Plant Circadian Networks: Methods and Protocols

ISBN-13: 9781493906994 / Angielski / Twarda / 2014 / 361 str.

Dorothee Staiger

Opis

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.

Spis treści

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 Külahoglu and Andrea Bräutigam

 

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 Köster, 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

 

9AthaMap Web Tools for the Analysis of Transcriptional and Post-Transcriptional Gene Expression Regulation in Arabidopsis thaliana

Reinhard Hehl and Lorenz Bülow

 

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. Salomé, Maria Bernal and Ute Krämer

 

17. Assessing Redox State and Reactive Oxygen Species in Circadian Rhythmicity

Katharina König, 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 Ibáñez, Naoki Takata and Maria E. Eriksson

 

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

Mikael Johansson, Naoki Takata, Cristian Ibáñez 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