Circadian Rhythms (eBook)

front cover 1
copyright 5
Table of Contents 6
front matter 11
Contributors to Volume 393 11
Preface 17
body 42
Section I: Genetic Approaches to Circadian Clocks 42
[1] Analysis of Circadian Rhythms in Overview of Assays and Genetic and Molecular Biological Manipulation 44
Abstract 1 44
Introduction 1 44
Rhythms in Neurospora 45
Overview of Molecular Events in the Neurospora Circadian Cycle 46
Assays for Rhythmicity in Neurospora 48
Analysis via Genetic and Molecular Genetic Techniques 52
Concluding Remarks 1 59
References 1 60
[2] Circadian Genetics in the Model Higher Plant, 64
Abstract 2 64
Introduction 2 64
Circadian Screens Using Luciferase 66
Circadian Screen Measuring Stomatal Rhythms 73
Testing Circadian Rhythms of Mutants Identified in Other Screens 73
Reverse Genetics 74
References 2 75
[3] Genetic Screens for Clock Mutants in 76
Abstract 3 76
Introduction 3 77
Strategies for Mutagenesis 79
Genetic Crosses to Generate Genotypes for a Screen 82
Detection of Mutant Circadian Phenotypes 88
Validation of Candidate Lines Identified in Genetic Screens 95
Concluding Comments 3 97
References 3 98
[4] Systems Approaches to Biological Rhythms in Drosophila 102
Abstract 4 102
Introduction 4 103
The Circadian Clock of the Fly: Genes and Their Products, Considered in Part from Systems Perspectives 109
Clock-Controlled Genes: Tentative Steps That Move the Subject from Central Pacemaking Concerns out into the System as a Whole 120
The Multicellular System Operating within the Brain of to Regulate Behavioral Rhythmicity 134
Input Systems Subserving Clock Resetting in 155
Actions of Rhythm-Related Genes During Drosophila Development 171
The Rhythm System of Drosophila as Defined Genetically Influences Weakly Appreciable Circadian Phenotypes, as Well as Noncircadian but Temporally Based Characters 184
The Rhythm System, as Defined Genetically, Influences Elements of Biology with No Particular Temporal Components 197
Conclusion 4 208
Acknowledgments 4 209
References 4 209
[5] Analysis of Circadian Rhythms in Zebrafish 227
Abstract 5 227
Introduction 5 227
General Methods 5 228
Locomotor Activity Rhythms 230
Bioluminescence Rhythms in 233
Transgenic Zebrafish 233
Bioluminescence Rhythms in Live Larval Zebrafish 235
Bioluminescence Rhythms in Cultured Organs 235
Recapitulating the Zebrafish Clock in Cultured Cells 236
Establishment of the Z3 Cell Line 236
Culture Conditions for Z3 Cells 237
Other Zebrafish-Derived Cells for Circadian Studies 238
Molecular Methods 5 239
Retroviral Infection 5 241
Preparation of Nuclear Extracts 243
References 5 244
[6] Genetic Manipulation of Circadian Rhythms in Xenopus 246
Abstract 6 246
Introduction 6 246
Transgenic Method 248
Measurement of Circadian Outputs 252
Concluding Remarks 6 258
References 6 258
[7] Forward Genetic Screens to Identify Circadian Rhythm Mutants in Mice 260
Abstract 7 260
Introduction 7 260
Strain Choice 261
ENU Safety Procedures 262
ENU Preparation 263
Injections 7 263
Breeding Strategies 264
The Efficiency of Scanning the Genome to Detect a Recessive Mutant 266
Production Throughput 268
Mutant Heritability Tests 269
Acknowledgments 7 270
References 7 270
[8] Methods to Record Circadian Rhythm Wheel Running Activity in Mice 271
Abstract 8 271
Introduction 8 271
Strain Choice 272
Facilities and Equipment Needed for a Circadian 272
Rhythm Screen 272
Experimental Design and Throughput 275
Data Analysis 8 278
Acknowledgments 8 279
References 8 279
[9] Genetic Approaches to Human Behavior 280
Abstract 9 280
Introduction 9 280
Identifying Mendelian Circadian Variants 283
Approaches to Complex Genetics 287
Challenges of Behavioral Genetics 288
Acknowledgments 9 290
References 9 290
[10] Enhanced Phenotyping of Complex Traits with a Circadian Clock Model 292
Abstract 10 292
Introduction 10 292
The Network Model 295
Clock Mutants 300
Conclusions 10 304
Acknowledgments 10 305
References 10 305
Section II: Tracking Circadian Control of Gene Activity 307
[11] Real-Time Reporting of Circadian-Regulated Gene Expression by Luciferase Imaging in Plants and Mammalian Cells 309
Abstract 11 309
Introduction 11 309
Plants 310
Mammalian Cells 312
Data Analysis 11 323
Acknowledgments 11 326
References 11 326
[12] Real-Time Luminescence Reporting of Circadian Gene Expression in Mammals 328
Abstract 12 328
Introduction 12 328
Animals and Cells 329
Tissue Culture 330
Recording Medium 332
Recording Apparatuses 333
Data Analysis 12 339
Conclusion 12 339
Acknowledgment 12 340
References 12 340
[13] Transgenic cAMP Response Element Reporter Flies for Monitoring Circadian Rhythms 342
Abstract 13 342
Introduction 13 342
Methods 13 344
Results 13 347
Discussion 13 351
References 13 352
[14] Analysis of Circadian Output Rhythms of Gene Expression in Neurospora and Mammalian Cells in Culture 355
Abstract 14 355
Introduction 14 355
DNA Microarray Analysis of Clock Control in Mammalian 367
Cell Culture 367
Concluding Remarks 14 377
References 14 377
[15] Molecular and Statistical Tools for Circadian Transcript Profiling 381
Abstract 15 381
Array Platforms 381
Experimental Design 382
Independent Verification of Microarray Results 389
Molecular Techniques 391
Data Analysis Techniques 394
Acknowledgments 15 404
References 15 404
[16] RNA Profiling in Circadian Biology 406
Abstract 16 406
Introduction 16 406
Experimental Design and Wet Work 407
Experimental Methodology—Dry Work 410
Recommendations 16 414
References 16 414
Section III: Molecular Cycles: Clock Protein Rhythms 417
[17] Analysis of Posttranslational Regulations in the Neurospora Circadian Clock 419
Abstract 17 419
Introduction 17 419
Posttranslational Regulations in the Neurospora Circadian Clock 420
Description of Methods 423
Concluding Remarks 17 431
Acknowledgments 17 431
References 17 431
[18] Analyzing the Degradation of PERIOD Protein by the Ubiquitin-Proteasome Pathway in Cultured Drosophila Cells 434
Abstract 18 434
Overview of Different Mechanisms Mediating the Degradation of Clock Proteins by the Ubiquitin/Proteasome Pathway 434
Analyzing dPER Degradation by the UPP in Cultured Drosophila Cells 437
Concluding Remarks 18 444
Acknowledgments 18 444
References 18 445
[19] Casein Kinase I in the Mammalian Circadian Clock 448
Abstract 19 448
Introduction 19 449
Bacterial Expression and Purification of an Active Form of CKI" 449
Examination of mPER2 Stability in Tissue Culture Cells 452
Induce mPER2 Phosphorylation and Degradation by Phosphatase Inhibition with Calyculin A 452
Analyzing mPER2 Protein Degradation in Xenopus Egg Extracts 455
Concluding Remarks 19 457
References 19 457
[20] Nucleocytoplasmic Shuttling of Clock Proteins 458
Abstract 20 458
Nuclear Localization Signals in Clock Proteins 459
Nuclear Export Signals (NES) in Clock Proteins 464
Nucleocytoplasmic Shuttling of Clock Proteins 465
Nucleocytoplasmic Shuttling and the Heterokaryon Assay 466
Clock Protein Dynamics: Nucleocytoplasmic Shuttling by FLIP 468
Functionality of Clock Protein Shuttling 472
Acknowledgments 20 474
References 20 474
Section IV: Anatomical Representation of Neural Clocks 476
[21] Techniques that Revealed the Network of the Circadian Clock of Drosophila 478
Abstract 21 478
Immunocytochemistry 478
Reporter Gene Expression in Clock Neurons 479
Genetic Manipulations That Identified Clock Neurons Acting as 483
Circadian Pacemakers for Behavioral Rhythmicity 483
Ectopic Expression of Clock and Clock-Related Genes 485
Role of Peripheral Oscillators 486
Concluding Remarks 21 487
References 21 487
[22] The Suprachiasmatic Nucleus is a Functionally Heterogeneous Timekeeping Organ 490
Abstract 22 490
The Brain’s Clock as a Construct 490
In the Beginning: Anatomical Heterogeneity but Functional Homogeneity 492
Reducing SCN Tissue to Cells and Slices 493
SCN Tissue Organization and Heterogeneous Gene Expression 494
Dissection of the Retinorecipient Subdivision of the SCN 496
Heterogeneity of Phase at Tissue and Single-Cell Levels 497
Building a Global View: From Clock Genes to Circadian Behavior 499
From Center to Network 499
Acknowledgments 22 500
References 22 500
Section V: Mosaic Circadian Systems 505
[23] Transplantation of Mouse Embryo Fibroblasts: An Approach to Study the Physiological Pathways Linking the Suprachiasmatic Nucleus and Peripheral Clocks 507
Abstract 23 507
Signaling Pathways and Peripheral Clock 507
Outline of the Procedure 508
Preparation of Mouse Embryo Fibroblasts from Single Mouse Embryo 509
Preparation of Condensed MEF–Collagen Matrix 512
Subcutaneous Implantation Procedure 514
Analysis of Circadian Gene Expression by RNase Protection Assay and 515
Hybridization 23 515
References 23 515
[24] Mouse Chimeras and Their Application to Circadian Biology 516
Abstract 24 516
Introduction 24 517
Properties of Aggregation Chimeric Mice 518
A Study of Clock Chimeras Principles for Circadian Studies 519
Using Chimeras to Study Intercellular Interactions in Circadian Systems 520
General Applications for Chimeras in Circadian Studies 522
Technique 524
Summary 24 528
References 24 528
Section VI: Peripheral Circadian Clocks 531
[25] Measuring Circadian Rhythms in Olfaction Using Electroantennograms 533
Abstract 25 533
Introduction 25 533
Electroantennogram Apparatus Setup 535
Preparing to Record EAG Responses 538
Recording Electroantennograms 541
Conclusion 25 543
References 25 545
[26] Circadian Effects of Timed Meals (and Other Rewards) 547
Abstract 26 547
Introduction 26 547
Entrainment of Locomotor Activity by Meal Feeding 548
Entrainment of Peripheral Organs by Meal Feeding 550
The Search for the Feeding-Entrainable Oscillator 552
Might Entrainment of the FEO Be Entrainment by Reward? 553
Are the FEO and Methamphetamine-Inducible Oscillator the Same Clock? 555
Is It ‘‘Reward’’ After All? 556
Acknowledgments 26 557
References 26 557
[27] Peripheral Clocks and the Regulation of Cardiovascular and Metabolic Function 562
Abstract 27 562
The Emerging Importance of Peripheral Clocks 562
NPAS2 and Other Candidate Members of the Core Clock in the Periphery 563
ChIP Analysis of Promoter Occupancy 564
Analysis of Circadian Rhythms by Serum Shock Analysis 565
Zeitgeber, Circadian Time, and Constant Darkness: Lights on, Lights off ? 566
Isolation of RNA from Murine Aorta 567
Circadian Variation in Metabolism and Diabetes 569
Adapting Metabolic Assays to Assess Circadian Variations in Mice 569
Blood Pressure Studies 572
Circadian Profiles in Cardiovascular Physiology and Disease 572
Conclusion 27 574
References 27 574
Section VII: Cell and Tissue Culture System 578
[28] Circadian Gene Expression in Cultured Cells 580
Abstract 28 580
Introduction 28 580
Monitoring Circadian Gene Expression in Cultured Cells 583
Choice of Cell Line 590
Conclusions and Perspectives 28 591
Acknowledgments 28 592
References 28 592
[29] Cell Culture Models for Oscillator and Pacemaker Function: Recipes for Dishes with Circadian Clocks? 595
Abstract 29 595
Biological Clocks in Vertebrates 595
Molecular Clockworks 597
Avian Pineal Gland 598
Methods in Pinealocyte Culture 599
Mammalian Suprachiasmatic Nucleus and Primary Cell Culture 602
Immortalized SCN2.2 Cell Line 603
Shocked Fibroblast Model 610
Relative Merits of Different Cell Culture Approaches 611
Acknowledgments 29 612
References 29 612
[30] Analysis of Circadian Mechanisms in the Suprachiasmatic Nucleus by Transgenesis and Biolistic Transfection 616
Abstract 30 616
Organotypic Slices of Suprachiasmatic Nuclei 617
Dissection Medium 618
Culture Medium 618
Real-Time Recording of Circadian Activity in Organotypic SCN Slice 619
Recording Medium 621
Fluorescent Imaging of Circadian Gene Expression in the SCN Organotypical Slice 622
Biolistic Transfection of SCN Organotypical Slices 623
Imaging Circadian Gene Expression Using Biolistically Transfected Reporter Genes 627
Acknowledgments 30 628
References 30 628
[31] Oligodeoxynucleotide Methods for Analyzing the Circadian Clock in the Suprachiasmatic Nucleus 630
Abstract 31 630
Introduction 31 630
Analysis of SCN Rhythmicity In Vivo and In Vitro 631
Targeted Deletion of Clock Genes 633
Antisense Oligodeoxynucleotides and Small Interfering RNA as Tools to Investigate Gene Function in Circadian Timekeeping 635
Decoy Oligodeoxynucleotides as Tools to Investigate Transcriptional Control in Circadian Timekeeping 638
Conclusions 31 641
Acknowledgments 31 641
References 31 642
[32] Assaying the Drosophila Negative Feedback Loop with RNA Interference in S2 Cells 647
Abstract 32 647
Introduction 32 647
Methodology 32 650
Transient Transfection 652
Generating Stable Cell Lines 655
References 32 658
[33] Role of Neuronal Membrane Events in Circadian Rhythm Generation 660
Abstract 33 660
Introduction 33 660
Input Pathways and Entrainment 661
Role of Transmembrane Ionic Fluxes in Rhythm Generation 666
Output and Rhythm Expression 670
Concluding Remarks 33 673
References 33 673
Section VIII: Intercellular Signaling 680
[34] A Screen for Secreted Factors of the Suprachiasmatic Nucleus 682
Abstract 34 682
Introduction 34 682
General Strategy 683
Signal Sequence Trap 684
Behavioral Screen for a Possible Role of SCN Factors in Regulating Locomotor Activity 693
Acknowledgments 34 698
References 34 699
[35] Genetic and Biochemical Strategies for Circadian Control 700
Abstract 35 700
Introduction 35 700
Genetic Approaches to Studying Clock Control Elements 701
Biochemical Strategies for Identifying mRNA Targets of Clock-Regulated RNA-Binding Proteins 711
Appendix 35 715
Acknowledgments 35 716
References 35 716
[36] Membranes, Ions, and Clocks: Testing the Njus-Sulzman-Hastings Model of the Circadian Oscillator 719
Abstract 36 719
Membrane Model for the Circadian Clock 720
Testing the Membrane Model in the Molluscan Eye 720
Testing the Membrane Model in the Mammalian Suprachiasmatic Nucleus 721
Testing the Membrane Model in Drosphila melanogaster 724
Detailed Procedure for Electrical Silencing of Drosophila Pacemaker Neurons with a dORK(delta) Potassium Channel 726
Conclusions 36 727
Acknowledgments 36 727
References 36 728
Section IX: Photoresponsive Clocks 731
[37] Mammalian Photoentrainment: Results, Methods, and Approaches 733
Abstract 37 733
Introduction 37 733
Investigating Photopigments 740
Methods for Action Spectroscopy 742
Phase Shifting in the rd/ rd cl Mouse 752
Conclusions 37 757
References 37 758
[38] Cryptochromes and Circadian Photoreception in Animals 762
Abstract 38 762
Introduction 38 762
Mammalian Cryptochromes 765
Zebrafish Cryptochromes 774
Cryptochrome 778
Conclusions 38 778
Acknowledgments 38 779
References 38 779
[39] Nonvisual Ocular Photoreception in the Mammal 782
Abstract 39 782
Historical Introduction 782
The Melanopsin Hypothesis 783
The Cryptochrome Hypothesis 785
References 39 789
Section X: Sleeping Flies 792
[40] Essentials of Sleep Recordings in Moving Beyond Sleep Time 794
Abstract 40 794
Introduction 40 794
Procedure 795
Constraints 796
Basic Characteristics of Sleep 799
Sleep Deprivation 803
Sexual Dimorphism 805
Conclusions 40 805
Acknowledgment 40 806
References 40 806
[41] Drosophila melanogaster: An Insect Model for Fundamental Studies of Sleep 807
Abstract 41 807
Introduction 41 807
Baseline Sleep: Locomotor Assay and Videography 809
Sleep Deprivation and Rebound 811
Arousal Threshold 813
Sleep Intensity 814
Pharmacological Studies 815
Electrophysiology Studies 816
Sleep-Relevant Genes 817
Shortcomings and Future Prospects 822
Acknowledgments 41 824
References 41 824
Section XI: Circadian Biology of Populations 829
[42] Molecular Evolution and Population Genetics of Circadian Clock Genes 831
Abstract 42 831
Introduction 42 831
Phylogenetic Analysis 832
Neutrality Tests 837
Polymorphism in Human Clock Genes 842
Quantitative Trait Loci Analysis 842
Statistical Resampling Methods in Molecular Evolution 843
Interspecific Transformations 844
Protein Alignments and Predictions 845
Conclusions 42 846
Computer Program for Phylogeny and Molecular Evolution 846
Acknowledgments 42 847
References 42 847
[43] Testing the Adaptive Value of Circadian Systems 852
Abstract 43 852
Background 43 852
Adaptive Significance of Clocks 855
Tests of Adaptive Significance 858
Natural Selection and the Evolution of Clocks: ‘‘Escape from Light?’’ 865
For Future Studies 867
Acknowledgments 43 869
References 43 869
Section XII: Circadian Clocks Affecting Noncircadian Biology 872
[44] A ‘‘Bottom-Counting’’ Video System for Measuring Cocaine-Induced Behaviors in 874
Abstract 44 874
Introduction 44 874
Behavioral Scoring 875
Bottom-Counting Assay 876
Automated Carousel and Image Capture 880
Proof of Principle 881
References 44 884
[45] The Circadian Clock and Tumor Suppression by Mammalian Period Genes 885
Abstract 45 885
Introduction 45 885
Genetic Studies Demonstrated that mPER1 and mPER2 are Circadian Regulators 886
Noncircadian Phenotypes of mPer1 and mPer2 Mutant Mice 888
Tumor Suppression Function of mPER2 889
Circadian Clock Regulates Cell Cycle Genes 890
New Links Between Growth Regulators and Circadian Clock 892
Acknowledgments 45 893
References 45 893
back matter 895
Author Index 895
Index 936