Difference between revisions of "Team:DTU-Denmark/Design"
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<h2>Design</h2> | <h2>Design</h2> | ||
| − | <p><div>The LEAP project is based on building a software that can create synthetic promoter libraries around any set or subset of organisms. We chose to develop promoters for Aspergillus niger, since work in this organism is underrepresented in iGEM, but well represented in the biotech industry[1]</div></p> | + | <p><div>The LEAP project is based on building a piece of software that can create synthetic promoter libraries around any set or subset of organisms. We chose to develop promoters for <i>Aspergillus niger</i>, since work in this organism is underrepresented in iGEM, but well represented in the biotech industry.[1]</div></p> |
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| − | <p>Multiple design decisions were made for the synthetic LEAP promoters created in this project. With software and models, we are able to create different synthetic promoters but to | + | <p>Multiple design decisions were made for the synthetic LEAP promoters created in this project. With software and models, we are able to create different synthetic promoters but in order for them to be of any value, these promoters must be usable for further work within industry or academia. To make sure our promoters would be of actual use in the real world, we contacted representatives from both biotech companies and research institutions as described in the <a href="https://2019.igem.org/Team:DTU-Denmark/Integrated_Human_Practices" target="_blank">integrated Human Practices</a> page. Their feedback on which features were especially important for promoters, enabled us to define some important design criteria for our software, proHMMoter, in order to produce promoters with the desired features. Some of the most important features of the synthetic LEAP promoters are shown in the figure below:</a> |
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| − | <img alt="" src="https://static.igem.org/mediawiki/2019/ | + | <img id="designlinesfig1" alt="" src="https://static.igem.org/mediawiki/2019/a/af/T--DTU-Denmark--designfigtest1.svg"> |
| − | <img alt="figure | + | <img alt="This difure is connected to the one below it. The figure shows a promoter with the following considerations." src="https://static.igem.org/mediawiki/2019/d/df/T--DTU-Denmark--Designfigure1promoter.svg" class="df1promoter"> |
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| − | <div class="df2 df2promoter"><p><b>Domestication:</b> Compatibility with different assembly methods is important, especially since we want to ensure that the promoters can be used as a new part within an existing design.</p></div> | + | <div class="df2 df2promoter"><p><b>Domestication:</b><br> Compatibility with different assembly methods is important, especially since we want to ensure that the promoters can be used as a new part within an existing design. With the software behind LEAP, we will enable everyone to define which assembly standards they want the promoters to comply with.</p></div> |
| − | <div class="df2 df3promoter"><p><b>Different promoter dynamics:</b><p> | + | <div class="df2 df3promoter"><p><b>Different promoter dynamics:</b><p> Basing promoter design on different genes enables the software to create promoters with different dynamics. This enables the creation of promoters that can be activated under different conditions such as a specific growth phase. |
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<div class="df2 df5promoter"><p><b>Cross species activity:</b><p> | <div class="df2 df5promoter"><p><b>Cross species activity:</b><p> | ||
| − | It was important | + | It was important for the generated promoters to be easily transferable among any selected group of organisms, which is why the fundamental design of the software was based on homology modeling. This allows the user to include any number of organisms without compromising their core organisms. |
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| + | <a href="https://2019.igem.org/Team:DTU-Denmark/Model" target="_blank"> | ||
| + | <img title="Click to go to model" alt="The model takes all of these features into account." src="https://static.igem.org/mediawiki/2019/b/b8/T--DTU-Denmark--designcomputerfig1.svg" class="df1computer"></a> | ||
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| − | <p>Click here to read more about how we built a new test device for future iGEM teams to use in testing fungal promoters using Type IIS restriction enzymes. You can also read more about our different strategies for cloning and expressing our promoters in Aspergillus niger </p> | + | <p>Click here to read more about how we built a new test device for future iGEM teams to use in testing fungal promoters using Type IIS restriction enzymes. You can also read more about our different strategies for cloning and expressing our promoters in <i>Aspergillus niger</i> </p> |
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<img src="https://static.igem.org/mediawiki/2019/c/cd/T--DTU-Denmark--design_promoter_design_1.svg" /> | <img src="https://static.igem.org/mediawiki/2019/c/cd/T--DTU-Denmark--design_promoter_design_1.svg" /> | ||
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| − | <p>Click here to read more about the requirements we defined for our promoters, and the reasoning behind them. You can also read about | + | <p>Click here to read more about the requirements we defined for our promoters, and the reasoning behind them. You can also read about which genes the different LEAP promoters are based on, and which considerations we had for these selections. </p> |
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| − | <p>Click here to read more about | + | <p>Click here to read more about which design considerations were made for measuring our promoter output, and which experiments this lead us to perform. |
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Latest revision as of 21:28, 21 October 2019
Design
Multiple design decisions were made for the synthetic LEAP promoters created in this project. With software and models, we are able to create different synthetic promoters but in order for them to be of any value, these promoters must be usable for further work within industry or academia. To make sure our promoters would be of actual use in the real world, we contacted representatives from both biotech companies and research institutions as described in the integrated Human Practices page. Their feedback on which features were especially important for promoters, enabled us to define some important design criteria for our software, proHMMoter, in order to produce promoters with the desired features. Some of the most important features of the synthetic LEAP promoters are shown in the figure below:
Domestication:
Compatibility with different assembly methods is important, especially since we want to ensure that the promoters can be used as a new part within an existing design. With the software behind LEAP, we will enable everyone to define which assembly standards they want the promoters to comply with.
Different promoter dynamics:
Basing promoter design on different genes enables the software to create promoters with different dynamics. This enables the creation of promoters that can be activated under different conditions such as a specific growth phase.
Differentiated promoter strength:
With proHMMoter, the software behind LEAP, it is possible to create promoters with varying strengths, but with similar promoter dynamics.
Cross species activity:
It was important for the generated promoters to be easily transferable among any selected group of organisms, which is why the fundamental design of the software was based on homology modeling. This allows the user to include any number of organisms without compromising their core organisms.
Click here to read more about how we built a new test device for future iGEM teams to use in testing fungal promoters using Type IIS restriction enzymes. You can also read more about our different strategies for cloning and expressing our promoters in Aspergillus niger
Click here to read more about the requirements we defined for our promoters, and the reasoning behind them. You can also read about which genes the different LEAP promoters are based on, and which considerations we had for these selections.
Click here to read more about which design considerations were made for measuring our promoter output, and which experiments this lead us to perform.
Click here to read more about the requirements we defined for our promoters, and the reasoning behind them. You can also read about what genes the different LEAP promoters are based on, and what considerations we had for these selections.
Click here to read more about how we built a new test device for future iGEM teams to use in testing fungal promoters using Type IIS restriction enzymes. You can also read more about our different strategies for cloning and expressing our promoters in Aspergillus niger
Click here to read more about what design considerations were made for measuring our promoter output, and which experiments this let us to perform.
(1) Siddiqui, S: Protein Production: Quality Control and Secretion Stress Response. New and Future Developments in Microbial Biotechnology and Bioengineering: Aspergillus System Properties and Applications, 2016. pp. 257-266
