Deliverables
Construction plan for synthetic biological modules optogenetic sensors (WP1) inserted into them.
Report on the agenda, list of participants of the kick-off meeting
Deliver a quantitative (mathematical) description of the optogenetic systems and provide an optimization strategy to meet the required quantitative and dynamic responses or 2D control of stem cells.
Set up of a project web site and decide on a logo.
Initial version of image analysis modules. Construction and training of deep convolutional networks for the segmentation of the desired structures (2D-islands, differentiated/undifferentiated single cells and cap mesenchymes of kidneys).
Synthetic biological modules for locomotion, adhesion, proliferation, apoptosis and folding, with optogenetic sensors (WP1) inserted into them.
Fully characterization of light-regulated gene expression systems in terms of kinetics, dynamic range and sensitivity in HEK293 and 6TA3 cells.
Hardware and software for patterned illumination setup. DMD (“digital micromirror device”) based illumination system with multiple wavelengths and optimize it for mammalian cells. Automated procedures to align the coordinate systems of the sample and the DMD. Design of control interfaces to enable simple and reliable device operation.
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Publications
Author(s): Melinda Liu Perkins, Dirk Benzinger, Murat Arcak, Mustafa Khammash
Published in: Nature Communications, 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-15166-3
Author(s): Rebecca E McKenzie
Emma M Keizer
Jochem N A Vink
Jasper van Lopik
Ferhat Büke
Vera Kalkman
Christian Fleck
Sander J Tans
Stan J J Brouns
Published in: Molekular Systems Biology, 2022, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.202110680
Author(s): Christie JM and Zurbriggen MD
Published in: New Phytologist, 229,6, 2020, Page(s) 3108-3115, ISSN 1469-8137
Publisher: Wiley
DOI: 10.1111/nph.17008
Author(s): Armin Baumschlager, Marc Rullan, Mustafa Khammash
Published in: Nature Communications, 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-17677-5
Author(s): Nikolai Kahle, David J. Sheerin, Patrick Fischbach, Leonie‐Alexa Koch, Philipp Schwenk, Dorothee Lambert, Ryan Rodriguez, Konstantin Kerner, Ute Hoecker, Matias D. Zurbriggen, Andreas Hiltbrunner
Published in: The Plant Journal, 104/4, 2020, Page(s) 1038-1053, ISSN 0960-7412
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/tpj.14979
Author(s): Jonas Pleyer, Christian Fleck
Published in: Frontiers of Physics - Biophysics, 2022, ISSN 2296-424X
Publisher: Frontiers Media
DOI: 10.3389/fphy.2022.968409
Author(s): Armin Baumschlager, Mustafa Khammash
Published in: Advanced Biology, 5/5, 2021, Page(s) 2000256, ISSN 2701-0198
Publisher: Wiley
DOI: 10.1002/adbi.202000256
Author(s): Jamie Davies
Published in: Proceedings of the IEEE, 2022, ISSN 1558-2256
Publisher: Institute of Electrical and Electronics Engineers
DOI: 10.1109/jproc.2021.3137077
Author(s): Edoardo Romano, Armin Baumschlager, Emir Bora Akmeriç, Navaneethan Palanisamy, Moustafa Houmani, Gregor Schmidt, Mehmet Ali Öztürk, Leonard Ernst, Mustafa Khammash, Barbara Di Ventura
Published in: Nature Chemical Biology, 17/7, 2021, Page(s) 817-827, ISSN 1552-4450
Publisher: Nature Publishing Group
DOI: 10.1038/s41589-021-00787-6
Author(s): David Golonka, Patrick Fischbach, Siddhartha G. Jena, Julius R. W. Kleeberg, Lars-Oliver Essen, Jared E. Toettcher, Matias D. Zurbriggen, Andreas Möglich
Published in: Communications Biology, 2/1, 2019, ISSN 2399-3642
Publisher: Springer Nature
DOI: 10.1038/s42003-019-0687-9
Author(s): Tang K
Beyer HM
Zurbriggen MD
Gärtner W
Published in: Chemical Reviews, 2021, ISSN 1520-6890
Publisher: ACS Publications
DOI: 10.1021/acs.chemrev.1c00194
Author(s): Tim Blomeier, Patrick Fischbach, Leonie‐Alexa Koch, Jennifer Andres, Miguel Miñambres, Hannes Michael Beyer, Matias Daniel Zurbriggen
Published in: Advanced Biology, 5/5, 2021, Page(s) 2000307, ISSN 2701-0198
Publisher: Wiley
DOI: 10.1002/adbi.202000307
Author(s): Davies JA, Elhendawi M, Palakkan A, Sallam M
Published in: Current Opinion in Biomedical Engineering, 2021, ISSN 2468-4511
Publisher: Elsevier
DOI: 10.1016/j.cobme.2021.100334
Author(s): McKenzie, Rebecca E, Emma M Keizer, Jochem N A Vink, Jasper van Lopik, Vera Kalkman, Christian Fleck, Sander J Tans, and Stan J J Brouns
Published in: biorxiv, July 21, 2021, 2021, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2021.07.21.453200