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A graphical user interface to design high-throughput optogenetic experiments with the optoPlate-96

Nature Protocols volume 15, pages 2785–2787 (2020)Cite this article

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arising from: Bugaj, L. J. & Lim, W. A. Nature Protocols https://www.nature.com/articles/s41596-019-0178-y (2019)

The application of molecular optogenetic switches for the perturbation of biological systems has resulted in unprecedented insights into cellular signaling processes1,2,3,4,5,6,7. However, the common practice of using microscopes or light-emitting diode (LED) panels as illumination sources for controlling light-responsive proteins makes parallelization of experiments difficult, thus complicating the acquisition of high-throughput data needed for the quantitative understanding of biological systems.

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Fig. 1: Overview of the optoConfig-96 workflow.

Data availability

The image data used to generate the correction matrices for the 24-well plate adapter are available upon request. The calculated correction matrices are available online at https://www.github.com/WeberSynBioLab/optoConfig-96.

Code availability

optoConfig-96 is available at https://www.github.com/WeberSynBioLab/optoConfig-96, along with the most up-to-date version of the user guide (Supplementary Manual).

References

  1. Bugaj, L. J. et al. Cancer mutations and targeted drugs can disrupt dynamic signal encoding by the Ras-Erk pathway. Science 361, eaao3048 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  2. de Beco, S. et al. Optogenetic dissection of Rac1 and Cdc42 gradient shaping. Nat. Commun. 9, 1–13 (2018).

    Google Scholar 

  3. Zhou, X. X., Fan, L. Z., Li, P., Shen, K. & Lin, M. Z. Optical control of cell signaling by single-chain photoswitchable kinases. Science 355, 836–842 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  4. Yousefi, O. S. et al. Optogenetic control shows that kinetic proofreading regulates the activity of the T cell receptor. eLife 8, e42475 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  5. Tischer, D. K. & Weiner, O. D. Light-based tuning of ligand half-life supports kinetic proofreading model of T cell signaling. eLife 8, e42498 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  6. Zhang, P. et al. Chronic optogenetic induction of stress granules is cytotoxic and reveals the evolution of ALS-FTD pathology. eLife 8, e39578 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  7. Kolar, K., Knobloch, C., Stork, H., Žnidarič, M. & Weber, W. OptoBase: a web platform for molecular optogenetics. ACS Synth. Biol. 7, 1825–1828 (2018).

    Article  CAS  PubMed  Google Scholar 

  8. Bugaj, L. J. & Lim, W. A. High-throughput multicolor optogenetics in microwell plates. Nat. Protoc. 14, 2205–2228 (2019).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We thank J. Schmidt, D. Renz and L. Breh (technical workshop of the Faculty of Biology, University of Freiburg, Germany) for assembling the optoPlates-96 and 3D printing of the 24-well plate adapter. We also thank A. Fischer, C. Jerez-Longres, L. Lataster, H. Mohsenin and N. Urban for testing optoConfig-96. This work was supported in part by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy CIBSS–EXC-2189, Project ID 390939984. This work was supported in part by the Excellence Initiative of the Deutsche Forschungsgemeinschaft (GSC–4, Spemann Graduate School) and in part by the Ministry for Science, Research and Arts of the State of Baden-Wuerttemberg.

Author information

Authors and Affiliations

  1. Faculty of Biology, University of Freiburg, Freiburg, Germany

    Oliver S. Thomas, Maximilian Hörner & Wilfried Weber

  2. Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany

    Oliver S. Thomas, Maximilian Hörner & Wilfried Weber

  3. Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany

    Oliver S. Thomas & Wilfried Weber

Authors
  1. Oliver S. Thomas
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  2. Maximilian Hörner
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  3. Wilfried Weber
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Contributions

O.S.T., M.H. and W.W. conceptualized optoConfig-96. O.S.T. wrote the software. M.H. designed and characterized the 24-well plate adapter. M.H. and W.W. supervised the project. O.S.T., M.H. and W.W. wrote and edited the manuscript.

Corresponding authors

Correspondence to Maximilian Hörner or Wilfried Weber.

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The authors declare no competing interests.

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Peer review information Nature Protocols thanks Andreas Möglich and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

Supplementary Notes 1 and 2, Supplementary Manual and Supplementary References

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Thomas, O.S., Hörner, M. & Weber, W. A graphical user interface to design high-throughput optogenetic experiments with the optoPlate-96. Nat Protoc 15, 2785–2787 (2020). https://doi.org/10.1038/s41596-020-0349-x

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