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

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             <img src="https://static.igem.org/mediawiki/2021/3/3d/T--NCTU_Formosa--Design.svg">
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             <img src="https://static.igem.org/mediawiki/2021/e/e1/T--NCTU_Formosa--medal1021.png">
 
         </div>
 
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         <div class="main-content">
 
         <div class="main-content">
 
             <img src="https://static.igem.org/mediawiki/2021/0/02/T--NCTU_Formosa--next.png" id="nextBottom" />
 
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             <div class="section s1">
 
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                 <h1 class="topic" id="topic1">Overview</h1>
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                 <h1 class="topic" id="topic1">Gold</h1>
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                    <h2 class="subtopic" id="topic1">Integrated Human Practices</h2>
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                        <p>
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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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                        </p>
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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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                    <h2 class="subtopic" id="topic1">Project Modeling</h2>
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                        <p>
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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
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                              Optimization Model
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                        </p>
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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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                    <h2 class="subtopic" id="topic1">Proof of Concept</h2>
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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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                    <h2 class="subtopic" id="topic1">Partnership</h2>
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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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                    <h2 class="subtopic" id="topic1">Education & Communication</h2>
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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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                        <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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                    <h2 class="subtopic" id="topic1">Collaboration</h2>
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                    <h2 class="subtopic" id="topic1">Human Practices</h2>
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                    <h2 class="subtopic" id="topic1">Proposed Implementation</h2>
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                <h1 class="topic" id="topic1">Bronze</h1>
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                    <h2 class="subtopic" id="topic1">Competition Deliverables</h2>
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                    <h2 class="subtopic" id="topic1">Attributions</h2>
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                    <h2 class="subtopic" id="topic1">Project Description</h2>
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                    <h2 class="subtopic" id="topic1">Contribution</h2>
  
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            <div id="video" style="padding-bottom: 5%;">
 
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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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                     &#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>
+
                     &#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 amount of bacteria which cause tooth decay and periodontal disease. When the amount of bacteria decrease, 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.
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                </p>
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                <h1 class="topic" >DenTeeth</h1>
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                <h1 class="subtopic" id="topic1"><i>E .coli</i> DenTeeth</h1>
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                <p id="p1">
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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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                <p id="p1">
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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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                <p id="p1">
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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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                <p id="p1">
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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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                            <th>Organisms\Peptide</th>
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                            <th>A</th>
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                            <th>C</th>
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                            <th>D</th>
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                            <th>E</th>
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                            <th>F</th>
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                            <th>G</th>
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                            <th>H</th>
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                            <th>I</th>
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                            <th>K</th>
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                            <th>P</th>
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                            <th>R</th>
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                            <th>Y</th>
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                        </tr>
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                      <tr>
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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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                      <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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                <h1 class="subtopic" >STATH</h1>
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                <p id="p1">
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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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Revision as of 00:38, 22 October 2021


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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

See the Proof of Concept page for more information!

Partnership

See the Partnership page for more information!

Education & Communication

See the Communication page for more information!

Excellence in Another Area

See the Excellence_in_Another_Area page for more information!

Silver

Engineering Success

Collaboration

Human Practices

Proposed Implementation

Bronze

Competition Deliverables

Attributions

Project Description

Contribution

  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 amount of bacteria which cause tooth decay and periodontal disease. When the amount of bacteria decrease, 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.

Reference

  1. Mounika Basavaraju, Vidya SagarSisnity et al.(2016)”Quorum quenching: Signal jamming in dental plaque biofilms”Journal of dental sciences 11(4):349-352
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