Chronobiology: Biological Timekeeping

Jay C. Dunlap, Jennifer J. Loros, and Patricia J. DeCoursey

2004
382 pages, 278 illustrations
paper

About This Title

The study of how solar- and lunar-related rhythms are governed by living pacemakers within organisms constitutes the scientific discipline of chronobiology. Parallel to the familiar spatial cellular structure of living cells, temporal, or time, organization is a vital part of the survival and normal functioning of every species. Adaptations evolved by organisms to cope with regular geophysical cycles in their environment are evident in nearly every aspect of their lives. In fact, biological timekeeping is a core property of life on a revolving planet.

Few fields encompass the breadth of science that is associated with chronobiology. Chronobiologists are at the cutting edge of fields ranging from microbial genetics to ethology to treatment of human psychiatric illnesses. Recognizing that no individual could do justice to the field in writing a comprehensive text, a group of editors with a wide range of experience has collaborated to produce Chronobiology. Chapters have been planned and written by the editors and by teams of specialists.

The text begins with a general introduction to the formalisms and vocabulary that describe circadian rhythmicity. The behavioral and ecological importance of rhythms is introduced, followed by discussion of the theoretical bases of the fundamental properties that define a circadian rhythm. Circannual rhythms and photoperiodic responses in plants and animals are examined next. A central block of four chapters develops the comparative anatomy, physiology, genetics, and molecular biology of organisms with circadian clocks. Examples at all levels of organization are drawn from the real world and from current and classic research. A pair of chapters then develops the basic circadian organization of human beings and the relevance of circadian biology to human welfare. A final chapter looks to the future by exploring six cutting-edge areas of research.

The book’s highly readable style reduces technical terminology to a minimum and does not require background in neuroscience or mathematics. Illustrations and photographs are used liberally to elucidate conceptually difficult points, and the text makes use of actual data sets to explain basic principles. A collection of color plates condenses the overarching themes of the book into four colorful collages.

About the Author(s)

Jay C. Dunlap is Chairman of the Department of Genetics at Dartmouth Medical School. An early interest in the physiology of marine organisms drew him to graduate work with J. W. Hastings at Harvard, where he first became fascinated with biological clocks and with the genetic dissection of complex biological phenomena. Dr. Dunlap has co-edited 16 books in genetics and published over 100 articles on the genetics and the molecular biology of circadian systems. A recipient of the Honma International Prize for Circadian Rhythms Research, he has served on the editorial board of the Journal of Biological Rhythms, and as president of the Society for Research on Biological Rhythms.

Jennifer J. Loros is Professor of Biochemistry and of Genetics at Dartmouth Medical School. A lifelong interest in horticulture led to graduate work on circadian biological clocks at the University of California, Santa Cruz and postdoctoral research at Dartmouth. She serves as Associate Editor for the journal Genetics and on the Advisory Board for the Journal of Biological Rhythms, and received the Aschoff's Rule Award for her contributions to understanding circadianly regulated gene expression. Dr. Loros's lab explores the genetic and molecular underpinning of circadian timing systems, the means through which fungal and mammalian clocks control gene expression and organismal behavior, and molecular mechanisms of the clock's response to environmental stimuli.

Patricia J. DeCoursey is Distinguished Professor of Biology in the Department of Biological Sciences at the University of South Carolina. Her early interests in ornithology led her to Cornell University for undergraduate studies in zoology. She completed a Ph.D. in zoology and biochemistry at the University of Wisconsin, Madison, and then carried out postdoctoral research with Jürgen Aschoff at the Max-Planck Institute for Behavioral Physiology in Erling-Andech, Germany. Dr. DeCoursey was member in 1985 of the original Organizing Committees for both the Journal of Biological Rhythms and the Society for Research on Biological Rhythms. She served two terms as SRBR’s Secretary, and has been active on the Advisory Boards of both groups. Her career-long interests in chronobiology have centered on behavioral, physiological, and ecological aspects of circadian rhythms, primarily in mammals.

Reviews and Commentary

“[This] book is a tour de force. … Dunlap, Loros, and DeCoursey lucidly describe the history of the field while deftly explaining the complex processes of rhythm generation and synchronization to environmental light cues, and their physiological significance. They cover the wide array of organisms that express circadian rhythmicity, from cyanobacteria to humans. The text draws on the expertise of some 50 of the brightest minds in the field, so there is no chapter that stands out as being shallow or bereft of detail. Chronobiology is appropriate for upper-division university students or introductory graduate courses.”
—Vincent M. Cassone, BioScience

“This superbly edited, richly illustrated book would be properly employed as a textbook for courses focused on chronobiology. . . . In summary, this fascinating synthesis of the field should find a wide audience and become a useful resource on biological timing for many years to come.”
—Jadwiga Giebultowicz, Integrative and Comparative Biology

“Too long neglected as an important part of all biological systems, chronobiology now has a textbook that should appeal to students and instructors at all levels and that researchers in diverse fields should have as an important reference tool. It is well written, includes much up-to-date information, and offers valuable insights into how biological timekeeping affects life from the genetic to organismal level. Highly recommended for graduate and advanced undergraduate students, as well as a vital acquisition for academic libraries.”
—Life Science Book Review

“The science of chronobiology weaves a fascinating and fundamentally important thread through the tapestry of molecular biology, biochemistry, cell biology, neuroscience, evolution, animal behavior, plant biology, the biology of unicellular organisms, medicine, and agriculture. Yet, despite intense interest in biological rhythms and the clocks that control them (see almost any recent issue of Science or Nature), this book is the first and only comprehensive review of chronobiology in over two decades, and simply the best treatment of the discipline ever produced. This much-needed text is both an outstanding primer for students and an excellent resource for scientists and medical practitioners. At last—here is the book needed time and time again!”
—Michael S. Grace, Florida Institute of Technology

“On a first quick pass through the book I noticed that each chapter was a construct of many contributors—about 70 in all, mostly leading chronobiology researchers. . . . The presentation reads smoothly . . . and is well-organized. . . . All of the topics that must be covered in a text on chronobiology are present. And the production of the book is superb. . . . In a nutshell, I take my hat off to the many contributors and the publisher for their efforts. The stated goal of the preface has been accomplished—the field now has its much-needed textbook.”
—John D. Palmer, Nature

“This extremely important work fills a deep void in the scientific literature—it is the first to treat this rapidly expanding discipline in more than two decades of intense research. Lucid text, excellent figures, and up-to-date references make this a must-read for anyone seriously interested in animal behavior, functional neuroscience, or fascinatingly complex outputs of molecular and cellular biological machinery.”
—M. S. Grace, Choice

“Chronobiology is an excellent book for undergraduate and graduate students and even scientists in other disciplines who want to discover how chronobiology might be affecting their fields of interest.”
—Biology Digest

1. Overview of Biological Timing from Unicells to Humans
All known organisms have the capacity to respond to internal and environmental information. One class of responses, called biological timekeeping, interfaces a living, internal, self-sustained clockworks with corrective factors of an organism's rhythmic habitat. This chapter reviews the long-standing human interest in time measurement and sets the stage for a systematic coverage of the basic principles of chronobiology, a multidisciplinary science that studies the neural and humoral basis of biological clocks from the molecular to the population levels.
Author: Patricia J. DeCoursey

2. The Behavioral Ecology and Evolution of Biological Timing Systems
Biological timing in organisms is undoubtedly shaped by natural selection. The resultant overt rhythms include daily circadian, lunar-related, or annual periodicities that are highly adaptive for survival of a species in its habitat niche. This chapter describes the various functions of these environmentally synchronized living pacemakers, which may act as alarm clocks, as continuous chronometers for time-compensated navigation, to gate life-history events, or to anticipate and coordinate the multiple physiological functions within an organism.
Author: Patricia J. DeCoursey
Contributors: Paul Heideman, Teresa Horton, Theresa Lee, Stéphan Reebs, and Laura Smale

3. Fundamental Properties of Circadian Rhythms
A careful examination of the major defining characteristics of circadian rhythms can afford insight into both the utility of a clock and into the molecular mechanism of the oscillator. Drawing examples from classic papers and the current literature, this chapter describes the three fundamental characteristics of circadian rhythms—persistence, temperature compensation, and entrainment. The theory of continuous and discrete entrainment is developed to help show how limit cycles are used to model circadian rhythms.
Authors: Carl Hirschie Johnson, Jeffrey Elliott, Russell Foster, Ken-Ichi Honma, and Richard Kronauer

4. Circannual Rhythms and Photoperiodism
The lives of most plants and animals are organized on a seasonal schedule, or circannual rhythm, that is endogenous in many organisms. This chapter chronicles the discovery and description of circannual rhythms and photoperiodic responses in plants and animals and how they are adaptive to organisms. The comparative physiological bases of photoperiodic responses in higher plants, insects, birds, and mammals are covered.
Authors: Bruce Goldman, Eberhard Gwinner, Fred J. Karsch, David Saunders, Irving Zucker, and Gregory F. Ball
Contributors: C. Robertson McClung and Herbert Underwood

5. Functional Organization of Circadian Systems in Multicellular Animals
To tell time accurately, biological clocks must be based on a self-sustained oscillator and they must remain in phase with local environmental time. A systematic phylogenetic survey establishes that different species use many different structural components for timekeeping. Every circadian system consists of a basic cellular oscillator, dedicated sensory receptors that convey environmental information to calibrate the clock to local time, and a neural/humoral output messenger system to communicate with behavioral effectors. Current research is illuminating the complexity of this system and the degree of feedback loops acting on it. The recent discovery of semi-autonomous and local peripheral circadian pacemakers has greatly expanded the view of circadian regulation.
Author: Patricia J. DeCoursey
Contributors: Gene Block, Gerta Fleissner, Günther Fleissner, Michael Menaker, Robert Y. Moore, Terry Page, Kathleen Siwicki, and Herbert Underwood

6. Cell Physiology of Circadian Timing Systems in Metazoan Animals
The study of the cellular basis of circadian physiology is one of the most challenging aspects of the entire field. Three species have proven highly favorable as model organisms for the in vitro study of cellular mechanisms. This chapter examines the circadian systems of the ocular pacemaker of the marine snail, Bulla; the pineal gland of the newly hatched domestic chicken; and the SCN pacemaker of several laboratory rodents. In all known cases, individual pacemaker cells are independent oscillators that are electrically coupled for a stable, unified output signal to regulate other damped oscillators and effector organs.
Author: Patricia J. DeCoursey
Contributors: Gene Block, David Earnest, Michael Lehman, Johanna H. Meijer, Terry Page, Rebecca Prosser, Till Roenneberg, William J. Schwartz, Rae Silver, Tony van den Pol, and Martin Zatz

7. Molecular Biology of Circadian Pacemaker Systems
Over the past two decades, biochemical, genetic, and molecular studies have to a surprising degree elucidated the molecular bases of rhythmicity in cyanobacteria, fungi, animals, and plants. This chapter first lays out the theoretical and historical antecedents for this work. A brief primer on genetics and molecular biology then sets the stage for an up-to-date discussion of the components and design principles underlying the coupled feedback loop oscillators that form the basis for circadian rhythmicity in important model systems and in humans.
Author: Jay C. Dunlap
Contributors: Susan Golden, Carl Hirschie Johnson, Takao Kondo, C. P. Kyriacou, C. Robertson McClung, Hitoshi Okamura, Amita Sehgal, Joseph S. Takahashi, Chuck Weitz, and Mike Young

8. Adapting to Life on a Rotating World at the Gene Expression Level
In all organisms the adaptive significance of circadian rhythmicity is due to the ability of clocks to control the behavior and metabolism of cells, and thereby of organisms. Building on the molecular foundation laid in previous chapters, this chapter returns to the biology of circadian systems by examining the molecular biology of circadian output, the means through which clocks make their presence felt within an organism. Examples from prominent model systems are used to explain mechanisms of circadian output control and of feedback from output back to input or to the oscillator.
Authors: Jennifer Loros, J. Woodland Hastings, and Ueli Schibler
Contributors: Carla Green, Susan Golden, F. Rob Jackson, David Morse, and William Schwartz

9. Human Circadian Organization
Chapter 9 explores human circadian biology. Realization of the commonality of function of circadian systems in organisms as diverse as protists and nonhuman mammalian vertebrates has provided much insight into human circadian function. The SCN of the hypothalamus is the primary pacemaker, and light input for entrainment is exclusively through the retina. The many rhythmic behavioral and physiological functions regulated in part or in whole by the SCN include body temperature, the activity rhythm and sleep–wake cycle, endocrine secretion, and melatonin levels. A developmental progression in circadian performance from birth to old age is evident.
Authors: James M. Waterhouse and Patricia J. DeCoursey
Contributors: Torbjorn Åkerstedt, Josephine Arendt, Charles Czeisler, Derk-Jan Dijk, David Dinges, and Kenneth P. Wright

10. The Relevance of Circadian Rhythms for Human Welfare
Humans are basically day-active mammals with an 8-hour consolidated sleep period. This chapter examines circadian stresses that are the product of the 24-hour society found in many industrialized countries. Research is needed both for clinical treatment of circadian dysfunctions and to minimize deleterious effects in healthy individuals engaged in biologically abnormal activities such as night work and shift work, jet flight across time zones, or life in extreme arctic locales. Encouraging progress has been made using circadian principles to diagnose and treat chronopathological conditions, particularly sleep and mood disorders.
Authors: James M. Waterhouse and Patricia J. DeCoursey
Contributors: Josephine Arendt, Scott Campbell, William J. M. Hrushesky, Björn Lemmer, Alfred Lewy, Michael Terman, Thomas A. Wehr, and Anna Wirz-Justice

11. Looking Forward
The text closes with six themes that illustrate possible directions of circadian research in the near future. Since sleep deficits magnify health conditions, especially among the elderly, the development of treatment based on circadian principles will be important. Phylogenetic and ecological studies will give a better understanding of the origins and functions of sleep in animals. Simple animal models will replace humans in many aspects of circadian molecular and behavioral research. Increased emphasis will be placed on the study of peripheral pacemakers in contrast to central, primary pacemakers, especially in mammals. Multidisciplinary molecular–behavioral techniques, such as those involving transgenic chimeras, will be used to study circadian mechanism. Circadian principles in relation to the photic and thermal pollution of Earth may help cope with the pressing issues of ecosystem integrity and loss of biodiversity.
Author: Patricia J. DeCoursey
Contributors: Joan Hendricks and Fred W. Turek

Glossary
Species lists
• English Common Name to Latin Name
• Latin Name to English Common Name
Acknowledgments
Index

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