Cypergenetic Tissue Engineering

Deliverables

Optimised switches 1. generation

Optimized and customized optical switches for spatiotemporal control of stem cell fate

Construction plans for optogenetic synthetic modules

Construction plan for synthetic biological modules optogenetic sensors (WP1) inserted into them.

Kick-off meeting

Report on the agenda, list of participants of the kick-off meeting

Improved image analysis

Improved image analysis modules

Quantitative description of the optogenetic systems

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.

Web site and logo

Set up of a project web site and decide on a logo.

Image analysis modules

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).

Image sets of optical-controlled cell sheet morphogenesis

Image sets for the morphogenesis of simple cell sheets imposed by closedloop optical control

Synthetic modules controlling cell fate

Synthetic biological modules for locomotion, adhesion, proliferation, apoptosis and folding, with optogenetic sensors (WP1) inserted into them.

Model for cell islands

Optimalcontrol model for growth control of flat cell islands

Model for stem cell differentiation

Optimalcontrol model for spatial stem cell differentiation

Characterization of light-regulated gene expression systems

Fully characterization of light-regulated gene expression systems in terms of kinetics, dynamic range and sensitivity in HEK293 and 6TA3 cells.

Tested optogenetic cells

Mammalian cell lines carrying one of the modules from D21 tested with allover illumination

Patterned illumination

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.

Publications

Synthetic morphology with agential materials

Author(s): Jamie Davies, Michael Levin
Published in: Nature Reviews Bioengineering, Issue 1, 2023, Page(s) 46-59, ISSN 2731-6092
Publisher: SpringerNature
DOI: 10.1038/s44222-022-00001-9

Cell-in-the-loop pattern formation with optogenetically emulated cell-to-cell signaling

Author(s): Melinda Liu Perkins, Dirk Benzinger, Murat Arcak, Mustafa Khammash
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-15166-3

Unlocking the potential of optogenetics in microbial applications

Author(s): Moritz Benisch; Stephanie K Aoki; Mustafa Khammash
Published in: Current Opinion in Microbiology, 77, Issue 6, 2024, ISSN 1369-5274
Publisher: Elsevier BV
DOI: 10.1016/j.mib.2023.102404

Single cell variability of CRISPR-Cas interference and adaptation

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: Molecular Systems Biology, 2022, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.202110680

Optogenetics in Plants

Author(s): Christie JM and Zurbriggen MD
Published in: New Phytologist, Issue 229,6, 2020, Page(s) 3108-3115, ISSN 1469-8137
Publisher: Wiley
DOI: 10.1111/nph.17008

Exploiting natural chemical photosensitivity of anhydrotetracycline and tetracycline for dynamic and setpoint chemo-optogenetic control

Author(s): Armin Baumschlager, Marc Rullan, Mustafa Khammash
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-17677-5

COLD REGULATED 27 and 28 are targets of CONSTITUTIVELY PHOTOMORPHOGENIC 1 and negatively affect phytochrome B signalling

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, Issue 104/4, 2020, Page(s) 1038-1053, ISSN 0960-7412
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/tpj.14979

Agent-Based Models in Cellular Systems

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

Platforms for Optogenetic Stimulation and Feedback Control

Author(s): Kumar, Sant, and Mustafa Khammash
Published in: Frontiers in Bioengineering and Biotechnology, Issue 10, 2022, ISSN 2296-4185
Publisher: Frontiers
DOI: 10.3389/fbioe.2022.918917

Synthetic Biological Approaches for Optogenetics and Tools for Transcriptional Light‐Control in Bacteria

Author(s): Armin Baumschlager, Mustafa Khammash
Published in: Advanced Biology, Issue 5/5, 2021, Page(s) 2000256, ISSN 2701-0198
Publisher: Wiley
DOI: 10.1002/adbi.202000256

Synthetic Morphogenesis: introducing IEEE journal readers to programming living mammalian cells to make structures

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

Engineering AraC to make it responsive to light instead of arabinose

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, Issue 17/7, 2021, Page(s) 817-827, ISSN 1552-4450
Publisher: Nature Publishing Group
DOI: 10.1038/s41589-021-00787-6

Deconstructing and repurposing the light-regulated interplay between Arabidopsis phytochromes and interacting factors

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, Issue 2/1, 2019, ISSN 2399-3642
Publisher: Springer Nature
DOI: 10.1038/s42003-019-0687-9

The red edge: Bilin-binding photoreceptors as optogenetic tools and fluorescence reporters

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

Blue Light‐Operated CRISPR/Cas13b‐Mediated mRNA Knockdown (Lockdown)

Author(s): Tim Blomeier, Patrick Fischbach, Leonie‐Alexa Koch, Jennifer Andres, Miguel Miñambres, Hannes Michael Beyer, Matias Daniel Zurbriggen
Published in: Advanced Biology, Issue 5/5, 2021, Page(s) 2000307, ISSN 2701-0198
Publisher: Wiley
DOI: 10.1002/adbi.202000307

Renal engineering: strategies to address the problem of the ureter

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

Diya – A universal light illumination platform for multiwell plate cultures

Author(s): Sant Kumar; Stanislav Anastassov; Stephanie K. Aoki; Johannes Falkenstein; Ching-Hsiang Chang; Timothy Frei; Peter Buchmann; Paul Argast; Mustafa Khammash
Published in: iScience, 26 (10), Issue 17, 2024, ISSN 2589-0042
Publisher: Elsevier BV
DOI: 10.1016/j.isci.2023.107862

Stratified tissue biofabrication by rotational internal flow layer engineering

Author(s): Ian Holland; Wenmiao Shu; Jamie A Davies
Published in: Holland , I , Shu , W & Davies , J A 2023 , ' Stratified tissue biofabrication by rotational internal flow layer engineering ' , Biofabrication . https://doi.org/10.1088/1758-5090/ace2ed, Issue 17, 2023, ISSN 1758-5082
Publisher: IOS Press
DOI: 10.1088/1758-5090/ace2ed

Deliverables

Publications

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