Difference between revisions of "Team:CCU Taiwan/Poster"

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<div class="section full first_text" id="title">
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<img src="https://static.igem.org/mediawiki/2020/f/fb/T--Example--Poster_Title.png">
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<div class="info">
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<div class="title">DENDETX</div>
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<div class="text">You should list all authors and their affiliations here. You can also add the project's abstract.</div>
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<div class="section full" id="goals">
 
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<img src="https://static.igem.org/mediawiki/2020/6/6e/T--Example--Poster_Introduction.png">
 
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<div class="title">Project Goals</div>
 
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<div class="text">
 
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<li>Develop a rapid test for dengue fever to improve treatment outcomes.</li>
 
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<li>Develop a method to mass-produce peptides for virus recognition, reducing cost.</li>
 
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<li>Raise awareness of dengue fever in scientifically illiterate and high-risk groups.</li>
 
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<div style="padding: 20px 0px; width:95%; margin:auto; font-size:14px;">
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<div class="section half" id="introduction">
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<h1> Poster: CCU_Taiwan </h1>
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<img src="https://static.igem.org/mediawiki/2020/6/6e/T--Example--Poster_Introduction.png">
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<br><br>
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<div class="info">
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<div class="title">Introduction</div>
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<div class="text">
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Dengue fever occurs in tropical and subtropical regions. Half of the world population is now at risk, with 390 million infections every year, causing dengue fever to be listed by WHO as a top 10 health threat.
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Dengue fever can progress into more serious conditions like dengue hemorrhagic fever (DHF), which has a 20% mortality rate. If conditions continue to worsen, patients experience dengue shock syndrome (DSS), which has a mortality rate up to 40%. An estimated 500,000 patients develop DHF or DSS, resulting in about 25,000 deaths every year.
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Taiwan is in the area under the threat of dengue virus. From 2014 to 2015, there were over 44,000 confirmed cases during a dengue fever outbreak that spread from Tainan to other cities, causing 228 deaths. Recently, there was local transmission of dengue fever in Taoyuan, showing that the potentially affected population keeps increasing.
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There is no specific treatment or vaccine for dengue, and health care systems are still facing a challenge from dengue fever.
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<div class="section half" id="inspiration">
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<img src="https://static.igem.org/mediawiki/2020/6/6e/T--Example--Poster_Introduction.png">
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<div class="info">
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<div class="title">Inspiration: Interaction between the CLEC5A and E protein suggest proteins might be effective in detection</div>
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<div class="text">
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After infection by the dengue virus, a nonstructural protein, NS1, appears in blood serum early in the infection. The current method of detecting dengue fever uses antibodies to recognize NS1 antigens. Nevertheless, the cost of the antibodies is high, the antibodies are hard to purify, and the procedure of making antibodies is time-consuming.
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We took a step back to seek an alternative. We aimed to find something smaller and easier to produce to detect dengue virus instead of using antibodies. Symptoms of DHF and DSS result from interaction between C-type lectin domain, family 5, member A (CLEC5A) on macrophages and the envelope protein (E proteins) of dengue virus.
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We found the sequences from CLEC5A most likely to bind the dengue virus and confirmed this using Rosetta simulations. We believe these peptides have potential to detect the dengue virus.
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We designed a detection kit with these peptides that can bind to the E protein of dengue virus. This would allow people who may have dengue fever or live in an outbreak region of dengue fever to get treatment or protection and control the spread early.
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<h3> Poster Template </h3>
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<div class="section third" id="lae">
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<p> This poster template will let you create an interactive poster! The poster is divided in two parts: the visual overview on the left and the documentation on the right. The visual overview is broken down into sections that the user can click on. When a user clicks on a poster section in the visual overview, the documentation on the right will display the text and graphics associated with this section of the poster. You can find the documentation on how to use this template, as well as an example here: <a href="https://2020.igem.org/Competition/Deliverables/Poster">https://2020.igem.org/Competition/Deliverables/Poster</a></p>
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<img src="https://static.igem.org/mediawiki/2020/f/f3/T--Example--Poster_Inspiration.png">
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<div class="info">
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<div class="title">Linear Array Epitope</div>
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<div class="text">
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Linear array epitope (LAE) is a technique to produce tandem-repeated sequences (TRSs). After the procedure, the TRSs would be expressed as a long-chain peptide which can be cleaved by an enzyme, resulting in many identical peptides.
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<br><br>
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<b>The procedure of LAE: </b>
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<ol>
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<li>Design DNA oligo primers.</li>
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<li>Template-repeated PCR (TR-PCR).</li>
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<li>Adaptor PCR (AD-PCR).</li>
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</ol>
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For the primer design, TR-PCR primers need to be partially complementary to each other and AD-PCR primers need to have restriction sites.
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In TR-PCR, those primers act as both primer and template and they are partially complementary. The TRSs can be produced during the PCR cycling process. In AD-PCR, restriction sites need be introduced into the products of TR-PCR by adding the AD-PCR primers in PCR.
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<div class="section third" id="parts">
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<img src="https://static.igem.org/mediawiki/2020/c/c5/T--Example--Poster_Problem.png">
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<div class="info">
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<div class="title">Parts</div>
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<div class="text">
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The BioBrick of TRSs is composed of T7 promoter, lac operator, thrombin site, TRSs, and His tag.
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The BioBrick of E protein is composed of a T7 promoter, lac operator, thrombin site, E protein gene, HA tag, and His tag.
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The BioBrick of CLEC5A is composed of a T7 promoter, lac operator, thrombin site, CLEC5A gene, Myc tag, and His tag.
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Our peptides and proteins were expressed in E. Coli with T7 promotor and lac operator, which can be induced by IPTG. The thrombin site was included to remove unnecessary sections. The His tag was used in Western blot to confirm the expression of protein, and the HA tag and myc tag were utilized for purification.
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<div class="section third" id="modeling">
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<img src="https://static.igem.org/mediawiki/2020/9/90/T--Example--Poster_Idea.png">
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<div class="info">
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<div class="title">Modeling: Interaction between the tandem-repeated sequence peptide and E protein</div>
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<div class="text">
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<b>Purpose:</b>
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<br>
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Our goal is to design a peptide of tandem-repeated sequence (PTRSs) to imitate the binding of CLEC5A to the E protein from the dengue virus. In order to ensure the PTRSs and the E protein interact, all the structure of PTRSs and proteins and their interactions were modeled using Rosetta.
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<br><br>
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<b>Method and Results:</b>
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<ol>
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<li>The structure of E protein (Figure 1) from a local strain (PL046) was generated using RosettaCM (comparative modeling with Rosetta) based on the crystal structure (PDB: 1OAN).</li>
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<li>The structures of PTRSs were predicted purely based on their sequences using the <i>ab initio</i> method in Rosetta, and the representative structures are shown in Figure 2.</li>
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<li>The most probable structure of the PTRS were identified by clustering.</li>
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<li>The interactions between the PTRSs and the E protein were evaluated using global protein-protein docking. The 100 most frequent docking sites are shown in Figure 3.</li>
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</ol>
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Figure 1. The homologous structure of PL046 E protein (cyan) based on the deposited structure (PDB: 1OAN) magenta.
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Figure 2. The representative structures of a PTRS.
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Figure 3. The best 100 results (based on the Rosetta score) of PTRS docking to PL046 E protein (red). The space above the plane (grey) indicates the external surface of the virion, where the interactions occur.
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<b>Modeling: Interaction between gold nanoparticles</b>
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<br>
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<b>Purpose:</b>
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<br>
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A potential weakness of our design is that peptides on the gold nanoparticles and on the glass fiber compete for the same binding sites on the E protein. If the E proteins on the virus particles are fully covered by gold nanoparticles, there would be no sites available to interact with the peptides attached to the glass fiber. Hence, we need to understand if this situation would hinder development of our kit.
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<br><br>
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<b>Method:</b>
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<br>
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We used DLVO theory to calculate the repulsion between gold nanoparticles to estimate the number of gold nanoparticles that would bind to a virus particle. The structure of dengue virus is icosahedral, and there are nine E proteins on each surface. The distances between the potential binding sites can be obtained from the structure in the protein data bank (1K4R).
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DLVO theory can be described as follows,
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<b>W<sub>total</sub>(D) = W<sub>a</sub>(D) + W<sub>r</sub>(D) = -AR/12D + 2πεε<sub>0</sub>R&Psi;<sub>&delta;</sub><sup>2</sup>exp(-κD)</b>
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<br><br>
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W<sub>total</sub>(D): total energy<br>
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W<sub>a</sub>(D): van der Waals interaction energy<br>
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W<sub>r</sub>(D): electrostatic interaction energy<br>
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A: Hamaker constant = 2.5×10<sup>-19</sup> J<br>
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R: radius = 1.3x10<sup>-8</sup> m (based on the size of gold nanoparticles)<br>
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C: center to center distance<br>
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D: C-R<br>
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ε: permittivity of vacuum = 8.854x10<sup>-12</sup> F/m<br>
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ε<sub>0</sub>: dielectric of solution = 80.4 (at 20°C)<br>
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&Psi;<sub>&delta;</sub><sup>2</sup>: Stern layer potential (zeta potential) = 1.794 mV<br>
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κ<sup>-1</sup>: diffuse layer thickness = 7.95x10<sup>-10</sup> m
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<br><br>
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We took several representative positions on adjoining faces of the icosahedron to calculate the interactions between the gold nanoparticles based on DLVO theory.
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<br><br>
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<b>Results:</b>
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The total energies are all positive, indicating repulsive forces, (Table 1) and these total energies are also larger than the typical biological interactions (~0.5 kcal/mol or 3.49 x10-21 J). The results suggest that there will always be free faces on the virus particles to interact with the peptides conjugated on the test line.
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Table 1. Energies of the gold nanoparticles between representative positions.
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<div class="section half" id="product">
 
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<img src="https://static.igem.org/mediawiki/2020/6/6e/T--Example--Poster_Introduction.png">
 
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<div class="info">
 
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<div class="title">The detection kit - DENDETX</div>
 
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<div class="text"> Introduce your project and your team's goals.</div>
 
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<div class="section half" id="results">
 
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<img src="https://static.igem.org/mediawiki/2020/6/6e/T--Example--Poster_Introduction.png">
 
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<div class="info">
 
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<div class="title">Results</div>
 
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<div class="text"> Introduce your project and your team's goals.</div>
 
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<div class="row">
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<div class="section third" id="hp">
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<img src="https://static.igem.org/mediawiki/2020/f/f3/T--Example--Poster_Inspiration.png">
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<div class="info">
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<div class="title">Human Practices</div>
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<div class="text"> What inspired your team? What motivated you to work on this particular project? </div>
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<div class="section third" id="inclusion">
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<img src="https://static.igem.org/mediawiki/2020/c/c5/T--Example--Poster_Problem.png">
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<div class="info">
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<div class="title">Inclusion</div>
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<div class="text"> What is the problem your team is working to solve? How does it affect the world? </div>
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<div class="info">
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<div class="title">References</div>
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<img src="https://static.igem.org/mediawiki/2020/f/fb/T--Example--Poster_Title.png">
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<div class="text"> How are you going to solve the problem? Where did the idea come from? </div>
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<div class="info">
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<!--Write the title of the section -->
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<div class="title"> Poster Title</div>
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<!--Write the text explaining this section -->
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<div class="text">You should list all authors and their affiliations here. You can also add the project's abstract.</div>
 
</div>
 
</div>
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</div>
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<!--This is the second row of the poster, it contains the introduction section --->
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<div class="section full" id="introduction">
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<img src="https://static.igem.org/mediawiki/2020/6/6e/T--Example--Poster_Introduction.png">
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<!--Info: Place the title and text for this section, it will appear when the user clicks on it-->
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<div class="info">
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<!--Write the title of the section -->
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<div class="title"> Introduction </div>
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<!--Write the text explaining this section -->
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<div class="text"> Introduce your project and your team's goals.</div>
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</div>
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</div>
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</div>
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<!--This is the third row of the poster, it contains the inspiration, problem and idea sections --->
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<div class="row">
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<div class="section third" id="inspiration">
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<!--Here is the image used for the third width section, the size is:  400 x 200 pixels  -->
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<img src="https://static.igem.org/mediawiki/2020/f/f3/T--Example--Poster_Inspiration.png">
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<!--Info: Place the title and text for this section, it will appear when the user clicks on it-->
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<div class="info">
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<!--Write the title of the section -->
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<div class="title"> Inspiration </div>
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<!--Write the text explaining this section -->
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<div class="text"> What inspired your team? What motivated you to work on this particular project? </div>
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</div>
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</div>
  
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<p id="section_text"></p>
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<img src="https://static.igem.org/mediawiki/2020/c/c5/T--Example--Poster_Problem.png">
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<!--Info: Place the title and text for this section, it will appear when the user clicks on it-->
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<div class="info">
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<div class="title"> Problem </div>
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<!--Write the text explaining this section -->
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<div class="text"> What is the problem your team is working to solve? How does it affect the world? </div>
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</div>
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</div>
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<div class="section third" id="idea">
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<img src="https://static.igem.org/mediawiki/2020/9/90/T--Example--Poster_Idea.png">
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<!--Info: Place the title and text for this section, it will appear when the user clicks on it-->
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<div class="info">
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<div class="title">Idea </div>
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<!--Write the text explaining this section -->
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<div class="text"> How are you going to solve the problem? Where did the idea come from? </div>
 
</div>
 
</div>
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</div>
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</div>
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<!--This is the fourth row of the poster, it contains the engineering section --->
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<div class="row">
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<!-- This creates a full width section with the id 'engineering' --->
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<div class="section full" id="engineering">
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<img src="https://static.igem.org/mediawiki/2020/0/02/T--Example--Poster_Engineering.png">
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<!--Info: Place the title and text for this section, it will appear when the user clicks on it-->
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<div class="info">
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<!--Write the title of the section -->
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<div class="title"> Engineering</div>
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<!--Write the text explaining this section -->
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<div class="text"> Here you can explain the engineering process behind your project. </div>
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</div>
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</div>
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</div>
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<!--This is the fifth row of the poster, it contains the three nameless sections --->
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<div class="row">
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<div class="section third" id="section_1">
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<img src="https://static.igem.org/mediawiki/2020/5/53/T--Example--Poster_Section1.png">
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<!--Info: Place the title and text for this section, it will appear when the user clicks on it-->
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<div class="info">
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<!--Write the title of the section -->
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<div class="title"> Section 1 </div>
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<!--Write the text explaining this section -->
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<div class="text"> Use this section to explain whatever you would like! Suggestions: Safety, Human Practices, Measurement, etc. </div>
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</div>
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</div>
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<div class="section third" id="section_2">
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<img src="https://static.igem.org/mediawiki/2020/e/ec/T--Example--Poster_Section2.png">
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<!--Info: Place the title and text for this section, it will appear when the user clicks on it-->
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<div class="info">
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<!--Write the title of the section -->
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<div class="title"> Section 2 </div>
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<!--Write the text explaining this section -->
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<div class="text"> Use this section to explain whatever you would like! Suggestions: Safety, Human Practices, Measurement, etc. </div>
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</div>
 
</div>
 
</div>
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<div class="section third" id="section_3">
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<img src="https://static.igem.org/mediawiki/2020/9/9e/T--Example--Poster_Section3.png">
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<!--Info: Place the title and text for this section, it will appear when the user clicks on it-->
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<div class="info">
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<!--Write the title of the section -->
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<div class="title"> Section 3 </div>
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<!--Write the text explaining this section -->
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<div class="text"> Use this section to explain whatever you would like! Suggestions: Safety, Human Practices, Measurement, etc. </div>
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</div>
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</div>
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</div>
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<!--This is the sixth row of the poster, it contains the results and references sections --->
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<div class="row">
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<div class="section two_thirds" id="results">
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<img src="https://static.igem.org/mediawiki/2020/b/b0/T--Example--Poster_Results.png">
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<!--Info: Place the title and text for this section, it will appear when the user clicks on it-->
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<div class="info">
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<!--Write the title of the section -->
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<div class="title"> Results</div>
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<!--Write the text explaining this section -->
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<div class="text"> What did your team achieve? What do you plan to work on moving forward? </div>
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</div>
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</div>
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<img src="https://static.igem.org/mediawiki/2020/f/fa/T--Example--Poster_References.png">
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<!--Info: Place the title and text for this section, it will appear when the user clicks on it-->
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<div class="info">
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<!--Write the title of the section -->
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<div class="title">References and Acknowledgements</div>
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Revision as of 07:15, 9 November 2020

Poster: CCU_Taiwan



Poster Template

This poster template will let you create an interactive poster! The poster is divided in two parts: the visual overview on the left and the documentation on the right. The visual overview is broken down into sections that the user can click on. When a user clicks on a poster section in the visual overview, the documentation on the right will display the text and graphics associated with this section of the poster. You can find the documentation on how to use this template, as well as an example here: https://2020.igem.org/Competition/Deliverables/Poster

Poster Title
You should list all authors and their affiliations here. You can also add the project's abstract.
Introduction
Introduce your project and your team's goals.
Inspiration
What inspired your team? What motivated you to work on this particular project?
Problem
What is the problem your team is working to solve? How does it affect the world?
Idea
How are you going to solve the problem? Where did the idea come from?
Engineering
Here you can explain the engineering process behind your project.
Section 1
Use this section to explain whatever you would like! Suggestions: Safety, Human Practices, Measurement, etc.
Section 2
Use this section to explain whatever you would like! Suggestions: Safety, Human Practices, Measurement, etc.
Section 3
Use this section to explain whatever you would like! Suggestions: Safety, Human Practices, Measurement, etc.
Results
What did your team achieve? What do you plan to work on moving forward?
References and Acknowledgements
If not already cited in other sections of your poster, what literature sources did you reference on this poster? Who helped or advised you?