Two new volumes of Methods in Enzymology continue the legacy of this premier serial with quality chapters authored by leaders in the field. Circadian Rhythms and Biological Clocks Part A and Part B is an exceptional resource for anybody interested in the general area of circadian rhythms. As key elements of timekeeping are conserved in organisms across the phylogenetic tree, and our understanding of circadian biology has benefited tremendously from work done in many species, the volume provides a wide range of assays for different biological systems. Protocols are provided to assess clock function, entrainment of the clock to stimuli such as light and food, and output rhythms of behavior and physiology. This volume also delves into the impact of circadian disruption on human health. Contributions are from leaders in the field who have made major discoveries using the methods presented here.
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Table of Contents
1. Studying Circadian Rhythm and Sleep Using Genetic Screens in DrosophilaSofia Axelrod, Lino Saez and Michael W. Young
2. Dissecting the Mechanisms of the Clock in Neurospora
Jennifer Hurley, Jennifer J. Loros and Jay C. Dunlap
3. High Throughput and Quantitative Approaches for Measuring Circadian Rhythms in Cyanobacteria Using Bioluminescence
Ryan K. Shultzaberger, Mark L. Paddock, Takeo Katsuki, Ralph J. Greenspan and Susan S. Golden
4. Using Circadian Entrainment to Find Cryptic Clocks
Zheng Eelderink-Chen, Maria Olmedo, Jasper Bosman and Martha Merrow
5. Wavelet-based Analysis of Circ adian Behavioral Rhythms
Tanya L. Leise
6. Genetic Analysis of Drosophila Circadian Behavior in Semi-Natural Conditions
Edward W Green, Emma K O'Callaghan, Mirko Pegoraro, J Douglas Armstrong, Rodolfo Costa3 and Charalambos P Kyriacou
7. Methods to Study Molecular Mechanisms of the Neurospora Circadian Clock
Joonseok Cha, Mian Zhou, and Yi Liu
8. Detecting KaiC Phosphorylation Rhythms of the Cyanobacterial Circadian Oscillator in Vitro and in Vivo
Yong-Ick Kim, Joseph S. Boyd, Javier Espinosa, and Susan S. Golden
9. The Role of Casein Kinase I in the Drosophila Circadian Clock
Jeffrey L. Price, Jin-Yuan Fan, Andrew Keightley and John C. Means
10. Purification and Analysis of PERIOD Protein Complexes of the Mammalian Circadian Clock
Jin Young Kim, Pieter Bas Kwak, Michael Gebert, Hao A. Duong and Charles J. Weitz
11. Best Practices for Fluorescence Microscopy of the Cyanobacterial Circadian Clock
Susan E. Cohen, Marcella L. Erb, Joe Pogliano and Susan S. Golden
12. Structural and Biophysical Methods to Analyze Clock Function and Mechanism
Martin Egli
13. Identification of Small Molecule Modulators of the Circadian Clock
Tsuyoshi Hirota and Steve A. Kay
14. ChIP-Seq and RNA-Seq Methods to Study Circadian Control of Transcription in Mammals
Joseph S. Takahashi, Vivek Kumar , Prachi Nakashe, Nobuya Koike, Hung-Chung Huang, Carla B. Green, and Tae-Kyung Kim
15. Chipping away at the Drosophila Clock
Jian Zhou, Wangjie Yu and Paul E. Hardin
16. Considerations for RNA-seq Analysis of Circadian Rhythms
Jiajia Li, Gregory R Grant, John B Hogenesch and Michael E Hughes
17. RNA-Seq Profiling of Small Numbers of Drosophila Neurons
Katharine Abruzzi, Xiao Chen, Emi Nagoshi, Abby Zadina, and Michael Rosbash
18. Analysis of Circadian Regulation of Poly(A) Tail Length
Shihoko Kojima and Carla B. Green
19. Sample Preparation for Phosphoproteomic Analysis of Circadian Time Series in Arabidopsis Thaliana
Johanna Krahmer, Matthew M Hindle, Sarah F Martin, Thierry Le Bihan and Andrew J Millar
