Circadian Rhythms and Biological Clocks Part A
- 1st Edition, Volume 551 - January 27, 2015
- Latest edition
- Editor: Amita Sehgal
- Language: English
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 Biologica… Read more
- 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.
- 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
- Chapter One: Studying Circadian Rhythm and Sleep Using Genetic Screens in Drosophila
- 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
- Chapter Seven: Methods to Study Molecular Mechanisms of the Neurospora Circadian Clock
- 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
- Chapter Fourteen: ChIP-seq and RNA-seq Methods to Study Circadian Control of Transcription in Mammals
- Author Index
- Subject Index
"…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
- Edition: 1
- Latest edition
- Volume: 551
- Published: January 27, 2015
- Language: English
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