Methods in Enzymology. Volume 393. Circadian Rhythms. Michael W. Young

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1 Methods in Enzymology Volume 393 Circadian Rhythms Michael W. Young

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3 CONTRIBUTORS TO VOLUME 393 PREFACE VOLUME IN SERIES x i XVI I 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 Genetic Screens for Clock Mutants JEFFREY L. PRICE 3 5 in Drosophila 4. Systems Approaches to Biological Rhythms JEFFREY C. HALL 61 in Drosophila 5. Analysis of Circadian Rhythms in Zebrafish JUN HIRAYAMA, MAKi KANEKO, LUCA CARDONE, GREGORY CAHILL, AN D PAOLO SASSONE-CORSI Genetic Manipulation of Circadian Rhythms NAOTo HAYASAKA, in Xenopus SILVIA 1. LARUE, AND CARLA B. GREEN Forward Genetic Screens to Identify Circadian SANDRA M. SIEPKA AND Rhythm Mutants in Mice JOSEPH S. TAKAHASHI Methods to Record Circadian Rhythm Wheel SANDRA M. SIEPKA AND Running Activity in Mice JOSEPH S. TAKAHASHI Genetic Approaches to Human Behavior Louis J. PTACEK, CHRISTOPHER R. JONES, AND YING-Hui Fu Enhanced Phenotyping of Complex Traits MARTHA MERROw AND with a Circadian Clock Model TILL ROENNEBERG 251

4 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 Real-Time Luminescence Reporting of SHIN YAMAZAKI AND Circadian Gene Expression in Mammals JOSEPH S. TAKAHASHI 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 Molecular and Statistical Tools for Circadian HERMAN WIJNEN, Transcript Profiling FELIX NAEF, AN D MICHAEL W. YOUNG 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 37 9 Neurospora Circadian Clock 18. Analyzing the Degradation of PERIOD HYUK WAN Ko AND Protein by the Ubiquitin-Proteasome ISAAC EDERY 39 4 Pathway 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 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 9 the Circadian Clock of Drosophila 22. The Suprachiasmatic Nucleus is a Functionally RAE SILVER AN D Heterogeneous Timekeeping Organ WILLIAM J. SCHWARTZ 451

5 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 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 Circadian Effects of Timed Meals (and ALEC J. DAVIDSON, Other Rewards) OZGUR TATAROGLU, AND MICHAEL MENAKER 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 Cell Culture Models for Oscillator and DAVID J. EARNEST AN D Pacemaker Function : Recipes for Dishes VINCENT M. CASSONE 55 8 with 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 Oligodeoxynucleotide Methods for Analyzing SHELLEY A. TISCHKAU AND the Circadian Clock in the Suprachiasmatic MARTHA U. GILLETTE 593 Nucleu s 32. Assaying the Drosophila Negative Feedback PIPAT NAWATHEAN, Loop with RNA Interference in S2 Cells JEROME S. MENET, AN D MICHAEL ROSBASH Role of Neuronal Membrane Events GABRIELLA B. LUNDKVIST in Circadian Rhythm Generation SID GENE D. BLOCK 623

6 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 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 D BIKEM AKTEN Membranes, Ions, and Clocks: Testing the MICHAEL N. NITABACH, TODD Njus-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 Cryptochromes and Circadian Photoreception CARRIE L. PARTCH AN D in Animals Azlz SANCAR Nonvisual Ocular Photoreception in the RussELL N. VAN GELDER 74 6 Mammal Section X. Sleeping Flies 40. Essentials of Sleep Recordings in Drosophila : Rozl ANDRETIC AND Moving Beyond Sleep Time PAUL J. SHAW 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 Testing the Adaptive Value of CARL HIRSCHIE JOHNSON 81 8 Circadian Systems

7 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 The Circadian Clock and Tumor CHENG CHI LEE 852 Suppression by Mammalian Period Gene s AUTHOR INDEX 86 3 SUBJECT INDEX 905