Livrables
Optimized and customized optical switches for spatiotemporal control of stem cell fate
Construction plans for optogenetic synthetic modulesConstruction plan for synthetic biological modules optogenetic sensors (WP1) inserted into them.
Kick-off meetingReport on the agenda, list of participants of the kick-off meeting
Improved image analysisImproved image analysis modules
Quantitative description of the optogenetic systemsDeliver 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.
Web site and logoSet up of a project web site and decide on a logo.
Image analysis modulesInitial 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).
Image sets of optical-controlled cell sheet morphogenesisImage sets for the morphogenesis of simple cell sheets imposed by closedloop optical control
Synthetic modules controlling cell fateSynthetic biological modules for locomotion, adhesion, proliferation, apoptosis and folding, with optogenetic sensors (WP1) inserted into them.
Model for cell islandsOptimalcontrol model for growth control of flat cell islands
Model for stem cell differentiationOptimalcontrol model for spatial stem cell differentiation
Characterization of light-regulated gene expression systemsFully characterization of light-regulated gene expression systems in terms of kinetics, dynamic range and sensitivity in HEK293 and 6TA3 cells.
Tested optogenetic cellsMammalian cell lines carrying one of the modules from D21 tested with allover illumination
Patterned illuminationHardware 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.
Publications
Auteurs:
Jamie Davies, Michael Levin
Publié dans:
Nature Reviews Bioengineering, Numéro 1, 2023, Page(s) 46-59, ISSN 2731-6092
Éditeur:
SpringerNature
DOI:
10.1038/s44222-022-00001-9
Auteurs:
Melinda Liu Perkins, Dirk Benzinger, Murat Arcak, Mustafa Khammash
Publié dans:
Nature Communications, Numéro 11/1, 2020, ISSN 2041-1723
Éditeur:
Nature Publishing Group
DOI:
10.1038/s41467-020-15166-3
Auteurs:
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
Publié dans:
Molecular Systems Biology, 2022, ISSN 1744-4292
Éditeur:
Nature Publishing Group
DOI:
10.15252/msb.202110680
Auteurs:
Christie JM and Zurbriggen MD
Publié dans:
New Phytologist, Numéro 229,6, 2020, Page(s) 3108-3115, ISSN 1469-8137
Éditeur:
Wiley
DOI:
10.1111/nph.17008
Auteurs:
Armin Baumschlager, Marc Rullan, Mustafa Khammash
Publié dans:
Nature Communications, Numéro 11/1, 2020, ISSN 2041-1723
Éditeur:
Nature Publishing Group
DOI:
10.1038/s41467-020-17677-5
Auteurs:
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
Publié dans:
The Plant Journal, Numéro 104/4, 2020, Page(s) 1038-1053, ISSN 0960-7412
Éditeur:
Blackwell Publishing Inc.
DOI:
10.1111/tpj.14979
Auteurs:
Jonas Pleyer, Christian Fleck
Publié dans:
Frontiers of Physics - Biophysics, 2022, ISSN 2296-424X
Éditeur:
Frontiers Media
DOI:
10.3389/fphy.2022.968409
Auteurs:
Armin Baumschlager, Mustafa Khammash
Publié dans:
Advanced Biology, Numéro 5/5, 2021, Page(s) 2000256, ISSN 2701-0198
Éditeur:
Wiley
DOI:
10.1002/adbi.202000256
Auteurs:
Jamie Davies
Publié dans:
Proceedings of the IEEE, 2022, ISSN 1558-2256
Éditeur:
Institute of Electrical and Electronics Engineers
DOI:
10.1109/jproc.2021.3137077
Auteurs:
Edoardo Romano, Armin Baumschlager, Emir Bora Akmeriç, Navaneethan Palanisamy, Moustafa Houmani, Gregor Schmidt, Mehmet Ali Öztürk, Leonard Ernst, Mustafa Khammash, Barbara Di Ventura
Publié dans:
Nature Chemical Biology, Numéro 17/7, 2021, Page(s) 817-827, ISSN 1552-4450
Éditeur:
Nature Publishing Group
DOI:
10.1038/s41589-021-00787-6
Auteurs:
David Golonka, Patrick Fischbach, Siddhartha G. Jena, Julius R. W. Kleeberg, Lars-Oliver Essen, Jared E. Toettcher, Matias D. Zurbriggen, Andreas Möglich
Publié dans:
Communications Biology, Numéro 2/1, 2019, ISSN 2399-3642
Éditeur:
Springer Nature
DOI:
10.1038/s42003-019-0687-9
Auteurs:
Tang K
Beyer HM
Zurbriggen MD
Gärtner W
Publié dans:
Chemical Reviews, 2021, ISSN 1520-6890
Éditeur:
ACS Publications
DOI:
10.1021/acs.chemrev.1c00194
Auteurs:
Tim Blomeier, Patrick Fischbach, Leonie‐Alexa Koch, Jennifer Andres, Miguel Miñambres, Hannes Michael Beyer, Matias Daniel Zurbriggen
Publié dans:
Advanced Biology, Numéro 5/5, 2021, Page(s) 2000307, ISSN 2701-0198
Éditeur:
Wiley
DOI:
10.1002/adbi.202000307
Auteurs:
Davies JA, Elhendawi M, Palakkan A, Sallam M
Publié dans:
Current Opinion in Biomedical Engineering, 2021, ISSN 2468-4511
Éditeur:
Elsevier
DOI:
10.1016/j.cobme.2021.100334
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