Difference between revisions of "Team:Oxford/Test/Practices"

(Undo revision 184330 by Duke of hildas (talk))
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<div class="container-fluid page-heading">
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    <div class="container-fluid page-heading">
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    <h3>Practices</h3>
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        <h3>Practices</h3>
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</div>
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    </div>
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<div class="container-fluid">
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    <div class="container-fluid">
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    <div class="row">
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        <div class="row">
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        <div class="col-md-9">
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            <div class="col-md-9">
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            <div class="section" id="introduction">
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                <div class="section" id="introduction">
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                <div class="slim">
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                    <div class="slim">
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                    <h2>Introduction</h2>
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                        <h2>Introduction</h2>
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                    <p>
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                        <p>
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                        Our project relies on a three way conversation between the team, the public and experts. It touches every aspect of the project, from our choice of application to the details of our delivery system. We promoted Synthetic Biology and iGEM through outreach programs to inspire the next generation.
+
                            Our project relies on a three way conversation between the team, the public and experts. It touches every aspect of the project, from our choice of application to the details of our delivery system. We promoted Synthetic Biology and iGEM through outreach programs to inspire the next generation.
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                    </p>
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                        </p>
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                    <p>
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                        <p>
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                        Urinary tract infections are a huge problem globally with millions of cases reported each year. We’re producing a guide for everything you need to know about urinary tract infections, as well as a treatment to beat antibiotics, which are rapidly becoming ineffective.
+
                            Urinary tract infections are a huge problem globally with millions of cases reported each year. We’re producing a guide for everything you need to know about urinary tract infections, as well as a treatment to beat antibiotics, which are rapidly becoming ineffective.
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                    </p>
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                        </p>
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                    <p>
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                        <p>
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                        We want to make our website as accessible as possible to all readers, regardless of their level of expertise. Words with a <a class="definition" title="Dotted Blue Underline" data-content="Yep, just like this one.">dotted blue underline</a> will show a definition when you hover over them.
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                            We want to make our website as accessible as possible to all readers, regardless of their level of expertise. Words with a <a class="definition" title="Dotted Blue Underline" data-content="Yep, just like this one.">dotted blue underline</a> will show a definition when you hover over them.
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                    </p>
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                        </p>
 +
                    </div>
 
                 </div>
 
                 </div>
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            </div>
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                <div class="section-spacer"></div>
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            <div class="section-spacer"></div>
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                <div class="section" id="public-interaction">
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            <div class="section" id="project-choice">
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                    <div class="slim">
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                <div class="slim">
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                        <h2>Public Interaction</h2>
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                    <h2>Project Choice</h2>
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                    </div>
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                     <div id="project-choice-approaching-the-public">
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                     <div id="public-interaction-project-choice">
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                             <h3>Approaching the Public</h3>
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                        <div class="slim">
 +
                             <h3>Project Choice</h3>
 
                             <p>
 
                             <p>
 
                                 To decide on our project idea, we sent out an initial questionnaire to the public to hear about what they thought about synthetic biology. We asked what big problems they wanted solving. We took the questionnaire to schools, to the streets and to our friends.
 
                                 To decide on our project idea, we sent out an initial questionnaire to the public to hear about what they thought about synthetic biology. We asked what big problems they wanted solving. We took the questionnaire to schools, to the streets and to our friends.
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                                 A large proportion of our responses expressed concern for how Synthetic Biology would be used in society, with several references to the issues of contamination and exploitation for profit. With this in mind, we constructed a second questionnaire about our project, to test whether the public would get behind it.
 
                                 A large proportion of our responses expressed concern for how Synthetic Biology would be used in society, with several references to the issues of contamination and exploitation for profit. With this in mind, we constructed a second questionnaire about our project, to test whether the public would get behind it.
 
                             </p>
 
                             </p>
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                    </div>
 
−
                        <div id="project-choice-approaching-the-public-initial-feedback">
 
−
                              <h4>Initial Feedback</h4>
 
−
                              <p>
 
−
                                  We sent a second questionnaire to find out more about whether the public would use a Solution from synthetic biology to treat Urinary tract infections. We asked more about whether they had heard of genetic engineering or synthetic biology, and how much they trust a recommended treatment by a doctor. In collaboration with UCL, we also filmed some of these responses on the street. The results were overwhelmingly positive.
 
−
                              </p>
 
 
                         </div>
 
                         </div>
−
                     <div id="project-choice-our-inspiration">
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                    </div>
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                            <h3>Our Inspiration</h3>
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                     <div id="public-interaction-initial-feedback">
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                            <p>
+
                         <div class="slim">
−
                            </p>
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                             <h3>Initial Feedback</h3>
−
                         <div id="project-choice-our-inspiration-jorge-talk">
+
−
                             <h4>Jorge Talk</h4>
+
 
                             <p>
 
                             <p>
 +
                                We sent a second questionnaire to find out more about whether the public would use a Solution from synthetic biology to treat Urinary tract infections. We asked more about whether they had heard of genetic engineering or synthetic biology, and how much they trust a recommended treatment by a doctor. In collaboration with UCL, we also filmed some of these responses on the street. The results were overwhelmingly positive.
 
                             </p>
 
                             </p>
 
                         </div>
 
                         </div>
−
                        <div id="project-choice-our-inspiration-churchill">
+
                    </div>
−
                             <h4>Churchill Hospital, Oxford</h4>
+
                </div>
 +
                <div class="section-spacer"></div>
 +
                <div class="section" id="medical-professionals">
 +
                    <div class="slim">
 +
                        <h2>Talking to Medical Professionals</h2>
 +
                        <p>
 +
                            Now that we were confident that the public would benefit from our idea, we set out designing our constructs. We visited nurses at the JR hospital in Oxford and the UTI clinic in London to get the Doctors on board; this discussion is essential for the success of the project.
 +
                        </p>
 +
                        <div id="medical-professionals-churchill">
 +
                             <h3>Churchill Hospital, Oxford</h3>
 
                             <p>
 
                             <p>
 
                                 Our first visit to the hospital was to the outpatient clinic during which we spoke with Jan, one of the nurses on the ward. Jan told us about a case of a person getting septicaemia as a result of a urinary infection. The patient had received antibiotics for seven days and had come back for a check up. Their urine sample was clear and all seemed fine but then the patient had started to shake. The bacteria were now in their blood as it had travelled back up the ureter to the kidney. Even though this was a rare case, it was shocking to hear about such a serious case and made our project feel very relevant.
 
                                 Our first visit to the hospital was to the outpatient clinic during which we spoke with Jan, one of the nurses on the ward. Jan told us about a case of a person getting septicaemia as a result of a urinary infection. The patient had received antibiotics for seven days and had come back for a check up. Their urine sample was clear and all seemed fine but then the patient had started to shake. The bacteria were now in their blood as it had travelled back up the ureter to the kidney. Even though this was a rare case, it was shocking to hear about such a serious case and made our project feel very relevant.
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                             </p>
 
                             </p>
 
                         </div>
 
                         </div>
−
                         <div id="project-choice-our-inspiration-jr"
+
                         <div id="medical-professionals-jr">
−
                             <h4>John Radcliffe Hospital, Oxford</h4>
+
                             <h3>The John Radcliffe Hospital, Oxford</h3>
 
                             <p>
 
                             <p>
 
                                 We still wanted to learn more about urinary infections as well as to get some feedback from nurses abourtour idea. We organized a trip to the Adams Ward (Geratology) to learn more about how urinary infections affect elderly people.
 
                                 We still wanted to learn more about urinary infections as well as to get some feedback from nurses abourtour idea. We organized a trip to the Adams Ward (Geratology) to learn more about how urinary infections affect elderly people.
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                                 <li>If you are to kill all of the pathogenic bacteria in the urinary tract, will that make fungal infections more likely?</li>
 
                                 <li>If you are to kill all of the pathogenic bacteria in the urinary tract, will that make fungal infections more likely?</li>
 
                             </ul>
 
                             </ul>
 +
                        </div>
 
                     </div>
 
                     </div>
−
                    <div id="project-choice-the-problem">
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                </div>
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                            <h3>The Problem</h3>
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                <div class="section-spacer"></div>
 +
                <div class="section" id="patients">
 +
                    <div class="slim">
 +
                        <h2>Talking to Patients</h2>
 +
                        <div class="quote quote-right">
 
                             <p>
 
                             <p>
 +
                                the process is not very different to using antibiotics
 
                             </p>
 
                             </p>
−
                    </div>
+
                        </div>
−
                    <div id="project-choice-our-solution">
+
−
                          <h3>Our Solution</h3>
+
−
                          <p>
+
−
                          </p>
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−
                    </div>
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−
                </div>
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            </div>
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−
            <div class="section-spacer"></div>
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            <div class="section" id="project-viability">
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                <div class="slim">
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−
                    <h2>Project Viability</h2>
+
−
                    <p>
+
−
                    </p>
+
−
                    <div id="project-viability-will-our-idea-work">
+
−
                        <h3>Will Our Idea Work?</h3>
+
 
                         <p>
 
                         <p>
 +
                            During the process of talking to medical professionals, the importance of talking to patients as well was clear to us. On one occasion we spoke with Mavis, a patient staying on the Bedford Ward at the John Radcliffe Hospital. Her experience of urinary infections was that she had only suffered from them before having a catheter; since having a catheter fitted she hadn’t had any problems of infection. Her catheter was in place for up to 10 weeks. This enforced the importance of being able to keep our bacteria alive for a sustained period of time. When we asked her about treating infection with bacteria she said she would be happy to if it had been recommended to her by a doctor and told us that it is not dissimilar to using antibiotics.
 
                         </p>
 
                         </p>
 
                     </div>
 
                     </div>
−
                    <div id="project-viability-ethics">
+
                </div>
−
                         <h3>Ethics</h3>
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                <div class="section-spacer"></div>
 +
                <div class="section" id="further-feedback">
 +
                    <div class="slim">
 +
                         <h2>Further Feedback</h2>
 
                         <p>
 
                         <p>
 +
                            We are still designing a delivery system for our UTI treatment. We plan on asking the public to select from a variety of options, and then to design our treatment around the most popular one.
 
                         </p>
 
                         </p>
 
                     </div>
 
                     </div>
−
                    <div id="project-viability-the-uti-clinic">
+
                </div>
−
                         <h3>The UTI Clinic</h3>
+
                <div class="section-spacer"></div>
 +
                <div class="section" id="outreach">
 +
                    <div class="slim">
 +
                         <h2>Outreach</h2>
 
                         <p>
 
                         <p>
 +
                            To promote Synthetic Biology and iGEM, we’ve used a variety of approaches.
 
                         </p>
 
                         </p>
 
                     </div>
 
                     </div>
−
                     <div id="project-viability-delivery-method">
+
                     <div id="outreach-uniq-workshop">
−
                         <h3>Delivery Method</h3>
+
                         <div class="slim">
−
                        <p>
+
                            <h3>UNIQ Workshop</h3>
−
                        </p>
+
                            <p>
 +
                                We met with 40 prospective Oxford students to teach them about Synthetic Biology. The students had in interest in Biochemistry but knew nothing about iGEM. We hammered home the key message of Synthetic Biology - that we achieve more progress by expanding a registry of standardised biological parts - through a 15 minute introductory presentation on BioBricks. We then split them into groups and gave each one a mentor from our iGEM team. We worked through questions to test their understanding in a tutorial style and asked them to explain the constructs of previous iGEM teams. They finished by presenting their findings to each other.
 +
                            </p>
 +
                        </div>
 
                     </div>
 
                     </div>
−
                     <div id="project-viability-increasing-awareness">
+
                     <div id="outreach-abr-school-talk">
−
                         <h3>Increasing Awareness</h3>
+
                         <div class="slim">
 +
                            <h3>UTC Oxfordshire</h3>
 +
                            <p>
 +
                                A couple of us gave a presentation on antibiotic resistance to a class of GCSE students from UTC Oxfordshire (a local school specialising in science) at the Natural History Museum in Oxford, The Pitt Rivers Museum. Our talk covered the discovery of antibiotics, the advantages of them (including their use in laboratory work), how they work, and how bacteria can evolve to gain resistance to them, as well as concepts such as horizontal gene transfer and the consequences of antibiotic resistance on our everyday lives. It also covered our project outline, and pros and cons of Solution, showing how it should help combat antibiotic resistance. At the end, we held a discussion between the students and our team about antibiotic resistance, and their perception of the concern. We also asked how they would feel about using our engineered bacteria, and the response was positive, with most of the students saying that if their doctor recommended the treatment, they would be open to using it.
 +
                            </p>
 +
                        </div>
 +
                    </div>
 +
                </div>
 +
                <div class="section-spacer">
 +
                </div>
 +
                <div class="section" id="videos">
 +
                    <div class="slim">
 +
                        <h2>Videos</h2>
 
                         <p>
 
                         <p>
−
                             To promote Synthetic Biology and iGEM, we’ve used a variety of approaches.
+
                             We’ve produced the following videos to promote our project and help future teams:
 
                         </p>
 
                         </p>
−
                         <div id="project-viability-increasing-awareness-uniq-workshop">
+
                         <ul>
−
                                 <h4>UNIQ Workshop</h4>
+
                            <li>
−
                                 <p>
+
                                Introduction to Oxford iGEM
−
                                     We met with 40 prospective Oxford students to teach them about Synthetic Biology. The students had in interest in Biochemistry but knew nothing about iGEM. We hammered home the key message of Synthetic Biology - that we achieve more progress by expanding a registry of standardised biological parts - through a 15 minute introductory presentation on BioBricks. We then split them into groups and gave each one a mentor from our iGEM team. We worked through questions to test their understanding in a tutorial style and asked them to explain the constructs of previous iGEM teams. They finished by presenting their findings to each other.
+
                                <video width="640" height="480" controls>
 +
                                    <source src="OxiGEM_Consulting_the_public.mp4‎" type="video/mp4">
 +
                                        Your browser does not support the video tag.
 +
                                 </video>
 +
                            </li>
 +
                            <li>
 +
                                 <p class="animating">
 +
                                     Stochastic Modelling Tutorial (<a href="https://www.youtube.com/watch?v=xMy8oqP5Mis"> link</a>)<br>
 
                                 </p>
 
                                 </p>
−
                        </div>
+
                             </li>
−
                        <div id="project-viability-increasing-awareness-utc-oxfordshire">
+
                         </ul>
−
                                <h4>UTC Oxfordshire</h4>
+
−
                                <p>
+
−
                                    A couple of us gave a presentation on antibiotic resistance to a class of GCSE students from UTC Oxfordshire (a local school specialising in science) at the Natural History Museum in Oxford, The Pitt Rivers Museum. Our talk covered the discovery of antibiotics, the advantages of them (including their use in laboratory work), how they work, and how bacteria can evolve to gain resistance to them, as well as concepts such as horizontal gene transfer and the consequences of antibiotic resistance on our everyday lives. It also covered our project outline, and pros and cons of Solution, showing how it should help combat antibiotic resistance. At the end, we held a discussion between the students and our team about antibiotic resistance, and their perception of the concern. We also asked how they would feel about using our engineered bacteria, and the response was positive, with most of the students saying that if their doctor recommended the treatment, they would be open to using it.
+
−
                                </p>
+
−
                        </div>
+
−
                        <div id="project-viability-increasing-awareness-bbc-radio-oxford">
+
−
                             <h4>BBC Radio Oxford</h4>
+
−
                         </div>
+
 
                     </div>
 
                     </div>
 +
                </div>
 +
                <div class="section" id="references">
 +
                    <h2>References</h2>
 +
                    <ol>
 +
                        <li>
 +
                            [1] You can see all of our responses <a href="https://docs.google.com/document/d/1MAzVkPVVGAbAbFMIN9OIvZtC4vBpGkW2et9W3omnkzM/edit?usp=sharing">here</a>.
 +
                        </li>
 +
                    </ol>
 
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Revision as of 17:59, 8 September 2015

Practices

Introduction

Our project relies on a three way conversation between the team, the public and experts. It touches every aspect of the project, from our choice of application to the details of our delivery system. We promoted Synthetic Biology and iGEM through outreach programs to inspire the next generation.

Urinary tract infections are a huge problem globally with millions of cases reported each year. We’re producing a guide for everything you need to know about urinary tract infections, as well as a treatment to beat antibiotics, which are rapidly becoming ineffective.

We want to make our website as accessible as possible to all readers, regardless of their level of expertise. Words with a dotted blue underline will show a definition when you hover over them.

Public Interaction

Project Choice

To decide on our project idea, we sent out an initial questionnaire to the public to hear about what they thought about synthetic biology. We asked what big problems they wanted solving. We took the questionnaire to schools, to the streets and to our friends.

Examples of their suggestions for the applications of synthetic biology include bacteria which:

  • Remove carbon dioxide from the atmosphere
  • Target and kill cancerous cells
  • Help treat Alzheimer's disease
  • Produce energy
  • Sew up holes in clothes
  • Produce teeth glue
  • Indicate how long someone has been dead for
  • Combat antibiotic resistance

Of our responses, around 40 were related to Medicine and Health [1]. This led us to choose that track for our project. However, it was our team member George Driscoll’s work at the UTI clinic in London which helped us to select UTIs as a specific cause. Due to the un-aesthetic nature of the infection, it often receives less attention with regard to research.

A large proportion of our responses expressed concern for how Synthetic Biology would be used in society, with several references to the issues of contamination and exploitation for profit. With this in mind, we constructed a second questionnaire about our project, to test whether the public would get behind it.

Initial Feedback

We sent a second questionnaire to find out more about whether the public would use a Solution from synthetic biology to treat Urinary tract infections. We asked more about whether they had heard of genetic engineering or synthetic biology, and how much they trust a recommended treatment by a doctor. In collaboration with UCL, we also filmed some of these responses on the street. The results were overwhelmingly positive.

Talking to Medical Professionals

Now that we were confident that the public would benefit from our idea, we set out designing our constructs. We visited nurses at the JR hospital in Oxford and the UTI clinic in London to get the Doctors on board; this discussion is essential for the success of the project.

Churchill Hospital, Oxford

Our first visit to the hospital was to the outpatient clinic during which we spoke with Jan, one of the nurses on the ward. Jan told us about a case of a person getting septicaemia as a result of a urinary infection. The patient had received antibiotics for seven days and had come back for a check up. Their urine sample was clear and all seemed fine but then the patient had started to shake. The bacteria were now in their blood as it had travelled back up the ureter to the kidney. Even though this was a rare case, it was shocking to hear about such a serious case and made our project feel very relevant.

Jan also made the following points:

  • People with infections have a catheter because they need a way to empty the bladder; else the urine travels up the ureter and back into the bladder
  • If a patient becomes septic the catheter has to be removed or can be fatal
  • UTIs are not just contracted by the catheter and it is important to also consider community based UTIs
  • “UTIs are very common and can be quite painful”
  • No separate ward for UTIs – they are treated in every ward
  • The protocol for treatment is to take a urine sample, see if there is an infection, and prescribe antibiotics that the bacteria are most sensitive to
  • Elderly hospital wards are likely to have many cases of UTIs

We took a lot from this initial conversation. We went onto investigating the pros and cons of the current methods of treating urinary infections and compared these to what Solution could offer. We realized that we needed to consider the catheter more from a hospital/medical perspective as up to this point we had confused its function, thinking it was more to do with administering medication rather than emptying the bladder. Following this meeting, the design of the catheter became an integral part of the project.

The John Radcliffe Hospital, Oxford

We still wanted to learn more about urinary infections as well as to get some feedback from nurses abourtour idea. We organized a trip to the Adams Ward (Geratology) to learn more about how urinary infections affect elderly people.

First interview with Laura Evans, Adams Ward

What is the procedure for treating UTIs?

  1. Dip urine
  2. If the test comes back as positive, treat with a wide spectrum antibiotic
  3. Whether or not the catheter is inserted with prophylactic antibiotic treatment is the doctor’s decision

What happens when a patient tests positive for a urinary infection?

Whether or not the catheter is removed if a patient tests positive for a urinary infection depends largely on the reason that the catheter has been fitted. On the whole, the catheter remains fitted and the patient is treated with a large dose of antibiotics.

Is antibiotic resistance a problem?

Yes, particularly on this ward. As we treat elderly patients with recurring infections, their UTIs are frequently resistant to antibiotic treatment. We try different combinations of antibiotics but recurring infections are a significant problem.

Our project involves designing a catheter that prevents the formation of a biofilm on its surface. What do you think of this idea?

A catheter like that would be useful, but it depends on how long your catheter would work for. Patients can have catheters fitted for 3 months or longer. Catheters are also removed for other reasons, for example if they become blocked. Blockage is particularly an issue when the patient is suffering from a urinary infection.

Laura’s response regarding how long a catheter remains in place spurred us into researching how we could keep our Solution bacteria alive. This is what we found.

Biochemistry Department

To gain a further insight into the feasibility of Solution, we gave two talks during the summer, one at the termly Corpus Christi College Biochemistry talks and another to a group of alumni from the Oxford Biochemistry department. Two important questions arose from these talks:

  • Have you considered whether the proteins you planning on secreting are immunogenic?
  • If you are to kill all of the pathogenic bacteria in the urinary tract, will that make fungal infections more likely?

Talking to Patients

the process is not very different to using antibiotics

During the process of talking to medical professionals, the importance of talking to patients as well was clear to us. On one occasion we spoke with Mavis, a patient staying on the Bedford Ward at the John Radcliffe Hospital. Her experience of urinary infections was that she had only suffered from them before having a catheter; since having a catheter fitted she hadn’t had any problems of infection. Her catheter was in place for up to 10 weeks. This enforced the importance of being able to keep our bacteria alive for a sustained period of time. When we asked her about treating infection with bacteria she said she would be happy to if it had been recommended to her by a doctor and told us that it is not dissimilar to using antibiotics.

Further Feedback

We are still designing a delivery system for our UTI treatment. We plan on asking the public to select from a variety of options, and then to design our treatment around the most popular one.

Outreach

To promote Synthetic Biology and iGEM, we’ve used a variety of approaches.

UNIQ Workshop

We met with 40 prospective Oxford students to teach them about Synthetic Biology. The students had in interest in Biochemistry but knew nothing about iGEM. We hammered home the key message of Synthetic Biology - that we achieve more progress by expanding a registry of standardised biological parts - through a 15 minute introductory presentation on BioBricks. We then split them into groups and gave each one a mentor from our iGEM team. We worked through questions to test their understanding in a tutorial style and asked them to explain the constructs of previous iGEM teams. They finished by presenting their findings to each other.

UTC Oxfordshire

A couple of us gave a presentation on antibiotic resistance to a class of GCSE students from UTC Oxfordshire (a local school specialising in science) at the Natural History Museum in Oxford, The Pitt Rivers Museum. Our talk covered the discovery of antibiotics, the advantages of them (including their use in laboratory work), how they work, and how bacteria can evolve to gain resistance to them, as well as concepts such as horizontal gene transfer and the consequences of antibiotic resistance on our everyday lives. It also covered our project outline, and pros and cons of Solution, showing how it should help combat antibiotic resistance. At the end, we held a discussion between the students and our team about antibiotic resistance, and their perception of the concern. We also asked how they would feel about using our engineered bacteria, and the response was positive, with most of the students saying that if their doctor recommended the treatment, they would be open to using it.

Videos

We’ve produced the following videos to promote our project and help future teams:

  • Introduction to Oxford iGEM

  • Stochastic Modelling Tutorial ( link)

References

  1. [1] You can see all of our responses here.