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

 
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                 <h1 class="topic" id="topic1">Biobrick design</h1>
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                 <h1 class="topic" id="topic1">Overview</h1>
  
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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 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.
+
                     &#8195;&#8195;With quorum sensing and repressible promoter, our biobrick has a time span to achieve oral inhibition 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>
 +
                </p>
 +
                <h1 class="topic" >DenTeeth</h1>
 +
                <h1 class="subtopic" id="topic1"><i>E .coli</i> DenTeeth</h1>
 +
                <p id="p1">
 +
                    &#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>
 +
                </p>
 +
                <h1 class="subtopic" >Expression conditions : Under high temperature</h1>
 +
                <p id="p1">
 +
                    &#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>
 +
                </p>
 +
                <h1 class="subtopic">Expression adjustment : Quorum sensing</h1>
 +
                <p id="p1">
 +
                    &#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.
 +
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>
 +
                </p>
 +
                <h1 class="subtopic" >LL-37 antimicrobial peptide</h1>
 +
                <p id="p1">
 +
                    &#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>
 +
 
 +
                </p>
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                <div class="table-scroll">
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                <table>
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                        <tr>
 +
                            <th>Organisms\Peptide</th>
 +
                            <th>A</th>
 +
                            <th>C</th>
 +
                            <th>D</th>
 +
                            <th>E</th>
 +
                            <th>F</th>
 +
                            <th>G</th>
 +
                            <th>H</th>
 +
                            <th>I</th>
 +
                            <th>K</th>
 +
                            <th>P</th>
 +
                            <th>R</th>
 +
                            <th>Y</th>
 +
                        </tr>
 +
                      <tr>
 +
                            <td>Homo sapiens</td>
 +
                            <td>GCC</td>
 +
                            <td>TGC</td>
 +
                            <td>GAC</td>
 +
                            <td>GAG</td>
 +
                            <td>TTC</td>
 +
                            <td>GGC</td>
 +
                            <td>CAC</td>
 +
                            <td>ATC</td>
 +
                            <td>AAG</td>
 +
                            <td>CCC</td>
 +
                            <td>AGG</td>
 +
                            <td>TAC</td>
 +
                        </tr>
 +
                      <tr>
 +
                            <td><i>E. coli</i></td>
 +
                            <td>GCT</td>
 +
                            <td>GCG</td>
 +
                            <td>ATG</td>
 +
                            <td>AAT</td>
 +
                            <td>TTG</td>
 +
                            <td>GCC</td>
 +
                            <td>ATA</td>
 +
                            <td>TTA</td>
 +
                            <td>AAA</td>
 +
                            <td>CCG</td>
 +
                            <td>CGC</td>
 +
                            <td>TAT</td>
 +
                        </tr>
 +
                </table>
 +
                </div>
 +
                <div class="sub">Table 1. The comparison of the codon in homo sapiens and in <i>E. coli</i>.</div>
 +
                <h1 class="subtopic">BMP2</h1>
 +
                <p id="p1">
 +
                    &#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>
 +
 
 +
                </p>
 +
                <h1 class="subtopic" >STATH</h1>
 +
                <p id="p1">
 +
                    &#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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{{NCTU_Formosa/footer}}
 
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Latest revision as of 03:12, 22 October 2021


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Overview

  With quorum sensing and repressible promoter, our biobrick has a time span to achieve oral inhibition 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.

DenTeeth

E .coli DenTeeth

  DenTeeth is the revolution of E. coli BL21. Since E. coli 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.

Expression conditions : Under high temperature

  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.

Expression adjustment : Quorum sensing

  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. 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).

LL-37 antimicrobial peptide

  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.

Organisms\Peptide A C D E F G H I K P R Y
Homo sapiens GCC TGC GAC GAG TTC GGC CAC ATC AAG CCC AGG TAC
E. coli GCT GCG ATG AAT TTG GCC ATA TTA AAA CCG CGC TAT
Table 1. The comparison of the codon in homo sapiens and in E. coli.

BMP2

  By binding to different receptors, it can promote the restoration of gums and the regeneration of tooth bones. We also optimize it with codons.

STATH

  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.

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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