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Plant Circadian Networks

Methods and Protocols

  • Book
  • © 2022

Overview

Editors:
  1. Dorothee Staiger

    1. Department of Biology, University of Bielefeld, Bielefeld, Germany

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    You can also search for this editor in PubMed   Google Scholar

  2. Seth Davis

    1. Department of Biology, University of York, Heslington, UK

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    You can also search for this editor in PubMed   Google Scholar

  3. Amanda Melaragno Davis

    1. Department of Biology, University of York, Heslington, UK

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2398)

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Table of contents (19 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Circadian Rhythm: Phase Response Curve and Light Entrainment

    • Xiaodong Xu, Li Yuan, Qiguang Xie
    Pages 1-13

  3. Period Estimation and Rhythm Detection in Timeseries Data Using BioDare2, the Free, Online, Community Resource

    • Tomasz Zieliński, Johnny Hay, Andrew J. Millar
    Pages 15-32Open Access

  4. Detection and Analysis of Circadian Rhythms Via Prompt Chlorophyll Fluorescence

    • Yuri Dakhiya, Rachel Green
    Pages 33-45

  5. High Spatial Resolution Luciferase Imaging of the Arabidopsis thaliana Circadian Clock

    • Mark Greenwood, Anthony J. W. Hall, James C. W. Locke
    Pages 47-55

  6. Agrobacterium-Mediated Seedling Transformation to Measure Circadian Rhythms in Arabidopsis

    • Michael K. Y. Ting, Reimo Zoschke, Michael J. Haydon
    Pages 57-64

  7. Measurement of Luciferase Rhythms in Soybean Hairy Roots

    • Qiguang Xie, Yu Wang, Li Yuan, Xiaodong Xu
    Pages 65-73

  8. ODE (Ordinary Differential Equation) Models for Plant Circadian Networks: What the Models Are and How They Should Be Used

    • Jonathan W. Pitchford, Paula Avello
    Pages 75-88

  9. How to Detect QTLs in the Plant Circadian Clock

    • Muhammad Usman Anwer, Marcel Quint
    Pages 89-97

  10. Measuring Hypocotyl Length in Arabidopsis

    • James Ronald, Seth Jon Davis
    Pages 99-106

  11. High-Throughput Extraction and Enzymatic Determination of Sugars and Fructans in Fructan-Accumulating Plants

    • Kallyne A. Barros, Masami Inaba, Auxiliadora Oliveira Martins, Ronan Sulpice
    Pages 107-119

  12. Simple Nuclei Preparation and Co-immunoprecipitation Procedures for Studying Protein Abundance and Interactions in Plant Circadian Time Courses

    • Akane Kubota, Young Hun Song, Takato Imaizumi
    Pages 121-134

  13. Chromatin Immunoprecipitation Protocol for Circadian Clock Proteins

    • Sally Adams, Isabelle A. Carré
    Pages 135-150

  14. A High-Throughput 3′-Tag RNA Sequencing for Large-Scale Time-Series Transcriptome Studies

    • Xiaoyu Weng, Thomas E. Juenger
    Pages 151-172

  15. Experimental Design for Time-Series RNA-Seq Analysis of Gene Expression and Alternative Splicing

    • Nikoleta A. Tzioutziou, Allan B. James, Wenbin Guo, Cristiane P. G. Calixto, Runxuan Zhang, Hugh G. Nimmo et al.
    Pages 173-188

  16. Using Tandem Affinity Purification to Identify Circadian Clock Protein Complexes from Arabidopsis

    • Maria L. Sorkin, Dmitri A. Nusinow
    Pages 189-203

  17. Firefly Luciferase Complementation-Based Analysis of Dynamic Protein-Protein Interactions Under Diurnal and Circadian Conditions in Arabidopsis

    • Qiguang Xie, Qiao Wang, Xiaodong Xu
    Pages 205-213

  18. Monitoring Seasonal Bud Set, Bud Burst, and Cold Hardiness in Populus

    • Mikael Johansson, Naoki Takata, Cristian Ibáñez, Maria E. Eriksson
    Pages 215-226

  19. The Perennial Clock Is an Essential Timer for Seasonal Growth Events and Cold Hardiness

    • Mikael Johansson, Cristian Ibáñez, Naoki Takata, Maria E. Eriksson
    Pages 227-242

  20. Correction to: Period Estimation and Rhythm Detection in Timeseries Data Using BioDare2, the Free, Online, Community Resource

    • Tomasz Zieliński, Johnny Hay, Andrew J. Millar
    Pages C1-C1Open Access
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Keywords

About this book


This second edition provides new and updated protocols to investigate clock-controlled parameters including period estimations and entrainment measurements and modelling. Chapters detail promoter activity using luciferase reporters, fluorescent-tagging of clock proteins and cellular imaging, protein level measurements, regulated RNA splicing detection, post-translational modifications, protein-protein interactions, and protein DNA/chromatin interactions. Additional chapters focus on seasonal processes like hypocotyl growth and flowering time control in annuals and trees, and techniques on soybean. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols.

Authoritative and practical, Plant Circadian Networks: Methods and Protocols, Second Edition is designed not only for the chronobiology community dealing with circadian biology but also for the plant community in general. 

“Period estimation and rhythm detection in timeseries data using BioDare2, the free, online, community resource” is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.


Editors and Affiliations

  • Department of Biology, University of Bielefeld, Bielefeld, Germany

    Dorothee Staiger

  • Department of Biology, University of York, Heslington, UK

    Seth Davis, Amanda Melaragno Davis

Bibliographic Information

  • Book Title: Plant Circadian Networks

  • Book Subtitle: Methods and Protocols

  • Editors: Dorothee Staiger, Seth Davis, Amanda Melaragno Davis

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-1912-4

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2022

  • Hardcover ISBN: 978-1-0716-1911-7Published: 22 October 2021

  • Softcover ISBN: 978-1-0716-1914-8Published: 23 October 2022

  • eBook ISBN: 978-1-0716-1912-4Published: 21 October 2021

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: XI, 245

  • Number of Illustrations: 17 b/w illustrations, 33 illustrations in colour

  • Topics: Plant Sciences

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