Difference between revisions of "Team:DTU-Denmark/Design"

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<h1>Design</h1>
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Design is the first step in the design-build-test cycle in engineering and synthetic biology. Use this page to describe the process that you used in the design of your parts. You should clearly explain the engineering principles used to design your project.
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<img src="https://static.igem.org/mediawiki/2019/7/7b/T--DTU-Denmark--designheader2.svg" title="Illustration of different considerations made for the design of promoters in aspergillus" style="margin-top:75px;max-width:70%;margin-right:auto; margin-left:auto;display: block;
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<h2>Design</h2>
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<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 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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<h3>What should this page contain?</h3>
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  <img id="designlinesfig1" alt="" src="https://static.igem.org/mediawiki/2019/a/af/T--DTU-Denmark--designfigtest1.svg">
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<li>Explanation of the engineering principles your team used in your design</li>
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  <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><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>
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  <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 df4promoter"><p><b>Differentiated promoter strength:</b><p> With proHMMoter, the software behind LEAP, it is possible to create promoters with varying strengths, but with similar promoter dynamics.   
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      <div class="df2 df5promoter"><p><b>Cross species activity:</b><p>
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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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<h3>Inspiration</h3>
 
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<li><a href="https://2016.igem.org/Team:MIT/Experiments/Promoters">2016 MIT</a></li>
 
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<li><a href="https://2016.igem.org/Team:BostonU/Proof">2016 BostonU</a></li>
 
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<li><a href="https://2016.igem.org/Team:NCTU_Formosa/Design">2016 NCTU Formosa</a></li>
 
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<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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        <a href="https://2019.igem.org/Team:DTU-Denmark/Design_Plasmid">Vector design</a>
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          <img src="https://static.igem.org/mediawiki/2019/7/70/T--DTU-Denmark--design_vector_design.svg"/>
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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 <i>Aspergillus niger</i> </p>
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        <a href="https://2019.igem.org/Team:DTU-Denmark/Design_Promoter">Promoter Design</a>
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          <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 which genes the different LEAP promoters are based on, and which considerations we had for these selections.  </p>
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        <a href="https://2019.igem.org/Team:DTU-Denmark/Design_Measurement">Measurement design</a>
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          <div class="button-image"> <img src="https://static.igem.org/mediawiki/2019/4/4c/T--DTU-Denmark--design_test_design.svg" style="height:100%;"/></div>
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            <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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        <a href="https://2019.igem.org/Team:DTU-Denmark/Design_Promoter">Promoter Design</a>
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          <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 what genes the different LEAP promoters are based on, and what considerations we had for these selections.  </p>
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        </div>
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<div class="one_whole underordnede">
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        <a href="https://2019.igem.org/Team:DTU-Denmark/Design_Plasmid">Vector design</a>
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          <img src="https://static.igem.org/mediawiki/2019/7/70/T--DTU-Denmark--design_vector_design.svg"/>
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            </div>
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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>
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        <a href="https://2019.igem.org/Team:DTU-Denmark/Design_Measurement">Measurement design</a>
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          <div class="button-image"> <img src="https://static.igem.org/mediawiki/2019/4/4c/T--DTU-Denmark--design_test_design.svg" style="height:100%;"/></div>
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            </div>
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            <p>Click here to read more about what design considerations were made for measuring our promoter output, and which experiments this let us to perform. 
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<p style=" font-size:14px;"><br><br>
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(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</p>
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                    <h5>Useful links</h5>
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Latest revision as of 21:28, 21 October 2019

Design

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 Aspergillus niger, since work in this organism is underrepresented in iGEM, but well represented in the biotech industry.[1]

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:

This difure is connected to the one below it. The figure shows a promoter with the following considerations.

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.

The model takes all of these features into account.
Vector design

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

Promoter Design

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.

Measurement design

Click here to read more about which design considerations were made for measuring our promoter output, and which experiments this lead us to perform.

Promoter Design

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.

Vector design

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

Measurement design

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

The logos of our three biggest supporters, DTU Blue Dot, Novo Nordisk fonden and Otto Mønsted fonden The logos of all of our sponsors, DTU, BioNordica, Eurofins Genomics, Qiagen, NEB New England biolabs, IDT Integrated DNA technologies and Twist bioscience