Difference between revisions of "Team:Oxford/Design"

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    <h3>Practices</h3>
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    <div class="container-fluid page-heading" style="background-image: url(https://static.igem.org/mediawiki/2015/8/8a/Ox_Keeptesting.jpg)">
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        <h3>Design</h3>
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    <div class="row">
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        <div class="col-md-9">
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    <div class="container-fluid">
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            <div class="section" id="introduction">
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        <div class="row">
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            <div class="col-md-9">
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                 <div class="slim">
 
                 <div class="slim">
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                     <div class="section" id="introduction">
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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.
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                            Following on from all of the safety research we conducted we put that knowledge into designing a catheter in order to get our proteins  (DNase and DispB) into the urinary track where we want them.
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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.
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                            Designing a novel method of getting our bacteria into the urinary tract was a big consideration during the beginning stages of our project. The approach of delivering our bacteria directly through the catheter into the bladder would probably be the most effective. However we found that the biofilm also forms on the outside of the catheter so in our design we attempted to tackle the biofilm from outside and in.
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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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                            While our bacteria could potentially be used to a large range of different pipes to tackle a growing world problem with biofilms we decide to focus on a medical application for them. We focused on the problem of urinary tract infections as a member of our team, George Driscoll, had seen first hand the extreme impact it can have on people’s, especially women’s lives.
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                    </p>
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                        </p>
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                </div>
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                        <div class="quote quote-right">
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            </div>
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                            <p>“Biofilms are shit and a big problem in the world” </p>
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            <div class="section-spacer"></div>
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                            <h3>Ria Dinsdale<br>Catheter Fanatic</h3>
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            <div class="section" id="project-choice">
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                         </div>
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                <div class="slim">
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                        <p>
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                    <h2>Project Choice</h2>
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                            Our catheter would have a three-pronged attack on the biofilm. First the biofilm forming in the lining of the bladder, then the biofilm beginning to form on the outside of the catheter itself, and finally attacking the biofilm trying to form on the inside walls of the catheter.
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                    <div id="project-choice-approaching-the-public">
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                        </p>
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                             <h3>Approaching the Public</h3>
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                        <p>
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                            Our initial research into the current designs of catheter began online, where we started to get a better understanding of the size that we were working with. We looked into the problems with insertion, removal and general life with having a catheter in place. Through out the design process we attempted to keep these constantly in our mind in order to create something that would not only help with infection but was practical for the patient, doctor and manufacturer.
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                        </p>
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                        <p>
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                            To get some more first hand experience of how small a catheter is we purchased a catheter. This made us realise how small our containment method would have to be. As UTIs mainly affect women we decided to buy a 14F female Foley catheter. This gave us a much better idea of the size we were working with i.e. very small. Knowing this leads us to adjust the chemical that we were hoping to use to make the beads that will contain our bacteria.
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                        </p>
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                        <p>
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                            The idea of having a containment method as part of our project was first realised during the safety research as it would be dangerous to allow free bacteria into the human body. This could lead to possible fatal consequence as the bacteria could mutate and you don’t know what will happen in several generations.
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                        </p>
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                        <p>
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                            However to reduce the risk of infect we would not be able to access the beads for the duration on the catheter being in place, as this could allow for foreign bacteria to get into the urinary tract and cause greater infection. Therefore any nutrients that the bacteria would need have to be present in the beads, or be available from the urine running through the catheter.
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                        </p>
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                        <p>
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                            The bacteria would have to be able to survive for 3 months so in an ideal world we would have been able to test the bacteria in the beads, for 3 months, however the time scale of the project did not allow us to do that as the concept of the beds was not realised until the later stages of the project. We would have also liked to tested whether or not the bead would remain in tack out of the CaCl2 for 3 months, and potential storage methods for the beads. Freezing the beads was however tested and found to be unsuccessful.
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                        </p>
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                        <p>
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                            The gel must not be toxic to humans that we would have to make sure of, relates to the safety of the catheter. If we use a silicone polymer either as a sheet or in fibres then many medical devices are made from silicone due to its inert characteristics and the fact that it doesn’t cause any unwanted side effects. Therefore this fits in with the safety side of the project. Catheters themselves are made from silicon so it shows that they are safe to put into the body.
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                        </p>
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                    </div>
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                    <div class="section" id="beads">
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                        <h2>Beads containing Bacteria</h2>
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                        <div id="beads-intro">
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                             <h3>Introduction</h3>
+
 
                             <p>
 
                             <p>
−
                                 In order to stop the biofilm forming on the inside of the catheter it will contain beads that have our bacteria encapsulated inside of them however the protein is still able to diffuse out. This is needed as a way to contain the bacteria so they won’t be free in the urinary tract and therefore cause potential health problems for the patient.
+
                                 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.
 
                             </p>
 
                             </p>
 
                             <p>
 
                             <p>
−
                                 These beads could also be contained outside the body inside a bag of sterile water; this bag would then be plugged into a 3-way Foley catheter. This solution would then be washed through the catheter and into the bladder, therefore tackling any infection that may be present in the lining of the bladder.
+
                                 Examples of their suggestions for the applications of synthetic biology include bacteria which:
 
                             </p>
 
                             </p>
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                             <div class="image image-right">
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                             <ul>
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                                 <img src="https://static.igem.org/mediawiki/2015/6/66/Ox_Beads_design.JPG" />
+
                                 <li>Remove carbon dioxide from the atmosphere</li>
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                                 <p>First attempt at making the beads using Sodium Alginate</p>
+
                                <li>Target and kill cancerous cells</li>
−
                             </div>
+
                                <li>Help treat Alzheimer's disease</li>
 +
                                <li>Produce energy</li>
 +
                                <li>Sew up holes in clothes</li>
 +
                                <li>Produce teeth glue</li>
 +
                                <li>Indicate how long someone has been dead for</li>
 +
                                 <li>Combat antibiotic resistance</li>
 +
                             </ul>
 
                             <p>
 
                             <p>
−
                                 To see our process of designing and making the beads, look <a href="#">here.</a>
+
                                 Of our responses, around 40 were related to Medicine and Health [<a href="#PRef1">1</a>]. 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.
 
                             </p>
 
                             </p>
 
                             <p>
 
                             <p>
−
                                 One problem with using an alginate to encapsulate the bacteria is that they are only structurally sound over a short period of time and break down over longer periods. This poses a problem, as the beads could therefore not be used to treat urinary tract infections were the catheter is to remain in place for up to 3 months.
+
                                 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>
 +
                    </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>
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                        <div id="beads-proof">
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                    <div id="project-choice-our-inspiration">
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                             <h3>Proof of Principle</h3>
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                             <h3>Our Inspiration</h3>
 
                             <p>
 
                             <p>
−
                                Our first aim was to be able to make beads that would be small enough to fit inside of a catheter.
 
 
                             </p>
 
                             </p>
 +
                    </div>
 +
                        <div id="project-choice-our-inspiration-jorge-talk">
 +
                            <h4>Jorge Talk</h4>
 
                             <p>
 
                             <p>
−
                                To do this we got several catheters from the local hospital and cut one open.
 
 
                             </p>
 
                             </p>
 +
                        </div>
 +
                        <div id="project-choice-our-inspiration-churchill">
 +
                            <h4>Churchill Hospital, Oxford</h4>
 
                             <p>
 
                             <p>
−
                                 We then wanted to show that we could get the bacteria inside of the beads. To do this we created beads that contained fluorescent bacteria. The bacteria we used were from the interlab study, 20K MG, 20K deltaF, 20K DH5 and as a negative control we used MG(-).
+
                                 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.
 
                             </p>
 
                             </p>
 
                             <p>
 
                             <p>
−
                                 Sets of the beads were made up for 3 days and the fluorescence was measured using the GFP protocol on the Flurostar machine.
+
                                 Jan also made the following points:
 
                             </p>
 
                             </p>
 +
                            <ul>
 +
                                <li>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</li>
 +
                                <li>If a patient becomes septic the catheter has to be removed or can be fatal</li>
 +
                                <li>UTIs are not just contracted by the catheter and it is important to also consider community based UTIs</li>
 +
                                <li>“UTIs are very common and can be quite painful”</li>
 +
                                <li>No separate ward for UTIs – they are treated in every ward</li>
 +
                                <li>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</li>
 +
                                <li>Elderly hospital wards are likely to have many cases of UTIs</li>
 +
                            </ul>
 
                             <p>
 
                             <p>
−
                                 From the data it can be shown that the wells that contain a beads made with fluorescent bacteria encapsulated have a much higher fluorescence than the beads made without any bacteria and the beads made with the negative control bacteria. Therefore we can conclude that the bacteria are encapsulated inside of the beads.
+
                                 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.
 
                             </p>
 
                             </p>
 
                         </div>
 
                         </div>
 +
                        <div id="project-choice-our-inspiration-jr">
 +
                            <h4>John Radcliffe Hospital, Oxford</h4>
 +
                            <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.
 +
                            </p>
 +
                            <div id="project-choice-our-inspiration-jr-evans">
 +
                                <h4>First interview with Laura Evans, Adams Ward</h4>
 +
                                <p>
 +
                                    What is the procedure for treating UTIs?
 +
                                </p>
 +
                                <ol class="interview-response">
 +
                                    <li><em>Dip urine</em></li>
 +
                                    <li><em>If the test comes back as positive, treat with a wide spectrum antibiotic</em></li>
 +
                                    <li><em>Whether or not the catheter is inserted with prophylactic antibiotic treatment is the doctor’s decision</em></li>
 +
                                </ol>
 +
                                <p>
 +
                                    What happens when a patient tests positive for a urinary infection?
 +
                                </p>
 +
                                <p class="interview-response">
 +
                                    <em>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.</em>
 +
                                </p>
 +
                                <p>
 +
                                    Is antibiotic resistance a problem?
 +
                                </p>
 +
                                <p class="interview-response">
 +
                                    <em>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.</em>
 +
                                </p>
 +
                                <p>
 +
                                    Our project involves designing a catheter that prevents the formation of a biofilm on its surface. What do you think of this idea?
 +
                                </p>
 +
                                <p class="interview-response">
 +
                                    <em>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.</em>
 +
                                </p>
 +
                                <p>
 +
                                    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.
 +
                                </p>
 +
                            </div>
 +
                        </div>
 +
                    <div id="project-choice-the-problem">
 +
                            <h3>The Problem</h3>
 +
                            <p>
 +
                                Following our inspiring visits to the Churchill and John Radcliffe hospitals, we wanted to find out the public thought about the problem of antibiotic resistance. We posed the question:
 +
                                <em>To what extent do you feel that antibiotic resistance is a problem that needs addressing in society today?</em>
 +
                                <div class="image image-full">
 +
                                    <img src="https://static.igem.org/mediawiki/2015/d/dd/Ox_Q2_antibiotic_resistance.png">
 +
                                </div>
 +
                                <p>
 +
                                    Our survey clearly shows that, according to the general public, antibiotic resistance is an important problem that needs solving. Therefore we felf it was a useful area to direct our project towards. One of our team members, George, worked in a UTI clinic over the summer of 2014, so he knows first-hand that UTIs are a big problem for a lot of people and that, in severe cases, current methods of treatment are inadequate. When he brought this to our attention, we thought it was worthwile trying to find a solution to this problem.
 +
                                </p>
 +
                            </p>
 
                     </div>
 
                     </div>
−
                     <div class="section" id="semi">
+
                        <div id="project-choice-the-problem-experts">
−
                        <h2>Semi-Permeable Membrane</h2>
+
                            <h4>Feedback from Oxford Experts</h4>
 +
                            <p>
 +
                              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:
 +
                            </p>
 +
                            <ul>
 +
                              <li>Have you considered whether the proteins you planning on secreting are immunogenic?</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>
 +
                        </div>
 +
                     <div id="project-choice-our-solution">
 +
                          <h3>Our Solution</h3>
 +
                          <p>
 +
                          </p>
 +
                    </div>
 +
                </div>
 +
            </div>
 +
            <div class="section-spacer"></div>
 +
            <div class="section" id="project-viability">
 +
                <div class="slim">
 +
                    <h2>Project Viability</h2>
 +
                    <p>
 +
                        Now that we had decided on our project choice, we needed to find out if it wolud be feasible and, if so, what obstacles we wolud need to overcome.
 +
                    </p>
 +
                    <div id="project-viability-bacterial-sustainability">
 +
                        <h3>Bacterial Sustainability</h3>
 
                         <p>
 
                         <p>
−
                            A selectively permeable would be used inside the catheter to contain the beads in a compartment. This membrane would supply a second physical defence against the bacteria getting into the urinary tract as well as a method for containing the beads. The membrane would be similar to the membrane used in a dialysis machine, therefore the urine and protein could diffuse through it but the bacteria would remain contained. Our largest protein is roughly 40 kDa so therefore the membrane that we use would have to have pores with a large enough diameter to allow it through. Membranes for dialysis tubing is made of several different materials, for example, polysulfone, polyethersulfone (PES), etched polycarbonate, or collagen. The pores would also have to be large enough to allow through all the components on the urine otherwise you would get a build up in the catheter and therefore could cause potential problems.
+
                          We made our first steps in the right direction after visiting the Bedford Ward at the John Radcliffe Hospital. We spoke with one of the catheterised patients there called Mavis. She admitted to having had urinary infections in the past, but said she had not contracted a UTI since having a catheter fitted.
 
                         </p>
 
                         </p>
 
                         <p>
 
                         <p>
−
                            For our catheter a polysulfone would be best for our membrane as it is most commonly used in the medical profession and in dialysis machines. You can therefore control the size of the pores in the synthesis and so be able to form the pores size that was required.
+
                          We found that Mavis would possibly use the same catheter 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 class="section" id="coating">
+
                     <div id="project-viability-ethics">
−
                         <h2>Coating</h2>
+
                         <h3>Ethics</h3>
 
                         <p>
 
                         <p>
−
                             To stop the biofilm forming on the outside of the catheter the idea would to immobilize it into a gel that would be attached to the outer surface of the catheter. One idea would be to form the gel into fibres and therefore could then be wrapped around the outside of the catheter that would adhere with some kind of medical grade adhesive. These fibres would therefore have a large surface area to volume ratio ensuring that there was greater diffusion of the DNase and DispB out of the gel therefore tackling the infection as quickly as possible.
+
                             To find out the public opinion on our project, we sent out a questionnaire to over 150 people, asking: <em>'If your doctor recommended a treatment for an infection, which involved the use of bacteria that had been engineered to treat the infection, would you use it?'</em>. We also asked this question to a number of medical professionals during our visits to hospitals and clinics.
 
                         </p>
 
                         </p>
 
                         <p>
 
                         <p>
−
                             This idea has been used in previous catheters that are currently on the market. These coatings have, and do, contain silver nanoparticles, antibiotics etc etc
+
                             Whilst the majority of feedback was very positive, we did encounter some valuable criticism, as shown in the graph below. Most medical professionals we spoke to had positive responses, though one nurse did have certain reservations about our idea.
 
                         </p>
 
                         </p>
 +
                        <div class="image image-full">
 +
                            <img src="https://static.igem.org/mediawiki/2015/1/15/Ox_Q2_doctor_recommendation.png">
 +
                        </div>
 
                         <p>
 
                         <p>
−
                             Idea would be to encase our bacteria in a thin sol-gel film, which would keep it contained on the catheter but be able to maintain its activity from inside the gel. The properties of the gel could be selected so that it would be hydrophilic, this would aid in the insertion of the catheter and comfort for the patient when the catheter was in place. This would contain the bacteria but it would still be able to produce the protein and it would still be able to diffuse out. This is where our kill switch design would be particularly useful as if the bacteria were to escape the matrix then the kill switch would be able to cause the bacteria to die. In the time that we have in order to complete our project, synthesising these isn’t something we could attempt however there are papers that have shown it to work.
+
                             This proportion of negative feedback, although small, highlighted to us that our dialogue with the public needed to be improved. We believe that, through improving people's understanding of our project, we can convince pessimists that genetic engineering is now a force for good. This also led us onto holding talks to student groups, which you can find in the <a href="#project-viability-increasing-awareness">Increasing Awareness</a> section below.
 
                         </p>
 
                         </p>
 
                         <p>
 
                         <p>
−
                             Coatings seem to be hydrophilic polymers, e.g. hydrogels. This is because when the coating comes in contact with water the gel swells slightly and the surface becomes smooth and slipper therefore easing insertion.
+
                             Nevertheless, this is very encouraging data for our project, and again highlights the importance of gaining support from doctors, because without their backing, this project is likely never to become as common a treatment as antibiotics.
 
                         </p>
 
                         </p>
 +
                    </div>
 +
                    <div id="project-viability-the-uti-clinic">
 +
                        <h3>The UTI Clinic</h3>
 
                         <p>
 
                         <p>
−
                            Another potential for a coating would be to make the fibres out of the Sodium Alginate. This would need testing.
 
−
 
 
                         </p>
 
                         </p>
 
                     </div>
 
                     </div>
−
                     <div class="section" id="man">
+
                     <div id="project-viability-delivery-method">
−
                         <h2>Manufacturing</h2>
+
                         <h3>Delivery Method</h3>
 
                         <p>
 
                         <p>
−
                             Currently catheters are very cheap to produce, find out how much, therefore as part of our project we decided to look into how we could introduce the beads into the pipe during the manufacturing process. We spoken to a mechanical engineer, Steven Dinsdale, and he help us with a design for a machine that could do this. The machine would use the technique of extrusion to make the tube and then a second cooled inflow tube would introduce the beads. This would hopefully keep the bacteria cool enough so they are not killed yet the polymer would be hot enough to melt and then form the tube.
+
                             Now that we had focused our project towards treatment of CAUTIs, we needed a suitable catheter design. We needed some method by which we could expose the catheter, and bladder, to our anti-microbial proteins, and in a safe manner.
 
                         </p>
 
                         </p>
−
                         <div class="image image-full">
+
                         <p>
−
                            <img src="https://static.igem.org/mediawiki/2015/b/b5/Ox_Steve.PNG" />
+
                            First, we considered the idea of having our bacteria implanted within the patient, in the confines of the catheter. It was of paramount importance that we make sure the bacteria would be safely contained, and not be able to escape into the bladder to cause further infection.
−
                             <p>Manufacturing idea from mechanical engineer Steven Dinsdale</p>
+
                        </p>
 +
                        <p>
 +
                            Our team member Ria Dinsdale made the suggestion of using sol-gel as a possible method of containment. Despite being a very convincing idea, we found that it would be too difficult to design under the time restraints of the summer.
 +
                        </p>
 +
                        <p>
 +
                            However, we subseqently found an alternative containment method,
 +
                            which we resurrected from the Oxford iGEM 2014 project 'DCMation'. Our predecessors' project also had to find a method of bacterial containment.
 +
                        </p>
 +
                    </div>
 +
                        <div id="project-viability-delivery-method-biobeads">
 +
                            <h4>BioBeads</h4>
 +
                            <div class="image image-right">
 +
                                    <img src="https://static.igem.org/mediawiki/2015/6/66/Ox_Beads_design.JPG" />
 +
                                    <p>First attempt at making the beads using Sodium Alginate</p>
 +
                            </div>
 +
                             <p>
 +
                                The 2014 team encapsulated their bacteria in agarose to form BioBeads. These BioBeads were then given an outer coating of cellulose acetate, to allow flow of molecules into and out of the bead, whilst preventing the escape of their bacteria.
 +
                            </p>
 +
                            <p>
 +
                                This year, we have been able to significantly improve the BioBead concept, by changing our inner material to sodium alginate, and our outer material to polystyrene; something which is still a work in progress. For full details on our developements on BioBeads, check out our <a href="https://2015.igem.org/Team:Oxford/Design">Design</a> page!
 +
                            </p>
 
                         </div>
 
                         </div>
 +
                        <div id="project-viability-delivery-method-catheter-design">
 +
                            <h2>Catheter design</h2>
 +
                            <p>
 +
                                Currently catheters are very cheap to produce, find out how much, therefore as part of our project we decided to look into how we could introduce the beads into the pipe during the manufacturing process. We spoken to a mechanical engineer, Steven Dinsdale, and he help us with a design for a machine that could do this. The machine would use the technique of extrusion to make the tube and then a second cooled inflow tube would introduce the beads. This would hopefully keep the bacteria cool enough so they are not killed yet the polymer would be hot enough to melt and then form the tube.
 +
                            </p>
 +
                            <div class="image image-full">
 +
                                <img src="https://static.igem.org/mediawiki/2015/b/b5/Ox_Steve.PNG" />
 +
                                <p>Manufacturing idea from mechanical engineer Steven Dinsdale</p>
 +
                            </div>
 +
                            <p>
 +
                                Potential problems:
 +
                            </p>
 +
                            <ul>
 +
                                <li>If this design were used for catheter production the bacteria would potentially not survive the sterilisation process at the end of the manufacturing.</li>
 +
                                <li>Steps further down in the manufacturing process could harm out bacteria.</li>
 +
                                <li>The bacteria may not survive in storage due to the length of time stored, temperature, etc</li>
 +
                            </ul>
 +
                        </div>
 +
                    <div id="project-viability-increasing-awareness">
 +
                        <h3>Increasing Awareness</h3>
 
                         <p>
 
                         <p>
−
                             Potential problems:
+
                             To promote Synthetic Biology and iGEM, we’ve used a variety of approaches.
 
                         </p>
 
                         </p>
−
                         <ul>
+
                         <div id="project-viability-increasing-awareness-uniq-workshop">
−
                            <li>If this design were used for catheter production the bacteria would potentially not survive the sterilisation process at the end of the manufacturing.</li>
+
                                <h4>UNIQ Workshop</h4>
−
                            <li>Steps further down in the manufacturing process could harm out bacteria.</li>
+
                                <p>
−
                            <li>The bacteria may not survive in storage due to the length of time stored, temperature, etc</li>
+
                                    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.
−
                         </ul>
+
                                </p>
 +
                        </div>
 +
                        <div id="project-viability-increasing-awareness-utc-oxfordshire">
 +
                                <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>
 
             </div>
 
             </div>
−
            <div class="col-md-3 contents-sidebar">
+
        </div>
−
                <ul id="sidebar" class="nav nav-stacked" data-spy="affix">
+
        <div class="col-md-3 contents-sidebar">
−
                    <li><a href="#introduction">Introduction</a></li>
+
            <ul id="sidebar" class="nav nav-stacked" data-spy="affix">
−
                    <li>
+
                <li><a href="#introduction">Introduction</a></li>
−
                         <a href="#beads">Beads</a>
+
                <li><a href="#project-choice">Project Choice</a>
−
                        <ul class="nav nav-stacked">
+
                    <ul class="nav nav-stacked">
−
                            <li><a href="#beads-intro">Introduction</a></li>
+
                         <li><a href="#project-choice-approaching-the-public">Approaching the Public</a>
−
                             <li><a href="#beads-proof">Proof of Principle</a></li>
+
                            <ul class="nav nav-stacked">
−
                         </ul>
+
                                <li><a href="#project-choice-approaching-the-public-initial-feedback">Initial Feedback</a></li>
−
                    </li>
+
                             </ul>
−
                     <li><a href="#semi">Semi-Permeable Membrane</a></li>
+
                        </li>
−
                    <li><a href="#coating">Coating</a></li>
+
                        <li><a href="#project-choice-our-inspiration">Our Inspiration</a>
−
                    <li><a href="#man">Manufacturing</a></li>
+
                            <ul class="nav nav-stacked">
−
                </ul>
+
                                <li><a href="#project-choice-our-inspiration-jorge-talk">Jorge Talk</a></li>
−
             </div>
+
                                <li><a href="#project-choice-our-inspiration-churchill">Churchill Hospital, Oxford</a></li>
 +
                                <li><a href="#project-choice-our-inspiration-jr">John Radcliffe Hospital, Oxford</a>
 +
                                    <ul class="nav nav-stacked">
 +
                                      <li><a href="#project-choice-our-inspiration-jr-evans">First Interview with Laura Evans, Adams Ward<li></a>
 +
                                    </ul>
 +
                                </li>
 +
                            </ul>
 +
                         </li>
 +
                        <li><a href="#project-choice-the-problem">The Problem</a>
 +
                            <ul class="nav nav-stacked">
 +
                                <li><a href="#project-choice-the-problem-experts">Feedback from Oxford Experts</a></li>
 +
                            </ul>
 +
                        </li>
 +
                        <li><a href="#project-choice-our-solution">Our Solution</a></li>
 +
                     </ul>
 +
                </li>
 +
                <li><a href="#project-viability">Project Viability</a>
 +
                      <ul class="nav nav-stacked">
 +
                          <li><a href="#project-viability-bacterial-sustainability">Bacterial Sustainability </a></li>
 +
                          <li><a href="#project-viability-ethics">Ethics</a></li>
 +
                          <li><a href="#project-viability-the-uti-clinic">The UTI Clinic</a></li>
 +
                          <li><a href="#project-viability-delivery-method">Delivery Method</a>
 +
                              <ul class="nav nav-stacked">
 +
                                  <li><a href="#project-viability-delivery-method-biobeads">BioBeads</a></li>
 +
                                  <li><a href="#project-viability-delivery-method-catheter-design">BioBeads</a></li>
 +
                              </ul>
 +
                          </li>
 +
                          <li><a href="#project-viability-increasing-awareness">Increasing Awareness</a>
 +
                              <ul class="nav nav-stacked">
 +
                                  <li><a href="#project-viability-increasing-awareness-uniq-workshop">UNIQ Workshop</a></li>
 +
                                  <li><a href="#project-viability-increasing-awareness-utc-oxfordshire">UTC Oxfordshire</a></li>
 +
                                  <li><a href="#project-viability-increasing-awareness-bbc-radio-oxford">BBC Radio Oxford</a></li>
 +
                              </ul>
 +
                          </li>
 +
                      </ul>
 +
                </li>
 +
             </ul>
 
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Revision as of 12:14, 10 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.

Project Choice

Approaching the Public

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.

Our Inspiration

Jorge Talk

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.

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.

The Problem

Following our inspiring visits to the Churchill and John Radcliffe hospitals, we wanted to find out the public thought about the problem of antibiotic resistance. We posed the question: To what extent do you feel that antibiotic resistance is a problem that needs addressing in society today?

Our survey clearly shows that, according to the general public, antibiotic resistance is an important problem that needs solving. Therefore we felf it was a useful area to direct our project towards. One of our team members, George, worked in a UTI clinic over the summer of 2014, so he knows first-hand that UTIs are a big problem for a lot of people and that, in severe cases, current methods of treatment are inadequate. When he brought this to our attention, we thought it was worthwile trying to find a solution to this problem.

Feedback from Oxford Experts

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?

Our Solution

Project Viability

Now that we had decided on our project choice, we needed to find out if it wolud be feasible and, if so, what obstacles we wolud need to overcome.

Bacterial Sustainability

We made our first steps in the right direction after visiting the Bedford Ward at the John Radcliffe Hospital. We spoke with one of the catheterised patients there called Mavis. She admitted to having had urinary infections in the past, but said she had not contracted a UTI since having a catheter fitted.

We found that Mavis would possibly use the same catheter 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.

Ethics

To find out the public opinion on our project, we sent out a questionnaire to over 150 people, asking: 'If your doctor recommended a treatment for an infection, which involved the use of bacteria that had been engineered to treat the infection, would you use it?'. We also asked this question to a number of medical professionals during our visits to hospitals and clinics.

Whilst the majority of feedback was very positive, we did encounter some valuable criticism, as shown in the graph below. Most medical professionals we spoke to had positive responses, though one nurse did have certain reservations about our idea.

This proportion of negative feedback, although small, highlighted to us that our dialogue with the public needed to be improved. We believe that, through improving people's understanding of our project, we can convince pessimists that genetic engineering is now a force for good. This also led us onto holding talks to student groups, which you can find in the Increasing Awareness section below.

Nevertheless, this is very encouraging data for our project, and again highlights the importance of gaining support from doctors, because without their backing, this project is likely never to become as common a treatment as antibiotics.

The UTI Clinic

Delivery Method

Now that we had focused our project towards treatment of CAUTIs, we needed a suitable catheter design. We needed some method by which we could expose the catheter, and bladder, to our anti-microbial proteins, and in a safe manner.

First, we considered the idea of having our bacteria implanted within the patient, in the confines of the catheter. It was of paramount importance that we make sure the bacteria would be safely contained, and not be able to escape into the bladder to cause further infection.

Our team member Ria Dinsdale made the suggestion of using sol-gel as a possible method of containment. Despite being a very convincing idea, we found that it would be too difficult to design under the time restraints of the summer.

However, we subseqently found an alternative containment method, which we resurrected from the Oxford iGEM 2014 project 'DCMation'. Our predecessors' project also had to find a method of bacterial containment.

BioBeads

First attempt at making the beads using Sodium Alginate

The 2014 team encapsulated their bacteria in agarose to form BioBeads. These BioBeads were then given an outer coating of cellulose acetate, to allow flow of molecules into and out of the bead, whilst preventing the escape of their bacteria.

This year, we have been able to significantly improve the BioBead concept, by changing our inner material to sodium alginate, and our outer material to polystyrene; something which is still a work in progress. For full details on our developements on BioBeads, check out our Design page!

Catheter design

Currently catheters are very cheap to produce, find out how much, therefore as part of our project we decided to look into how we could introduce the beads into the pipe during the manufacturing process. We spoken to a mechanical engineer, Steven Dinsdale, and he help us with a design for a machine that could do this. The machine would use the technique of extrusion to make the tube and then a second cooled inflow tube would introduce the beads. This would hopefully keep the bacteria cool enough so they are not killed yet the polymer would be hot enough to melt and then form the tube.

Manufacturing idea from mechanical engineer Steven Dinsdale

Potential problems:

  • If this design were used for catheter production the bacteria would potentially not survive the sterilisation process at the end of the manufacturing.
  • Steps further down in the manufacturing process could harm out bacteria.
  • The bacteria may not survive in storage due to the length of time stored, temperature, etc

Increasing Awareness

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.

BBC Radio Oxford