Plant Circadian Networks by Staiger, Dorothee; Davis, Seth; Davis, Amanda Melaragno;

Long description:

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.

Table of Contents:

Circadian Rhythm: Phase Response Curve and Light Entrainment.- Period Estimation and Rhythm Detection in Timeseries Data Using BioDare2, the Free, Online, Community Resource.- Detection and Analysis of Circadian Rhythms Via Prompt Chlorophyll Fluorescence.- High Spatial Resolution Luciferase Imaging of the Arabidopsis thaliana Circadian Clock.- Agrobacterium-mediated seedling transformation to measure circadian rhythms in Arabidopsis.- Measurement of Luciferase Rhythms in Soybean Hairy Roots.-ODE (ordinary differential equation) Models for Plant Circadian Networks: What The Models Are, and How They Should Be Used.- How to Detect QTLs in the Plant Circadian Clock.- Measuring Hypocotyl Length in Arabidopsis.- High Throughput Extraction and Enzymatic Determination of Sugars and Fructans In Fructan-Accumulating Plants.- Simple Nuclei Preparation and Co-Immunoprecipitation Procedures for Studying Protein Abundance and Interactions In Plant Circadian Time Courses.- Chromatin Immunoprecipitation Protocol for Circadian Clock Proteins.- A high-throughput 3′-Tag RNA Sequencing for Large-Scale Time-Series Transcriptome Studies.- Experimental Design for Time-Series RNA-seq Analysis of Gene Expression and Alternative Splicing.- Using tandem affinity purification to identify circadian clock protein complexes from Arabidopsis.- Firefly Luciferase Complementation-Based Analysis of Dynamic Protein-Protein Interactions under Diurnal and Circadian Conditions in Arabidopsis.- Monitoring Seasonal Bud Set, Bud Burst, and Cold Hardiness in Populus.- The Perennial Clock Is an Essential Timer for Seasonal Growth Events and Cold Hardiness.