Circadian Clocks: Methods and Protocols

Preface: Designing a Circadian Experiment
Table of Contents...
Contributing Authors...

Part I Measuring and Modeling Physiological and Behavioral Rhythms

1. Real-Time In Vitro Fluorescence Anisotropy of the Cyanobacterial Circadian Clock
Joel Heisler, Archana Chavan, Yong-Gang Chang, and Andy LiWang

2. Inductively Coupled Plasma Mass Spectrometry for Elemental Analysis in Circadian Biology
Alessandra Stangherlin, Jason Day, and John O'Neill

3. The Assessment of Circadian Rhythms within the Immune System
Chlo?C. Nobis, Marc Cuesta, Jean-Fran蔞is Daudelin, Genevi鋦e Dubeau-Laram嶪, Diane B. Boivin, Nathalie Labrecque, and Nicolas Cermakian

4. Measuring Circadian Rhythms in Human Cells
Ngoc-Hien Du and Steven A. Brown

5. Measuring the Effects of Circadian Rhythm-Related Manipulations on Depression-Like Behavior in Rodents: Forced Swim and Tail Suspension Tests
Chelsea A. Vadnie, Lauren M. DePoy, and Colleen A. McClung

6. Asking the Clock: How to Use Information from Questionnaires for Circadian Phenotyping
C幨ine Vetter, Eva C. Winnebeck, and Till Roenneberg

7. Simple Kinetic Models in Molecular Chronobiology
J. Patrick Pett, P嶚 O. Westermark, and Hanspeter Herzel

Part II Genome-Wide Analyses in Circadian Biology

8. Searching Novel Clock Genes using RNAi-Based Screening
Bert Maier, Stephan Lorenzen, Anna-Marie Finger, Hanspeter Herzel, and Achim Kramer

9. Chromatin Immunoprecipitation (ChIP) from Mouse Liver Nuclei
Sara S. Fonseca Costa and Jgen A. Ripperger

10. Using GRO-seq to Measure Circadian Transcription and Discover Circadian Enhancers
Bin Fang, Dongyin Guan, and Mitchell A. Lazar

11. Circadian Metabolomics from Breath
Steven A. Brown and Pablo M-L Sinues

12. A Lipidomics View of Circadian Biology
Rona Aviram, Chunyan Wang, Xianlin Han, and Gad Asher

13. Circadian Lipidomics: Analysis of Lipid Metabolites Around-The-Clock
Ursula Loizides-Mangold, Volodymyr Petrenko, and Charna Dibner

14. Phosphoproteome and Proteome Sample Preparation from Mouse Tissues for Circadian Analysis
Franziska Bring, Sean J. Humphrey and Maria S. Robles

15. Circadian Phosphorylation of CLOCK and BMAL1
Hikari Yoshitane and Yoshitaka Fukada

Part III Imaging and Manipulating Brain Clocks

16. Fluorescence Live Imaging of Drosophila Circadian Pacemaker Neurons
Virginie Sabado and Emi Nagoshi

17. Monitoring Electrical Activity in Drosophila Circadian Output Neurons
Annika F. Barber and Amita Sehgal

18. Light Input to the Mammalian Circadian Clock
Adam A. Dannerfjord, Laurence A. Brown, Russell G. Foster, and Stuart N. Peirson

19. Acute In Vivo Multi-Electrode Recordings from the Mouse Suprachiasmatic Nucleus
Joshua Mouland, Lauren Walmsley, Timothy M. Brown, and Robert J. Lucas

20. Perforated Multi-Electrode Array Recording in Hypothalamic Brain Slices
Mino D. C. Belle, Beatriz Ba隳-Otalora and Hugh D. Piggins

21. Collection of Mouse Brain Slices for Bioluminescence Imaging of Circadian Clock Networks
Jennifer A. Evans, David K. Welsh, and Alec J. Davidson

22. Computational Analysis of PER2:: LUC Imaging Data
Tanya L. Leise

23. Electrophysiological Approaches to Studying the Suprachiasmatic Nucleus
Stephan Michel, Takahiro J. Nakamura, Johanna H. Meijer, and Christopher S. Colwell

24. Optogenetic Methods for the Study of Circadian Rhythms
Jeff R. Jones, Michael C. Tackenberg, and Douglas G. McMahon