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| − | <li><a href="#ove">Overview</a></li> | + | <li><a href="#bro">Bronze</a></li> |
| − | <li><a href="#int">Introduction</a></li> | + | <li><a href="#sli">Silver</a></li> |
| − | <li> | + | <li><a href="#gol">Gold</a></li> |
| − | <a href="# mec"> Mechanism</a> | + | |
| − | <ul>
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| − | <li><a href="#nov">Liquid Sample without Virus</a></li>
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| − | <li><a href="#vi">Liquid Sample with Virus</a></li>
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| − | </ul>
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| − | </li>
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| | <article> | | <article> |
| − | <section id="ove"> | + | <p>We summarize our achievements fulfilling the criteria of the medals as follows:</p> |
| − | <h2>Overview</h2> | + | <h3>Abbreviations</h3> |
| − | <p>Dengue fever has been a severe problem in Taiwan for a long time, but there is still no vaccine to prevent it and no medicine to cure it. Therefore, we tried to tackle this problem by producing the peptides of the tandem repeat sequences (PTRSs) that can bind to the envelope protein (E protein) of the dengue virus, providing an alternative opportunity for detection and prevention.</p> | + | <p>AuNP: gold nanoparticle<br>CLEC5A: C-type lectin domain, family 5, member A<br>E protein: dengue virus envelope protein<br>LAE: linear array epitope<br>PTRS: peptide of tandem-repeated sequence<br>TR-PCR: template-repeat PCR<br>TRS: tandem-repeated sequence</p> |
| | + | <section id="bro"> |
| | + | <h2>Bronze</h2> |
| | + | <h3>Competition Deliverables</h3> |
| | + | <ul> |
| | + | <li>Wiki: Visit our Wiki pages to see a complete description of what we have done this year.</li> |
| | + | <li>Poster: Check our Poster page to see the interactive poster.</li> |
| | + | <li>Presentation Video: Enjoy our Presentation video to see a summary of our project.</li> |
| | + | <li>Project Promotion Video: Our Project promotion video explains the importance of our project.</li> |
| | + | <li>Judging Form: We have filed this judging form properly before the deadline.</li> |
| | + | </ul> |
| | <br> | | <br> |
| − | <p>Currently, no dengue virus detection kits are made in Taiwan. Thus, our team decided to develop a detection kit for dengue virus. We used PTRSs to capture the targets in our detection kit instead of commonly used antibodies. The following are the advantages of PTRSs compared to antibodies.</p> | + | <h3>Project Description</h3> |
| | <ul> | | <ul> |
| − | <li><b>Lower cost</b></li> | + | <li>We chose dengue fever as our topic because it is listed as a top 10 health threat by WHO, and Taiwan is in the region under the threat of dengue fever.</li> |
| − | <p>PTRSs are shorter and have a simpler structure than antibodies. Thus, the production costs of PTRSs are much lower.</p>
| + | <li>Since there is no effective medicine for dengue fever, our main goal is to detect the dengue virus early to keep patients from developing severe symptoms.</li> |
| − | <li><b>Longer storage</b></li> | + | <li>We found that the interaction between CLECE5A and the envelope protein of the dengue virus is the key leading to severe dengue. We developed a detection kit based on this interaction.</li> |
| − | <p>Because PTRSs are linear and short sequence, they are not easily denatured. </p> | + | <li>We produced peptides using a PCR technique, LAE, which could massively produce peptides as the detection agents in the detection kit.</li> |
| − | <li><b>Fast production</b></li> | + | <li>We used Rosetta to simulate the interactions between the PTRSs with E protein to confirm our proposed design.</li> |
| − | <p>The production of antibodies requires injection of antigens into a mouse or a rabbit. After injection, several months are required to produce the antibodies. This procedure is too complex and time consuming. We use linear array epitope (LAE) to produce PTRSs, which can greatly reduce the production time, especially with the short sequences and simple structures of PTRSs.</p>
| + | <li>We consulted with professional experts and governmental agencies to make the design of our detection kit more effective.</li> |
| − | <li><b>Easy modification</b></li> | + | |
| − | <p>A big advantage of PTRSs is that they can be modified easily. If the dengue virus mutates, we can rapidly change PTRSs to detect the mutated strain.</p> | + | |
| | </ul> | | </ul> |
| | + | <br> |
| | + | <h3>Attributions</h3> |
| | + | <p>Check our Attributions page to see who helped us. We appreciate the all the support we have received.</p> |
| | + | <br> |
| | + | <h3>Contribution</h3> |
| | + | <p>We provide a novel PCR method, LAE, to produce TRS.</p> |
| | </section> | | </section> |
| | <br> | | <br> |
| − | <section id="int"> | + | <section id="sil"> |
| − | <h2>Introduction</h2> | + | <h2>Silver</h2> |
| − | <p>We use a lateral flow immunochromatographic assay like the one used in a pregnancy test, mounted with PTRSs to detect the dengue virus. Our detection kit consists of the sample pad, conjugate pad, test line, control line, and absorbent pad. The sample pad and absorbent pad are made of cellulose fibers, the conjugate pad is made of glass fiber and the test line and the control line are on the other glass fiber. The functions of these pads are:</p> | + | <h3>Engineering Success</h3> |
| | <ul> | | <ul> |
| − | <li>Sample pad is where the liquid sample is placed.</li> | + | <li></li> |
| − | <li>Conjugate pad is where the dengue virus reacts with PTRSs.</li> | + | <li></li> |
| − | <li>Test line indicates a positive result.</li> | + | <li></li> |
| − | <li>Control line ensures that the detection kit is reliable.</li> | + | <li></li> |
| − | <li>Absorbent pad absorbs water and prevents the backflow.</li> | + | <li></li> |
| | </ul> | | </ul> |
| − | </section>
| |
| − | <br>
| |
| − | <section>
| |
| − | <div id="mec">
| |
| − | <h2>Mechanism</h2>
| |
| − | <p>Two PTRSs that can bind with the dengue virus E protein are required. The first PTRSs (PTRS-1) is attached to gold nanoparticles and placed on the conjugate pad. The second PTRSs (PTRS-2) is placed on the test line. E proteins from the dengue virus are expressed and conjugated on the control line.</p>
| |
| − | <br>
| |
| − | <p>Since both PTRSs bind to the E proteins, if present, dengue virus will bind to PTRS-1 which are attached to the gold nanoparticles on the conjugate pad, then bind to PTRS-2 on the test line. PTRS-1, with the attached nanoparticles, will always bind to the E proteins on the control line.</p>
| |
| − | <br>
| |
| − | <p>Gold nanoparticles appear red when they aggregate, and the red color is visible with the naked eye, as shown in Figure 1.</p>
| |
| − | <div id="imginfo">
| |
| − | <img width="80%" src="https://static.igem.org/mediawiki/2020/4/49/T--CCU_Taiwan--Design_0.png">
| |
| − | <p>Figure 1. Components of the detection kit</p>
| |
| − | </div>
| |
| − | </div>
| |
| | <br> | | <br> |
| − | <div id="nov"> | + | <h3>Collaboration</h3> |
| − | <h3>Liquid Sample without Virus</h3> | + | <ul> |
| − | <p>Figure 2 shows how the detection kit works when the liquid sample does not contain dengue virus. Because there are no virus particles in the liquid sample, PTRS-1 conjugated on gold nanoparticles bind to nothing and flow past the test line. When flowing to the control line, where the E proteins are located, PTRS-1 bind to the E proteins. An aggregation of gold nanoparticles attached to PTRS-1 leads to a red band on the control line.</p> | + | <li>Check our Collaborations page to see who collaborated with us.</li> |
| − | </div>
| + | <li>We mentored NYMU Taipei on using Rosetta for protein modeling and docking.</li> |
| − | <div id="imginfo">
| + | <li>We helped Mingdao iGEM 2020 to examine the metabolites produced by oral bacteria while they provided us green fluorescent proteins (GFPs) as mock E proteins to test the affinity between them and the test line.</li> |
| − | <img width="80%" src="https://static.igem.org/mediawiki/2020/6/69/T--CCU_Taiwan--Design1_1.gif">
| + | <li>We collaborated with Team iGEM IISER Berhampur, which is also working on dengue, to jointly carry out a global survey on dengue. They also helped us to translate our children’s storybook into Hindi.</li> |
| − | <p>Figure 2. Mechanism in absence of dengue virus</p>
| + | </ul> |
| − | </div> | + | |
| | <br> | | <br> |
| − | <div id="vi"> | + | <h3>Human Practices</h3> |
| − | <h3>Liquid Sample with Virus</h3> | + | <ul> |
| − | <p>Figure 3 shows how the detection kit works when the liquid sample contains dengue virus. PTRS-1 conjugated on gold nanoparticles bind to the virus particles in the conjugated pad. When the virus particles reach the test line, the unbound virus surface can interact with PTRS-2 attached to the test line. These restricted virus particles lead to an aggregation of gold nanoparticles, which results in a red band indicating a positive result. The residual gold nanoparticles then flow to the control line. A red band can be found on the control line also due to the aggregation of gold nanoparticles.</p> | + | <li>Check our Human Practices page to see how we connected with society.</li> |
| − | </div> | + | <li>To ensure that our project is socially responsible and could have a substantial impact, we consulted with various government officials, experts and the public to consider how our project would fit into the communities and health care systems.</li> |
| − | <div id="imginfo"> | + | </ul> |
| − | <img width="80%" src="https://static.igem.org/mediawiki/2020/b/b7/T--CCU_Taiwan--Design2_1.gif">
| + | <br> |
| − | <p>Figure 3. Mechanism in presence of dengue virus</p> | + | <h3>Proposed Implementation</h3> |
| − | </div> | + | <ul> |
| | + | <li>Check our Implementation page to see how we plan to implement our project.</li> |
| | + | <li>We targeted our customers and planned a distribution network by establishing the supply chain of our product.</li> |
| | + | <li>We considered how to realize the whole picture by setting goals, both short term and long term.</li> |
| | + | <li>We considered various challenges we would meet when implementing it in society.</li> |
| | + | </ul> |
| | </section> | | </section> |
| | <br> | | <br> |
| − | <hr>
| + | <section id="gol"> |
| − | <section id="ref" style="word-break:break-all; word-wrap:break-all;"> | + | <h2>Gold</h2> |
| − | <h4>References</h4> | + | <h3>Integrated Human Practices</h3> |
| − | <p>Baeumner, Antje J.; Schlesinger, Nicole A.; Slutzki, Naomi S.; Romano, Joseph; Lee, Eun Mi; Montagna, Richard A. Biosensor for dengue virus detection: Sensitive, rapid, and serotype specific. American Chemical Society. Doi: 10.1021/ac015675e<br> | + | <ul> |
| − | Horstick, Olaf; Tozan, Yesim; Wilder-Smith, Annelies. Reviewing Dengue: Still a Neglected Tropical Disease? PLOS Neglected Tropical Diseases. Doi: 10.1371/journal.pntd.0003632<br>
| + | <li>Check our Human Practices page to see how expert opinions shaped our project.</li> |
| − | Lim, Jong Min; Kim, Ji Hong; Ryu, Myung Yi; Cho, Chae Hwan; Park, Tae Jung; Park, Jong Pil. An electrochemical peptide sensor for detection of dengue fever biomarker NS1. Analytica Chimica Acta. Doi: 10.1016/j.aca.2018.04.005<br>
| + | <li>We consulted with Taiwan Food and Drug Administration (TFDA) and Dengue Prevention and Control Center to understand their needs and optimized our product accordingly.</li> |
| − | Mazbahul Kabir; Syamal Raychaudhuri; James William Needham; Stanislaw Morkowski. Lateral Flow Assaysystemand Methods Forts Use. United States Patent and Trademark Office. Patent No.: US 8, 399, 261 B2<br>
| + | <li>We have obtained substantial advice from experts in scientific fields, who directed us how to improve the use of AuNPs in the detection kit.</li> |
| − | Wang, Hsi Kai; Tsai, Cheng Han; Chen, Kuan Hung; Tang, Chung Tao; Leou, Jiun Shyang; Li, Pi Chun; Tang, Yin Liang; Hsieh, Hsyue Jen; Wu, Han Chung; Cheng, Chao Min. Cellulose-based diagnostic devices for diagnosing serotype-2 dengue fever in human serum. WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Doi: 10.1002/adhm.201300150
| + | </ul> |
| − | </p> | + | <br> |
| | + | <h3>Project Modeling</h3> |
| | + | <ul> |
| | + | <li>Details are shown on our Model page.</li> |
| | + | <li>We used Rosetta to generate the structures of the peptides and proteins and simulate their interactions.</li> |
| | + | <li>We employed DLVO theory to calculate the repulsion between gold nanoparticles to confirm there is no chance that two AuNPs could attach to adjoining faces on the virions, which could have prevented binding to the test line.</li> |
| | + | </ul> |
| | + | <br> |
| | + | <h3>Science Communication</h3> |
| | + | <ul> |
| | + | <li>Check our Science Communication page to see how we conducted our educational activities.</li> |
| | + | <li>We created a children’s storybook talking about viruses in Chinese, then translated it into English and Hindi. Those languages are the first three most-spoken languages in the world.</li> |
| | + | <li>We created a podcast program talking about synthetic biology for the younger generation.</li> |
| | + | <li>We recorded a Taiwanese Hokkien audio to disseminate knowledge of dengue for senior citizens.</li> |
| | + | </ul> |
| | + | <br> |
| | + | <h3>Excellence in Another Area</h3> |
| | + | <ul> |
| | + | <li>Check our Science Communication and Inclusivity pages to see how we invited traditionally underrepresented communities to participate in science.</li> |
| | + | <li>We filmed a glove puppetry show to disseminate knowledge of dengue, in a unique collaboration with a professional troupe performing this traditional Chinese art form.</li> |
| | + | <li>We provided science education opportunities to inmates in a juvenile correction school. </li> |
| | + | </ul> |
| | </section> | | </section> |
| | </article> | | </article> |
We summarize our achievements fulfilling the criteria of the medals as follows:
Abbreviations
AuNP: gold nanoparticle
CLEC5A: C-type lectin domain, family 5, member A
E protein: dengue virus envelope protein
LAE: linear array epitope
PTRS: peptide of tandem-repeated sequence
TR-PCR: template-repeat PCR
TRS: tandem-repeated sequence
Bronze
Competition Deliverables
- Wiki: Visit our Wiki pages to see a complete description of what we have done this year.
- Poster: Check our Poster page to see the interactive poster.
- Presentation Video: Enjoy our Presentation video to see a summary of our project.
- Project Promotion Video: Our Project promotion video explains the importance of our project.
- Judging Form: We have filed this judging form properly before the deadline.
Project Description
- We chose dengue fever as our topic because it is listed as a top 10 health threat by WHO, and Taiwan is in the region under the threat of dengue fever.
- Since there is no effective medicine for dengue fever, our main goal is to detect the dengue virus early to keep patients from developing severe symptoms.
- We found that the interaction between CLECE5A and the envelope protein of the dengue virus is the key leading to severe dengue. We developed a detection kit based on this interaction.
- We produced peptides using a PCR technique, LAE, which could massively produce peptides as the detection agents in the detection kit.
- We used Rosetta to simulate the interactions between the PTRSs with E protein to confirm our proposed design.
- We consulted with professional experts and governmental agencies to make the design of our detection kit more effective.
Attributions
Check our Attributions page to see who helped us. We appreciate the all the support we have received.
Contribution
We provide a novel PCR method, LAE, to produce TRS.
Silver
Engineering Success
Collaboration
- Check our Collaborations page to see who collaborated with us.
- We mentored NYMU Taipei on using Rosetta for protein modeling and docking.
- We helped Mingdao iGEM 2020 to examine the metabolites produced by oral bacteria while they provided us green fluorescent proteins (GFPs) as mock E proteins to test the affinity between them and the test line.
- We collaborated with Team iGEM IISER Berhampur, which is also working on dengue, to jointly carry out a global survey on dengue. They also helped us to translate our children’s storybook into Hindi.
Human Practices
- Check our Human Practices page to see how we connected with society.
- To ensure that our project is socially responsible and could have a substantial impact, we consulted with various government officials, experts and the public to consider how our project would fit into the communities and health care systems.
Proposed Implementation
- Check our Implementation page to see how we plan to implement our project.
- We targeted our customers and planned a distribution network by establishing the supply chain of our product.
- We considered how to realize the whole picture by setting goals, both short term and long term.
- We considered various challenges we would meet when implementing it in society.
Gold
Integrated Human Practices
- Check our Human Practices page to see how expert opinions shaped our project.
- We consulted with Taiwan Food and Drug Administration (TFDA) and Dengue Prevention and Control Center to understand their needs and optimized our product accordingly.
- We have obtained substantial advice from experts in scientific fields, who directed us how to improve the use of AuNPs in the detection kit.
Project Modeling
- Details are shown on our Model page.
- We used Rosetta to generate the structures of the peptides and proteins and simulate their interactions.
- We employed DLVO theory to calculate the repulsion between gold nanoparticles to confirm there is no chance that two AuNPs could attach to adjoining faces on the virions, which could have prevented binding to the test line.
Science Communication
- Check our Science Communication page to see how we conducted our educational activities.
- We created a children’s storybook talking about viruses in Chinese, then translated it into English and Hindi. Those languages are the first three most-spoken languages in the world.
- We created a podcast program talking about synthetic biology for the younger generation.
- We recorded a Taiwanese Hokkien audio to disseminate knowledge of dengue for senior citizens.
Excellence in Another Area
- Check our Science Communication and Inclusivity pages to see how we invited traditionally underrepresented communities to participate in science.
- We filmed a glove puppetry show to disseminate knowledge of dengue, in a unique collaboration with a professional troupe performing this traditional Chinese art form.
- We provided science education opportunities to inmates in a juvenile correction school.
