. rangeli, which does not cause disease in humans.
 Yes
Polymerase Chain Reaction (PCR)
  • Molecular detection of T. cruzi DNA is performed using a combination of three real-time PCR assays.
  • Acceptable specimen types are EDTA blood, heart biopsy tissue or cerebrospinal fluid.
  • Allows high sensitivity in the acute phase
  • Allows the presence of T.cruzi to be accurately distinguished from T. rangeli
  • Allows direct detection of infection and easy interpretation of results
  • High variation in accuracy and lack of international quality controls
  • High cost and complexity means it is not practical to use in a clinical practice
  • Further validation is needed to prove whether PCR is suitable to diagnose the chronic phase of Chagas
 Yes
Serological tests
  • Detection of antibodies against T. cruzi
  • Includes techniques such as indirect fluorescent antibody (IFA) test, a commercial enzyme immunoassay (EIA) and immunochromatographic tests
  • Can be used for acute phase and chronic phase
  • High specificity and sensitivity
  • Commercialised and approved for use by WHO
  • Low-cost formats are available
  • Cross reactivity can occur with diseases, such as leishmaniasis and schistosomiasis
  • Performance of these tests is lower than reported by their manufacturer, especially against specific strains of T. cruzi
  • Not suitable for immunocompromised patients and newborns
 No

We also spoke to Professor Dias Borges Lalwani is professor of epidemiology at the Faculty of pharmaceutical sciences at UFAM, whose contact details were forwarded to us by the AQA Amazonas team. We were fortunate enough to be able to arrange a Skype meeting with Jaila, which helped us contextualise the problem of Chagas highlighting the difficulty of seeking diagnosis given non-specific early disease symptoms.


Why congenital Chagas disease?

We spoke to Dr Alonso-Vega of the University of San Simón, Cochabamba who ran the National Congenital Chagas Disease Programme in Bolivia from 2004-2009, and is an expert in congenital Chagas. Dr Alonso-Vega’s Chagas Disease Program recommended the need for a new congenital diagnostic. She gave us specific guidance for implementation of our diagnostic device in Bolivia and confirmed the suitability of our congenital test in Bolivian hospitals, where most deliveries occur.


We first contacted Professor Yves Carlier early on in our project to gain more information about the pathology of congenital Chagas disease. Professor Carlier is a researcher in infectious diseases and clinical immunology at the Université Libre de Bruxelles. He re-emphasised the need for a diagnostic for neonates, strengthening our resolve to focus on congenital Chagas disease. He also informed us about the benefits of diagnosing Chagas disease in neonates, such as that treatment with benznidazole cures around 100% of babies if given before one year of age but not later in life.


We also learnt that Chagas treatment for under 15’s is free, giving us confidence that our diagnostic would be accessible and impactful in containing Chagas if provided in a hospital setting. Our discussion with her further emphasised the requirement for a rapid point of care test that would allow treatment of infected newborns to begin before they left the hospital.


How did we develop our design?

Based on our findings from the OpenPlant conference, we established a set of criteria for our applied design - the 4 E’s (‘Effectiveness’, ‘Ease of use’, ‘Economics’ and ‘Environment & Safety’).


Prototyping involved extensive consideration of various design iterations. We progressed from paper to cardboard to 3D printing - at each stage of this process, we were able to iron out flaws in our design and to incorporate new features from our evaluations.

Read more here.

What is our solution?

Our current kit meets our criteria established from our 4E’s framework: it is effective, easy-to-use, economically viable and environmentally safe. Furthermore, it incorporates many of the recommendations provided to us by the experts we contacted. Our solution is a rapid, point-of-care diagnostic for congenital Chagas disease which can easily be used by any healthcare professional.


Following extensive design and development, we produced a 3D prototype version of our kit. We spoke to Tim Ring, the vice president of safe-tec sales and marketing who generously sent us MICROSAFE® pipette samples so we could test the compatibility of these with our kit design. These pipettes are advantageous for blood collection and allowed us to test our applied design more rigorously.


Our 3D prototype design was refined by the healthcare professionals we contacted for evalutation. The insights from Sarah Dragonetti (Registered Nurse) and Dr. Ben Riley (General Practice doctor) were hugely useful in assessing and refining the practicality of our diagnostic kit, consequently improving our applied design.

Read more here.

How will we implement our design?

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.


We received invaluable advice from David Sprent, an expert in International Supply Chain, and Juan Solano and Alfons Van Woerkom, representatives of the Global Fund who advised us on evaluating costs of manufacture, transport and taxation of a kit for end use by the Bolivian healthcare system.


We consulted with HeLEX, (Centre for Health, Law and Emerging Technologies) and with InSIS (Institute for Science, Innovation and Society). InSIS researches and informs key contemporary and emerging issues and processes of social, scientific, and technological change. The insights from both HeLEX and InSIS were highly useful in evaluating the ethical and social issues related to our project, and heavily influenced our applied design.


Professor Keith Pardee has worked on cell-free technologies, and he informed us how cell-free systems could solve a lot of issues around safety and cost.


Dr Piers Millett is a Senior Research Fellow at the Future of Humanity Institute, and he introduced us to the concept of platform technologies and how this could be applied to our project. This provides a good way of fast tracking future developments because the platform will already have met regulatory approval, therefore allowing the device to be more rapidly adapted for other diseases.


Read more here.

References

Carlier, Y. and Truyens, C. 2017 Maternal-fetal transmission of Trypanosoma cruzi. Second Edition, American Trypanosomiasis Chagas Disease: One Hundred Years of Research: Second Edition. Second Edition. Elsevier Inc. doi: 10.1016/B978-0-12-801029-7.00024-1.

Cencig, S. et al. 2012 ‘Evaluation of benznidazole treatment combined with nifurtimox, posaconazole or AmBisome?? in mice infected with Trypanosoma cruzi strains’, International Journal of Antimicrobial Agents. Elsevier B.V., 40(6), pp. 527–532. doi: 10.1016/j.ijantimicag.2012.08.002.