Difference between revisions of "Team:NCTU Formosa/Criteria"

 
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                <h1 class="topic" id="topic1">Overview</h1>
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                 <video autoplay muted loop poster="https://2021.igem.org/File:T--NCTU_Formosa--Biobrick_total.svg" id="vid1">
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                     <source src="https://static.igem.org/mediawiki/2021/2/27/T--NCTU_Formosa--biobrick_video_final.mp4" type="video/mp4">
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                    <img src="https://static.igem.org/mediawiki/2021/d/de/T--NCTU_Formosa--gold.png?fbclid=IwAR0xmz7hIetUEgRQvSh9VGFp78dY-J3UFQu_Y7nq9WB1N0zqMqVa5K24Vhs" title="Edward Jenner" alt="Design">
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                     <img src="https://static.igem.org/mediawiki/2021/5/55/T--NCTU_Formosa--bronze.png?fbclid=IwAR16CVBFIk25A7aABRGr78gdhc140abiqAO-2zbWZC5BgVY7CHFbRyfQqng" title="fauxels" alt="hp">
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                 <h1 class="topic" id="topic1">Gold</h1>
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                <p id="p1">
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                    <h2 class="subtopic" id="topic1">Integrated Human Practices</h2>
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                    &#8195;&#8195;With quorum sensing and repressible promoter, our biobrick has a time span to achieve oral sterilization and restoration. With the increase of oral bacteria, it will activate the antimicrobial peptide LL-37 to inhibit the large number of bacteria that cause tooth decay and periodontal disease. When the number of bacteria decreases, it will activate BMP2 and STATH to repair gums and help tooth remineralization. This mechanism can avoid the formation of biofilm during the remineralization process, and it also can achieve the best efficient restoration on the condition of fewer bacteria.<br>
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                        <p>
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                 <h1 class="topic" >DenTeeth</h1>
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                     &#8195;&#8195;To ensure our project caters to the needs of the actual situation, we visit the animal shelter and invite professors in the dentistry and veterinary medicine department to discuss the concept of the project. After deciding to focus on canine oral health first, we visited Hsinchu City Animal Protection and Health Inspection Office. Due to the lack of oral medical resources, many dogs suffer from oral-related diseases. After the visit, the idea of making their life more comfortable becomes firmer. Throughout the discussion with Prof. Cheng Hen-Li, we choose the antimicrobial peptide inhibiting the growth of P.gingivalis. In interviewing with Prof. Liu, Pin-Chen recommended adding our engineered bacteria into the dental bone, making dental medical treatment simpler and less intrusive. Besides, Prof. Liu, Pin-Chen instructs us it is difficult to calculate a suitable dental bone feeding frequency. Thus, we construct an Efficiency Optimization Model for precise dental bone feeding.
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                <h1 class="subtopic" id="topic1"><i>E .coli</i> DenTeeth</h1>
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                        </p>
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                <p id="p1">
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                        <a href="https://2021.igem.org/Team:NCTU_Formosa/Human_Practices">See the Human Practices page for more information!</a>
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                    &#8195;&#8195;DenTeeth is the revolution of <i>E. coli</i> BL21. Since <i>E. coli</i> BL21 is a colony that has the properties that have the high-level expression of recombinant proteins, we can test our protein function more efficiently. <br>
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                </p>
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                <h1 class="subtopic" >Expression conditions : Under high temperature</h1>
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                     &#8195;&#8195;The RBS of BBa_K3736001 (Quorum sensing sequence) needs to exceed 37 degrees to enable its mRNA to begin translation and initiate quorum sensing regulation. In this way, we can ensure that our engineered bacteria can operate in a specific temperature range. When it develops into a commodity in the future, it can also reduce the production of antimicrobial peptides before entering the body of a warm-blooded animal, making it stable and easy to store.<br>
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                </p>
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                <h1 class="subtopic">Expression adjustment : Quorum sensing</h1>
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                    &#8195;&#8195;When the LuxR protein produced by BBa_K3736001 (Quorum sensing sequence) binds to the AHL produced by all bacteria, it can prompt the Plux promoter of BBa_K3736002 (Inhibition sequence) to start transcription, so that BBa_K3736002 (Inhibition sequence) can be expressed when there are more bacteria.
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When the tetR protein in BBa_K3736002 (Inhibition sequence) is expressed, the Ptet promoter of BBa_K3736003 (Restoration sequence) will be inhibited to achieve the antagonistic effect of BBa_K3736002 (Inhibition sequence) and BBa_K3736003 (Restoration sequence).<br>
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                </p>
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                <h1 class="subtopic" >LL-37 antimicrobial peptide</h1>
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                    &#8195;&#8195;LL-37 is an antimicrobial peptide from humans, to improve its performance, we performed codon harmonization. The optimized sequence of codons will be more suitable for expression by our engineered strains than the natural sequence.<br>
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                </p>
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                    <h2 class="subtopic" id="topic1">Project Modeling</h2>
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                <table>
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                    &#8195;&#8195; Oral cavity is a hotbed for pathogens of periodontal diseases, as the goal of modelling is to simulate the microenvironment incorporated with Denteeth, mainly the overturn of pathogens, and make predictions on their extinction. Therefore, we compute the competing bacterial growing patterns, and the killing effect on pathogens. Also, we propose a renew rate of the final product, considering the biobrick design in Danteeth, including quorum sensing, target peptide expression. Altogether, the model enables Danteeth to optimize continually with the help of reinforcement AI. The model consists of two parts: 1. Prediction Model 2. Efficiency Optimization Model.
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                            <th>Organisms\Peptide</th>
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                        <a href="https://2021.igem.org/Team:NCTU_Formosa/Model">See the Model page for more information!</a>
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                            <th>A</th>
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                    <h2 class="subtopic" id="topic1">Proof of Concept</h2>
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                            <th>C</th>
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                        <p>
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                            <th>D</th>
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                    &#8195;&#8195;DenTeeth can produce antimicrobial peptides, LL-37 when the concentration of bacteria in the mouth is higher. After the growth of bacteria is inhibited, STATH and BMP2 will express, maintaining a high calcium level in saliva, and repairing soft tissues in the oral cavity. Therefore, oral problems, especially periodontal disease can be successfully prevented.
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                            <th>E</th>
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                         </p>
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                            <th>F</th>
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                         <p>
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                            <th>G</th>
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                    &#8195;&#8195;We proved our concept with a meticulous process which can be roughly divided into three parts: Model, Lab Work, and Device design. Combining modeling results and predictions with our lab work, we enable to make DenTeeth work as we imagined. We could further prove that DenTeeth can be implemented in the real world for daily usages
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                            <th>H</th>
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                        </p>
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                            <th>I</th>
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                        <a href="https://2021.igem.org/Team:NCTU_Formosa/Proof_Of_Concept">See the Proof of Concept page for more information!</a>
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                            <th>K</th>
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                    <h2 class="subtopic" id="topic1">Partnership</h2>
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                            <th>P</th>
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                    <img class="images" src="https://static.igem.org/mediawiki/2021/3/30/T--NCTU_Formosa--partnerhsip_flow_chart.png?fbclid=IwAR1RJFE8Mbcp3LhzCDDNYcn2a5gkhWzX-J1CzopuulshSnOcpuJq9v2F-wk">
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                            <th>R</th>
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                    <p>
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                            <th>Y</th>
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                        &#8195;&#8195;Throughout this year, we collaborate with NTHU on a set of shared objectives related to both of our projects. This partnership is both vital to our project, without each other's help, we wouldn't complete our projects smoothly. In the partnership, we help NTHU in culturing the callus of Pinus armandii. On the other hand, NTHU helps us in the measurement of the O.D. value of the E. coli and the excitation/emission wavelength of RFP and GFP.
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                         </tr>
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                    </p>
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                      <tr>
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                        <a href="https://2021.igem.org/Team:NCTU_Formosa/Partnership">See the Partnership page for more information!</a>
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                            <td>Homo sapiens</td>
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                            <td>GCC</td>
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                            <td>TGC</td>
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                            <td>GAC</td>
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                            <td>GAG</td>
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                            <td>TTC</td>
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                            <td>GGC</td>
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                            <td>CAC</td>
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                            <td>ATC</td>
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                            <td>AAG</td>
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                            <td>CCC</td>
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                            <td>AGG</td>
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                            <td>TAC</td>
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                         </tr>
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                            <td><i>E. coli</i></td>
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                            <td>GCT</td>
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                            <td>GCG</td>
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                            <td>ATG</td>
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                            <td>AAT</td>
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                            <td>TTG</td>
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                            <td>GCC</td>
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                            <td>ATA</td>
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                            <td>TTA</td>
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                            <td>AAA</td>
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                            <td>CCG</td>
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                            <td>CGC</td>
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                            <td>TAT</td>
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                        </tr>
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                </table>
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                </div>
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                <div class="sub">Table 1. The comparison of the codon in homo sapiens and in <i>E. coli</i>.</div>
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                <h1 class="subtopic">BMP2</h1>
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                <p id="p1">
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                    &#8195;&#8195;By binding to different receptors, it can promote the restoration of gums and the regeneration of tooth bones. We also optimize it with codons.<br>
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                </p>
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                    <h2 class="subtopic" id="topic1">Education & Communication</h2>
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                <h1 class="subtopic" >STATH</h1>
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                    <img class="images" src="https://static.igem.org/mediawiki/2021/1/16/T--NCTU_Formosa--NCTU_presentation2.jpg">
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                     &#8195;&#8195;STATH is a protein that humans prevent the precipitation of calcium phosphate, we also optimize its codons. Its properties can reduce the risk of calculus for teeth soaked in supersaturated calcium and phosphorus saliva.<br>
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                        &#8195;&#8195;This year, our science communication held virtual meetups, operated a synthetic biology channel, and interacted with future iGEMers who will hopefully inherit our goals, etc. Science communication helps us share our knowledge with the public, check if we understand our project thoroughly, and making more people know iGEM.
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                    </p>
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                 </p>
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                        <a href="https://2021.igem.org/Team:NCTU_Formosa/Communication">See the Communication page for more information!</a>
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                    <h2 class="subtopic" id="topic1">Excellence in Another Area</h2>
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                    <img class="images" src="https://static.igem.org/mediawiki/2021/d/d1/T--NCTU_Formosa--towel_white.svg?fbclid=IwAR0CSTfw-4nEFIYBuOyTdA4sV6PJxqo17HQhW4gNXXwI9a6vbVrFAczHOTk">
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                     <p>
 +
                        &#8195;&#8195;This year, our science communication held virtual meetups, operated a synthetic biology channel, and interacted with future iGEMers who will hopefully inherit our goals, etc. Science communication helps us share our knowledge with the public, check if we understand our project thoroughly, and making more people know iGEM.
 +
                    </p>
 +
                        <a href="https://2021.igem.org/Team:NCTU_Formosa/Excellence_in_Another_Area">See the Excellence_in_Another_Area page for more information!</a>
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                <h1 class="topic" id="topic1">Silver</h1>
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                    <h2 class="subtopic" id="topic1">Engineering Success</h2>
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                    <a href="https://2021.igem.org/Team:NCTU_Formosa/Excellence_in_Another_Area">See the Excellence_in_Another_Area page for more information!</a>
 +
                    <h2 class="subtopic" id="topic1">Collaboration</h2>
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                    <a href="https://2021.igem.org/Team:NCTU_Formosa/Excellence_in_Another_Area">See the Excellence_in_Another_Area page for more information!</a>
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                    <h2 class="subtopic" id="topic1">Human Practices</h2>
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                    <a href="https://2021.igem.org/Team:NCTU_Formosa/Excellence_in_Another_Area">See the Excellence_in_Another_Area page for more information!</a>
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                    <h2 class="subtopic" id="topic1">Proposed Implementation</h2>
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                    <a href="https://2021.igem.org/Team:NCTU_Formosa/Excellence_in_Another_Area">See the Excellence_in_Another_Area page for more information!</a>
 +
                 <h1 class="topic" id="topic1">Bronze</h1>
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                    <h2 class="subtopic" id="topic1">Competition Deliverables</h2>
 +
                    <a href="https://2021.igem.org/Team:NCTU_Formosa/Excellence_in_Another_Area">See the Excellence_in_Another_Area page for more information!</a>
 +
                    <h2 class="subtopic" id="topic1">Attributions</h2>
 +
                    <a href="https://2021.igem.org/Team:NCTU_Formosa/Excellence_in_Another_Area">See the Excellence_in_Another_Area page for more information!</a>
 +
                    <h2 class="subtopic" id="topic1">Project Description</h2>
 +
                    <a href="https://2021.igem.org/Team:NCTU_Formosa/Excellence_in_Another_Area">See the Excellence_in_Another_Area page for more information!</a>
 +
                    <h2 class="subtopic" id="topic1">Contribution</h2>
 +
                    <a href="https://2021.igem.org/Team:NCTU_Formosa/Excellence_in_Another_Area">See the Excellence_in_Another_Area page for more information!</a>
 
                  
 
                  
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                <h1 class="topic-r">Reference</h1>
 
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                    <li class="ref">Mounika Basavaraju, Vidya SagarSisnity et al.(2016)”Quorum quenching: Signal jamming in dental plaque biofilms”Journal of dental sciences 11(4):349-352</li>
 
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Latest revision as of 02:59, 22 October 2021


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dog Design hp

Gold

Integrated Human Practices

  To ensure our project caters to the needs of the actual situation, we visit the animal shelter and invite professors in the dentistry and veterinary medicine department to discuss the concept of the project. After deciding to focus on canine oral health first, we visited Hsinchu City Animal Protection and Health Inspection Office. Due to the lack of oral medical resources, many dogs suffer from oral-related diseases. After the visit, the idea of making their life more comfortable becomes firmer. Throughout the discussion with Prof. Cheng Hen-Li, we choose the antimicrobial peptide inhibiting the growth of P.gingivalis. In interviewing with Prof. Liu, Pin-Chen recommended adding our engineered bacteria into the dental bone, making dental medical treatment simpler and less intrusive. Besides, Prof. Liu, Pin-Chen instructs us it is difficult to calculate a suitable dental bone feeding frequency. Thus, we construct an Efficiency Optimization Model for precise dental bone feeding.

See the Human Practices page for more information!

Project Modeling

   Oral cavity is a hotbed for pathogens of periodontal diseases, as the goal of modelling is to simulate the microenvironment incorporated with Denteeth, mainly the overturn of pathogens, and make predictions on their extinction. Therefore, we compute the competing bacterial growing patterns, and the killing effect on pathogens. Also, we propose a renew rate of the final product, considering the biobrick design in Danteeth, including quorum sensing, target peptide expression. Altogether, the model enables Danteeth to optimize continually with the help of reinforcement AI. The model consists of two parts: 1. Prediction Model 2. Efficiency Optimization Model.

See the Model page for more information!

Proof of Concept

  DenTeeth can produce antimicrobial peptides, LL-37 when the concentration of bacteria in the mouth is higher. After the growth of bacteria is inhibited, STATH and BMP2 will express, maintaining a high calcium level in saliva, and repairing soft tissues in the oral cavity. Therefore, oral problems, especially periodontal disease can be successfully prevented.

  We proved our concept with a meticulous process which can be roughly divided into three parts: Model, Lab Work, and Device design. Combining modeling results and predictions with our lab work, we enable to make DenTeeth work as we imagined. We could further prove that DenTeeth can be implemented in the real world for daily usages

See the Proof of Concept page for more information!

Partnership

  Throughout this year, we collaborate with NTHU on a set of shared objectives related to both of our projects. This partnership is both vital to our project, without each other's help, we wouldn't complete our projects smoothly. In the partnership, we help NTHU in culturing the callus of Pinus armandii. On the other hand, NTHU helps us in the measurement of the O.D. value of the E. coli and the excitation/emission wavelength of RFP and GFP.

See the Partnership page for more information!

Education & Communication

  This year, our science communication held virtual meetups, operated a synthetic biology channel, and interacted with future iGEMers who will hopefully inherit our goals, etc. Science communication helps us share our knowledge with the public, check if we understand our project thoroughly, and making more people know iGEM.

See the Communication page for more information!

Excellence in Another Area

  This year, our science communication held virtual meetups, operated a synthetic biology channel, and interacted with future iGEMers who will hopefully inherit our goals, etc. Science communication helps us share our knowledge with the public, check if we understand our project thoroughly, and making more people know iGEM.

See the Excellence_in_Another_Area page for more information!

Silver

Engineering Success

See the Excellence_in_Another_Area page for more information!

Collaboration

See the Excellence_in_Another_Area page for more information!

Human Practices

See the Excellence_in_Another_Area page for more information!

Proposed Implementation

See the Excellence_in_Another_Area page for more information!

Bronze

Competition Deliverables

See the Excellence_in_Another_Area page for more information!

Attributions

See the Excellence_in_Another_Area page for more information!

Project Description

See the Excellence_in_Another_Area page for more information!

Contribution

See the Excellence_in_Another_Area page for more information!
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