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Plant Circadian Networks: Methods and Protocols

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

Series: Methods in Molecular Biology Volume: 1158

By: Dorothee Staiger (Editor)

372 pages, 47 colour & 30 b/w illustrations, 14 tables

Humana Press

Hardback | May 2014 | #218009 | ISBN-13: 9781493906994
Availability: Usually dispatched within 1-2 weeks Details
NHBS Price: £89.50 $113/€106 approx

About this book

Plant Circadian Networks: Methods and Protocols provides a collection of protocols to investigate clock-controlled parameters including transcript and small RNA levels, promoter activity using luciferase reporters, protein levels and posttranslational modification, protein-protein interaction, in vivo DNA-protein interaction and RNA-protein interaction, cellular redox state, Ca2+ levels, and innate immune responses. Furthermore, the use of bioinformatics resources is described to evaluate high throughput data sets and to integrate the data into an overarching picture of circadian networks in the cell. Additional chapters focus on seasonal processes like flowering time control, and techniques on trees, moss and algae.

Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Plant Circadian Networks: Methods and Protocols is designed not only for the chronobiology community dealing with circadian biology but also for the plant community in general.


Contents

1. Measurement of Luciferase Rhythms C. Robertson McClung and Qiguang Xie
2. Online Period Estimation and Determination of Rhythmicity in Circadian Data, using the BioDare Data Infrastructure Anne Moore, Tomasz Zielinski and Andrew J. Millar
3. Global Profiling of the Circadian Transcriptome using Microarrays Polly Yingshan Hsu and Stacey L. Harmer
4. ChIP-Seq Analysis of Histone Modifications at the Core of the Arabidopsis Circadian Clock Jordi Malapeira and Paloma Mas
5. Quantitative Transcriptome Analysis using RNA-seq Canan Kulahoglu and Andrea Brautigam
6. Rapid and Parallel Quantification of Small and Large RNA Species Corinna Speth and Sascha Laubinger
7. The RIPper Case - Identification of RNA Binding Protein Targets by RNA Immunoprecipitation Tino Koster, Meike Haas and Dorothee Staiger
8. A Protocol for Visual Analysis of Alternative Splicing in RNA-Seq Data using Integrated Genome Browser Alyssa A. Gulledge, Hiral Vora, Ketan Patel and Ann E. Loraine
9. AthaMap Web Tools for the Analysis of Transcriptional and Post-Transcriptional Gene Expression Regulation in Arabidopsis thaliana Reinhard Hehl and Lorenz Bulow
10. Analysis of mRNA Translation States in Arabidopsis over the Diurnal Cycle by Polysome Microarray Anamika Missra and Albrecht G von Arnim
11. Immunoprecipitation-based Analysis of Protein-protein Interactions Corinna Speth, Luis A. A. Toledo-Filho and Sascha Laubinger
12. Comparative Phosphoproteomics to Identify Targets of the Clock-Relevant Casein Kinase 1 in C. reinhardtii Flagella Jens Boesger, Volker Wagner, Wolfram Weisheit and Maria Mittag
13. Pulsed Induction of Circadian Clock Genes in Arabidopsis Seedlings Stephen M. Knowles, Sheen X. Lu and Elaine M. Tobin
14. The use of Fluorescent Proteins to Analyze Circadian Rhythms Ekaterina Orkat, Miriam Hassidim and Rachel M. Green
15. Measuring Circadian Oscillations of Cytosolic-free Calcium in Arabidopsis thaliana Timothy J. Hearn and Alex A.R. Webb
16. Circadian Life without Micronutrients: Effects of Altered Micronutrient Supply on Clock Function in Arabidopsis Patrice A. Salome, Maria Bernal and Ute Kramer
17. Assessing Redox State and Reactive Oxygen Species in Circadian Rhythmicity Katharina Konig, Helena Galliardt, Marten Moore, Patrick Treffon, Thorsten Seidel and Karl-Josef Dietz
18. Circadian Regulation of Plant Immunity to Pathogens Robert A. Ingle and Laura C. Roden
19. Determination of Photoperiodic Flowering Time Control in Arabidopsis and Barley Alexander Steffen, Andreas Fischer and Dorothee Staiger
20. The Perennial Clock is an Essential Timer for Seasonal Growth Events and Cold Hardiness Mikael Johansson, Cristian Ibanez, Naoki Takata and Maria E. Eriksson
21. Monitoring Seasonal Bud Set, Bud Burst and Cold Hardiness in Populus Mikael Johansson, Naoki Takata, Cristian Ibanez and Maria E. Eriksson
22. Transformation and Measurement of Bioluminescence Rhythms in the Moss Physcomitrella patens Setsuyuki Aoki, Ryo Okada and Santosh B. Satbhai
23. Modeling and Simulating the Arabidopsis thaliana Circadian Clock Using XPP-AUTO Christoph Schmal, Jean-Christophe Leloup and Didier Gonze


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