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| <b>Presented by DTU BioBuilders 2020</b> | | <b>Presented by DTU BioBuilders 2020</b> |
− | <p style="font-size:13px">Daniel Bavnhøj<sup>a</sup>, Peter Bing<sup>a</sup>, Clara Drachmann<sup>b</sup>, Martí M. Gómez<sup>b</sup>, Cecilia D. V. Graae<sup>a</sup>, Bira A. Khan<sup>a</sup>, Niels M. Knudsen<sup>a</sup>, Lucas Levassor<sup>a</sup>, Margrethe Mærsk-Møller<sup>b</sup>, Victoria V. Nissen<sup>a</sup>, Christine Pedersen<sup>a</sup>, Cecilie A. N. Thystrup<sup>b</sup>, Timian Rindal<sup>a</sup> </p> | + | <p style="font-size:13px">Daniel Bavnhøj<sup>a</sup>, Peter Bing<sup>a</sup>, Clara Drachmann<sup>b</sup>, Martí M. Gómez<sup>b</sup>, Cecilia D. V. Graae<sup>a</sup>, Bira A. Khan<sup>a</sup>, Niels MK<sup>a</sup>, Lucas Levassor<sup>a</sup>, Margrethe Mærsk-Møller<sup>b</sup>, Victoria V. Nissen<sup>a</sup>, Christine Pedersen<sup>a</sup>, Cecilie A. N. Thystrup<sup>b</sup>, Timian Rindal<sup>a</sup> </p> |
| <p style="font-size:10px"> <sup>a</sup>DTU Bioengineering, <sup>b</sup>DTU Health Tech, Technical University of Denmark </p> | | <p style="font-size:10px"> <sup>a</sup>DTU Bioengineering, <sup>b</sup>DTU Health Tech, Technical University of Denmark </p> |
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| <div class="title"> Model and Software</div> | | <div class="title"> Model and Software</div> |
| <!--Write the text explaining this section --> | | <!--Write the text explaining this section --> |
− | <div class="text"> <p align="justify">To aid our parts characterization, we developed two models for studying the morphological features of <i>Aspergillus niger</i>, both based on our experimental data. </p> | + | <div class="text"> <p align="justify">To aid our parts characterization, we developed two models for studying the morphological features of <i>Aspergillus niger</i>, both based on our experimental data. The first model, <b>Morphologizer</b>, automatically analyzes microscopic images of mycelia. The second model, <b>Mycemulator</b>, is a stochastic model that simulates mycelial growth based on morphological parameters, including some from the Morphologizer. </p> |
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| <center><figure> <img style="width:80%" src="https://static.igem.org/mediawiki/2020/5/53/T--DTU-Denmark--Poster_imageana.png" class="center"><figcaption><p align="justify"><i> Showcase of our first model, Morphologizer. The model analyzes microscope images of mycelia, converts them into graph objects, and extracts morphological features of interest from the graph, such as the number of branches, branching angles, and hyphal curvature. </i></p></figcaption></figure></center> | | <center><figure> <img style="width:80%" src="https://static.igem.org/mediawiki/2020/5/53/T--DTU-Denmark--Poster_imageana.png" class="center"><figcaption><p align="justify"><i> Showcase of our first model, Morphologizer. The model analyzes microscope images of mycelia, converts them into graph objects, and extracts morphological features of interest from the graph, such as the number of branches, branching angles, and hyphal curvature. </i></p></figcaption></figure></center> |
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− | <center><figure> <img style="width:80%" src="https://static.igem.org/mediawiki/2020/0/06/T--DTU-Denmark--Poster_ATCC.gif" class="center"><figcaption><p align="justify"><i> Here, we demonstrate our final simulation of ATCC 1015 based on parameters obtained from both experimental measurements and microscopic image analysis. The substrate gradient is shown in green, i.e. the greener the higher substrate concentration and the mycelium is shown in purple with newer hyphal elements in lighter colors. </i></p></figcaption></figure></center> | + | <center><figure> <img style="width:80%" src="https://static.igem.org/mediawiki/2020/0/06/T--DTU-Denmark--Poster_ATCC.gif" class="center"><figcaption><p align="justify"><i>Showcase of our second model, Mycemulator. A stochastic simulation of background strain ATCC 1015 based on parameters obtained from both experimental measurements and microscopic image analysis. The substrate gradient is shown in green, i.e. the greener the higher substrate concentration and the mycelium is shown in purple with newer hyphal elements in lighter colors. </i></p></figcaption></figure></center> |
| </div> | | </div> |
| </div> | | </div> |
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| <p align="justify"><b>New morphology strains</b><br> | | <p align="justify"><b>New morphology strains</b><br> |
− | We have made 9 new morphology strains and characterized their performance as cell factories based on growth and protein secretion when grown in BioLectors and Bioreactors. We even showed that some of our new strains, the three novel strains were <i>gul-1</i> was knocked-out, had to three-fold increased protein production compared to the reference strain. | + | We have made 9 new morphology strains and characterized their performance as cell factories based on growth and protein secretion when grown in BioLectors and Bioreactors. We even showed that some of our new strains, the three novel strains were <i>gul-1</i> was knocked-out, had up to three-fold increased protein production compared to the reference strain. |
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| <b>Morphological toolbox for <i>A. niger</i></b><br> | | <b>Morphological toolbox for <i>A. niger</i></b><br> |
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| <b>Analysis of fungal microscopic images</b><br> | | <b>Analysis of fungal microscopic images</b><br> |
− | We have developed Morphologizer - a tool for analyzing microscope images of mycelia. Using Morphologizer, one can extract growth parameters of any fungal strain. | + | We have developed Morphologizer - a tool for analyzing microscope images of mycelia. Using Morphologizer, one can easily and automatically estimate morphological parameters for a fungal strain. |
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| <b>Simulation of mycelial growth</b><br> | | <b>Simulation of mycelial growth</b><br> |
− | We have developed Mycemulator - a model that can simulate mycelial growth based on real life parameters - for example extracted by Morphologizer. </p> | + | We have developed Mycemulator - a model that can simulate mycelial growth based on real-world parameters - for example the parameters estimated by our Morphologizer model. </p> |
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| </div> | | </div> |