ClockTutorial #2: Basic Concepts and Terms

From the Archives
This is the second in the series of posts designed to provide the basics of the field of Chronobiology. See the first part: ClockTutorial #1 – What Is Chronobiology and check out the rest of them here – they will all, over time, get moved to this blog.

Here is a brief overview of the concepts and terms used in the field of chronobiology. I will write much more detailed accounts of various aspects of it in the future.
Seasons of the year, phases of the moon, high and low tides, and alternation between night and day are examples of cyclic changes in the environment. Each presents a different set of challenges to the animals. For instance, day and night are two different environments that force animals to evolve two different sets of physiological and behavioral adaptations. Homeostasis implies a relatively stable defense of a set-point value of a physiological parameter. Different times (of day, year etc.) demand different levels of physiological activity. Rheostasis addresses the controlled change of a set-point. Almost every biochemical, physiological and behavioral function shows a daily cycle. Geophysical cycles are highly predictable (in contrast with meteor hits), so organisms evolved timing mechanisms – biological clocks (and calendars) – that correspond to the durations of periodic events in nature. Thus, physiological and behavioral states are synchronized to the outside world. Types of cycles can be circadian (about a day), long-period/low-frequency cycles are infradian (e.g., circalunar, circannual), and short-period/high-frequency cycles are ultradian (e.g., circatidal, circahoral = about an hour).
It is advantageous for animals to predict, and not merely react to changes in the environment. Along with synchronization to the outside world (external synchronization), biological clocks also synchronize events within the body (internal synchronization), e.g,. ensure that time of hormone release coincides with the time when the hormone receptor is available at the cell membrane of the target tissue, etc. Another function of the biological clock is to put a time-stamp on memories, i.e., it functions as cognitive organ of time-perception. If an event happens to an animal that impacts its potential fitness, the animal will remember not only what happened and where, but also when (time of day). Continuously Consulted Clocks are used for sun-compass orientation and navigation, e.g., in migratory birds and in honeybees (time-sense). As the Sun moves across the horizon over the course of a day, animals that orient using the Sun as a reference point use the internal clock to compensate for the Sun’s movement.
Entrainment is synchronization of the internal time to the external time. The cues from the environment are called Zeitgebers (zeit = time, geber = giver, German). Light-dark cycles are the most potent cues in almost all organisms. A variety of other cues, e.g., temperature cycles and social cues can entrain biological rhythms in animals in which it is an ecologically relevant cue.
Freerunning rhythms are expressed in constant conditions in complete isolation from all time cues. Biological rhythms are endogenous, i.e., generated by the organism itself and inherent (have a genetic basis). The period of the freerunning rhythm is independent of temperature, i.e., it exhibits a phenomenon called temperature compensation.
Almost every cell has a clock. Pacemakers are specialized tissues responsive to environmental cues. They send neural or chemical signals to other (peripheral) clocks in the body. Pacemaker cells (unlike the cells of peripheral oscillators) can cycle indefinitely in isolation, i.e., in a dish.
Circadian organization refers to the fact that one or more pacemakers drive the rhythms in all other cells, i.e, the circadian system is a complex system composed on one of more pacemakers as well as myriads of peripherals oscillators in all other cells of the body. Pacemakers communicate with each other, entrain the peripheral clocks, and recieve feedback from the periphery.
Pacemakers in invertebrates reside in the eyes, optic lobes, or in the brain. Pacemakers in vertebrates are suprachiasmatic nuclei (SCN) located in the hypothalamus on the base of the brain, the pineal organ, and the retina of the eye. In mammals the SCN is the only pacemaker. Retina is the only source of light information, it also contains a (peripheral) clock, and makes hormone melatonin which usually does not leak into the circulation but regulates physiological events within the eye. In mammals, the pineal is not a pacemaker, yet it secretes melatonin rhythmically under the daily stimulation from the SCN. The intestine is another organ in the body capable of producing melatonin. It almost never leaks into circulation but regulates events withing the intestinal tract.
Circadian photoreception in mammals is not through rods and cones (though they appear to play a modifying role), but via about 1000 retinal ganglion cells that contain photopigments melanopsin and cryptochrome. These cells project their axons to the circadian pacamekers in the SCN, to the brain centers controlling pupillary reflex (narrowing of pupils in bright light), and brain centers controlling mood (thus you are depressed if you live in a dark place, e.g., prison).
In non-mammalian vertebrates (hagfish, lampreys, fish, amphibians, reptiles and birds) the suprachiasmatic area is often not sufficient, i.e., it is just one of several pacemakers working together to produce rhythms at the level of the organism. Pineal organ is the pacemaker in many non-mammalian animals and retina is the pacemaker in some animals. Photoreception occurs via eyes (ganglion cells, as in mammals, see above), directly photosensitive pineal, and extraretinal photoreceptors found deep inside the brain.
Photoperiodism is measurement of daylength as a seasonal cue (e.g, for migration, reproduction, fattening, molting and hibernation). In mammals the circadian clock measures duration of nightly melatonin release. In other animals it is known that the clock is involved but is not well understood how.
Circannual rhythms are endogenous annual cycles. Photoperiodism is sometimes thought to be a mechanism for entrainment of circannual rhythms to the external annual cycle. The role of circadian system in generation of circannual rhythms is iffy at best. Very little is known about the mechanism of generation of circalunar and circatidal rhythms, while chronobiologists, as a rule, shy away from trying to explain such long cycles as multiannual rhythms of eclosion in periodic cicadas or flowering of bamboo.
Jet-lag is a consequence of long-distance flights over multiple time zones, while shift-lag is a consequence of rotating work shifts. Both lead to internal desynchronization of various pacemakers and peripheral clocks, e.g., SCN shifts fast to the new time zone or work schedule, while clocks in liver and GI tract shift very slowly. As a result, there is greater incidence of ulcers, heart attacks and cancer in long-term shift-workers. Circadian system is also involved in some psychiatric disorders, e.g., bipolar disease, and seasonal affective disorder (SAD).

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