chronobiology
clock | August 17, 2006This 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 | August 16, 2006Different strokes occur at different times
Different types of strokes occur most often at different times of day say scientists at Iwate Medical University in Iwate, Japan.
The team based their findings on data from 12,957 cases of first-ever stroke diagnosed by CT or MRI scans and drawn from the Iwate Stroke Registry between 1991 and 1996.The researchers chose patients who had experienced cerebral infarctions, or ischemic strokes, where cells die because blood flow to the brain is restricted, and two kinds of hemorrhagic strokes: intercerebral hemorrhages that occur within the brain, and…
clock | August 16, 2006This April 16, 2005 post gives you links to further online resources and literature on entrainment and Phase-Response Curves, as well as a link to a database of PRCs so you can play with them yourself.
One of the most useful chronobiological databases available online is the PRC Atlas. Compiled by Dr.Carl Johnson of Vanderbilt University, it contains hundreds of published and unpublished Phase-Response Curves. One can sort the Curves by species or by type of stimulus (e.g., light pulses, pulses of varius chemicals, dark pulses on constant-light background, etc.) and one is also able to…
clock | August 16, 2006This 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 firt 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 | August 16, 2006This is the fifth post in a series about mechanism of entrainment. Orignally 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 | August 16, 2006The 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 | August 16, 2006The 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 | August 16, 2006This 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 | August 16, 2006This post from February 03, 2005 covers the basic concepts and terms on entrainment.
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 entrainment of rhythms to environmental periodicities.
Entrainment is a process by which a biological…
clock | August 15, 2006
This post from March 27, 2006 starts with some of my old research and poses a new hypothesis.
The question of animal models
There are some very good reasons why much of biology is performed in just a handful of model organisms. Techniques get refined and the knowledge can grow incrementally until we can know quite a lot of nitty-gritty details about a lot of bioloigcal processes. One need not start from Square One with every new experiment with every new species. One should, of course, occasionally test how generalizable such findings are to other organisms, but the value of models is…
clock | August 15, 2006
One of the assumptions in the study of circadian organization is that, at the level of molecules and cells, all vertebrate (and perhaps all animal) clocks work in roughly the same way. The diversity of circadian properties is understood to be a higher-level property of interacting multicelular and multi-organ circadian systems: how the clocks receive environmental information, how the multiple pacemakers communicate and synchronize with each other, how they convey the temporal information to the peripheral clocks in all the other cells in the body, and how perpheral clocks generate…
clock | August 15, 2006
This post, from January 25, 2006, describes part of the Doctoral work of my lab-buddy Chris.
Mammals have only one circadian pacemaker - the suprachiasmatic nucleus (SCN). Apparently all the other cells in the body contain circadian clocks, too, but only the SCN drives all the overt rhythms. Without the SCN, there are no rhythms - the peripheral clocks either get out of phase with each other, or their clocks stop ticking altogether.
If you place various tissues in a dish, the SCN cycles indefinitely. All other tissues are capable of only a few oscillations in the absence of a daily signal…
clock | August 15, 2006
One of the important questions in the study of circadian organization is the way multiple clocks in the body communicate with each other in order to produce unified rhythmic output.
In the case of mammals, the two pacemakers are the left and the right suprachiasmatic nucleus (SCN). The tow nuclei are anatomically close to each other and have direct nerve connections between them, so it is not difficult to imagine how the two clocks manage to remain continuously coupled (syncronized) to each other and, together, produce a single output, thus synchronizing all the rhythms in the body.
In the…
clock | August 14, 2006Going 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 | August 14, 2006
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 | August 14, 2006
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 | August 14, 2006
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. For…
clock | August 14, 2006As I announced last week, this week will be All Clocks All The Time. Why?
First, I need to move some of the old posts from Circadiana over here, at a faster rate than I've been doing so far. Second, I'll be quite busy this week. Third, I need to hype myself up for the final effort at my Dissertation so blogging about any other topic would be counter-productive (not that it's not gonna happen...)
So, here is the deal. Over the next five days I will repost some old and write some new posts on three big topics in Chronobiology: circadian organization, entrainment and photoperiodism.…
clock | August 10, 2006This is an interesting idea:
A novel way to advance the circadian cycle has been proposed as a way to solve the problem associated with the early starting times of middle and high schools. It has been recognized for some time that teen age students do not really wake up until well past the time they physically arrive at school. Researchers at Brown University have found that the student's blood contains large amounts of the sleep hormone, melatonin. Researchers at the Lighting Innovations Institute of John Carroll University are seeking funding to carry out a study to find out if their method…
clock | August 10, 2006A nice new study on ecological aspects of circadian rhythms:
To a tiny tadpole, life boils down to two basic missions: eat, and avoid being eaten. But there's a trade-off. The more a tadpole eats, the faster it grows big enough to transform into a frog; yet finding food requires being active, which ups the odds of becoming someone else's dinner.
Scientists have known that prey adjust their activity levels in response to predation risk, but new research by a University of Michigan graduate student shows that internal factors, such as biorhythms, temper their responses.
Michael Fraker, a…