Preface Contributors I. Overviews. 1. Light, photoreceptors and circadian clocks Russell G. Foster, Mark W. Hankins and Stuart N. Peirson 2. Statistical analysis of biological rhythm data Harold B. Dowse II. Rhythmic Readouts. 3. Rhythmic conidiation in Neurospora crassa. Cas Kramer 4. Monitoring and analyzing Drosophila circadian locomotor activity. Mauro A. Zordan, Clara Benna and Gabriella Mazzotta. 5. Automated video image analysis of larval zebrafish locomotor rhythms. Gregory M. Cahill 6. Locomotor activity in rodents. Gianluca Tosini 7. Analysis of circadian leaf movement rhythms in Arabidopsis thaliana. Kieron D. Edwards and Andrew J. Millar 8. Detection of rhythmic bioluminescence from luciferase reporters in cyanobacteria. Shannon R. Canales, Jayna L. Ditty, Eugenia M. Clerico and Susan S. Golden 9. Analysis of rhythmic gene expression in adult Drosophila using the firefly-luciferase reporter gene. Ralf Stanewsky 10. Monitoring circadian rhythms in Arabidopsis thaliana using luciferase reporter genes. Anthony Hall and Paul Brown III. Identification of Clock Genes. 11. Specialized techniques for site directed mutagenesis in cyanobacteria Eugenia M. Clerico, Jayna L. Ditty and Susan S. Golden 12. Novel strategies for the identification of clock genes in Neurospora with insertional mutagenesis Kruno Sveric, Moyra Mason, Till Roenneberg and Martha Merrow 13. Mutagenesis with Drosophila Patrick Emery 14. Mutagenesis in Arabidopsis. Jodi Maple and Simon G. Moller 15. Yeast-two-hybrid screening. Jodi Maple and Simon G. Moller 16. Microarrays: quality control and hybridization protocol. Ken-ichiro Uno and Hiroki R. Ueda 17. Microarrays: statistical methods for circadian rhythms. Rikuhiro Yamada and Hiroki R. Ueda 18. Identification of clock genes using difference gel electrophoresis (DIGE). Natasha A. Karp and Kathryn S. Lilley IV. Gene Expression: RNA. 19. Isolation of total RNA from Neurospora mycelium. Cas Kramer 20. RNA extraction from Drosophila heads. Patrick Emery 21. Extraction of plant RNA. Michael G. Salter and Helen E. Conlon 22. RNA Extraction from mammalian tissues. Stuart N. Peirson and Jason N. Butler 23. Northern analysis of sense and antisense frequency RNA in Neurospora crassa. Cas Kramer 24. RNase protection assay. Patrick Emery 25. Quantitative PCR. Stuart N. Peirson and Jason N. Butler V. Gene Expression: Proteins. 26. Protein extraction, fractionation and purification from cyanobacteria. Natalia B. Ivleva and Susan S. Golden 27. Protein extraction from Drosophila heads. Patrick Emery 28. Plant protein extraction. Helen E. Conlon and Michael G. Salter 29. Protein extraction from mammalian tissues. Choogon Lee 30. Western blotting. Choogon Lee 31. Co-immunoprecipitation (coIP) assay. Choogon Lee 32. In vitro phosphorylation and kinase assays in Neurospora crassa. Lisa Franchi, Giuseppe Macino VI. In vitro Systems. 33. Basic protocols for Drosophila S2 cell line: maintenance and transfection M. Fernanda Ceriani 34. Co-immunoprecipitation on Drosophila cells in culture M. Fernanda Ceriani 35. Basic protocols for zebrafish cell lines: maintenance and transfection. Daniela Vallone, Cristina Santoriello, Srinivas Babu Gondi and Nicholas S. Foulkes 36. Manipulation of mammalian cell lines for circadian studies. Filippo Tamanini 37. Reporter assays. M. Fernanda Ceriani 38. Use of firefly luciferase activity assays to monitor circadian molecular rhythms in vivo and in vitro. Wangjie Yu and Paul E. Hardin 39. SCN cultures that maintain rhythmic properties in vitro. K. Tominaga-Yoshino, T. Ueyama and H. Okamura VII. Microscopy analysis. 40. RNA in situ hybridisations on Drosophila whole mounts. Corinna Wulbeck and Charlotte Helfrich-Forster 41. In situ hybridisation of SCN slices. Horacio O. de la Iglesia 42. Immunohistochemistry in Drosophila, sections and whole mounts. Charlotte Helfrich-Forster 43. Immunocytochemistry on SCN slices Marta Munoz Llamosas 44. Immunofluorescence analysis of circadian protein dynamics in cultured mammalian cells. Filippo Tamanini
