Difference between revisions of "Team:Valencia UPV/Improve"
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| − | + | <section style="/* background-color: #353535; *//* background-image: url("https://previews.123rf.com/images/bogdanhoda/bogdanhoda1504/bogdanhoda150400014/38730978-test-tubes-in-clinic-pharmacy-and-medical-research-laboratory-with-male-scientist-using-pipette.jpg"); *//* background-size: 100%; */height:44.2em;margin-top: 0em;padding-top: 1.1em;" class="height-90 parallax"> | |
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| − | <a class="anchorOffset" id="story"></a> | + | <a class="anchorOffset" id="story"></a> |
| − | <section class="feature-large" style="padding-top: 6em; padding-bottom: 50px; outline: none;" data-scroll-id="story" tabindex="-1"> | + | <section class="feature-large" style="padding-top: 6em; padding-bottom: 50px; outline: none;" data-scroll-id="story" tabindex="-1"> |
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| − | padding-left: 2em;padding-right: 2em;"> | + | padding-left: 2em;padding-right: 2em;"> |
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| − | + | <h3 style=" | |
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| − | + | font-weight: 700; | |
| − | + | font-size: 40px; | |
| − | + | margin-bottom: 0.2em; | |
| − | ">Part Improvement</h3> | + | ">Part Improvement</h3> |
| − | + | <p> | |
| − | <p> | + | During the development of the iGEM project, when designing our <a href="https://2018.igem.org/Team:Valencia_UPV/Part_Collection" target="_blank">Part Collection</a>, we decided to offer Printeria users a <b>wide range of reporter proteins</b> that they could use in their experiments. Of all of them, it calls our attention that some reporter proteins such as the <b>YFP did not present much information</b> about their use and experimentation, compared to the well-known GFP or sfGFP. |
| − | The BioBrick chosen to be improved was the YFP coding sequence: <a href="http://parts.igem.org/Part:BBa_K592101"> BBa_K592101</a>. To do this, we first standardized the part to be compatible with the <a href="https://2018.igem.org/Team:Valencia_UPV/GB3"> GoldenBraid 3.0</a> assembly method creating the part <a href="http://parts.igem.org/Part:BBa_K2656021"> BBa_K2656021</a>. Then, we created the part <a href="http://parts.igem.org/Part:BBa_K2656020"> BBa_K2656020</a>. This part is the CDS of the YFP with the addition of the degradation tag ssRA LVA. | + | </p> |
| + | <p> | ||
| + | Because of this reason, the Printeria team has carried out <b>several experiments using YFP</b> as a reporter protein in order to better characterize it, obtaining the maximum information about that part. Throughout the project we have obtained its <a href="https://2018.igem.org/Team:Valencia_UPV/Experiments#imSpectral" target="_blank"><b>excitation and emission spectra</b></a>, as well as the <a href="https://2018.igem.org/Team:Valencia_UPV/Experiments#comparison" target="_blank"><b>MEFL/cell factor</b></a> that allows us to convert FOD into equivalent molecules (MEFL). | ||
| + | </p> | ||
| + | |||
| + | <p> | ||
| + | However, we decided to go a step further and <b>design a new part by adding a degradation LVA tag to YFP sequence</b>, which increases the action of proteases and causes <b>faster degradation</b>. The BioBrick chosen to be improved was the YFP coding sequence: <a href="http://parts.igem.org/Part:BBa_K592101"> BBa_K592101</a>. To do this, we first standardized the part to be compatible with the <a href="https://2018.igem.org/Team:Valencia_UPV/GB3"> GoldenBraid 3.0</a> assembly method creating the part <a href="http://parts.igem.org/Part:BBa_K2656021"> BBa_K2656021</a>. Then, we created the part <a href="http://parts.igem.org/Part:BBa_K2656020"> BBa_K2656020</a>. This part is the CDS of the YFP with the addition of the degradation tag ssRA LVA. | ||
| − | </p> | + | </p> |
| − | <p> | + | <p> |
| − | To test the effect of the degradation tag, we designed an <a href="https://2018.igem.org/Team:Valencia_UPV/Model#tag_exp">experiment</a> with which we measured the increase in protein degradation due to this tag. To perform this experiment, we assembled two composite parts with the same promoter, RBS and terminator: | + | To test the effect of the degradation tag, we designed an <a href="https://2018.igem.org/Team:Valencia_UPV/Model#tag_exp">experiment</a> with which we measured the increase in protein degradation due to this tag. To perform this experiment, we assembled two composite parts with the same promoter, RBS and terminator: |
| − | </p> | + | </p> |
| − | <ul> | + | <ul> |
| − | <li> | + | <li> |
| − | <p> | + | <p> |
| − | <a href="http://parts.igem.org/Part:BBa_K2656112"> BBa_K2656112</a>: | + | <a href="http://parts.igem.org/Part:BBa_K2656112"> BBa_K2656112</a>: |
| − | </p> | + | </p> |
| − | </li> | + | </li> |
| − | + | <ul style=" | |
| − | padding-left: 3em !important;"> | + | padding-left: 3em !important;"> |
| − | + | <li><p><a href="http://parts.igem.org/Part:BBa_K2656004">BBa_K2656004</a>: the <a href="http://parts.igem.org/Part:BBa_J23106">J23106</a> promoter in its GoldenBraid compatible version from our <a href="https://2018.igem.org/Team:Valencia_UPV/Part_Collection">Part Collection</a></p></li> | |
| − | + | <li><p><a href="http://parts.igem.org/Part:BBa_K2656009">BBa_K2656009</a>: the <a href="http://parts.igem.org/Part:BBa_B0030">B0030</a> ribosome biding site in its GoldenBraid compatible version from our <a href="https://2018.igem.org/Team:Valencia_UPV/Part_Collection">Part Collection</a></p></li> | |
| − | + | <li><p><a href="http://parts.igem.org/Part:BBa_K2656021">BBa_K2656021</a>: The original part <a href="http://parts.igem.org/Part:BBa_K592101"> BBa_K592101</a> compatible with the GoldenBraid assembly method</p></li> | |
| − | + | <li><p><a href="http://parts.igem.org/Part:BBa_K2656026">BBa_K2656026</a>: the <a href="http://parts.igem.org/Part:BBa_B0015">B0015</a> transcriptional terminator in its GoldenBraid compatible version from our <a href="https://2018.igem.org/Team:Valencia_UPV/Part_Collection">Part Collection</a></p></li> | |
| − | </ul> | + | </ul> |
| − | <li> | + | <li> |
| − | <p> | + | <p> |
| − | <a href="http://parts.igem.org/Part:BBa_K2656111"> BBa_K2656111</a>: | + | <a href="http://parts.igem.org/Part:BBa_K2656111"> BBa_K2656111</a>: |
| − | </p> | + | </p> |
| − | </li> | + | </li> |
| − | + | <ul style=" padding-left: 3em !important;"> | |
| − | + | <li><p><a href="http://parts.igem.org/Part:BBa_K2656004">BBa_K2656004</a></p></li> | |
| − | + | <li><p><a href="http://parts.igem.org/Part:BBa_K2656009">BBa_K2656009</a></p></li> | |
| − | + | <li><p><a href="http://parts.igem.org/Part:BBa_K2656020">BBa_K2656020</a>: The original part with the added LVA ssRA degradation tag compatible with the GoldenBraid assembly method</p></li> | |
| − | + | <li><p><a href="http://parts.igem.org/Part:BBa_K2656026">BBa_K2656026</a></p></li> | |
| − | </ul> | + | </ul> |
| − | + | </ul></div> | |
| − | <p> Once the experiment was carried out, the results were plotted and Figure 1 was obtained, in which we can observe that the growth of the bacteria with both constructions was very similar, while the fluorescence had a clear variation.</p> | + | <p> Once the experiment was carried out, the results were plotted and Figure 1 was obtained, in which we can observe that the growth of the bacteria with both constructions was very similar, while the fluorescence had a clear variation.</p> |
| − | + | <img src="https://static.igem.org/mediawiki/2018/7/72/T--Valencia_UPV--optimization_exp1_YFP_graphUPV2018.png" /> | |
| − | <h6 style=" | + | <h6 style=" |
| − | + | text-align: left !important; | |
| − | "> Figure 1. Experimental results of the fluorescence comparison experiment between the transcriptional unit with BBa_K2656021 and the one with BBa_K2656020. </h6> | + | "> Figure 1. Experimental results of the fluorescence comparison experiment between the transcriptional unit with BBa_K2656021 and the one with BBa_K2656020. </h6> |
| − | <p>These data were optimized with our <a href="https://2018.igem.org/Team:Valencia_UPV/Model#const_models"> model</a> and the parameters from Table 1 were obtained. With these parameters it is possible to obtain that <b>the protein degradation of the protein with the LVA degradation tag is around twice as much as without the LVA degradation tag</b>. | + | <p>These data were optimized with our <a href="https://2018.igem.org/Team:Valencia_UPV/Model#const_models"> model</a> and the parameters from Table 1 were obtained. With these parameters it is possible to obtain that <b>the protein degradation of the protein with the LVA degradation tag is around twice as much as without the LVA degradation tag</b>. |
| − | <table> | + | <table> |
| − | <h6> Table 1. Optimized values of translation rate, degradation rate and dilution rate from experimental data </h6> <tbody><tr> | + | <h6> Table 1. Optimized values of translation rate, degradation rate and dilution rate from experimental data </h6> <tbody><tr> |
| − | + | <th><p>Optimized parameters</p></th> | |
| − | + | <th><p>Values</p></th> | |
| − | + | </tr> | |
| − | + | <tr> | |
| − | + | <td><p>Translation rate <b>p</b></p></td> | |
| − | + | <td> | |
| − | + | <ul> | |
| − | + | <li><p> | |
| − | + | For YFP with LVA tag <a href="http://parts.igem.org/Part:BBa_K2656020" target="_blank" style="padding-right: 0">BBa_K2656020</a>: p = 0.4622 min<sup>-1</sup> | |
| − | + | </p></li> | |
| − | + | <li><p> | |
| − | + | For YFP without LVA tag <a href="http://parts.igem.org/Part:BBa_K2656021" target="_blank" style="padding-right: 0">BBa_K2656021</a>: p = 1.053 min<sup>-1</sup> | |
| − | + | </p></li> | |
| − | + | </ul> | |
| − | + | </td></tr> | |
| − | + | <tr><td><p>PoI degradation rate <b>d<sub>p</sub></b></p></td> | |
| − | + | <td><p> | |
| − | + | </p><ul> | |
| − | + | <li><p> | |
| − | + | For YFP with LVA tag <a href="http://parts.igem.org/Part:BBa_K2656020" target="_blank" style="padding-right: 0">BBa_K2656020</a>: d<sub>p</sub> = 0.01492 min<sup>-1</sup> | |
| − | + | </p></li> | |
| − | + | <li><p> | |
| − | + | For YFP without LVA tag <a href="http://parts.igem.org/Part:BBa_K2656021" target="_blank" style="padding-right: 0">BBa_K2656021</a>: d<sub>p</sub> = 0.0080 min<sup>-1</sup> | |
| − | + | </p></li> | |
| − | + | </ul> | |
| − | + | <p></p></td> | |
| − | + | </tr> | |
| − | + | <tr> | |
| − | + | <td><p>Dilution rate <b><meta charset="utf-8">μ</b></p></td> | |
| − | + | <td><p> | |
| − | + | </p><ul> | |
| − | + | <li><p> | |
| − | + | For YFP with LVA tag <a href="http://parts.igem.org/Part:BBa_K2656020" target="_blank" style="padding-right: 0">BBa_K2656020</a>: <meta charset="utf-8">μ = 0.01166 min<sup>-1</sup> | |
| − | + | </p></li> | |
| − | + | <li><p> | |
| − | + | For YFP without LVA tag <a href="http://parts.igem.org/Part:BBa_K2656021" target="_blank" style="padding-right: 0">BBa_K2656021</a>: <meta charset="utf-8">μ = 0.01307 min<sup>-1</sup> | |
| − | + | </p></li> | |
| − | + | </ul> | |
| − | + | <p></p></td> | |
| − | + | </tr></tbody></table> | |
| − | <a href="https://static.igem.org/mediawiki/2018/7/73/T--Valencia_UPV--dp_ratioUPV2018.png" data-lightbox="true"> | + | <a href="https://static.igem.org/mediawiki/2018/7/73/T--Valencia_UPV--dp_ratioUPV2018.png" data-lightbox="true"> |
| − | + | <img src="https://static.igem.org/mediawiki/2018/7/73/T--Valencia_UPV--dp_ratioUPV2018.png" /> | |
| − | + | </a> | |
| − | + | </div> | |
| − | + | </div> | |
| − | + | </div> | |
| − | </section> | + | </section> |
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Revision as of 23:48, 9 October 2018
Part Improvement
During the development of the iGEM project, when designing our Part Collection, we decided to offer Printeria users a wide range of reporter proteins that they could use in their experiments. Of all of them, it calls our attention that some reporter proteins such as the YFP did not present much information about their use and experimentation, compared to the well-known GFP or sfGFP.
Because of this reason, the Printeria team has carried out several experiments using YFP as a reporter protein in order to better characterize it, obtaining the maximum information about that part. Throughout the project we have obtained its excitation and emission spectra, as well as the MEFL/cell factor that allows us to convert FOD into equivalent molecules (MEFL).
However, we decided to go a step further and design a new part by adding a degradation LVA tag to YFP sequence, which increases the action of proteases and causes faster degradation. The BioBrick chosen to be improved was the YFP coding sequence: BBa_K592101. To do this, we first standardized the part to be compatible with the GoldenBraid 3.0 assembly method creating the part BBa_K2656021. Then, we created the part BBa_K2656020. This part is the CDS of the YFP with the addition of the degradation tag ssRA LVA.
To test the effect of the degradation tag, we designed an experiment with which we measured the increase in protein degradation due to this tag. To perform this experiment, we assembled two composite parts with the same promoter, RBS and terminator:
BBa_K2656004: the J23106 promoter in its GoldenBraid compatible version from our Part Collection
BBa_K2656009: the B0030 ribosome biding site in its GoldenBraid compatible version from our Part Collection
BBa_K2656021: The original part BBa_K592101 compatible with the GoldenBraid assembly method
BBa_K2656026: the B0015 transcriptional terminator in its GoldenBraid compatible version from our Part Collection
BBa_K2656020: The original part with the added LVA ssRA degradation tag compatible with the GoldenBraid assembly method
Once the experiment was carried out, the results were plotted and Figure 1 was obtained, in which we can observe that the growth of the bacteria with both constructions was very similar, while the fluorescence had a clear variation.
Figure 1. Experimental results of the fluorescence comparison experiment between the transcriptional unit with BBa_K2656021 and the one with BBa_K2656020.
These data were optimized with our model and the parameters from Table 1 were obtained. With these parameters it is possible to obtain that the protein degradation of the protein with the LVA degradation tag is around twice as much as without the LVA degradation tag.
Optimized parameters |
Values |
|---|---|
Translation rate p |
|
PoI degradation rate dp |
|
Dilution rate μ |
|
