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Phytochromes pp 121–133Cite as

Basic Phytochrome B Calculations

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 2026))

Abstract

Mathematical models are important tools in helping us to understand complex biological systems. Models of phytochrome-regulated systems in Arabidopsis thaliana have shown the importance of dimerization, nuclear transport, and thermal/dark reversion in mediating phytochrome activity and plant development. Here we go through the steps required to calculate the steady-state amounts of phytochrome subspecies relative to the total phytochrome molecule population. Starting from a simplified two-state system we expand and apply the technique to the extended phytochrome dimer model. Additionally, we provide a Python package that can automatically calculate the proportion of phytochrome B in a particular state given specific experimental conditions.

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Change history

  • 22 June 2021

    In the original version of this book, Chapter 9 was inadvertently published with few errors in Table 2 data. This has now been rectified in this revised version of the book.

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Acknowledgments

We would like to thank Andreas Hiltbrunner and Rik van Rosmalen for testing the tool and for providing valuable feedback as to its usage and how it can be made easier for users. RWS is funded by FP7 Marie Curie Initial Training Network grant agreement number 316723 and EU Horizon 2020 grant agreement number 634942. CF is funded by HFSP Research grant RGP0025/2013.

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Authors and Affiliations

  1. Laboratory of Systems and Synthetic Biology, Wageningen UR, Wageningen, The Netherlands

    Robert W. Smith & Christian Fleck

  2. Sir William Dunn School of Pathology, University of Oxford, Oxford, UK

    Robert W. Smith

  3. Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland

    Christian Fleck

Authors
  1. Robert W. Smith
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  2. Christian Fleck
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Corresponding authors

Correspondence to Robert W. Smith or Christian Fleck .

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Editors and Affiliations

  1. Faculty of Biology, Institute of Biology II and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany

    Andreas Hiltbrunner

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Smith, R.W., Fleck, C. (2019). Basic Phytochrome B Calculations. In: Hiltbrunner, A. (eds) Phytochromes. Methods in Molecular Biology, vol 2026. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9612-4_9

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  • DOI: https://doi.org/10.1007/978-1-4939-9612-4_9

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9611-7

  • Online ISBN: 978-1-4939-9612-4

  • eBook Packages: Springer Protocols

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