Basic Phytochrome B Calculations

Robert W. Smith*, Christian Fleck

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapter

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.

Original languageEnglish
Title of host publicationPhytochromes
Subtitle of host publicationMethods and Protocols
EditorsAndreas Hiltbrunner
PublisherHumana Press Inc.
Pages121-133
Number of pages13
ISBN (Electronic)9781493996124
ISBN (Print)9781493996117
DOIs
Publication statusE-pub ahead of print - 18 Jul 2019

Publication series

NameMethods in Molecular Biology
Volume2026
ISSN (Print)1064-3745

Fingerprint

Phytochrome B
Phytochrome
Boidae
Plant Development
Cell Nucleus Active Transport
Dimerization
Arabidopsis
Theoretical Models
Hot Temperature
Population

Keywords

  • Computer programming
  • Mathematical modeling
  • Ordinary differential equations
  • Phytochromes

Cite this

Smith, R. W., & Fleck, C. (2019). Basic Phytochrome B Calculations. In A. Hiltbrunner (Ed.), Phytochromes: Methods and Protocols (pp. 121-133). (Methods in Molecular Biology; Vol. 2026). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-9612-4_9
Smith, Robert W. ; Fleck, Christian. / Basic Phytochrome B Calculations. Phytochromes: Methods and Protocols. editor / Andreas Hiltbrunner. Humana Press Inc., 2019. pp. 121-133 (Methods in Molecular Biology).
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Smith, RW & Fleck, C 2019, Basic Phytochrome B Calculations. in A Hiltbrunner (ed.), Phytochromes: Methods and Protocols. Methods in Molecular Biology, vol. 2026, Humana Press Inc., pp. 121-133. https://doi.org/10.1007/978-1-4939-9612-4_9

Basic Phytochrome B Calculations. / Smith, Robert W.; Fleck, Christian.

Phytochromes: Methods and Protocols. ed. / Andreas Hiltbrunner. Humana Press Inc., 2019. p. 121-133 (Methods in Molecular Biology; Vol. 2026).

Research output: Chapter in Book/Report/Conference proceedingChapter

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KW - Computer programming

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Smith RW, Fleck C. Basic Phytochrome B Calculations. In Hiltbrunner A, editor, Phytochromes: Methods and Protocols. Humana Press Inc. 2019. p. 121-133. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-9612-4_9