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Team:TAS Taipei/modeling - Revision history
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Xiaoyangkao2 at 09:20, 19 July 2014
2014-07-19T09:20:03Z
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <figcaption class='darkblue'>Figure 3:Circuit design of the three component repressilator we initially were going to use to regulate expression of c-Myc. The repressilator expresses c-Myc in an oscillatory fashion, so that there is not constant expression of c-Myc, and hence not constant induction of telomerase.</figcaption></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <figcaption class='darkblue'>Figure 3:Circuit design of the three component repressilator we initially were going to use to regulate expression of c-Myc. The repressilator expresses c-Myc in an oscillatory fashion, so that there is not constant expression of c-Myc, and hence not constant induction of telomerase.</figcaption></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </figure> </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </figure> </div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <p>The three component oscillator features three promoters that repress each other. With modeling, we first used the values showcased in <del class="diffchange diffchange-inline">Elowitz’s </del>paper from the BioModels databse on the repressilator and showed that the resulting system oscillated with the following equations and parameters:</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <p>The three component oscillator features three promoters that repress each other. With modeling, we first used the values showcased in <ins class="diffchange diffchange-inline">Elowitz's </ins>paper from the BioModels databse on the repressilator and showed that the resulting system oscillated with the following equations and parameters:</p></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h3>Alternatives to the three component oscillator</h3></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h3>Alternatives to the three component oscillator</h3></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h4>Self-Repressilator</h4></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h4>Self-Repressilator</h4></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <p>We first attempted to model the self-repressilator, which we know was an early design. The self-repressilator is significant because it lays the groundwork for the model of the two-component oscillator, which is really an expansion on the self-repressilator. The groundwork includes establishing the need for an explicit time delay, which is elaborated in the paper <del class="diffchange diffchange-inline">“Design </del>Principles of Biochemical <del class="diffchange diffchange-inline">Oscillators†</del>by Novak and Tyson. In this model, transcription is based on protein concentration in a previous point in time, to compensate for the time delay in transcription and translation. The explicit time delay was not needed in the three component oscillator because it established a time delay through a series of intermediates. The equations are as follows:</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <p>We first attempted to model the self-repressilator, which we know was an early design. The self-repressilator is significant because it lays the groundwork for the model of the two-component oscillator, which is really an expansion on the self-repressilator. The groundwork includes establishing the need for an explicit time delay, which is elaborated in the paper <ins class="diffchange diffchange-inline">"Design </ins>Principles of Biochemical <ins class="diffchange diffchange-inline">Oscillators" </ins>by Novak and Tyson. In this model, transcription is based on protein concentration in a previous point in time, to compensate for the time delay in transcription and translation. The explicit time delay was not needed in the three component oscillator because it established a time delay through a series of intermediates. The equations are as follows:</p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <img src="https://static.igem.org/mediawiki/2014hs/7/76/Image13.png"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <img src="https://static.igem.org/mediawiki/2014hs/7/76/Image13.png"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>Without the explicit time delay, the graph would look like this, which we know that it shouldn’t look like:</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>Without the explicit time delay, the graph would look like this, which we know that it shouldn’t look like:</p></div></td></tr>
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Xiaoyangkao2
http://2014hs.igem.org/wiki/index.php?title=Team:TAS_Taipei/modeling&diff=28158&oldid=prev
Xiaoyangkao2 at 09:18, 19 July 2014
2014-07-19T09:18:17Z
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>The amount of mRNA depends on the activity of the promoter transcribing the mRNA and the degradation rate of the mRNA. Promoter activity is described by the Hill equation, which can describe the effect of activation or repression by a transcription factor. </p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>The amount of mRNA depends on the activity of the promoter transcribing the mRNA and the degradation rate of the mRNA. Promoter activity is described by the Hill equation, which can describe the effect of activation or repression by a transcription factor. </p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <div class="col-lg-11 col-lg-offset-1"></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <div class="col-lg-11 col-lg-offset-1" <ins class="diffchange diffchange-inline">style='margin-bottom:15px;'</ins>></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h4>Repression:</h4></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h4>Repression:</h4></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h3 id='circuit_regulation'>Circuit Regulation</h3></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h3 id='circuit_regulation'>Circuit Regulation</h3></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <p>The circuit regulation section of modeling focuses on simulating the oscillating constructs that we came up with and approximating their behavior in real life. To oscillate, a system must have a balance between promoter strength and repressor half-life<del class="diffchange diffchange-inline">[12]</del>. In addition, a time delay of a sort, whether through a series of intermediates or through implementation of an explicit time delay in the model, is needed.<del class="diffchange diffchange-inline">[13] </del> Finally, the pattern of regulation must be sufficiently nonlinear(high cooperativity) for there to be oscillations.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <p>The circuit regulation section of modeling focuses on simulating the oscillating constructs that we came up with and approximating their behavior in real life. To oscillate, a system must have a balance between promoter strength and repressor half-life. In addition, a time delay of a sort, whether through a series of intermediates or through implementation of an explicit time delay in the model, is needed. Finally, the pattern of regulation must be sufficiently nonlinear(high cooperativity) for there to be oscillations.</p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h4>Three-component oscillator</h4></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h4>Three-component oscillator</h4></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <figure style='width:300px;'></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <figure style='width:300px;'></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>The two component oscillator is an expanded version of pLac-LacI self-Repressilator. The pLac-LacI represses itself and thus oscillates. Thus, TetR/RFP, which is expressed by pLac, will also oscillate. This means that expression of c-Myc will be oscillatory, because pTet is regulated by TetR. For experimental purposes, GFP took the place of c-Myc as a reporter to show oscillations.</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>The two component oscillator is an expanded version of pLac-LacI self-Repressilator. The pLac-LacI represses itself and thus oscillates. Thus, TetR/RFP, which is expressed by pLac, will also oscillate. This means that expression of c-Myc will be oscillatory, because pTet is regulated by TetR. For experimental purposes, GFP took the place of c-Myc as a reporter to show oscillations.</p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <p>The parameters that were used to construct the two component oscillator model were taken from a variety of sources. The promoter strengths were adjusted according to the ratios found by Drew Endy and other researchers, at a ratio of 650:395:40.<del class="diffchange diffchange-inline">[18] </del> The repressor half-life of LacI was adjusted to be shorter, based on the self-repressilator. In reality, this can be done by the application of ssrA tags, which can decrease the half-life of proteins.<del class="diffchange diffchange-inline">[19] </del> Finally, the dissociation constants of each protein and the cooperativity of TetR were altered based on the findings of the 2009 Aberdeen iGEM team.<del class="diffchange diffchange-inline">[20] </del> They found that the values of Kd(dissociation constant) cited in papers were too low because they conducted experiments in vitro instead of in vivo. Those experiments also did not take into account non-specific binding. The dissociation constants for LacI, TetR, and lambda CI were then estimated to be 700,7000, and 7000, respectively.<del class="diffchange diffchange-inline">[21] </del> Cooperativity of TetR was also found to be three instead of two.<del class="diffchange diffchange-inline">[22]</del></p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <p>The parameters that were used to construct the two component oscillator model were taken from a variety of sources. The promoter strengths were adjusted according to the ratios found by Drew Endy and other researchers, at a ratio of 650:395:40. The repressor half-life of LacI was adjusted to be shorter, based on the self-repressilator. In reality, this can be done by the application of ssrA tags, which can decrease the half-life of proteins. Finally, the dissociation constants of each protein and the cooperativity of TetR were altered based on the findings of the 2009 Aberdeen iGEM team. They found that the values of Kd(dissociation constant) cited in papers were too low because they conducted experiments in vitro instead of in vivo. Those experiments also did not take into account non-specific binding. The dissociation constants for LacI, TetR, and lambda CI were then estimated to be 700,7000, and 7000, respectively. Cooperativity of TetR was also found to be three instead of two.</p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>The two component oscillator is significant for two main reasons. First, its basis on pLac and LacI allows synchronization through the use of IPTG, making it easier for oscillations to actually bet tested. In addition, the system oscillated with the usage of more realistic parameters, contrary to the three component oscillator that tended towards equilibrium. These characteristics are shown in the graphs below:</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>The two component oscillator is significant for two main reasons. First, its basis on pLac and LacI allows synchronization through the use of IPTG, making it easier for oscillations to actually bet tested. In addition, the system oscillated with the usage of more realistic parameters, contrary to the three component oscillator that tended towards equilibrium. These characteristics are shown in the graphs below:</p></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h3 id='safety_switch'>Safety Termination</h3></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h3 id='safety_switch'>Safety Termination</h3></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <p>For the safety termination portion of our circuit, we express BRCA1 and Apoptin behind pSurvivin, which is a tumor-specific promoter.<del class="diffchange diffchange-inline">[23] </del> We were unable to produce a definite model that featured quantitative analysis, but were able to map out the mechanism for the safety mechanism. Apoptin induces apoptosis only in cancer cells, thus eliminating threat of metastasis.<del class="diffchange diffchange-inline">[24] </del>The wtBRCA1 protein product has been shown to interact with c-Myc.<del class="diffchange diffchange-inline">[25] </del> From the literature we have read, it seems to inhibit the hTERT promoter in multiple ways. BRCA1 has been shown to bind to c-Myc partially and inhibit its transcriptional and transformational activity in cells. BRCA1 is also suggested to inhibit hTERT promoter activity by binding to it.<del class="diffchange diffchange-inline">[26][27] </del> Thus, we have been able to piece together the following mechanism:</p> </div></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <p>For the safety termination portion of our circuit, we express BRCA1 and Apoptin behind pSurvivin, which is a tumor-specific promoter. We were unable to produce a definite model that featured quantitative analysis, but were able to map out the mechanism for the safety mechanism. Apoptin induces apoptosis only in cancer cells, thus eliminating threat of metastasis. The wtBRCA1 protein product has been shown to interact with c-Myc. From the literature we have read, it seems to inhibit the hTERT promoter in multiple ways. BRCA1 has been shown to bind to c-Myc partially and inhibit its transcriptional and transformational activity in cells. BRCA1 is also suggested to inhibit hTERT promoter activity by binding to it. Thus, we have been able to piece together the following mechanism:</p> </div></div></td></tr>
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Xiaoyangkao2
http://2014hs.igem.org/wiki/index.php?title=Team:TAS_Taipei/modeling&diff=28157&oldid=prev
Xiaoyangkao2 at 09:17, 19 July 2014
2014-07-19T09:17:07Z
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h3>General Format for Equations</h3></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h3>General Format for Equations</h3></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>For our project, we are modeling the rate of change in the number of proteins. This is dependent on translation of mRNA and the degradation rate of the proteins.</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>For our project, we are modeling the rate of change in the number of proteins. This is dependent on translation of mRNA and the degradation rate of the proteins.</p></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> <img src="https://static.igem.org/mediawiki/2014hs/c/c5/Image00.png"></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>The amount of mRNA depends on the activity of the promoter transcribing the mRNA and the degradation rate of the mRNA. Promoter activity is described by the Hill equation, which can describe the effect of activation or repression by a transcription factor. </p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>The amount of mRNA depends on the activity of the promoter transcribing the mRNA and the degradation rate of the mRNA. Promoter activity is described by the Hill equation, which can describe the effect of activation or repression by a transcription factor. </p></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> <div class="col-lg-11 col-lg-offset-1"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> <h4>Repression:</h4></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> <img src="https://static.igem.org/mediawiki/2014hs/1/18/Image11.png"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> <h4>Activation:</h4></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> <img src="https://static.igem.org/mediawiki/2014hs/4/47/Image09.png"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> </div></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h4>General Concepts</h4></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h4>General Concepts</h4></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>The maximum promoter strength, denoted by B, describes the rate of mRNA transcription and is listed in units of mRNA transcripts/min. The dissociation constant(Kd) describes the tendency of the transcription factor to separate into its subunits. Kd describes the binding affinity between the proteins and their target promoters. A higher Kd would mean that the protein has a hard time binding correctly to the promoter and a lower Kd would mean that it is comparatively easier for the protein to bind to its target promoter. Biologically, the Kd describes the concentration at which the promoter is 50% occupied. Lastly, the cooperativity, which is represented by n, describes the extent to which transcription factor binding will increase the attraction of the binding site to other transcription factors. A higher cooperativity would mean that binding of the regulating protein greatly increases the affinity of other regulators to bind. On a graph, that would mean that the system resembles a switch, showing a rapid change in state with a small difference in protein concentration.</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>The maximum promoter strength, denoted by B, describes the rate of mRNA transcription and is listed in units of mRNA transcripts/min. The dissociation constant(Kd) describes the tendency of the transcription factor to separate into its subunits. Kd describes the binding affinity between the proteins and their target promoters. A higher Kd would mean that the protein has a hard time binding correctly to the promoter and a lower Kd would mean that it is comparatively easier for the protein to bind to its target promoter. Biologically, the Kd describes the concentration at which the promoter is 50% occupied. Lastly, the cooperativity, which is represented by n, describes the extent to which transcription factor binding will increase the attraction of the binding site to other transcription factors. A higher cooperativity would mean that binding of the regulating protein greatly increases the affinity of other regulators to bind. On a graph, that would mean that the system resembles a switch, showing a rapid change in state with a small difference in protein concentration.</p></div></td></tr>
</table>
Xiaoyangkao2
http://2014hs.igem.org/wiki/index.php?title=Team:TAS_Taipei/modeling&diff=28148&oldid=prev
Xiaoyangkao2 at 08:45, 19 July 2014
2014-07-19T08:45:05Z
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h3>Citations</h3></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h3>Citations</h3></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del><p><del class="diffchange diffchange-inline">[1] </del>Zhao, Yong, Eladio Abreu, Jinyong Kim, Guido Stadler, Ugur Eskiocak, Michael P. Terns, Rebecca M. Terns, Jerry W. Shay, and Woodring E. Wright. "Processive and Distributive Extension of Human Telomeres by Telomerase under Homeostatic and Nonequilibrium Conditions." Molecular Cell, no. 42 (May 6, 2011): 297-307.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>Zhao, Yong, Eladio Abreu, Jinyong Kim, Guido Stadler, Ugur Eskiocak, Michael P. Terns, Rebecca M. Terns, Jerry W. Shay, and Woodring E. Wright. "Processive and Distributive Extension of Human Telomeres by Telomerase under Homeostatic and Nonequilibrium Conditions." Molecular Cell, no. 42 (May 6, 2011): 297-307.</p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> <p>[2] Ibid.</p></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>Harvard. "Key Numbers for Cell Biologists." B10NUMB3R5. http://www.google.com/url?q=http%3A%2F%2Fbionumbers.hms.harvard.edu%2FIncludes%2FKeyNumbersLinks.pdf&sa=D&sntz=1&usg=AFQjCNFyHaFJOqgspkVAHVMiHzUTU5Ky9A.</p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del><p><del class="diffchange diffchange-inline">[3] </del>Harvard. "Key Numbers for Cell Biologists." B10NUMB3R5. http://www.google.com/url?q=http%3A%2F%2Fbionumbers.hms.harvard.edu%2FIncludes%2FKeyNumbersLinks.pdf&sa=D&sntz=1&usg=AFQjCNFyHaFJOqgspkVAHVMiHzUTU5Ky9A.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>Oh, Stephen T., Saturo Kyo, and Laimonis A. Laimins. "Telomerase Activation by Human Papillomavirus Type 16 E6 Protein: Induction of Human Telomerase Reverse Transcriptase Expression through Myc and GC-Rich Sp1 Binding Sites." Journal of Virology 75, no. 12 (June 2001): 5559-66</p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del><p><del class="diffchange diffchange-inline">[4] </del>Oh, Stephen T., Saturo Kyo, and Laimonis A. Laimins. "Telomerase Activation by Human Papillomavirus Type 16 E6 Protein: Induction of Human Telomerase Reverse Transcriptase Expression through Myc and GC-Rich Sp1 Binding Sites." Journal of Virology 75, no. 12 (June 2001): 5559-66</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>Poole, Joseph C., Lucy G. Andrews, and Trygve O. Tollefsbol. "Activity, Function, and Gene Regulation of the Catalytic Subunit of Telomerase (hTERT)." Gene 269, nos. 1-2 (May 16, 2001): 1-12.</p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del><p><del class="diffchange diffchange-inline">[5] </del>Poole, Joseph C., Lucy G. Andrews, and Trygve O. Tollefsbol. "Activity, Function, and Gene Regulation of the Catalytic Subunit of Telomerase (hTERT)." Gene 269, nos. 1-2 (May 16, 2001): 1-12.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>Zou, Lin, Peng-Hui Zhang, Chun-Li Luo, and Zhi-Guang Tu. "Transcript Regulation of Human Telomerase Reverse Transcriptase by C-myc and Mad1." Acta Biochimica Et Biophysica Sinica 37, no. 1 (January 2005): 32-38.</p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del><p><del class="diffchange diffchange-inline">[6] </del>Zou, Lin, Peng-Hui Zhang, Chun-Li Luo, and Zhi-Guang Tu. "Transcript Regulation of Human Telomerase Reverse Transcriptase by C-myc and Mad1." Acta Biochimica Et Biophysica Sinica 37, no. 1 (January 2005): 32-38.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>Kapeli, Katannya, and Peter J. Hurlin. "Differential Regulation of N-Myc and c-Myc Synthesis, Degradation, and Transcriptional Activity by the Ras/Mitogen-activated Protein Kinase Pathway." The Journal of Biological Chemistry, no. 286 (September 9, 2011): 38498-508.</p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del><p><del class="diffchange diffchange-inline">[7] Harvard. "Key Numbers for Cell Biologists." B10NUMB3R5. http://www.google.com/url?q=http%3A%2F%2Fbionumbers.hms.harvard.edu%2FIncludes%2FKeyNumbersLinks.pdf&sa=D&sntz=1&usg=AFQjCNFyHaFJOqgspkVAHVMiHzUTU5Ky9A.</p></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>Chai, Juin Hsien, Yong Zhang, Wei Han Tan, Wee Joo Chng, Baojie Li, and Xueying Wang. "Supplemental Data Regulation of hTert by BCR-ABL at Multiple Levels in K562 Cells." BioMed Central. http://www.biomedcentral.com/content/supplementary/1471-2407-11-512-s1.pdf.</p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> <p>[8] Ibid</p></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>Purcell, Oliver, Claire S. Grierson, Mario di Bernardo, and Nigel J. Savery. "Temperature dependence of ssrA-tag mediated protein degradation." Journal of Biological Engineering 6, no. 10 (July 23, 2012).</p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> <p>[9] </del>Kapeli, Katannya, and Peter J. Hurlin. "Differential Regulation of N-Myc and c-Myc Synthesis, Degradation, and Transcriptional Activity by the Ras/Mitogen-activated Protein Kinase Pathway." The Journal of Biological Chemistry, no. 286 (September 9, 2011): 38498-508.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>Elowitz, Michael B., and Stanislas Leibler. "A Synthetic Oscillatory Network of Transcriptional Regulators." Nature 403 (January 20, 2000): 335-38.</p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del><p><del class="diffchange diffchange-inline">[10] </del>Chai, Juin Hsien, Yong Zhang, Wei Han Tan, Wee Joo Chng, Baojie Li, and Xueying Wang. "Supplemental Data Regulation of hTert by BCR-ABL at Multiple Levels in K562 Cells." BioMed Central. http://www.biomedcentral.com/content/supplementary/1471-2407-11-512-s1.pdf.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p><ins class="diffchange diffchange-inline">Novák</ins>, <ins class="diffchange diffchange-inline">Béla</ins>, and John J. Tyson. "Design Principles of Biochemical Oscillators." Nature Reviews, Molecular Cell Biology ser., 9 (December 2008): 981-91.</p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del><p><del class="diffchange diffchange-inline">[11] </del>Purcell, Oliver, Claire S. Grierson, Mario di Bernardo, and Nigel J. Savery. "Temperature dependence of ssrA-tag mediated protein degradation." Journal of Biological Engineering 6, no. 10 (July 23, 2012).</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>Endy, Drew E., J. C. Conboy, and C. C. Braff. "Promoter Characterization Experiments." Last modified April 22, 2008. Microsoft Word.</p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del><p><del class="diffchange diffchange-inline">[12] </del>Elowitz, Michael B., and Stanislas Leibler. "A Synthetic Oscillatory Network of Transcriptional Regulators." Nature 403 (January 20, 2000): 335-38.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>"Parameters." Team:Aberdeen_Scotland. http://www.google.com/url?q=http%3A%2F%2F2009.igem.org%2FTeam%3AAberdeen_Scotland%2Fparameters&sa=D&sntz=1&usg=AFQjCNG77BKYa2vSFwumEYhS6s_jWMAEKQ.</p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del><p><del class="diffchange diffchange-inline">[13] Novák</del>, <del class="diffchange diffchange-inline">Béla</del>, and John J. Tyson. "Design Principles of Biochemical Oscillators." Nature Reviews, Molecular Cell Biology ser., 9 (December 2008): 981-91.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>Yang, L., Z. Cao, F. Li, D. E. Post, E. G. Van Meir, H. Zhong, and W. C. Wood. "Tumor-specific Gene Expression Using the Survivin Promoter Is Further Increased by Hypoxia." Gene Therapy, no. 11 (2004): 1215-33.</p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del><p><del class="diffchange diffchange-inline">[14] Ibid</p></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>Sun Yat-Sen University. "Project/Design." iPS Cells Safeguard. Last modified 2013.https://2013.igem.org/Team:SYSU-China/Project/Design.</p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> <p>[15] Elowitz, Michael B., and Stanislas Leibler. "Repressilator." Unpublished manuscript, Princeton University, January 20, 2000. http://www.google.com/url?q=http%3A%2F%2Fwww.ebi.ac.uk%2Fbiomodels-main%2FBIOMD0000000012&sa=D&sntz=1&usg=AFQjCNGFLiZJXYrJcIBwjChGavz6UcD-LQ.</p></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>Blagosklonny, Mikhail V., Won G. An, Giovanni Melillo, Phuongmai Nguyen, Jane B. Trepel, and Leonard M. Neckers. "Regulation of BRCA1 by Protein Degradation." Oncogene 18, no. 47 (November 11, 1999): 6460-68.</p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> <p>[16] Novák, Béla, and John J. Tyson. "Design Principles of Biochemical Oscillators." Nature Reviews, Molecular Cell Biology ser., 9 (December 2008): 981-91.</p></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>Xiong, Jingbo, Saijun Fan, Qinghui Meng, Laura Schramm, Chenguang Wang, Boumedienne Bouzahza, Jinnian Zhou, Brian Zafonte, Itzhak D. Goldberg, Bassem R. Haddad, Richard G. Pestell, and Eliot M. Rosen. "BRCA1 Inhibition of Telomerase Activity in Cultured Cells."Molecular and Cellular Biology 23, no. 23 (December 2003): 8668-90</p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> <p>[17] Novák, Béla, and John J. Tyson. "Design Principles of Biochemical Oscillators." Nature Reviews, Molecular Cell Biology ser., 9 (December 2008): 981-91.</p></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> <p>[18] </del>Endy, Drew E., J. C. Conboy, and C. C. Braff. "Promoter Characterization Experiments." Last modified April 22, 2008. Microsoft Word.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del><p><del class="diffchange diffchange-inline">[19] Purcell, Oliver, Claire S. Grierson, Mario di Bernardo, and Nigel J. Savery. "Temperature dependence of ssrA-tag mediated protein degradation." Journal of Biological Engineering 6, no. 10 (July 23, 2012).</p></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> <p>[20] </del>"Parameters." Team:Aberdeen_Scotland. http://www.google.com/url?q=http%3A%2F%2F2009.igem.org%2FTeam%3AAberdeen_Scotland%2Fparameters&sa=D&sntz=1&usg=AFQjCNG77BKYa2vSFwumEYhS6s_jWMAEKQ.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del><p><del class="diffchange diffchange-inline">[21] Ibid</p></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> <p>[22] Ibid</p></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> <p>[23] </del>Yang, L., Z. Cao, F. Li, D. E. Post, E. G. Van Meir, H. Zhong, and W. C. Wood. "Tumor-specific Gene Expression Using the Survivin Promoter Is Further Increased by Hypoxia." Gene Therapy, no. 11 (2004): 1215-33.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del><p><del class="diffchange diffchange-inline">[24] </del>Sun Yat-Sen University. "Project/Design." iPS Cells Safeguard. Last modified<del class="diffchange diffchange-inline"></p></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> <p></del>2013.https://2013.igem.org/Team:SYSU-China/Project/Design.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> <p>[25] Blagosklonny, Mikhail V., Won G. An, Giovanni Melillo, Phuongmai Nguyen, Jane B. Trepel, and Leonard M. Neckers. "Regulation of BRCA1 by Protein Degradation." Oncogene 18, no. 47 (November 11, 1999): 6460-68.</p></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del><p><del class="diffchange diffchange-inline">[26] </del>Blagosklonny, Mikhail V., Won G. An, Giovanni Melillo, Phuongmai Nguyen, Jane B. Trepel, and Leonard M. Neckers. "Regulation of BRCA1 by Protein Degradation." Oncogene 18, no. 47 (November 11, 1999): 6460-68.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del><p><del class="diffchange diffchange-inline">[27] </del>Xiong, Jingbo, Saijun Fan, Qinghui Meng, Laura Schramm, Chenguang Wang, Boumedienne Bouzahza, Jinnian Zhou, Brian Zafonte, Itzhak D. Goldberg, Bassem R. Haddad, Richard G. Pestell, and Eliot M. Rosen. "BRCA1 Inhibition of Telomerase Activity in Cultured Cells."Molecular and Cellular Biology 23, no. 23 (December 2003): 8668-90</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
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Xiaoyangkao2
http://2014hs.igem.org/wiki/index.php?title=Team:TAS_Taipei/modeling&diff=28147&oldid=prev
Xiaoyangkao2 at 08:42, 19 July 2014
2014-07-19T08:42:37Z
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h4>Conclusion</h4></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h4>Conclusion</h4></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>Overall, the two component oscillator has a simpler design and is thus less constrained by differences of promoter strength, repressor half lives, and repressor dissociation constants. This makes the two component oscillator more realistically implementable. The oscillator also has an added benefit of easy synchronization with IPTG. Finally, after adjusting the parameters based on literature and tweaking LacI half-life with an ssrA tag, we were able to express the number of c-Myc proteins necessary to maintain telomere length.</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>Overall, the two component oscillator has a simpler design and is thus less constrained by differences of promoter strength, repressor half lives, and repressor dissociation constants. This makes the two component oscillator more realistically implementable. The oscillator also has an added benefit of easy synchronization with IPTG. Finally, after adjusting the parameters based on literature and tweaking LacI half-life with an ssrA tag, we were able to express the number of c-Myc proteins necessary to maintain telomere length.</p></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h3 id='safety_switch'>Safety Termination</h3></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h3 id='safety_switch'>Safety Termination</h3></div></td></tr>
</table>
Xiaoyangkao2
http://2014hs.igem.org/wiki/index.php?title=Team:TAS_Taipei/modeling&diff=28146&oldid=prev
Xiaoyangkao2 at 08:38, 19 July 2014
2014-07-19T08:38:04Z
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>The parameters that were used to construct the two component oscillator model were taken from a variety of sources. The promoter strengths were adjusted according to the ratios found by Drew Endy and other researchers, at a ratio of 650:395:40.[18] The repressor half-life of LacI was adjusted to be shorter, based on the self-repressilator. In reality, this can be done by the application of ssrA tags, which can decrease the half-life of proteins.[19] Finally, the dissociation constants of each protein and the cooperativity of TetR were altered based on the findings of the 2009 Aberdeen iGEM team.[20] They found that the values of Kd(dissociation constant) cited in papers were too low because they conducted experiments in vitro instead of in vivo. Those experiments also did not take into account non-specific binding. The dissociation constants for LacI, TetR, and lambda CI were then estimated to be 700,7000, and 7000, respectively.[21] Cooperativity of TetR was also found to be three instead of two.[22]</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>The parameters that were used to construct the two component oscillator model were taken from a variety of sources. The promoter strengths were adjusted according to the ratios found by Drew Endy and other researchers, at a ratio of 650:395:40.[18] The repressor half-life of LacI was adjusted to be shorter, based on the self-repressilator. In reality, this can be done by the application of ssrA tags, which can decrease the half-life of proteins.[19] Finally, the dissociation constants of each protein and the cooperativity of TetR were altered based on the findings of the 2009 Aberdeen iGEM team.[20] They found that the values of Kd(dissociation constant) cited in papers were too low because they conducted experiments in vitro instead of in vivo. Those experiments also did not take into account non-specific binding. The dissociation constants for LacI, TetR, and lambda CI were then estimated to be 700,7000, and 7000, respectively.[21] Cooperativity of TetR was also found to be three instead of two.[22]</p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>The two component oscillator is significant for two main reasons. First, its basis on pLac and LacI allows synchronization through the use of IPTG, making it easier for oscillations to actually bet tested. In addition, the system oscillated with the usage of more realistic parameters, contrary to the three component oscillator that tended towards equilibrium. These characteristics are shown in the graphs below:</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>The two component oscillator is significant for two main reasons. First, its basis on pLac and LacI allows synchronization through the use of IPTG, making it easier for oscillations to actually bet tested. In addition, the system oscillated with the usage of more realistic parameters, contrary to the three component oscillator that tended towards equilibrium. These characteristics are shown in the graphs below:</p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <figure style=''></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <figure style='<ins class="diffchange diffchange-inline">width:600px;</ins>'></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <img src='https://static.igem.org/mediawiki/2014hs/8/8d/Background_noise.jpg'></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <img src='https://static.igem.org/mediawiki/2014hs/8/8d/Background_noise.jpg'></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <figcaption class='darkblue'>Figure 10: Graph that shows the relationship between time and the protein concentrations of different cells without synchronization. Although only 15 proteins were simulated, it is clear from the graph that oscillatory behavior cannot be observed without synchronization.</figcaption></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <figcaption class='darkblue'>Figure 10: Graph that shows the relationship between time and the protein concentrations of different cells without synchronization. Although only 15 proteins were simulated, it is clear from the graph that oscillatory behavior cannot be observed without synchronization.</figcaption></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </figure></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </figure></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <figure style=''></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <figure style='<ins class="diffchange diffchange-inline">width:600px;</ins>'></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <img src='https://static.igem.org/mediawiki/2014hs/6/6e/Two-component_oscillator_with_reporter.jpg'></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <img src='https://static.igem.org/mediawiki/2014hs/6/6e/Two-component_oscillator_with_reporter.jpg'></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <figcaption class='darkblue'>Figure 11: Graph that shows the behavior of the two component oscillator. The blue line represents LacI, the yellow line represents TetR/RFP, and the green line represents GFP. The bacteria are synchronized with IPTG in this scenario, allowing for a clear observation of oscillatory behavior. This graph was also able to oscillate under the more realistic parameters that eliminated oscillatory behavior in the three component oscillator.</figcaption></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <figcaption class='darkblue'>Figure 11: Graph that shows the behavior of the two component oscillator. The blue line represents LacI, the yellow line represents TetR/RFP, and the green line represents GFP. The bacteria are synchronized with IPTG in this scenario, allowing for a clear observation of oscillatory behavior. This graph was also able to oscillate under the more realistic parameters that eliminated oscillatory behavior in the three component oscillator.</figcaption></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </figure></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </figure></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <figure style=''></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <figure style='<ins class="diffchange diffchange-inline">width:600px;</ins>'></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <img src='https://static.igem.org/mediawiki/2014hs/7/71/Htert_c-myc_two_component.jpg'></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <img src='https://static.igem.org/mediawiki/2014hs/7/71/Htert_c-myc_two_component.jpg'></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <figcaption class='darkblue'>Figure 12:Graph that shows the relationship between time and the expression of c-Myc and hTERT. hTERT is represented by the blue line, while c-Myc is represented by the purple line. hTERT concentration starts from zero but ascends rapidly due to an initial burst in c-Myc that matches the behavior of the oscillator; the initial burst in c-Myc is hard to observe here because of the long timespan of the graph. After the initial burst of c-Myc, its concentration oscillates between around 500 to 800 proteins, causing hTERT to level out at 1111 molecules, which is reasonably close to the minimum of 920 molecules we aimed to express.</figcaption></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <figcaption class='darkblue'>Figure 12:Graph that shows the relationship between time and the expression of c-Myc and hTERT. hTERT is represented by the blue line, while c-Myc is represented by the purple line. hTERT concentration starts from zero but ascends rapidly due to an initial burst in c-Myc that matches the behavior of the oscillator; the initial burst in c-Myc is hard to observe here because of the long timespan of the graph. After the initial burst of c-Myc, its concentration oscillates between around 500 to 800 proteins, causing hTERT to level out at 1111 molecules, which is reasonably close to the minimum of 920 molecules we aimed to express.</figcaption></div></td></tr>
</table>
Xiaoyangkao2
http://2014hs.igem.org/wiki/index.php?title=Team:TAS_Taipei/modeling&diff=28145&oldid=prev
Xiaoyangkao2 at 08:37, 19 July 2014
2014-07-19T08:37:29Z
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h4>Two Component Oscillator</h4></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h4>Two Component Oscillator</h4></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <<del class="diffchange diffchange-inline">p</del>><del class="diffchange diffchange-inline">As shown above</del>, two component oscillator is an expanded version of <del class="diffchange diffchange-inline">the </del>self-<del class="diffchange diffchange-inline">repressilator</del>. The pLac-LacI <del class="diffchange diffchange-inline">sequence was already shown to oscillate in the self-repressilator above</del>. Thus, TetR/RFP, which is expressed by pLac, will also oscillate. This means that expression of c-Myc will be oscillatory, because pTet is regulated by TetR. For experimental purposes, GFP took the place of c-Myc as a reporter to show oscillations. <del class="diffchange diffchange-inline"> </del></p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <<ins class="diffchange diffchange-inline">figure style='width:600px;margin-top:10px;'</ins>></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> <img src='https://static.igem.org/mediawiki/2014hs/c/cc/Image01.png'></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> <figcaption class='darkblue'>Figure 9:Construct of the two component oscillator. pLac expresses LacI</ins>, <ins class="diffchange diffchange-inline">creating oscillations that were observed in the self-repressilator. pLac also expresses TetR and RFP. TetR then goes on to inhibit pTet, which expresses c-Myc These oscillations can be observed by observing changes in color intensity In the experiments that were run in the lab, c-Myc was replaced GFP as a reporter, making it easier to observe oscillations, as the construct would alternate between red and green fluorescence.</figcaption></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </figure></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> <p>The </ins>two component oscillator is an expanded version of <ins class="diffchange diffchange-inline">pLac-LacI </ins>self-<ins class="diffchange diffchange-inline">Repressilator</ins>. The pLac-LacI <ins class="diffchange diffchange-inline">represses itself and thus oscillates</ins>. Thus, TetR/RFP, which is expressed by pLac, will also oscillate. This means that expression of c-Myc will be oscillatory, because pTet is regulated by TetR. For experimental purposes, GFP took the place of c-Myc as a reporter to show oscillations.</p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>The parameters that were used to construct the two component oscillator model were taken from a variety of sources. The promoter strengths were adjusted according to the ratios found by Drew Endy and other researchers, at a ratio of 650:395:40.[18] The repressor half-life of LacI was adjusted to be shorter, based on the self-repressilator. In reality, this can be done by the application of ssrA tags, which can decrease the half-life of proteins.[19] Finally, the dissociation constants of each protein and the cooperativity of TetR were altered based on the findings of the 2009 Aberdeen iGEM team.[20] They found that the values of Kd(dissociation constant) cited in papers were too low because they conducted experiments in vitro instead of in vivo. Those experiments also did not take into account non-specific binding. The dissociation constants for LacI, TetR, and lambda CI were then estimated to be 700,7000, and 7000, respectively.[21] Cooperativity of TetR was also found to be three instead of two.[22]</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>The parameters that were used to construct the two component oscillator model were taken from a variety of sources. The promoter strengths were adjusted according to the ratios found by Drew Endy and other researchers, at a ratio of 650:395:40.[18] The repressor half-life of LacI was adjusted to be shorter, based on the self-repressilator. In reality, this can be done by the application of ssrA tags, which can decrease the half-life of proteins.[19] Finally, the dissociation constants of each protein and the cooperativity of TetR were altered based on the findings of the 2009 Aberdeen iGEM team.[20] They found that the values of Kd(dissociation constant) cited in papers were too low because they conducted experiments in vitro instead of in vivo. Those experiments also did not take into account non-specific binding. The dissociation constants for LacI, TetR, and lambda CI were then estimated to be 700,7000, and 7000, respectively.[21] Cooperativity of TetR was also found to be three instead of two.[22]</p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>The two component oscillator is significant for two main reasons. First, its basis on pLac and LacI allows synchronization through the use of IPTG, making it easier for oscillations to actually bet tested. In addition, the system oscillated with the usage of more realistic parameters, contrary to the three component oscillator that tended towards equilibrium. These characteristics are shown in the graphs below:</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>The two component oscillator is significant for two main reasons. First, its basis on pLac and LacI allows synchronization through the use of IPTG, making it easier for oscillations to actually bet tested. In addition, the system oscillated with the usage of more realistic parameters, contrary to the three component oscillator that tended towards equilibrium. These characteristics are shown in the graphs below:</p></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> <figure style=''></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> <img src='https://static.igem.org/mediawiki/2014hs/8/8d/Background_noise.jpg'></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> <figcaption class='darkblue'>Figure 10: Graph that shows the relationship between time and the protein concentrations of different cells without synchronization. Although only 15 proteins were simulated, it is clear from the graph that oscillatory behavior cannot be observed without synchronization.</figcaption></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> </figure></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <figure style=''></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <figure style=''></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <img src='https://static.igem.org/mediawiki/2014hs/6/6e/Two-component_oscillator_with_reporter.jpg'></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <img src='https://static.igem.org/mediawiki/2014hs/6/6e/Two-component_oscillator_with_reporter.jpg'></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <figcaption class='darkblue'>Figure <del class="diffchange diffchange-inline">4</del>: Graph that shows the <del class="diffchange diffchange-inline">ideal </del>behavior of the <del class="diffchange diffchange-inline">three </del>component <del class="diffchange diffchange-inline">repressilator put forth by Elowitz and Leibler in 2000</del>. The blue line represents LacI, the <del class="diffchange diffchange-inline">red </del>line represents TetR, and the <del class="diffchange diffchange-inline">yellow </del>line represents <del class="diffchange diffchange-inline">lambda CI</del>. The <del class="diffchange diffchange-inline">values and equations </del>for <del class="diffchange diffchange-inline">the model were obtained from the BioModels Database</del>. <del class="diffchange diffchange-inline">The </del>graph was <del class="diffchange diffchange-inline">obtained by numerical integration using Mathematica</del>.</figcaption></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <figcaption class='darkblue'>Figure <ins class="diffchange diffchange-inline">11</ins>: Graph that shows the behavior of the <ins class="diffchange diffchange-inline">two </ins>component <ins class="diffchange diffchange-inline">oscillator</ins>. The blue line represents LacI, the <ins class="diffchange diffchange-inline">yellow </ins>line represents TetR<ins class="diffchange diffchange-inline">/RFP</ins>, and the <ins class="diffchange diffchange-inline">green </ins>line represents <ins class="diffchange diffchange-inline">GFP</ins>. The <ins class="diffchange diffchange-inline">bacteria are synchronized with IPTG in this scenario, allowing </ins>for <ins class="diffchange diffchange-inline">a clear observation of oscillatory behavior</ins>. <ins class="diffchange diffchange-inline"> This </ins>graph was <ins class="diffchange diffchange-inline">also able to oscillate under the more realistic parameters that eliminated oscillatory behavior in the three component oscillator</ins>.</figcaption></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </figure> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </figure></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <figure style=''></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <figure style=''></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <img src='https://static.igem.org/mediawiki/2014hs/<del class="diffchange diffchange-inline">f</del>/<del class="diffchange diffchange-inline">f0</del>/<del class="diffchange diffchange-inline">C</del>-<del class="diffchange diffchange-inline">Myc_and_hTERT_expression</del>.jpg'></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <img src='https://static.igem.org/mediawiki/2014hs/<ins class="diffchange diffchange-inline">7</ins>/<ins class="diffchange diffchange-inline">71</ins>/<ins class="diffchange diffchange-inline">Htert_c</ins>-<ins class="diffchange diffchange-inline">myc_two_component</ins>.jpg'></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <figcaption class='darkblue'>Figure <del class="diffchange diffchange-inline">5</del>: Graph that shows the <del class="diffchange diffchange-inline">ideal behavior of </del>the <del class="diffchange diffchange-inline">three component repressilator put forth by Elowitz </del>and <del class="diffchange diffchange-inline">Leibler in 2000</del>. <del class="diffchange diffchange-inline">The </del>blue line <del class="diffchange diffchange-inline">represents LacI</del>, the <del class="diffchange diffchange-inline">red </del>line <del class="diffchange diffchange-inline">represents TetR, and the yellow line represents lambda CI</del>. <del class="diffchange diffchange-inline">The values and equations for the model were obtained </del>from the <del class="diffchange diffchange-inline">BioModels Database. The </del>graph <del class="diffchange diffchange-inline">was obtained by numerical integration using Mathematica</del>.</figcaption></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <figcaption class='darkblue'>Figure <ins class="diffchange diffchange-inline">12</ins>:Graph that shows the <ins class="diffchange diffchange-inline">relationship between time and </ins>the <ins class="diffchange diffchange-inline">expression of c-Myc </ins>and <ins class="diffchange diffchange-inline">hTERT</ins>. <ins class="diffchange diffchange-inline">hTERT is represented by the </ins>blue line, <ins class="diffchange diffchange-inline">while c-Myc is represented by </ins>the <ins class="diffchange diffchange-inline">purple </ins>line. <ins class="diffchange diffchange-inline">hTERT concentration starts </ins>from <ins class="diffchange diffchange-inline">zero but ascends rapidly due to an initial burst in c-Myc that matches the behavior of the oscillator; the initial burst in c-Myc is hard to observe here because of the long timespan of </ins>the graph<ins class="diffchange diffchange-inline">. After the initial burst of c-Myc, its concentration oscillates between around 500 to 800 proteins, causing hTERT to level out at 1111 molecules, which is reasonably close to the minimum of 920 molecules we aimed to express</ins>.</figcaption></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </figure> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </figure></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
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</table>
Xiaoyangkao2
http://2014hs.igem.org/wiki/index.php?title=Team:TAS_Taipei/modeling&diff=28144&oldid=prev
Xiaoyangkao2 at 08:26, 19 July 2014
2014-07-19T08:26:42Z
<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h4>Self-Repressilator</h4></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h4>Self-Repressilator</h4></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>We first attempted to model the self-repressilator, which we know was an early design. The self-repressilator is significant because it lays the groundwork for the model of the two-component oscillator, which is really an expansion on the self-repressilator. The groundwork includes establishing the need for an explicit time delay, which is elaborated in the paper “Design Principles of Biochemical Oscillators†by Novak and Tyson. In this model, transcription is based on protein concentration in a previous point in time, to compensate for the time delay in transcription and translation. The explicit time delay was not needed in the three component oscillator because it established a time delay through a series of intermediates. The equations are as follows:</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>We first attempted to model the self-repressilator, which we know was an early design. The self-repressilator is significant because it lays the groundwork for the model of the two-component oscillator, which is really an expansion on the self-repressilator. The groundwork includes establishing the need for an explicit time delay, which is elaborated in the paper “Design Principles of Biochemical Oscillators†by Novak and Tyson. In this model, transcription is based on protein concentration in a previous point in time, to compensate for the time delay in transcription and translation. The explicit time delay was not needed in the three component oscillator because it established a time delay through a series of intermediates. The equations are as follows:</p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <img src="https://<del class="diffchange diffchange-inline">2014hs</del>.igem.org/<del class="diffchange diffchange-inline">File:</del>Image13.png"></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <img src="https://<ins class="diffchange diffchange-inline">static</ins>.igem.org/<ins class="diffchange diffchange-inline">mediawiki/2014hs/7/76/</ins>Image13.png"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>Without the explicit time delay, the graph would look like this, which we know that it shouldn’t look like:</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>Without the explicit time delay, the graph would look like this, which we know that it shouldn’t look like:</p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <figure style='width:600px;margin-top:10px;'></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <figure style='width:600px;margin-top:10px;'></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <img src='https://<del class="diffchange diffchange-inline">2014hs</del>.igem.org/<del class="diffchange diffchange-inline">File:</del>Image20.jpg'></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <img src='https://<ins class="diffchange diffchange-inline">static</ins>.igem.org/<ins class="diffchange diffchange-inline">mediawiki/2014hs/2/23/</ins>Image20.jpg'></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <figcaption class='darkblue'>Figure 7: Graph showing the relationship between time and LacI concentration. The system tends to equilibrium quickly without an explicit time delay in the equations.</figcaption></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <figcaption class='darkblue'>Figure 7: Graph showing the relationship between time and LacI concentration. The system tends to equilibrium quickly without an explicit time delay in the equations.</figcaption></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </figure> </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </figure> </div></td></tr>
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Xiaoyangkao2
http://2014hs.igem.org/wiki/index.php?title=Team:TAS_Taipei/modeling&diff=28143&oldid=prev
Xiaoyangkao2 at 08:25, 19 July 2014
2014-07-19T08:25:42Z
<p></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 08:25, 19 July 2014</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h4>Self-Repressilator</h4></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h4>Self-Repressilator</h4></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>We first attempted to model the self-repressilator, which we know was an early design. The self-repressilator is significant because it lays the groundwork for the model of the two-component oscillator, which is really an expansion on the self-repressilator. The groundwork includes establishing the need for an explicit time delay, which is elaborated in the paper “Design Principles of Biochemical Oscillators†by Novak and Tyson. In this model, transcription is based on protein concentration in a previous point in time, to compensate for the time delay in transcription and translation. The explicit time delay was not needed in the three component oscillator because it established a time delay through a series of intermediates. The equations are as follows:</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>We first attempted to model the self-repressilator, which we know was an early design. The self-repressilator is significant because it lays the groundwork for the model of the two-component oscillator, which is really an expansion on the self-repressilator. The groundwork includes establishing the need for an explicit time delay, which is elaborated in the paper “Design Principles of Biochemical Oscillators†by Novak and Tyson. In this model, transcription is based on protein concentration in a previous point in time, to compensate for the time delay in transcription and translation. The explicit time delay was not needed in the three component oscillator because it established a time delay through a series of intermediates. The equations are as follows:</p></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> <img src="https://2014hs.igem.org/File:Image13.png"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> <p>Without the explicit time delay, the graph would look like this, which we know that it shouldn’t look like:</p></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> <figure style='width:600px;margin-top:10px;'></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> <img src='https://2014hs.igem.org/File:Image20.jpg'></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> <figcaption class='darkblue'>Figure 7: Graph showing the relationship between time and LacI concentration. The system tends to equilibrium quickly without an explicit time delay in the equations.</figcaption></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> </figure> </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> <img src="https://static.igem.org/mediawiki/2014hs/d/da/Table_7.PNG"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> <p>We thus implemented the time delay, along with a change to LacI half-life to make the system oscillate:</p> </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> <figure style='width:600px;margin-top:10px;'></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> <img src='https://static.igem.org/mediawiki/2014hs/5/5c/Image12.jpg'></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> <figcaption class='darkblue'>Figure 8:Graph showing the relationship between time and LacI concentration. After including an explicit time delay of 10 minutes, the self-repressilator oscillated correctly. This was expected, as Novak and Tyson specified time delay as a criterion for oscillation in their review on biochemical oscillators. This graph is significant because it sets the foundation for the two component oscillator that will be discussed next.</figcaption></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> </figure> </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> <img src="https://static.igem.org/mediawiki/2014hs/3/3e/Table_8.PNG"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h4>Two Component Oscillator</h4></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h4>Two Component Oscillator</h4></div></td></tr>
</table>
Xiaoyangkao2
http://2014hs.igem.org/wiki/index.php?title=Team:TAS_Taipei/modeling&diff=28140&oldid=prev
Xiaoyangkao2 at 08:18, 19 July 2014
2014-07-19T08:18:47Z
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<td colspan='2' style="background-color: white; color:black;">Revision as of 08:18, 19 July 2014</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <img src="https://static.igem.org/mediawiki/2014hs/0/0d/Table_4.PNG"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <img src="https://static.igem.org/mediawiki/2014hs/0/0d/Table_4.PNG"></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <figure style='width:600px'></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <figure style='width:600px<ins class="diffchange diffchange-inline">;margin-top:10px;</ins>'></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <img src='https://static.igem.org/mediawiki/2014hs/a/a4/Nonideal_oscilator.jpg'></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <img src='https://static.igem.org/mediawiki/2014hs/a/a4/Nonideal_oscilator.jpg'></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <figcaption class='darkblue'>Figure 6:Graph that shows the behavior of the repressilator after implementing changes to promoter strength, repressor half-life, and constant of dissociaiton that try to simulate more realistic conditions. Any oscillations are quickly dampened and the system moves to equilibrium. This result affirmed our concerns about the oscillator and directed us to design an alternative oscillator that is more likely to oscillate in reality.</figcaption></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <figcaption class='darkblue'>Figure 6:Graph that shows the behavior of the repressilator after implementing changes to promoter strength, repressor half-life, and constant of dissociaiton that try to simulate more realistic conditions. Any oscillations are quickly dampened and the system moves to equilibrium. This result affirmed our concerns about the oscillator and directed us to design an alternative oscillator that is more likely to oscillate in reality.</figcaption></div></td></tr>
</table>
Xiaoyangkao2