Plant Circadian Networks: Methods and Protocols

ISBN-13: 9781071619117 / Angielski / Twarda / 2021 / 250 str.

Dorothee Staiger; Seth Davis; Amanda Melaragno Davis

Spis treści

1. Circadian Rhythm: Phase Response Curve and Light Entrainment

Xiaodong Xu, Li Yuan, and Qiguang Xie

 

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

Tomasz Zieliński, Johnny Hay, and Andrew J. Millar

 

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

Yuri Dakhiya and Rachel Green

 

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

Mark Greenwood, Anthony J.W. Hall, and James C.W. Locke

 

5. Agrobacterium-mediated seedling transformation to measure circadian rhythms in Arabidopsis

Michael K. Y. Ting, Reimo Zoschke, and Michael J. Haydon

 

6. Measurement of Luciferase Rhythms in Soybean Hairy Roots

Qiguang Xie, Yu Wang, Li Yuan, and Xiaodong Xu

 

7. ODE (ordinary differential equation) Models for Plant Circadian Networks: What The Models Are, and How They Should Be Used

Jonathan W. Pitchford and Paula Avello Fernandez

 

8. How to Detect QTLs in the Plant Circadian Clock

Muhammad Usman Anwer and Marcel Quint

 

9. Measuring Hypocotyl Length in Arabidopsis

James Ronald and Seth J. Davis

 

10. High Throughput Extraction and Enzymatic Determination of Sugars and Fructans In Fructan-Accumulating Plants

Kallyne A. Barros, Masami Inaba, Auxiliadora Oliveira Martins, and Ronan Sulpice

 

11. Simple Nuclei Preparation and Co-Immunoprecipitation Procedures for Studying Protein Abundance and Interactions In Plant Circadian Time Courses

Akane Kubota, Young Hun Song, and Takato Imaizumi

 

12. Chromatin Immunoprecipitation Protocol for Circadian Clock Proteins

Sally Adams and Isabelle A. Carré

 

13. A high-throughput 3′-Tag RNA Sequencing for Large-Scale Time-Series Transcriptome Studies

Xiaoyu Weng and Thomas E. Juenger

 

14. 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, and John W. S. Brown

 

15. Using tandem affinity purification to identify circadian clock protein complexes from Arabidopsis

Maria L. Sorkin and Dmitri A. Nusinow

 

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

Qiguang Xie, Qiao Wang, and Xiaodong Xu

 

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

Mikael Johansson, Naoki Takata, Cristian Ibáñez, and Maria E. Eriksson

 

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

Mikael Johansson, Cristian Ibáñez, Naoki Takata, and Maria E. Eriksson

Blurb

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.