Clock Tutorials
clock | April 15, 2008This post from February 03, 2005 covers the basic concepts and terms on entrainment. This is also the only blog post to date that I am aware of that was cited in a scientific paper.
Let's now continue our series of Clock Tutorials with an introduction to some phenomena (and related terms and concepts) observed in the laboratory in the course of doing standard circadian experiments. Such experiments usually involve either the study of properties of freerunning rhythms (check the old tutorials, especially CT2 and CT 4 for clarification of basic terms and concepts), or the analysis of…
clock | April 14, 2008
I wrote this post back on February 02, 2005 in order to drive home the point that the circadian clock is not a single organ, but an organ system comprised of all cells in the body linked in a hierarchical manner:
In the earliest days of chronobiology, the notion of circadian organization was quite simple. Somewhere inside the organism there was a clock. It was entrained by light via photoreceptors (e.g., the eye) and it drove the rhythms of various biochemical, physiological and behavioral events in the body:
Very soon this simple notion became difficult to sustain in light of new data.…
clock | April 13, 2008 I wrote this post back on January 23, 2005. It explains how clock biologists think and how they design their experiments:
So, are you ready to do chronobiological research? If so, here are some of the tips - the thought process that goes into starting one's research in chronobiology.
First, you need to pick a question. Are you interested in doing science out of sheer curiosity to discover stuff that nobody knew before (a very noble, but hard-to-fund pursuit)? Or would you prefer your work to be applicable to human medicine or health policy, veterinary medicine, conservation biology, or…
clock | April 12, 2008 This post is a modification from two papers written for two different classes in History of Science, back in 1995 and 1998. It is a part of a four-post series on Darwin and clocks. I first posted it here on December 02, 2004 and then again here on January 06, 2005:
II. Darwin on Time
There is a season for everything
And a time for every purpose under the heaven:
A time to be born, and a time to die:
A time to plant and a time to reap.... (Ecclesiastes)
In this section I will attempt to evaluate from Darwin's writings what he thought about the selective role of environmental periodicities…
clock | April 11, 2008This post about the origin, evolution and adaptive fucntion of biological clocks originated as a paper for a class, in 1999 I believe. I reprinted it here in December 2004, as a third part of a four-part post. Later, I reposted it here.
III. Whence Clocks?
Origin, Evolution, and Adaptive Function of Biological Clocks
The old saw about the early bird just goes to show that the worm should have stayed in bed. (Heinlein 1973)
Now darkness falls.
Quail chirps.
What use Hawk eyes?
(Basho)
Local/temporary and global/universal environments. In the study of adaptive functions, usually the question…
clock | April 10, 2008This post, originally published on January 16, 2005, was modified from one of my written prelims questions from early 2000.
EVOLUTIONARY PHYSIOLOGY OF BIOLOGICAL CLOCKS
"Circadian clocks allow organisms to predict, instead of merely react to, cyclic (predictable) changes in the environment". A sentence similar to this one is the opening phrase of many a paper in the field of chronobiology. Besides becoming a truth by virtue of frequent repetition, such a statement appeals to common sense. It is difficult to imagine a universe in which it was not true. Yet, the data supporting the above…
clock | April 9, 2008
This is the third in the series of posts designed to provide the basics of the field of Chronobiology. This post is interesting due to its analysis of history and sociology of the discipline, as well as a look at the changing nature of science. You can check out the rest of Clock Tutorials here.
It appears that every scientific discipline has its own defining moment, an event that is touted later as the moment of "birth" of the field. This can be a publication of a paper (think of Watson and Crick) or a book ("Origin of Species" anyone?). In the case of Chronobiology, it was the 1960…
clock | April 8, 2008
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…
clock | April 7, 2008 This is the first in a series of posts from Circadiana designed as ClockTutorials, covering the basics of the field of Chronobiology. It was first written on January 12, 2005:
There are traditionally three approaches to research and teaching of physiology: biochemical, energetic, and homeostatic. The three are by no means exclusive and all good physiologists will include all three in their work and teaching, but each with a different emphasis.
Biochemical approach is typical of human/medical physiology. Physiological mechanisms are described at lower and lower levels, until the molecules…
clock | August 12, 2007NBM found an excellent online article (which I have seen before but I forgot) depicting Phase-Response Curves (PRC) to injections of melatonin in humans, rodents and lizards.
Note how the shape is roughly opposite to that of a PRC to light pulses, i.e., at phases at which light elicits phase-delays, melatonin produces advances and vice versa:
The lizard PRC was actually constructed in our lab, about ten years before I joined. The article, though, gives the wrong reference to this:
Underwood, H. and M. Harless (1985). "Entrainment of the circadian activity rhythm of a lizard to melatonin…
clock | July 31, 2007Going into more and more detail, here is a February 11, 2005 post about the current knowledge about the circadian organization in my favourite animal - the Japanese quail.
Japanese quail (Coturnix coturnix japonica), also known as the Asian Migratory Quail, are gallinaceous birds from the family Phasianidae, until 1960s thought to be a subspecies of European migratory quail (Coturnix coturnix coturnix), but now considered to be a separate species, designated as Coturnix japonica. The breeding range of the wild population encompasses Siberia, Mongolia, northeastern China and Japan, while the…
clock | July 30, 2007 This post was originally written on February 11, 2005. Moving from relatively simple mammalian model to more complex systems.
I have previously described the basic properties of the circadian organization in mammals. Non-mammalian vertebrates (fish, amphibians, reptiles and birds) have more complex circadian systems than mammals. While the suprachiasmatic area remains a site of circadian pacemakers, it is, unlike in mammals, not the only such site.
The pineal organ, which in mammals is a purely secretory organ, is directly photosensitive in other vertebrates (with the exception of snakes)…
clock | July 27, 2007 This February 06, 2005 post describes the basic elements of the circadian system in mammals.
The principal mammalian circadian pacemaker is located in the suprachiasmatic nuclei (SCN) of the hypothalamus. The general area was first discovered in 1948 by Curt Richter who systematically lesioned a number of endocrine glands and brain areas in rats. The only time he saw an effect on circadian rhythms was when he lesioned a frontal part of hypothalamus (which is at the base of the brain) immediatelly above the optic chiasm (the spot where two optic nerves cross). Later studies in the 1970s…
clock | July 26, 2007
I wrote this post back on February 02, 2005 in order to drive home the point that the circadian clock is not a single organ, but an organ system comprised of all cells in the body linked in a hierarchical manner:
In the earliest days of chronobiology, the notion of circadian organization was quite simple. Somewhere inside the organism there was a clock. It was entrained by light via photoreceptors (e.g., the eye) and it drove the rhythms of various biochemical, physiological and behavioral events in the body:
Very soon this simple notion became difficult to sustain in light of new data.…
clock | July 25, 2007This post (written on August 13, 2005) describes the basic theory behind photoperiodism and some experimental protocols developed to test the theory.
Timely prediction of seasonal periods of weather conditions, food availability or predator activity is crucial for survival of many species. Although not the only parameter, the changing length of the photoperiod ('daylength') is the most predictive environmental cue for the seasonal timing of physiology and behavior, most notably for timing of migration, hibernation and reproduction. While rising spring temperatures may vary from year to year,…
clock | July 24, 2007This post (click on the icon) was originally written on May 07, 2005, introducing the topic of neuroendocrine control of seasonal changes in physiology and behavior.
So far, I have directed all my attention to daily - circadian - rhythms, and pretty much ignored other rhythms that correspond to other cycles in nature. Another obvious cycle in nature is the procession of seasons during a year.
Just as an environment during the day is different from the same environment during the night and thus requires different adaptations for survival, so the winter environment and the summer environment…
clock | July 23, 2007This is the sixth post in a series about mechanism of entrainment, running all day today on this blog. In order to understand the content of this post, you need to read the previous five installments. The original of this post was first written on April 12, 2005.
A Phase Response Curve (PRC) can be made in three ways:
One can construct a PRC for a single individual. If you have a reasonably long-lived organism, you can apply a number of light pulses over a period of time. The advantage is that you will always know the freerunning period of your organism, and you will know with absolute…
clock | July 20, 2007This is the fifth post in a series about mechanism of entrainment. Originally written on April 11, 2005.
If you look at the Phase Response Curve you made you see that, as you follow the curve through the 24-hour cycle, you first encounter a dead zone during the subjective day (VT0 - CT 12) during which light pulses exert no or little effect on the phase of the clock. The line, then, turns down (negative slope) into the delay portion of the curve until it reaches a maximal delay in the early night. It reverses its direction then and goes up (positive slope) until it reaches maximal phase-…
clock | July 19, 2007The fourth post in the series on entrainment, originally written on April 10, 2005, explains the step-by-step method of constructing a PRC.
After months of applying light pulses to your animals you are ready to analyze and plot your data. You will print out the actographs (see how in the post "On Methodology" in the "Clock Tutorials" category) and you will see many instances of phase-shifts, somewhat like the very last figure in this post.
For each light pulse you applied to each animal, you measure the direction of the phase-shift (i.e., if it was a delay or an advance) and the size of the…
clock | July 18, 2007The third post in the series on entrainment, first written on April 10, 2005, starts slowly to get into the meat of things...As always, clicking on the spider-clock icon will take you to the site of the original post.
In the previous post, I introduced the concept of entrainment of circadian rhythms to environmental cycles. As I stated there, I will focus on non-parametric effects of light (i.e., the timing of onsets and offsets of light) on the phase and period of the clock.
Entrainment is a mechanism that forces the internal period (&tau - tau) of the biological clock to assume the…