Circadian Rhythms and Biological Clocks Part A - 1st Edition - ISBN: 9780128012185, 9780128013410

Circadian Rhythms and Biological Clocks Part A, Volume 551

1st Edition

Serial Volume Editors: Amita Sehgal
eBook ISBN: 9780128013410
Hardcover ISBN: 9780128012185
Imprint: Academic Press
Published Date: 15th January 2015
Page Count: 488
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Table of Contents

  • Preface
  • Part I: Organismal Rhythms as Read-Outs of Clock Function
    • Chapter One: Studying Circadian Rhythm and Sleep Using Genetic Screens in Drosophila
      • Abstract
      • 1 Introduction: Studying Circadian Behavior in the Fruit Fly, Drosophila melanogaster
      • 2 Screening for Circadian Rhythm and Sleep Mutants
      • 3 Screening Techniques
      • Acknowledgments
    • Chapter Two: Dissecting the Mechanisms of the Clock in Neurospora
      • Abstract
      • 1 Introduction
      • 2 Molecular Mechanism of the Neurospora Circadian Oscillator
      • 3 Core Clock Components
      • 4 Conclusion
    • Chapter Three: High-Throughput and Quantitative Approaches for Measuring Circadian Rhythms in Cyanobacteria Using Bioluminescence
      • Abstract
      • 1 Theory
      • 2 Build a Computer-Controlled Turntable
      • 3 Use a Computer-Controlled Turntable
      • 4 Analyzing Data from Turntable
      • 5 Steps to Extract Reliable Quantitative Information from Bioluminescence Levels
      • Acknowledgments
    • Chapter Four: Using Circadian Entrainment to Find Cryptic Clocks
      • Abstract
      • 1 Introduction
      • 2 Methods
      • 3 Discussion
      • Acknowledgments
    • Chapter Five: Wavelet-Based Analysis of Circadian Behavioral Rhythms
      • Abstract
      • 1 Introduction
      • 2 Fourier and Wavelet Methods for Time Series Analysis
      • 3 Computations
      • 4 Concluding Remarks
    • Chapter Six: Genetic Analysis of Drosophila Circadian Behavior in Seminatural Conditions
      • Abstract
      • 1 Introduction
      • 2 Considerations for Studies Outside
      • 3 Simulating Natural Conditions in the Laboratory
      • Acknowledgments
  • Part II: Characterization of Molecular Clock Components
    • Chapter Seven: Methods to Study Molecular Mechanisms of the Neurospora Circadian Clock
      • Abstract
      • 1 Introduction
      • 2 Description of Methods
      • 3 Concluding Remarks
      • Acknowledgment
    • Chapter Eight: Detecting KaiC Phosphorylation Rhythms of the Cyanobacterial Circadian Oscillator In Vitro and In Vivo
      • Abstract
      • 1 Theory
      • 2 Equipment
      • 3 Materials
      • 4 Protocol
      • 5 Step 1: Expression of KaiA or KaiB in E. coli
      • 6 Step 2: Expression of KaiC in E. coli
      • 7 Step 3: Purification of KaiA or KaiB
      • 8 Step 4: Purification of KaiC
      • 9 Step 5: In vitro oscillation reaction
      • 10 Step 6: SDS-PAGE
      • 11 Step 7: Densitometry
      • 12 Detection of protein phosphorylation forms from in vivo cell extracts
      • 13 Equipment
      • 14 Materials
      • 15 Protocol
      • 16 Step 1: Preparation
      • 17 Step 2: Electrophoresis and Blotting
      • Acknowledgments
    • Chapter Nine: The Role of Casein Kinase I in the Drosophila Circadian Clock
      • Abstract
      • 1 Introduction
      • 2 Expression of Mutant Forms of DBT with the GAL4/UAS Binary Expression Method
      • 3 Expression of DBT in Drosophila S2 Cells for Analysis of DBT Kinase Activity
      • 4 Proteomic Approaches
    • Chapter Ten: Purification and Analysis of PERIOD Protein Complexes of the Mammalian Circadian Clock
      • Abstract
      • 1 General Strategy
      • 2 Extraction and Characterization of PER Complexes from Mouse Tissues
    • Chapter Eleven: Best Practices for Fluorescence Microscopy of the Cyanobacterial Circadian Clock
      • Abstract
      • 1 Introduction
      • 2 Materials
      • 3 Methods
      • Acknowledgments
    • Chapter Twelve: Structural and Biophysical Methods to Analyze Clock Function and Mechanism
      • Abstract
      • 1 Introduction
      • 2 Kai Protein Overexpression, Purification, Complex Formation, and Analysis by Denatured and Native Polyacrylamide Gel Electrophoresis
      • 3 Analytical Ultracentrifugation
      • 4 Dynamic Light Scattering
      • 5 Thin Layer Chromatography
      • 6 Mass Spectrometry
      • 7 Site-Directed Mutagenesis
      • 8 Fluorescence Techniques (Labeled Proteins, Anisotropy, and Fluorescence Resonance Energy Transfer)
      • 9 Electron Microscopy
      • 10 X-ray Crystallography
      • 11 Small-Angle X-ray and Neutron Scattering
      • 12 Nuclear Magnetic Resonance
      • 13 Hydrogen–Deuterium Exchange
      • 14 MD Simulations
      • 15 Modeling the In Vitro Oscillator
      • 16 Summary and Outlook
      • Acknowledgments
    • Chapter Thirteen: Identification of Small-Molecule Modulators of the Circadian Clock
      • Abstract
      • 1 Introduction
      • 2 Cell-Based Circadian Assay
      • 3 High-Throughput Screening System
      • 4 Circadian Screening
      • 5 Conclusion
  • Part III: Circadian Regulation of Gene and Protein Expression
    • Chapter Fourteen: ChIP-seq and RNA-seq Methods to Study Circadian Control of Transcription in Mammals
      • Abstract
      • 1 Critical Factors
      • 2 ChIP-seq Method for Mouse Liver
      • 3 RNA-Seq Method for Mouse Liver
    • Chapter Fifteen: ChIPping Away at the Drosophila Clock
      • Abstract
      • 1 Introduction
      • 2 Equipment
      • 3 Solutions
      • 4 Protocol
      • 5 Discussion
    • Chapter Sixteen: Considerations for RNA-seq Analysis of Circadian Rhythms
      • Abstract
      • 1 Introduction
      • 2 Results
      • 3 Conclusions
      • 4 Methods
      • Acknowledgments
    • Chapter Seventeen: RNA-seq Profiling of Small Numbers of Drosophila Neurons
      • Abstract
      • 1 Introduction
      • 2 Results/Methods
      • 3 Discussion
    • Chapter Eighteen: Analysis of Circadian Regulation of Poly(A)-Tail Length
      • Abstract
      • 1 Introduction
      • 2 Measurement of Poly(A)-Tail Length at a Genomewide Level
      • 3 Measurement of Poly(A)-Tail Length at a Single-Gene Level
      • 4 Materials
      • 5 Concluding Remarks
      • Acknowledgments
    • Chapter Nineteen: Sample Preparation for Phosphoproteomic Analysis of Circadian Time Series in Arabidopsis thaliana
      • Abstract
      • 1 Introduction
      • 2 Materials and Methods
      • 3 Results
      • 4 Discussion
      • 5 Conclusions
      • Acknowledgments
  • Author Index
  • Subject Index


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.

Key Features

  • Continues the legacy of this premier serial with quality chapters authored by leaders in the field
  • Covers research methods in biomineralization science
  • Keeping with the interdisciplinary nature of the circadian rhythm field, the volume includes diverse approaches towards the study of rhythms, from assays of biochemical reactions in unicellular organisms to monitoring of behavior in humans.


Biochemists, biophysicists, molecular biologists, analytical chemists, and physiologists.


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© Academic Press 2015
Academic Press
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"…these volumes provide a remarkable summary of the methods, experimental systems, and findings of cutting-edge research into circadian rhythms….an essential resource for all types of scientists studying chronobiology, as well as an informative read for anyone who wishes to understand better the ticking of their biological clock." --The Quarterly Review of Biology

Praise for the Series:
"Should be on the shelves of all libraries in the world as a whole collection." --Chemistry in Industry
"The work most often consulted in the lab." --Enzymologia
"The Methods in Enzymology series represents the gold-standard." --Neuroscience

Ratings and Reviews

About the Serial Volume Editors

Amita Sehgal Serial Volume Editor

Dr. Sehgal is the John Herr Musser Professor of Neuroscience and Director of a Program in Chronobiology at the Perelman School of Medicine, University of Pennsylvania. She has also been an Investigator of the Howard Hughes Medical Institute since 1997. Dr. Sehgal received her Ph.D. from the Graduate School of Medical Sciences, Cornell University, working with Dr. Moses Chao, and conducted her postdoctoral work with Dr. Michael Young at Rockefeller University. A major focus in her laboratory is the cellular and molecular basis of circadian rhythms, using the fruit fly, Drosophila melanogaster as a model system. Her laboratory also developed a Drosophila model for the study of sleep, which has been adopted by laboratories worldwide, and is rapidly provding insight into the regulation and function of sleep. In 2009, Dr. Sehgal was elected to the Institute of Medicine and in 2011 to the American Academy of Arts and Sciences.

Affiliations and Expertise

John Herr Musser Professor of Neuroscience; co-Director, Penn Medicine Neuroscience Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA