Methods in Enzymology

Volume 393

Circadian Rhythms

Michael W. Young

CONTRIBUTORS TO VOLUME 393 x i

PREFACE XVI I

VOLUME IN SERIES xix

Section I . Genetic Approaches to Circadian Clocks

1 . Analysis of Circadian Rhythms in Neurospora: JAY C. DUNLAP AN D

Overview of Assays and Genetic and

JENNIFER J . LOROS

3

Molecular Biological Manipulatio n

2 . Circadian Genetics in the Model Higher Plant, MEGAN M . SOUTHERN AND

Arabidopsis thaliana

ANDREW J . MILLAR

23

3. Genetic Screens for Clock Mutants

JEFFREY L. PRICE

3 5

in Drosophila

4. Systems Approaches to Biological Rhythms

JEFFREY C . HALL

61in Drosophila

5 . Analysis of Circadian Rhythms in Zebrafish

JUN HIRAYAMA, MAKi KANEKO,

LUCA CARDONE,

GREGORY CAHILL, AN D

PAOLO SASSONE-CORSI

186

6 . Genetic Manipulation of Circadian Rhythms NAOTo HAYASAKA ,

in Xenopus

SILVIA 1. LARUE, AND

CARLA B . GREEN

205

7 . Forward Genetic Screens to Identify Circadian SANDRA M . SIEPKA AND

Rhythm Mutants in Mice

JOSEPH S . TAKAHASHI

21 9

9 . Methods to Record Circadian Rhythm Wheel SANDRA M . SIEPKA AND

Running Activity in Mice

JOSEPH S . TAKAHASHI

230

9 . Genetic Approaches to Human Behavior

Louis J . PTACEK,

CHRISTOPHER R . JONES, AND

YING-Hui Fu

239

10. Enhanced Phenotyping of Complex Traits

MARTHA MERROw AND

with a Circadian Clock Model

TILL ROENNEBERG

251

Section II . Tracking Circadian Control of Gene Activity

11 . Real-Time Reporting of Circadian-Regulated DAVID K . WELSH,

Gene Expression by Luciferase Imaging in TAKATO IMAIZUMI, AND

Plants and Mammalian Cells

STEVE A . KAY

26 9

12. Real-Time Luminescence Reporting of

SHIN YAMAZAKI AND

Circadian Gene Expression in Mammals

JOSEPH S . TAKAHASHI

28 8

13. Transgenic cAMP Response Element

KANAE IIJIMA-ANDO AND

Reporter Flies for Monitoring

JERRY C . P. YIN

302

Circadian Rhythm s

14. Analysis of Circadian Output Rhythms of

GILES DUFFIELD ,

Gene Expression in Neurospora and

JENNIFER J . LORDS, AND

Mammalian Cells in Culture

JAY C . DUNLAP

31 5

15. Molecular and Statistical Tools for Circadian HERMAN WIJNEN ,

Transcript Profiling

FELIX NAEF, AN D

MICHAEL W. YOUNG

34 1

16. RNA Profiling in Circadian Biology

JOHN R. WALKER AN D

JOHN B . HOGENESCH

36 6

Section III . Molecular Cycles : Clock Protein Rhythms

17 . Analysis of Posttranslational Regulations in the YI Lro

379Neurospora Circadian Clock

18. Analyzing the Degradation of PERIOD

HYUK WAN Ko AND

Protein by the Ubiquitin-Proteasome

ISAAC EDERY

39 4Pathway in Cultured Drosophila Cells

19. Casein Kinase I in the Mammalian

ERIK J . EIDE, HEESEOG RANG ,

Circadian Clock

STEPHANIE CRAPO ,

MONICA GALLEGO, AN D

DAVID M. VIRSHUP

408

20. Nucleocytoplasmic Shuttling of Clock Proteins FILIPPO TAMANINI ,

KAZUHIRO YAGITA ,

HITOSIII OKAMURA, AND

GIJSBERTUS T. J . VAN DER

HORST

41 8

Section IV. Anatomical Representation of Neural Clock s

21 . Techniques that Revealed the Network of

CHARLOTTE HELFRICH-FÖRSTER 43 9the Circadian Clock of Drosophila

22 . The Suprachiasmatic Nucleus is a Functionally RAE SILVER AN D

Heterogeneous Timekeeping Organ

WILLIAM J . SCHWARTZ

451

Section V. Mosaic Circadian Systems

23. Transplantation of Mouse Embryo Fibroblasts : SEHYUNG CHO,

An Approach to Study the Physiological

IRENE YUJNOVSKY,

Pathways Linking the Suprachiasmatic

MASAO Doi, AND

Nucleus and Peripheral Clocks

PAOLO SASSONE-CoRSi

46 9

24. Mouse Chimeras and Their Application to

SHARON S . LOW-ZEDDIE S

Circadian Biology

AND JOSEPH S . TAKAHASHI

47 8

Section VI . Peripheral Circadian Clocks

25. Measuring Circadian Rhythms in Olfaction

PARTHASARATHY KRISHNAN ,

Using Electroantennograms

STUART E. DRYER, AND

PAUL E. HARDIN

49 5

26. Circadian Effects of Timed Meals (and

ALEC J . DAVIDSON ,

Other Rewards)

OZGUR TATAROGLU, AND

MICHAEL MENAKER

50 9

27. Peripheral Clocks and the Regulation of

R. DANIEL RUDIC ,

Cardiovascular and Metabolic Function

ANNE M . CURTIS ,

YAN CHENG, AND

GARRET FITZGERALD

524

Section VII . Cell and Tissue Culture System

28. Circadian Gene Expression in Cultured Cells EMI NAGOSHI ,

STEVEN A . BROWN ,

CHARNA DIBNER ,

BENOIT KORNMANN, AND

UELI SCHIBLER

543

29. Cell Culture Models for Oscillator and

DAVID J . EARNEST AN D

Pacemaker Function : Recipes for Dishes

VINCENT M . CASSONE

55 8with Circadian Clocks ?

30. Analysis of Circadian Mechanisms in the

MICHAEL H . HASTINGS ,

Suprachiasmatic Nucleus by Transgenesis

AKHILESH B . REDDY,

and Biolistic Transfection

DOUGLAS G . MCMAHON ,

AND ELISABETH S . MAYWOOD 579

31 . Oligodeoxynucleotide Methods for Analyzing SHELLEY A . TISCHKAU AND

the Circadian Clock in the Suprachiasmatic MARTHA U . GILLETTE

593Nucleu s

32. Assaying the Drosophila Negative Feedback PIPAT NAWATHEAN ,

Loop with RNA Interference in S2 Cells

JEROME S . MENET, AN D

MICHAEL ROSBASH

610

33. Role of Neuronal Membrane Events

GABRIELLA B . LUNDKVIST

in Circadian Rhythm Generation

SID GENE D . BLOCK

623

Section VIII . Intercellular Signaling

34. A Screen for Secreted Factors of the

ACHIM KRAMER,Suprachiasmatic Nucleus

FU-CHIA YANG ,

SEBASTIAN KRAVES, AN D

CHARLES J . WEITZ

64 5

35. Genetic and Biochemical Strategies for

F . RoB JACKSON,

Identifying Drosophila Genes That

GINKA K. GENOVA ,Function in Circadian Control

YANMEI HUANG,

YELENA KLEYNER ,

JOOWON SUH,

MARY A . ROBERTS ,

VASUDHA SUNDRAM, AN DBIKEM AKTEN

663

36. Membranes, Ions, and Clocks: Testing the

MICHAEL N . NITABACH, TODDNjus-Sulzman-Hastings Model of the

C. HOLMES, AND

Circadian Oscillator

JUSTIN BLAU

682

Section IX. Photoresponsive Clocks

37. Mammalian Photoentrainment: Results,

STUART N. PEIRSON ,

Methods, and Approaches

STEWART THOMPSON ,

MARK W . HANKINS, AND

RUSSELL G . FOSTER

69 7

38. Cryptochromes and Circadian Photoreception CARRIE L. PARTCH AN D

in Animals

Azlz SANCAR

72 6

39. Nonvisual Ocular Photoreception in the

RussELL N . VAN GELDER

74 6Mammal

Section X. Sleeping Flies

40 . Essentials of Sleep Recordings in Drosophila : Rozl ANDRETIC AND

Moving Beyond Sleep Time

PAUL J . SHAW

75 9

41 . Drosophila melanogaster: An Insect Model for KAREN S . Ho AN D

Fundamental Studies of Sleep

AMITA SEHGAL

772

Section XI . Circadian Biology of Populations

42. Molecular Evolution and Population

ERAN TAUBER AN D

Genetics of Circadian Clock Genes

CHARALAMBOS P . KYRIACOU 79 7

43 . Testing the Adaptive Value of

CARL HIRSCHIE JOHNSON

81 8Circadian Systems

Section XII. Circadian Clocks Affecting Noncircadian Biology

44. A "Bottom-Counting" Video System for

REBECCA GEORGE,

Measuring Cocaine-Induced Behaviors

KEVIN LEASE ,

in Drosophila

JAMES BURNETTE, AND

JAY HIRSH

84 1

45 . The Circadian Clock and Tumor

CHENG CHI LEE

852

Suppression by Mammalian Period Gene s

AUTHOR INDEX 86 3

SUBJECT INDEX 905