Clock Tutorials
clock | July 17, 2007This 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 | July 16, 2007This 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 | July 12, 2007 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 | July 11, 2007
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 | July 10, 2007
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 | July 9, 2007Considering 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 | July 9, 2007 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 | February 12, 2007 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 | January 27, 2007Considering 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 | October 4, 2006From November 01, 2005, a review of a review...
Here is a nice article in Washington Post - Ecological Niche May Dictate Sleep Habits - about the adaptive function of sleep.
It addresses some of the themes I am interested in.
First, the unfortunate fact is that sleep was initially defined by researchers of humans, i.e., medical researchers. Inevitably, the (electrophysiological) definition of sleep was thus saddled with unneccessary anthropocentric elements that for decades hampered the study of evolution of sleep.
I was present at the meeting (here in Biotechnology Center in RTP) several…
clock | August 17, 2006This 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 | 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, 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 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…