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<li class="nav-item dropdown"> | <li class="nav-item dropdown"> | ||
<a class="nav-link dropdown-toggle" href="#" id="navbarDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"> | <a class="nav-link dropdown-toggle" href="#" id="navbarDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"> | ||
− | + | Project | |
</a> | </a> | ||
<div class="dropdown-menu" aria-labelledby="navbarDropdown"> | <div class="dropdown-menu" aria-labelledby="navbarDropdown"> | ||
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<li class="nav-item dropdown"> | <li class="nav-item dropdown"> | ||
<a class="nav-link dropdown-toggle" href="#" id="navbarDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"> | <a class="nav-link dropdown-toggle" href="#" id="navbarDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"> | ||
− | Dry Lab | + | <span style="color:red">Dry Lab</span> |
</a> | </a> | ||
<div class="dropdown-menu" aria-labelledby="navbarDropdown"> | <div class="dropdown-menu" aria-labelledby="navbarDropdown"> | ||
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<br> | <br> | ||
<ul> | <ul> | ||
− | <li><span style="color:black;font-family:comfort;font-size:16px;"">1. Enzymatic Degradation of Antibiotics</span></li> | + | <li><span style="color:black;font-family:comfort;font-size:16px;"">1. Enzymatic Degradation of Antibiotics [Module 1]</span></li> |
− | <li><span style="color:black;font-family:comfort;font-size:16px;"">2. Reduction of Horizontal Gene Transfer</span></li> | + | <li><span style="color:black;font-family:comfort;font-size:16px;"">2. Reduction of Horizontal Gene Transfer [Module 2]</span></li> |
− | <li><span style="color:black;font-family:comfort;font-size:16px;"">3. DNA degradation and cell death (‘kill switch’)</span></li> | + | <li><span style="color:black;font-family:comfort;font-size:16px;"">3. DNA degradation and cell death (‘kill switch’) [Module 3]</span></li> |
</ul> | </ul> | ||
<br> | <br> | ||
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border: 1px solid blue; | border: 1px solid blue; | ||
border-radius: 10px; | border-radius: 10px; | ||
− | " href="#1" aria-controls="1" role="tab" data-toggle="tab"> | + | " href="#1" aria-controls="1" role="tab" data-toggle="tab">Module 1 |
</a></li> | </a></li> | ||
<li role="presentation"><a href="#2" style=" padding: 10px; | <li role="presentation"><a href="#2" style=" padding: 10px; | ||
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border: 1px solid blue; | border: 1px solid blue; | ||
border-radius: 10px; | border-radius: 10px; | ||
− | " aria-controls="2" role="tab" data-toggle="tab"> | + | " aria-controls="2" role="tab" data-toggle="tab">Module 2 |
</a></li> | </a></li> | ||
<li role="presentation"><a href="#3" style=" padding: 10px; | <li role="presentation"><a href="#3" style=" padding: 10px; | ||
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border: 1px solid blue; | border: 1px solid blue; | ||
border-radius: 10px; | border-radius: 10px; | ||
− | " aria-controls="3" role="tab" data-toggle="tab"> | + | " aria-controls="3" role="tab" data-toggle="tab">Module 3</a></li> |
</ul> | </ul> | ||
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<table class="tableizer-table"> | <table class="tableizer-table"> | ||
<thead><tr class="tableizer-firstrow"><th>Symbol</th><th>Description</th><th>Value</th></tr></thead><tbody> | <thead><tr class="tableizer-firstrow"><th>Symbol</th><th>Description</th><th>Value</th></tr></thead><tbody> | ||
− | <tr><td>K<sub> | + | <tr><td>K<sub>D</sub></td><td>Concentration of Drug at which the rate is half of V<sub>m</sub></td><td>16.83 uM</td></tr> |
<tr><td>K<sub>cat</sub></td><td>Rate constant for rate limiting step</td><td>0.58 * 46,000 = 26 s</td></tr> | <tr><td>K<sub>cat</sub></td><td>Rate constant for rate limiting step</td><td>0.58 * 46,000 = 26 s</td></tr> | ||
</tbody></table> | </tbody></table> | ||
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<p> | <p> | ||
− | <center><img class="bod" src="https:// | + | <center><img class="bod" src="https://static.igem.org/mediawiki/2020/b/b6/T--IISER-Tirupati_India--results201.png" alt="Module 1"></center> |
</p> | </p> | ||
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<p> | <p> | ||
− | <center><img class="bod" src="https://static.igem.org/mediawiki/2020/ | + | <center><img class="bod" src="https://static.igem.org/mediawiki/2020/b/b5/T--IISER-Tirupati_India--results97.png" alt="Module 1"></center> |
</p> | </p> | ||
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<p style="color:black;font-family:comfort;font-size:16px;"> | <p style="color:black;font-family:comfort;font-size:16px;"> | ||
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<p> | <p> | ||
− | <center><img class="bod" src="https://static.igem.org/mediawiki/2020/ | + | <center><img class="bod" src="https://static.igem.org/mediawiki/2020/6/65/T--IISER-Tirupati_India--results95.png" alt="Module 1"></center> |
</p> | </p> | ||
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<p> | <p> | ||
− | <center><img class="bod" src="https://static.igem.org/mediawiki/2020/ | + | <center><img class="bod" src="https://static.igem.org/mediawiki/2020/9/91/T--IISER-Tirupati_India--results99.png" alt="Module 1"></center> |
</p> | </p> | ||
<p style="color:black;font-family:comfort;font-size:16px;"> | <p style="color:black;font-family:comfort;font-size:16px;"> | ||
− | The above picture shows the different ways the virus activates the lytic cycle. The virus upon infecting the bacteria can directly activate the lytic cycle. Otherwise the virus waits for a while after infection until the conditions are ideal and then activates the lytic cycle. This is called the induced lytic cycle. All these populations go into a transient phase called the burst phase. This leads to the death of the bacterium and the release of virions and transduced particles. The transduced particle could contain the AMR gene or not depending on whether the AMR gene was packaged into the protein coat. | + | The above picture shows the different ways the virus activates the lytic cycle. The virus upon infecting the bacteria can directly activate the lytic cycle. Otherwise the virus waits for a while after infection until the conditions are ideal and then activates the lytic cycle. This is called the induced lytic cycle. All these populations go into a transient phase called the burst phase. This leads to the death of the bacterium and the release of virions and transduced particles. The transduced particle could contain the AMR gene or not depending on whether the AMR gene was packaged into the protein coat. A fraction of the virion population (N<sub>13</sub>) constitute the transduced particles. |
+ | |||
<br> | <br> | ||
</p> | </p> | ||
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<tr><td>b_fr_lys_in</td><td>Fraction of lysogens in inflowing bacteria</td><td>0.05</td><td>-</td></tr> | <tr><td>b_fr_lys_in</td><td>Fraction of lysogens in inflowing bacteria</td><td>0.05</td><td>-</td></tr> | ||
<tr><td>b_fr_lys_en</td><td>Fraction of lysogens in enteric bacteria (start)</td><td>0.013</td><td>-</td></tr> | <tr><td>b_fr_lys_en</td><td>Fraction of lysogens in enteric bacteria (start)</td><td>0.013</td><td>-</td></tr> | ||
− | <tr><td> | + | <tr><td>𝜆</td><td>growth rate of bacteria,</td><td>0.03</td><td>h<sup>-1</sup></td></tr> |
− | <tr><td> | + | <tr><td>𝛿</td><td>death rate of bacteria,</td><td>0.005</td><td>h<sup>-1</sup></td></tr> |
− | <tr><td>N</td><td>Population cap</td><td>10<sup>10</sup></td><td>-</td></tr> | + | <tr><td>N<sub>cap</sub></td><td>Population cap</td><td>10<sup>10</sup></td><td>-</td></tr> |
<tr><td>g_n</td><td>No. of AMR gene copies per bacterium</td><td>1</td><td>-</td></tr> | <tr><td>g_n</td><td>No. of AMR gene copies per bacterium</td><td>1</td><td>-</td></tr> | ||
<tr><td>pr_gpick_gntr _pl</td><td>Probability tp picks plasmid bearing AMR gene, per lytic cycle per bacterium</td><td>0.02</td><td>-</td></tr> | <tr><td>pr_gpick_gntr _pl</td><td>Probability tp picks plasmid bearing AMR gene, per lytic cycle per bacterium</td><td>0.02</td><td>-</td></tr> | ||
<tr><td>pr_tp_pl_est</td><td>Probability tp picks plasmid bearing AMR gene, per lytic cycle per bacterium</td><td>1</td><td>-</td></tr> | <tr><td>pr_tp_pl_est</td><td>Probability tp picks plasmid bearing AMR gene, per lytic cycle per bacterium</td><td>1</td><td>-</td></tr> | ||
− | <tr><td> | + | <tr><td>ph _frAMRtp</td><td>Fraction of to with AMR gene of</td><td>0.02</td><td>-</td></tr> |
− | + | ||
<tr><td>t_newi</td><td>Newly infected bacteria</td><td>1</td><td>h</td></tr> | <tr><td>t_newi</td><td>Newly infected bacteria</td><td>1</td><td>h</td></tr> | ||
<tr><td>t_tp</td><td>Bacteria process tp</td><td>1</td><td>h</td></tr> | <tr><td>t_tp</td><td>Bacteria process tp</td><td>1</td><td>h</td></tr> | ||
<tr><td>t_Itcl_v</td><td>Direct lytic cycle</td><td>0.3833</td><td>h</td></tr> | <tr><td>t_Itcl_v</td><td>Direct lytic cycle</td><td>0.3833</td><td>h</td></tr> | ||
<tr><td>t_Itcl_t</td><td>Lytic cycle after prophage induction</td><td>0.9583</td><td>h</td></tr> | <tr><td>t_Itcl_t</td><td>Lytic cycle after prophage induction</td><td>0.9583</td><td>h</td></tr> | ||
− | <tr><td> | + | <tr><td>t_lscl</td><td>Lysogenic cycle</td><td>100</td><td>h</td></tr> |
</tbody></table> | </tbody></table> | ||
</center> | </center> | ||
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<ol> | <ol> | ||
− | <li>Kim, Dae-Wi, et al. "A novel sulfonamide resistance mechanism by two-component flavin-dependent monooxygenase system in sulfonamide-degrading actinobacteria." Environment international 127 (2019): 206-215</li> | + | <li>1. Kim, Dae-Wi, et al. "A novel sulfonamide resistance mechanism by two-component flavin-dependent monooxygenase system in sulfonamide-degrading actinobacteria." Environment international 127 (2019): 206-215</li> |
− | <li>Mao, J., & Lu, T. (2016). Population-dynamic modeling of bacterial horizontal gene transfer by natural transformation. Biophysical journal, 110(1), 258-268.</li> | + | <li>2. Mao, J., & Lu, T. (2016). Population-dynamic modeling of bacterial horizontal gene transfer by natural transformation. Biophysical journal, 110(1), 258-268.</li> |
− | <li>Hendricks, C. W. (1972). Enteric bacterial growth rates in river water. Applied microbiology, 24(2), 168-174.</li> | + | <li>3. Hendricks, C. W. (1972). Enteric bacterial growth rates in river water. Applied microbiology, 24(2), 168-174.</li> |
− | <li>Menon, P., Billen, G., & Servais, P. (2003). Mortality rates of autochthonous and fecal bacteria in natural aquatic ecosystems. Water Research, 37(17), 4151-4158.</li> | + | <li>4. Menon, P., Billen, G., & Servais, P. (2003). Mortality rates of autochthonous and fecal bacteria in natural aquatic ecosystems. Water Research, 37(17), 4151-4158.</li> |
− | <li>Lu, N., Massoudieh, A., Liang, X., Kamai, T., Zilles, J. L., Nguyen, T. H., & Ginn, T. R. (2015). A kinetic model of gene transfer via natural transformation of Azotobacter vinelandii. Environmental Science: Water Research & Technology, 1(3), 363-374</li> | + | <li>5. Lu, N., Massoudieh, A., Liang, X., Kamai, T., Zilles, J. L., Nguyen, T. H., & Ginn, T. R. (2015). A kinetic model of gene transfer via natural transformation of Azotobacter vinelandii. Environmental Science: Water Research & Technology, 1(3), 363-374</li> |
− | <li>Zhong, X., Kro, J. E., Top, E. M., & Krone, S. M. (2010). Accounting for mating pair formation in plasmid population dynamics. Journal of theoretical biology, 262(4), 711-719.</li> | + | <li>6. Zhong, X., Kro, J. E., Top, E. M., & Krone, S. M. (2010). Accounting for mating pair formation in plasmid population dynamics. Journal of theoretical biology, 262(4), 711-719.</li> |
− | <li>Volkova, V. V., Lu, Z., Besser, T., & Gröhn, Y. T. (2014). Modeling the infection dynamics of bacteriophages in enteric Escherichia coli: estimating the contribution of transduction to antimicrobial gene spread. Applied and environmental microbiology, 80(14), 4350-4362</li> | + | <li>7. Volkova, V. V., Lu, Z., Besser, T., & Gröhn, Y. T. (2014). Modeling the infection dynamics of bacteriophages in enteric Escherichia coli: estimating the contribution of transduction to antimicrobial gene spread. Applied and environmental microbiology, 80(14), 4350-4362</li> |
</ol> | </ol> | ||
</p> | </p> | ||
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<tr><td>A</td><td>Arabinose sugar</td><td>Number of molecules of arabinose sugar outside the cell</td></tr> | <tr><td>A</td><td>Arabinose sugar</td><td>Number of molecules of arabinose sugar outside the cell</td></tr> | ||
<tr><td>X<sub>1</sub></td><td>Arabinose sugar bound to AraC</td><td>Number of A-AraC complexes in a cell</td></tr> | <tr><td>X<sub>1</sub></td><td>Arabinose sugar bound to AraC</td><td>Number of A-AraC complexes in a cell</td></tr> | ||
− | <tr><td> | + | <tr><td>θ<sub>1</sub></td><td>AraC protein bound to PBAD promoter</td><td>Number of actively repressed p-bad promoters in a cell</td></tr> |
− | <tr><td> | + | <tr><td>θ<sub>2</sub></td><td>A-AraC (arabinose sugar AraC complex) bound to 11 and 12 sites of DNA) near p-bad promoter (this actually releases the DNA loop to give free promoter)</td><td>Number of active PBAD promoters in a cell</td></tr> |
− | <tr><td> | + | <tr><td>θ<sub>3</sub></td><td>A-AraC-CC (arabinose sugar AraC complex bound to 11 and 12 sites and CAP-cAMP complex bound to the CAP binding site of DNA) near to P-bad promoter (this enhances the efficiency with which RNA polymerase binds to the promoter)</td><td>Number of promoters which have enhanced activity in a cell</td></tr> |
<tr><td>X<sub>2</sub></td><td>c-AMP molecules</td><td>Number of c-AMP molecules in a cell</td></tr> | <tr><td>X<sub>2</sub></td><td>c-AMP molecules</td><td>Number of c-AMP molecules in a cell</td></tr> | ||
<tr><td>E<sub>g</sub></td><td>External glucose</td><td>Number of moles of glucose sugar outside the cell</td></tr> | <tr><td>E<sub>g</sub></td><td>External glucose</td><td>Number of moles of glucose sugar outside the cell</td></tr> |
Latest revision as of 07:48, 16 December 2020