Cypergenetic Tissue Engineering

Livrables

Optimised switches 2. generation

Optimized and customized optical switches for spatio-temporal control of stem cell fate.

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.

Final optimized image analysis

Final optimized image analysis modules.

Kick-off meeting

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

Image sets of optical- controlled stem cell differentiation

Image sets demonstrating control of stem cell differentiation by closed-loop optical control.

Improved image analysis

Improved image analysis modules

Organoid model

Optimal-control model for growth control of renal organoids.

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.

Model predictive control algorithms

Model predictive control algorithms for growth control.

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.

Image sets of optical- controlled polarization/ ureter production in renal organoids

Image sets and quantitative measurements of the optical closed-loop control of polarization/ ureter production in renal organoids.

Publications

Synthetic morphology with agential materials

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

Engineering of Bidirectional, Cyanobacteriochrome-Based Light-Inducible Dimers (BICYCL)s

Auteurs: Jang, Jaewan, Kun Tang, Jeffrey Youn, Sherin McDonald, Hannes M. Beyer, Matias D. Zurbriggen, Maruti Uppalapati, and G. Andrew Woolley
Publié dans: Nature Methods, Numéro 20, 2023, ISSN 1548-7091
Éditeur: Nature Publishing Group
DOI: 10.1038/s41592-023-01764-8

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

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

Unlocking the potential of optogenetics in microbial applications

Auteurs: Moritz Benisch; Stephanie K Aoki; Mustafa Khammash
Publié dans: Current Opinion in Microbiology, 77, Numéro 6, 2024, ISSN 1369-5274
Éditeur: Elsevier BV
DOI: 10.1016/j.mib.2023.102404

Single cell variability of CRISPR-Cas interference and adaptation

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

Optogenetics in Plants

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

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

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

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

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

Agent-Based Models in Cellular Systems

Auteurs: Jonas Pleyer, Christian Fleck
Publié dans: Frontiers of Physics - Biophysics, 2022, ISSN 2296-424X
Éditeur: Frontiers Media
DOI: 10.3389/fphy.2022.968409

Platforms for Optogenetic Stimulation and Feedback Control

Auteurs: Kumar, Sant, and Mustafa Khammash
Publié dans: Frontiers in Bioengineering and Biotechnology, Numéro 10, 2022, ISSN 2296-4185
Éditeur: Frontiers
DOI: 10.3389/fbioe.2022.918917

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

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

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

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

Engineering AraC to make it responsive to light instead of arabinose

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

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

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

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

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

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

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

Renal engineering: strategies to address the problem of the ureter

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

Diya – A universal light illumination platform for multiwell plate cultures

Auteurs: Sant Kumar; Stanislav Anastassov; Stephanie K. Aoki; Johannes Falkenstein; Ching-Hsiang Chang; Timothy Frei; Peter Buchmann; Paul Argast; Mustafa Khammash
Publié dans: iScience, 26 (10), Numéro 17, 2024, ISSN 2589-0042
Éditeur: Elsevier BV
DOI: 10.1016/j.isci.2023.107862

Stratified tissue biofabrication by rotational internal flow layer engineering

Auteurs: Ian Holland; Wenmiao Shu; Jamie A Davies
Publié dans: 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, Numéro 17, 2023, ISSN 1758-5082
Éditeur: IOS Press
DOI: 10.1088/1758-5090/ace2ed

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