Methods in Enzymology Volume 393 Circadian Rhythms · Circadian Rhythms 14. Analysis of Circadian Output Rhythms of GILES DUFFIELD, Gene Expression in Neurospora and JENNIFER J. LORDS,

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


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


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

Methods in Enzymology Volume 393 Circadian Rhythms · Circadian Rhythms 14. Analysis of Circadian Output Rhythms of GILES DUFFIELD, Gene Expression in Neurospora and JENNIFER J. LORDS,

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