chronobiology
clock | September 10, 2006Do pilots get enough rest?:
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The federal rules on pilot duty hours and rest periods aren't the most comprehensible of reads.
One rule allows airlines to schedule pilots to fly for eight hours or less during a 24-hour period without a "rest period during those eight hours." Another gives pilots who fly for more than eight hours in a 24-hour stretch a break of at least twice the number of hours flown, either "at or before the end of" the eight hours. Pilots who fly more than eight hours during a 24-hour period must receive 18 hours of rest…
clock | September 8, 2006Fifth in the five-part series on clocks in bacteria, covering more politics than biology (from May 17, 2006):
In the previous posts in this series, I covered the circadian clocks in Synechococcus, potential circadian clocks in a couple of other bacteria, and the presence of clock genes (thus potentially clocks) in a number of other bacteria. But what happened to the microbiological workhorse, the Escherichia coli? Does it have a clock? Hasn't anyone checked?
Believe it or not, this question is colored by politics. But I have to give you a little background first. Latter half of the 19th…
clock | September 8, 2006
Fourth in the five-part series on clocks in bacteria (from April 30, 2006):
For decades, it was thought that prokaryotes did not have circadian clocks. Then, a clock was discovered in a unicellular cyanobacterium, Synechococcus (later also in Synechocystis [1] and Trichodesmium [2]) which quickly became an important model in the study of circadian rhythms in general. Still, it was thought, for ten years or so, that no other prokaryotes had a circadian clock. Recently, the clock genes were found in filamentous (chain-forming) cyanobacteria, as well as a whole host of other bacteria and…
clock | September 7, 2006
The third installment in the five-part series on clocks in bacteria (from April 19, 2006):
As you probably know, my specialty are birds, so writing this series on clocks in microorganisms was quite an eye-opener for me and I have learned a lot. The previous two posts cover the clocks in the cyanobacterium Synechococcus elongatus, the first bacterium in which circadian rhythms were discovered and, thus, the species most studied to date.
The work in Synechococcus has uncovered a cluster of three genes - kaiA, kaiB and kaiC - that are essential for circadian rhytmicity in this species. kaiA…
clock | September 6, 2006
Second post in a series of five (from April 05, 2006):
In the previous two posts, here and here, I have mentioned how the discovery of circadian clocks in Cyanobacteria changed the way we think about the origin and evolution of circadian clocks. Quite soon after the initial discovery, the team from Carl Johnson's laboratory published two papers [1,2] describing a more direct test of adaptive function of circadian clocks in the Synechococcus elongatus.
Wild-type and various clock-mutants in Synechoccocus, when raised in isolation in light-dark cycles, have comparable reproductive rates.…
clock | September 5, 2006
Hypotheses 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 | September 5, 2006
First in a series of five posts on clocks in bacteria (from March 08, 2006)...
As I stated in the introductory post on this topic, it was thought for a long time that prokaryotes were incapable of generating circadian rhythms. When it was discovered, in 1994 [1], that one group of prokaryotes, the cyanobacteria, possess a circadian clock, the news was greeted with great excitement. This was the first definitive demonstration of a circadian clock in a bacterium (I intend to revisit the E.coli saga in a later post).
All three hypotheses for the origin of the circadian clock suppose that it…
clock | September 4, 2006The first in a series of posts on circadian clocks in microorganisms (from February 23, 2006)...
Many papers in chronobiology state that circadian clocks are ubiqutous. That has been a mantra since at least 1960. This suggests that most or all organisms on Earth possess biological clocks.
In the pioneering days of chronobiology, it was a common practice to go out in the woods and collect as many species as possible and document the existence of circadian rhythms. Technical limitations certainly influenced what kinds of organisms were usually tested.
Rhythms of locomotor activity are the…
clock | September 1, 2006I rarely write about biological rhythms outside of circadian range (e.g., circannual, circalunar, circatidal rhythms etc.), but if you liked this post on lunar rhythms in antlions, you will probably also like this little review of lunar rhythms in today's Nature:
Pull of the Moon:
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Studies of fiddler crabs, for example, have shown that even when kept in the lab under constant light and temperature, the animals are still most active at the times that the tide would be out. A similar internal 'circalunar' clock is thought to tick inside many animals, running in synchrony…
clock | August 31, 2006Melatonin improves mood in winter depression:
Alfred Lewy and his colleagues in the OHSU Sleep and Mood Disorders Lab set out to test the hypothesis that circadian physiological rhythms become misaligned with the sleep/wake cycle during the short days of winter, causing some people to become depressed.
Usually these rhythms track to the later dawn in winter, resulting in a circadian phase delay with respect to sleep similar to what happens flying westward. Some people appear to be tracking to the earlier dusk of winter, causing a similar amount of misalignment but in the phase-advance…
clock | August 30, 2006Chad 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 | August 28, 2006
You 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 | August 26, 2006Bumble Bees Can Estimate Time Intervals:
In a finding that broadens our understanding of time perception in the animal kingdom, researchers have discovered that an insect pollinator, the bumble bee, can estimate the duration of time intervals. Although many insects show daily and annual rhythms of behavior, the more sophisticated ability to estimate the duration of shorter time intervals had previously been known only in humans and other vertebrates.
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Bees and other insects make a variety of decisions that appear to require the ability to estimate elapsed…
clock | August 21, 2006Three interesting press releases/news-reports today. Click on links to read the whole articles:
Daytime light exposure dynamically enhances brain responses:
Exposure to light is known to enhance both alertness and performance in humans, but little is understood regarding the neurological basis for these effects, especially those associated with daytime light exposure. Now, by exposing subjects to light and imaging their brains while they subsequently perform a cognitive test, researchers have begun to identify brain regions involved in the effects on brain function of daytime light exposure…
clock | August 21, 2006This list, written on December 17, 2005, is still quite up-to-date. There are also some more specialized books which are expensive, and many of those I'd like to have one day, but I cannot afford them (though I have placed a couple of them on my wish list, just in case I see a cheap copy come up for sale):
I know the holidays are coming in just a couple of days, but perhaps you still have time to order a book or two for your friends and family.
There are tons of books about sleep out there, mostly of suspect quality. Books about clocks tend to be either very old (thus out-dated) or far too…
clock | August 18, 2006One of the several hypotheses floating around over the past several years to explain the phenomenon of repeated wake-up events in hibernating animals although such events are very energy-draining, is the notion that the immune system needs to be rewarmed in order to fend off any potential bacterial invasions that may have occured while the animal was hibernating:
Now, a group of researchers provided a mathematical model that supports this hypothesis:
"A habit in some animals to periodically wake up while hibernating may be an evolutionary mechanism to fight bacterial infection, according to…
clock | August 18, 2006Chossat's Effect in humans and other animalsThis 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…
clock | August 17, 2006Many Commercial Drivers Have Impaired Performance Due To Lack Of Sleep
Truck drivers who routinely get too little sleep or suffer from sleep apnea show signs of fatigue and impaired performance that can make them a hazard on the road, according to a major new study by researchers at the University of Pennsylvania School of Medicine. The study results are published in the August 15th issue of the American Journal of Respiratory and Critical Care Medicine.
clock | August 17, 2006
This is a summary of my 1999 paper, following in the footsteps of the work I described here two days ago. The work described in that earlier post was done surprisingly quickly - in about a year - so I decided to do some more for my Masters Thesis.
The obvious next thing to do was to expose the quail to T-cycles, i.e., non-24h cycles. This is some arcane circadiana, so please refer to the series of posts on entrainment from yesterday and the two posts on seasonality and photoperiodism posted this morning so you can follow the discussion below:
There were three big reasons for me to attempt…
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,…