Clock Tutorials
clock | June 29, 2009Considering I've been writing textbook-like tutorials on chronobiology for quite a while now, trying always to write as simply and clearly as possible, and even wrote a Basic Concepts And Terms post, I am surprised that I never actually defined the term "biological clock" itself before, despite using it all the time.
Since the science bloggers started writing the 'basic concepts and terms' posts recently, I've been thinking about the best way to define 'biological clock' and it is not easy! Let me try, under the fold:
A biological clock is a structure that times regular re-occurence of…
clock | June 29, 2009 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 | May 3, 2008This April 09, 2006 post places another paper of ours (Reference #17) within a broader context of physiology, behavior, ecology and evolution.
The paper was a result of a "communal" experiment in the lab, i.e., it was not included in anyone's Thesis. My advisor designed it and started the experiment with the first couple of birds. When I joined the lab, I did the experiment in an additional number of animals. When Chris joined the lab, he took over the project and did the rest of the lab work, including bringin in the idea for an additional experiment that was included, and some of the…
clock | May 2, 2008Hypotheses leading to more hypotheses (from March 19, 2006 - the Malaria Day):
I have written a little bit about malaria before, e.g, here and here, but this is my special Malaria Action Day post, inspired by a paper [1] that Tara sent me some weeks ago and I never got to write about it till now.
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In a journal called "Medical Hypotheses" Kumar and Sharma [1] propose that jet-lagged travellers may be more susceptible to getting infected with malaria. They write:
Rapid travel across several time zones leads to…
clock | May 1, 2008You probably realize by now that my expertise is in clocks and calendars of birds, but blogging audience forces me to occasionally look into human clocks from a medical perspective. Reprinted below the fold are three old Circadiana posts about the connection between circadian clocks and the bipolar disorder, the third one being the longest and most involved. Here are the links to the original posts if you want to check the comments (especially the first comment on the third post):
January 18, 2005: Clocks and Bipolar Disorder
August 16, 2005: Bipolar? Avoid night shift
February 19, 2006:…
clock | April 30, 2008Microarrays have been used in the study of circadian expression of mammalian genes since 2002 and the consensus was built from those studies that approximately 15% of all the genes expressed in a cell are expressed in a circadian manner. I always felt it was more, much more.
I am no molecular biologist, but I have run a few gels in my life. The biggest problem was to find a control gene - one that does not cycle - to make the comparisons to. Actin, which is often used in such studies as control, cycled in our samples. In the end, we settled on one of the subunits of the ribosome as we…
clock | April 29, 2008This is going to be a challenging post to write for several reasons. How do I explain that a paper that does not show too much new stuff is actually a seminal paper? How do I condense a 12-page Cell paper describing a gazillion experiments without spending too much time on details of each experiment (as much as I'd love to do exactly that)? How do I review it calmly and critically without gushing all over it and waxing poetically about its authors? How do I put it in proper theoretical and historical perspective without unnecessarily insulting someone? I'll give it a try and we'll see…
clock | April 28, 2008
Chad wrote a neat history of (or should we say 'evolution of') clocks, as in "timekeeping instruments". He points out the biological clocks are "...sort of messy application, from the standpoint of physics..." and he is right - for us biologists, messier the better. We wallow in mess, cherish ambiguity and relish in complexity. Anyway, he is talking about real clocks - things made by people to keep time. And he starts with a simple definition of what a clock is:
In order to really discuss the physics of timekeeping, you need to strip the idea of a clock down to the absolute bare…
clock | April 27, 2008Considering I've been writing textbook-like tutorials on chronobiology for quite a while now, trying always to write as simply and clearly as possible, and even wrote a Basic Concepts And Terms post, I am surprised that I never actually defined the term "biological clock" itself before, despite using it all the time.
Since the science bloggers started writing the 'basic concepts and terms' posts recently, I've been thinking about the best way to define 'biological clock' and it is not easy! Let me try, under the fold:
A biological clock is a structure that times regular re-occurence of…
clock | April 26, 2008This is an appropriate time of year for this post (February 05, 2006)...
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So, why do I say that it is not surprising the exposure to bright light alleviates both seasonal depression and other kinds of depression, and that different mechanisms may be involved?
In mammals, apart from visual photoreception (that is, image formation), there is also non-visual photoreception. The receptors of the former are the rods and cones that you all learned about in middle school. The receptors for the latter are a couple of thousand Retinal Ganglion…
clock | April 25, 2008This 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 | April 24, 2008This 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 | April 23, 2008This 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 | April 22, 2008This 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 | April 21, 2008The 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 | April 20, 2008The 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…
clock | April 19, 2008This is the second in a series of posts on the analysis of entrainment, originally written on April 10, 2005.
The natural, endogenous period of circadian rhythms, as measured in constant conditions, is almost never exactly 24 hours. In the real world, however, the light-dark cycle provided by the Earth's rotation around its axis is exactly 24 hours long. Utility of biological clocks is in retaining a constant phase between environmental cycles and activities of the organism (so the organism always "does" stuff at the same, most appropriate time of day).
Thus, a mechanism must exist to…
clock | April 18, 2008Going 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 | April 17, 2008 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 | April 16, 2008 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…