Friday, June 09, 2006

This blog has (finally) gone to SEED

So, the day has finally arrived - the Big Move to SEED scienceblogs. Go check out the brand new front page and all the old and new bloggers there.

My new blog, a fusion of all three of my blogs, will be a new brand, with a new name - A Blog Around The Clock, reflecting my age and musical taste, my usual blogging frequency and the area of my scientific expertise, all in one title.

The Banner was designed by Carel Pieter Brest Van Kempen who also runs a delightful science/art blog Rigor Vitae.

The new URL is http://scienceblogs.com/clock/, the new Atom feed is http://scienceblogs.com/clock/atom.xml and the new RSS feed is http://scienceblogs.com/clock/index.xml.

Please change your bookmarks, blogrolls and newsfeeds to reflect this move.

As I said before, Circadiana and The Magic School Bus will be closed (but not deleted), while Science And Politics will slow down and will re-focus on local North Carolina topics, including local politics (which includes following the career of John Edwards), and perhaps an occasional post for my readers from the Balkans. If you are still interested in those topics, you are welcome to retain the bookmarks, blogrolls and newsfeeds for Science And Politics as well, but I will not be insulted if you do not, as my main blogging effort will be over there, on my new SB blog.

I encourage you to go and check all 24 newbies over on SEED - all wonderful bloggers you should read if you are interested in science. Let me introduce my new fraternity-mates to you:

Carl Zimmer, the NYTimes science/evolution reporter, is moving The Loom from here to here.

Matt Nisbett, an expert on political communication and writer of a monthly column for the Skeptical Inquirer Online is moving his blog Framing-Science from here to here.

My fellow North Carolinian, medblogger Abel PharmBoy, is moving Terra Sigillata from here to here.

James Hrynyshyn, another fellow North Carolinian, is moving Island Of Doubt from here to here.

My favourite cognitive psychology blogger Chris is moving Mixing Memory from here to here.

Philosopher of biology John Wilkins is moving Evolving Thoughts from here to here.

Mike The Mad Biologist is moving from here to here.

I thought that one of my favourite science bloggers George Wilkinson has quit blogging, but no, he is also moving Keat's Telescope from here to here.

Reveres, experts on Avian Flu, are moving Effect Measure from here to here.

Karmen is moving her beautiful Chaotic Utopia from here to here.

Sandra Porter is moving Discovering Biology In A Digital World from here to here.

Nick Anthis is moving The Scientific Activist from here to here.

Joseph is moving Corpus Callosum from here to here.

Jake Young, another one of several neuroscientists joining the team, is moving Pure Pedantry from here to here.

Shelley Batts, another neuroscientist, is moving Retrospectacle from here to here.

Evil Monkey is moving Neurotopia from here to here.

Mike Dunford is moving The Questionable Authority from here to here.

Mark Chu-Carroll is moving Good Math, Bad Math from here to here.

David Ng and Benjamin Cohen are moving from Science Creative Quarterly and Annals of Science to World's Fair.

The Cheerful Oncologist is moving from here to here.

Dr.Charles is moving the eponimous Examining Room from here to here.

Dr. X is moving Chemblog from here to here.

The rowdy bonobos from Dr. Joan Bushwell's Chimpanzee Refuge are moving from here to here.

Steinn, an astrophysicist, is moving Dynamics Of Cats from here to here.

Finally, Jonah Lerer is a SEED staffer, starting his own blog called The Frontal Cortex.

There were few surprises for me on this list. Two good blogfriends of mine (Revere and Mike the Mad Biologist) managed to keep me in the dark about their move until two days ago. On the other hand, two bloggers I thought were going to accept the invitation, are not on the list (yet?). Almost all of the others I knew about.

The SEED overlords intend to add more bloggers before the end of the year so keep an eye on SEED - that is where the SciBlogging action is going to be.

Thursday, June 08, 2006

Jet-lagged sports teams

Study says West coast teams have advantage:
Ingmundson, who is also a a diplomate with the American Board of Sleep Medicine, says western-based teams may have an advantage in sporting events in which cross-country road trips are invloved. He has found that a disruption in eastern teams` circadian rhythms – or internal clocks – may contribute directly to poor performances like Miami`s versus Dallas.

"The mechanism is relatively straightforward, at least superficially," explains Ingmundson. "Performance on many cognitive and motor tasks peaks in late afternoon. Teams travelling west to east to play night games are playing with their biological clocks set earlier, close to the most favorable time, and teams traveling from east to west are playing at relatively later point in their biological "day," conferring a relative handicap."
Read the rest...

Tuesday, June 06, 2006

Sleep News

Benefits of Power Napping

and

New research explores why we're sleepy after we eat

and

Serotonin, Acting In A Specific Brain Region, Promotes Sleep In Fruit Flies:
Researchers have found that the neurotransmitter serotonin, known to affect many behaviors, also appears to promote lasting, quality sleep in an animal model for understanding how sleep is regulated. While central to the lives of most animals, the proper regulation sleep remains a largely enigmatic process.
(The actual paper is here: A Sleep-Promoting Role for the Drosophila Serotonin Receptor 1A)

Friday, June 02, 2006

Take your iPod to bed

Interesting idea, via Sleep Disorders blog: a pre-recorded morning talk-show puts you to sleep because it is a distraction from Real Life worries that may otherwise keep you awake at night, yet no need to worry that you'll miss something interesting.

I need to try me some Diane Rehm show. With her slow, monotonous manner of talking, I bet she would put me to sleep in five seconds. It almost puts me to sleep while I'm driving!

Wednesday, May 31, 2006

Early Bird Gets The Worm....or Seed

(Image stolen from Xtinpore)

Well, I may not be the earliest bird, certainly not early enough to grab the worm, but I am early enough in the game to be able to get some seed, or more precisely SEED.

Yup, starting this Friday, this blog will fuse with my other two blogs (Science And Politics and The Magic School Bus) and move to the ever-growing Scienceblogs.com.

It does not work right now, but on Friday you will be able to access the new blog at this URL.

I'll give you the Feed once I get it, so you can all change your bookmarks, blogrolls and newsfeeds to the new address.

The complete archives of this blog will remain here as there are many incoming links, but I will slowly, over the next few months, republish some of the best Circadiana posts over there. I hope you all move there with me - the new blog will be even better (and prettier) than this one.

Update: Due to technical problems, the new blogs will nost start tomorrow (Friday) but later, hopefully Monday of next week. I'll keep you posted.

Wednesday, May 24, 2006

Eight Hours a Circadian Rhythm Do Not Make

There is a new study on PLoS - Biology that is getting some traction in the media and which caught my attention because it was supposed to be about circadian rhythms. So, I downloaded the paper and read it through to see what it is really about.

Well, it is a decent study, but, unfortunately, it has nothing to do with circadian rhythms. Many examples of tritrophic relationships involve parasitoids (usually small wasps) being attracted by plant volatiles which are released in response to herbivory by insect (usually moth) larvae. So, if a caterpillar munches on a plant, that plant releases chemicals which attract the wasps. When a wasp arrives, she injects her eggs into the caterpillar, often together with a cocktail of toxins or other chemicals that alter the development of the caterpillar, keeping it in the larval stage longer than normal, thus giving wasp eggs sufficient time to hatch and the little wasp larvae to eat their way out (and in the process devouring and killing the caterpillar).

It has also been known for a while now that wasps are strictly diurnal, i.e., they fly only during the day. It has also been known for a couple of years now that plants release the alarm chemicals mostly during the day. Production of this odors takes energy which would be wasted at night when the wasps are not active.

Activity of caterpillars is much harder to assess, and many people in the field swear that there is no diurnal rhythm of their activity, i.e., they are as likely to feed on leaves at night as during the day, though some mild rhtyhms were found in some species.

What this paper addresses is the problem with the previous studies of the caterpillar rhythms. Those were assessed on larvae placed on their host plants. Thus, those were not well-controlled experiments because apart from a light-dark cycle, the larvae were simultaneously exposed to signals generated by the plants.

So, in this paper, the larve were kept in cups and fed synthetic food. They were assayed in light and in darkness in a series of experiments, first in the absence of plants, then in the presence of uninjured plants, and finally in the presence of day-time and night-time volatiles released by either uninjured or insect-injured plants.

Result: the activity of caterpillars was affected by the presence of plants.

Larvae were more likely to hide in the presence of plants than in their absence, even more in the presence of day-time emissions than night-time emission from uninjured plants, and even more in the presence of day-time emissions from the injured plants, suggesting that plant volatiles, especially those produced during the day, and especially those produced by grazed plants, inhibit foraging activity of larvae and promote hiding activity of larvae. The statistics are nice and strong and the conclusion drawn from the data is correct.

If they framed it in this way, the study would be fine. But, for some unkown reason, they decided to frame the study within the context of "sexier" circadian research.
"Although many organisms show daily rhythms in their activity patterns, the mechanistic causes of these patterns are poorly understood."
is the first sentence of the Abstract of the paper that contains the statement even in the title: Plant Volatiles, Rather than Light, Determine the Nocturnal Behavior of a Caterpillar (PDF).

Their first reference is to the Saunders' book on Insect Clocks and most of the Introduction and Discussion treats the results of the paper in the circadian context.
"The caterpillars are believed to have evolved a nocturnal lifestyle in order to avoid predatory wasps that maraud throughout the day, but why they don't use light cues like most other organisms remains a mystery, Takabayashi says" in a press release.
Yet, their experimental methods cannot say anything about response of circadian rhythms to light in these caterpillars. Why?

First, there is nothing said about the pre-treatment. Were the insects kept in light-dark cycle, constant dark or constant light prior to the onset of the experiment? Were they kept on plants or on artifical diet prior to the onset of the experiment? This information is essential to evaluate how entrained their circadian rhythms were prior to the experiment.

Was the onset of the experiment at the lights-off, lights-on or some other phase of the pre-treatment cycle? Just swithing on or off the lights on them at just any time of day or night will not shift their clocks so fast, or even at all, depending on their phase response.

Even if they have a fast-resetting Type O Phase Response Curve (and there is no reason to believe they do - those are rare in the animal kingdom), monitoring the response for just eight hours is not enough - the clocks take much longer to reset.

There is a reason why circadian rhythms are monitored over many days, weeks, months or even years and why the data collected over the first 2-5 days after any kind of treatment (light transition, light pulse, injections of chemicals, etc.) are not used in statistical analysis - the researcher waits that long until the post-treatment rhythm stabilizes.

So, from their data, we cannot say if plant volatiles affect the circadian clock. We also cannot say if the caterpillar clock is or is not responsive to light. The data are consistent with the hypothesis that their clock is light-blind, but is equally consistent with the hypothesis that it is not. The data are consistent with the hypothesis that plant volatiles entrain the clock, but also consistent with the hypothesis that plant odors exert only a masking effect on the overt rhythm of activity - the hands of the clock - without affecting the underlying gears of the clock.

Carl Zimmer wisely avoids any discussion of circadian clocks in his excellent description of what the paper really shows on Loom. The behavior is affected by plant volatiles. Period. Excellent demonstration of the effect. No need to bring in the stuff that was not really addressed by the research, no matter how much the authors wish it may be so.

Most of the others just parrot the press release, e.g., Biology News, Brightsurf, Our Diagnosis, New Scientist, 3 Quarks daily, EurekAlert and Biology Blog.

Tangled Bank

Tangled Bank #54 is up on Science And Politics

Tuesday, May 23, 2006

Clock in the primate adrenal

From Afarensis, I got a new paper about circadian rhythms in primates: Twenty-four hour rhythmic gene expression in the rhesus macaque adrenal gland (PDF), by Dario Lemos, Jodi Downs and Henryk Urbanski.

The way the study is presented in the press release (now offline!), it sounds like this is a big surprising breakthrough, but I am not too impressed. The work is good and useful, but the findings are far from Earth-shattering.

Using microarrays, they have shown that expression of many genes cycle in a circadian manner in the adrenal glands of monkeys. The work is in vivo, and we have known for more than ten years that every cell in the body contains a clock and that clock genes cycle in every cell in our body. There was even a curious old study showing that there is a rhythm in red blood cells - no nucleus there!

Also, people have done time-series analysis of gene expression in various tissues using microarrays, and in each tissue those genes that code for proteins that are essential for that tissue's function show a circadian profile of expression (while the housekeeping genes do not). So, genes for liver enzymes cycle in the liver, genes that code for proteins involved in muscle contraction show circadian patterns of expression in muscle cells, etc. Genes that are not involved in that organ's main function are either expressed constituitively (at a constant level) or not expressed at all.

If you take any tissue out of the body and culture it, the rhythms persist, at least for several days, showing that all cells in our body are competent clocks, not just driven into rhythmicity by a daily signal from the SCN. This has been done with a number of tissues to date, including heart, lung, liver and fibroblasts.

I'd get really excited if, in their next study, they transplant an adrenal from one monkey to another and force all rhythms of the (SCN-lesioned) host to adopt the period and phase of the transplant - that would show that the adrenal is not just a clock (which is boring - every cell is a clock), but a pacemaker of the circadian system.

People in the field of chronobiology have targeted the adrenal as a potential pacemaker for a long time (since 1948 work by Curt Richter) and many experiments have been performed in the past in rodents and chickens (a friend of mine did his PhD dissertation on this topic) and all the results were always negative - adrenal is functioning as a peripheral clock, but not a pacemaker.

Sunday, May 21, 2006

Tangled Bank - last call for submissions

The Tangled Bank

The next edition of Tangled Bank is fast approaching - it will appear on my other blog Science And Politics on Wednesday May 24th, very early in the morning. The deadline is 23rd at 8pm ET.

I have only eight entries so far - come on, people! Out of more than 400 science-related blogs, I get only eight posts?

Some carnivals have very strict entry policies - Carnival of Liberals is limited to the 10 best posts, and I And The Bird is limited to one post per blogger. Some carnivals actively encourage multiple submissions from each blogger, e.g., Teaching Carnival, Circus of the Spineless and Animalcules. Most other carnivals are ambiguous about the rules and it is up to each host to spell those out.

I am one of those hosts who likes big carnivals and encourages multiple entries. So, for this Tangled Bank send your best. If you send 15 entries, I'll pick 2 or 3 I like the best, but do not be afraid to send in multiple suggestions. Also, you can nominate someone else's post if you think it is really good and deserves a broader audience.

Send your entries to: Coturnix1 AT aol DOT com

Wednesday, May 17, 2006

Project Exploration

You may have noticed a new button on my sidebar that looks like this:
Project Exploration

If you click on it, you will be transported to the homepage of one of my favourite science educational programs - the Project Exploration. This project is the brainchild of paleontologist Paul Sereno and his wife, historian and educator Gabrielle Lyons.

If you do not know who Paul Sereno is, you are probably not interested in dinosaurs at all, as he is the #1 Big Star of Dinosaur Paleontology. Among else, he has discovered Carcharodontosaurus saharicus, one of the largest dinosaur carnivores - the African version of T.rex. Jobaria tiguidensis is the best preserved skeleton of a long-necked dinosaur. Sarcosuchus imperator, better known as Supercroc was big enough crocodile to hunt and eat dinosaurs. He has also discovered Eoraptor lunensis and Herrerasaurus ischigualastensis, two of the oldest dino fossils belonging to some of the earliest dinosaurs. Deltadromeus agilis, discovered by Gabrielle Lyons, was one of the fastest dinosaurs ever.

I had a good fortune to see Sereno give a talk and briefly to introduce myself to him, at the 2000 meeting of the Society for Integrative and Comparative Biology in Chicago. My brother knows him much better, as he and Gabrielle knew each other from grad school. Thanks to their friendship I got, over the years, a bunch of informational materials from the Project Exploration, as well as some really cool stuff, like some Sahara sand, a small plant fossil and several T-shirts that you cannot buy - they are not for sale. One day when I get out of financial problems, I will make it an annual ritual to donate to their program, devoted to bringing excitement about science to inner-city schoolchildren, particularly minorities and girls. In the meantime, I hope that you donate. They do not take any money from the government and depend on individual donations for their operation. You can donate your money, or alternatives (stocks, time, work), easily through their website.

So, click on the button now, or whenever you want in the future, to see what they are doing, to get help if you are a science teacher, or to donate to a worthy cause.

Update: Tara reminds me that it may be important to show you their financial report, as well as the outcomes of their work:
Our programs are creating pipelines to future careers in science:

* Students participating in our field programs are graduating high school at an 18% higher rate than their peers.
* Students are pursuing science in college—25% of all students and 34% of our girls declare science as their major.
* The girls in our programs are pursuing science in college at five times the national average.

Clocks in Bacteria V: How about E.coli?

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 and the first half of the 20th century saw a number of researchers discovering circadian rhythms independently from each other. They came from different backgrounds and did research in a variety of questions in different organisms. There were botanists and entomologists, physiologists and ecologists, behavioral biologists and microbiologists, evolutionary biologists and physicians.

The founding moment of the field was the Cold Spring Harbour meeting in 1960, which produced the Proceedings (Cold Spring Harbor Symposia on Quantitative Biology: Volume XXV. Biological Clocks. New York: Cold Spring Harbor Press, 1960.) which is, arguably, the founding document of the field. It is there and then that everyone realized that they were all studying the same phenomenon, they agreed on common terminology, and learned from each other what became standard experimantal methods in the field.

Not much later, in the 1970s, the Society for Research in Biological Rhythms (SRBR) was formed and had its first meeting. Apart from wonderful talks and posters, and rambunctious partying, one of the key moments of the meeting was the election of the Society President. By that time, something akin to War of the Roses was going on in the field. The two candidates for the position were the leaders of the two factions.

One faction, led by Franz Halberg (who coined the term "circadian" among else), was medically minded and argued for a practical, applied approach to the study of rhythmic phenomena, coupling mathematical modelling with clinical studies in humans and some model animals like rats and mice. The other faction, led by Colin Pittendrigh (student of Theodozius Dobzhansky), came from an evolutionary, ecological and ethological tradition, arguing for an integrative and comparative approach to the study of the basic science of biological rhythms.

Fortunately for all, Pittendrigh won. The rest is history - chronobiology took off and nobody could stop its meteoric rise. The human/medical approach that plagued the sleep research for so many decades was avoided by chronobiology. But the bad blood between Pittendrighians and the Halbergians remained for a long time - it actually still simmers underneath the surface, especially among the seniors in the field. Most of the top researchers in the field, the meeting organizers, the Society officials, textbook writers, journal editors, and the plenary lecture speakers are Pittendrigh's academic children, grandchildren and great-grandchildren (OK, I am one, too).

When I mentioned, in the first post in this series, that it was believed for decades that bacteria had no clocks, I was just parroting the party line. But there were some people who thought otherwise all along. Here is what Franz Halberg himself says about the question of clocks in Echerichia coli:

A circadian rhythm in bacteria was documented time-microscopically in 1961 on impeccable data collected by Lore A. Rogers (a noted bacteriologist described by a Cosmos Club Vignette of December 1967 as "the bright star in the [U.S. Department of Agriculture's] scientific horizon before World War II"). Rogers' data stemmed from a fluid culture of E. coli, analyzed both by a periodogram and by power spectra, showing clear free-running circadians. Nonetheless, for years international symposia and cell chronobiologists in particular, including a committee formed by them in 1975, held the view that circadians are a property only of eukaryotes. I wrote to each committee member asking why they ignored the demonstration in E. coli and the extension of the finding by Sturtevant in John Pauly's laboratory in Arkansas. I regarded, and continue to regard the organizers as friends. Both Woody Hastings and the late Hans-Georg Schweiger thereafter extended their focus to circaseptans, documenting their open mind. Schweiger became a visiting professor at the University of Minnesota and was my house guest (and I his house and institute guest), and in later years cooperated extremely closely. A friend on the committee, however, wrote that he "ate crow" and noted that the "consensus" had been that there were "too many analyses" in the 1961 publication and again too much time-microscopy in the follow-up study, a thesis notwithstanding. The consensus was also in keeping with negative unpublished results by several symposium participants; so went the critique leading to the committee's decree that circadians are limited to eukaryotes. Jürgen Aschoff also responded by asking something like "Do you wish to hold us responsible for posterity?" I answered in a qualified affirmative, that the rules we postulate today may be revised tomorrow, always based on data. Microbial circadians abound today and constitute an active field of investigation.[1]
Ah, how diplomatically he had to put it for publication!

Well, I dug through Google Scholar, then through ISI Web of Science, and none of the papers Halberg mentions (see below) exist online - they are just too old. So, I cannot tell you now what I think about this question. Perhaps one day I'll be idle and have a lot of time and will dig out and photocopy the hardcopies of these papers at the library and check the data myself. For now, let's keep the question open.

Perhaps the 1930 data were nice and clear, while 1970s data not so because of decades of relaxed selection for rhythmicity in laboratory cultures of E.coli held in acyclic conditions in the incubators. Perhaps they just lost rhythms during the intervening four decades. A new test should, perhaps, be performed on fresh wild-caught Escherichia coli.

At least we know that short-period cycles can evolve in E.coli under artifical selection [7], so, even if they do not naturally have circadian clocks, we can make them evolve one and solve the political problem once and for all.

[1] Franz Halberg et al. Transdisciplinary unifying implications of circadian findings in the 1950s. Journal of Circadian Rhythms 2003, 1:2

[2] Halberg F, Conner RL: Circadian organization and microbiology: Variance spectra and a periodogram on behavior of Escherichia coli growing in fluid culture. Proc minn Acad Sci 1961, 29:227-239.

[3] Rogers LA, Greenbank GR: The intermittent growth of bacterial cultures. J Bacteriol 1930, 19:181-190.

[4] Halberg F, Cornélissen G: The spectrum of rhythms in microorganisms revisited. Chronobiologia 1991, 18:114.

[5] Sturtevant R: Circadian patterns in linear growth of Escherichia coli. Anat Rec 1973, 175:453.

[6] Sturtevant R: Circadian variability in Klebsiella demonstrated by cosinor analysis. Int J Chronobiol 1973, 1:141-146.

[7] Michael B. Elowitz and Stanislas Leibler, A synthetic oscillatory network of transcriptional regulators. Nature 403, 335-338 (20 January 2000)

Previously in this series:
Circadian Clocks in Microorganisms
Clocks in Bacteria I: Synechococcus elongatus
Clocks in Bacteria II: Adaptive Function of Clocks in Cyanobacteria
Clocks in Bacteria III: Evolution of Clocks in Cyanobacteria
Clocks in Bacteria IV: Clocks in other bacteria

Sunday, May 14, 2006

Tangled Bank - call for submissions

The Tangled BankNext edition of Tangled Bank, the blog carnival covering science, nature, medicine, environment and the intersection between science and society, will be held on Wednesday, May 24th, on my other blog, Science And Politics. Send your entries by Tuesday, May 23th at 5pm (Eastern) to: Coturnix1 AT aol DOT com.

Monday, May 08, 2006

Cory Doctorow on Circadiana

Cory Doctorow gave an interview to RedHat.com recently and mentioned Circadiana there. Although I am thrilled that he likes this place, he made two mistakes:

First, I am not a she.

Second, Circadiana has not tapered off - it is more active than ever!

Friday, May 05, 2006

Ambien + Phenergan + Driving = A Big No-No

Seems like there is a good deal of interest today in Rep Patrick Kennedy's one-car accident last evening that he has attributed to taking a combination of the prescription sleep aid, Ambien (zolpidem tartrate), and Phenergan (promethazine), an old phenothiazine antipsychotic drug most often used now to treat nausea and gastrointestinal upset.
Then, Abel PharmBoy proceeds to explains how Ambien and Phenergan work and ends on this note:
However, this should be a lesson to all who take Ambien that they should 1) go immediately to bed after taking the drug, 2) do not combine it with any other CNS depressant, including OTC antihistamines or alcohol, and 3) certainly do not drive an automobile after taking such a drug combination.

Alcohol is not necessary to explain this case... unless one is trying to make a tabloid story out of this unfortunate incident.

Wednesday, May 03, 2006

Smoking (and Quitting) affects the Perception of Time

I wrote before about the effects of circadian time and/or body temperature on time perception. But, did you know that being a smoker and being placed in a situation in which lighting up is prohibited can also warp the sense of the passage of time? Here are a couple of papers on that topic:

First, an older, 2003, study, as reported here:

Time Perception Impaired When Smokers Stop:
In a recent study, 20 daily smokers, who went without a cigarette for 24 hours, overestimated the duration of a 45 second interval. To the abstaining smokers, the interval felt approximately 50 percent longer than 45 seconds or more than one minute.
-----------------
In the study, 22 nonsmokers (12 male and 10 female), and 20 daily smokers (12 male and 8 female), ages 18 to 41, were asked to estimate the duration of a 45 second period of time in a laboratory setting. The smokers were asked to participate in two sessions, once while smoking as usual and once after having stopped for 24 hours.

During each session, the participants were given these instructions: "In a moment, I'm going to say 'start' and then I will say 'stop.' When I say 'stop,' please tell me how much time you think has gone by in seconds. Please try not to count, but just tell me how much time you feel has gone by. Do you have any questions? Ready? Start. [45 second elapse] Stop."

The time estimates made by the nonsmokers and the smokers before the abstinence period were similar and fairly accurate. However, after 24 hours without a cigarette, the smoker's accuracy declined significantly compared to both the nonsmokers and their own estimates before the abstinence period. There were no gender differences in any of the outcomes.

The researchers conclude, "That 24-hour cigarette smoking abstinence can alter perceptions of time in a healthy, young, non-clinical population of smokers emphasizes the need for future research to delineate the attention --altering effects of nicotine and nicotine withdrawal on addiction processes."
More recently, a 2005 paper on the same subject:

Sayette MA, Loewenstein G, Kirchner TR, Travis T., Effects of smoking urge on temporal cognition, Psychol Addict Behav. 2005 Mar;19(1):88-93.
The authors examined temporal aspects of smoking urge. In Experiment 1, smokers assigned to high- or low-urge conditions were informed they would be allowed to smoke in 2.5 min. They next completed measures of time perception. High-urge smokers reported 45 s to pass significantly more slowly than did low-urge smokers. In Experiment 2, the high-urge smokers from Experiment 1 anticipated that their urges would climb steadily over the next 45 min if they were not permitted to smoke. Another group of high-urge smokers actually reported their urges over 45 min. These urge ratings did not show the steady rise anticipated by the first group. Results suggest that smoking urge may affect time perception and that craving smokers overpredict the duration and intensity of their own future smoking urges if they abstain.
The latter paper is also analyzed and explained by Chris of Mixing Memory - you should go and read it here.

Sunday, April 30, 2006

Clocks in Bacteria IV: Clocks in other bacteria

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 archaea. However, having clock genes does not neccessarily translate into having a functioning clock - the genes may have other functions (e.g., photoreception, or DNA repair) in bacteria other than Synechococcus.

So, two recent papers tried to address this question - do photosynthetic bacteria exhibit circadian rhythms? And the results of the two studies, in two different species of bacteria, have some interesting similarities to each other, so let's look at them in parallel.

Van Praag et al.[3], used Rhodospirillum rubrum, a gram-negative purple non-sulfur bacteria. Min et al.[4], also chose a purple photosynthetic bacterium Rhodobacter sphaeroides. In the former, the measured output was hydrogenase uptake, while in the latter a battery of luciferase reporter genes was inserted in the genome - strains exhibiting fluoresecence (presumably those in which the construct got inserted behind a promoter) were used in the study.

In the first study (click on images to enlarge), hydrogenase uptake was measured in unoxic (anaerobic) conditions in constant light (LL) at 32oC, and in constant darkness at 32oC and 16oC. In each of the three conditions, a rhythm was observed. The period of the freerunning rhythms was markedly different between the three conditions. In LL-32oC, period was ultradian: 12.1 hours. In DD at 32oC, the period was also ultradian: 14.8 hours. Only in DD at 16oC was the rhythm within a circadian range: 23.4 hours.



In the second study, light output was measured in three experiments. In all three, bacteria were assayed in constant darkness at 23oC. In the first and second groups, bacteria were pre-treated and their putative clocks entrained by a warm-cold-warm cycle prior to release into constant conditions. In the third group, the pre-treatments was exposure to a light-dark cycle prior to release into constant conditions. The first group was tested under aerobic conditions, while the second and the thir group were tested under anaerobic conditions.

Again, rhythms were observed in all three groups. What was observed was a difference in phase at which the rhythm begins dependent on the type of entraining cycle preceding the testing. The most important difference, however, was the difference in the freerunning period between the aerobic and anaerobic treatments. In the aerobic group, period was circadian: 20.5 hours. In the anaerobic conditions, the period was ultradian: 10.6 and 12.7 in groups II and III respectively.


What does this all mean? Temperature, light and oxygenation all appeared to have an effect on period. These experiments are difficult to do - if one was working with rodents or insects, the natural thing would be to test a large number of animals at several different temperatures to test for the possible lack of temperature compensation of the circadian rhythm, as well as at several different light intensities to test for the Aschoff's Rule. It is possible that this is a circadian clock that is not well temperature compensated, that is extremely sensitive to light, and that is based on the red-ox environment.

The way the studies have been reported, it is not clear that the rhythms are actually circadian, or if it just happened that some of the rhythms fell into the circadian range by accident. What is clear is that these bacteria generate endogenous rhythms. Are these rhythms circadian or not, and if so, are they driven by core-clock genes kaiA, kaiB and kaiC remains to be elucidated in the future.

[1] Aoki S, Kondo T, Wada H, and Ishiura M (1997) Circadian rhythm of the cyanobacterium Synechocystis sp. strain PCC 6803 in the dark. J Bacteriology 179:5751-5755.

[2] Chen YB, Domonic B, Mellon MT, and Zehr JP (1998) Circadian rhythm of nitrogenase gene expression in the diazotrophic filamentous nonheterocystous cyanobacterium Trichodesmium sp. strain IMS 101. J Bacteriology 180:3598-3605.

[3] Esther Van Praag, Robert Degli Agosti and Reinhard Bachofen, Rhythmic Activity of Uptake Hydrogenase in the Prokaryote Rhodospirillum rubrum, JOURNAL OF BIOLOGICAL RHYTHMS, Vol. 15 No. 3, June 2000 218-224

[4] Hongtao Min, Haitao Guo, Jin Xiong, Rhythmic gene expression in a purple photosynthetic bacterium, Rhodobacter sphaeroides, FEBS Letters 579 (2005) 808–812

Previously in this series:
Circadian Clocks in Microorganisms
Clocks in Bacteria I: Synechococcus elongatus
Clocks in Bacteria II: Adaptive Function of Clocks in Cyanobacteria
Clocks in Bacteria III: Evolution of Clocks in Cyanobacteria

Monday, April 24, 2006

Politics of Periodicity

How I wish I could see this seminar at The Johns Hopkins University:

Thurs., April 27, 4 p.m. "Circadian Oscillators in the Brain: Politics of Periodicity," a Biology seminar with Eric Herzog, Washington University; 100 Mudd. HW

Eric is a great speaker - I wonder what is he going to talk about! I am assuming that "politics" refers to the "negotiation" between different types of clock cells in the mammalian SCN, each with a different endogenous period, as to what period will the final output have. This will entail signalling mechanisms between cells, I assume, as well as phase-shifting properties of the cells.

Anyone there at John Hopkins who can go, watch and blog this?

Sunday, April 23, 2006

Drinking mothers - perpetually jet-lagged offspring

Prenatal alcohol exposure can alter circadian rhythms in offspring
Children with fetal alcohol spectrum disorders (FASD) suffer from a variety of behavioral alterations. For example, they may exhibit alterations in sleeping and eating patterns, which may indicate that their circadian systems which control biological rhythms have been affected by alcohol exposure during development. A rodent study in the May issue of Alcoholism: Clinical & Experimental Research confirms that alcohol exposure during a period equivalent to the third human trimester influences the ability to synchronize circadian rhythms to light cues.

--------------------snip------------------

For this study, researchers exposed male Sprague-Dawley rats to 6.0 g/kg of alcohol per day (n = 8), using an artificial rearing procedure, from postnatal days four through nine. The alcohol level represented heavy binge drinking. An artificially reared control group (n = 8) and a normally reared control group (n = 8) were also included in the study design. At 10 to 12 weeks of age, wheel-running behavior was continuously measured for eight days under a 12-hour light/12-hour dark (LD) cycle. Then the cycle was delayed by six hours and the rats were exposed to a new LD cycle for an additional six days. Their adjustment to the new cycle was evaluated.

------------snip---------------------

"This is the equivalent to a person undergoing exposure to 'jet lag,'" noted Earnest. "Basically, if you take a human and go across a number of time zones from east to west, similar to the light/dark cycle of these animals, some people will shift quickly, and some will not, and may even experience some physical problems or illness because of effects on their immune system. The responses of the alcohol-treated animals indicated that they resynchronized to the shifted light/dark cycle more slowly than the control animals."

The implications of these results for humans, added Earnest, are much broader than the term "jet lag" might indicate. "These individuals are going to have difficulties, in terms of their ability to function, while traveling across time zones and also during shift work," he said. "There are a couple of prominent examples in history regarding this: the Exxon Valdez and Chernobyl. The captain of the Exxon Valdez was not only working shift work, but he was drinking too, and unable to maintain a normal, necessary performance. With Chernobyl, the shift-work schedules were inappropriate and, at the time that the accident happened, poor mental and physical performances contributed to the disaster."

The underlying message, said Thomas, is that drinking alcohol during pregnancy can have long-lasting damaging effects to the offspring. "There is currently no known safe amount of alcohol that can be consumed during pregnancy, so it is best to abstain from alcohol drinking during pregnancy. We need to better understand the mechanisms of this dysfunction to determine if there are ways to mitigate the circadian dysfunction and behavioral dysregulation associated with developmental alcohol exposure."

Saturday, April 22, 2006

Sleepwalking with Ambien

Evil Monkey of the Neurotopia blog has a good rundown on the recent finding that patients on Ambien walk and eat in their sleep.

Friday, April 21, 2006

Sleep Photoblogging

I've seen this picture on a gazillion Lefty blogs this morning and was toying with the idea of posting it here with a snarky remark. Now that Sleepdoctor has it up, I cannot be left behind, so here it is:
Vice President, dreaming of quail...

The end of Polyphasic Sleep

Michael Breus PHD, ABSM, of Sleep Disorders Blog looks at Steve Pavlina's end of the Polyphasic Sleep Experiment. From what I've seen, everyone who tried it quit in the end. Nobody lasted long enough for any negative physical consequences to kick-in (phase-shifting the clock several times a day every day for months is most definitely not good for your health in the long term).

They all quit for social reasons - you cannot live out of sync with the family and the rest of the civilization. Read whar Dr.Breus has to say in: Sleep Hacker Backs Off.

Wednesday, April 19, 2006

Clocks in Bacteria III: Evolution of Clocks in Cyanobacteria

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 positively regulates the kaiBC promoter and overexpression of kaiC represses the kaiBC promoter. Deletion of any one of the three genes leads to the complete loss of rhythmicity.

Synechococcus is a unicellular cyanobacterium. It was thought that circadian clock evolved in it due to incompatibility between nitrogen fixation and photosynthesis. Thus, temporal separation of these two processes was needed, phosynthesis occuring only during the day, while nitrogen fixation was relagated to the night time. It is known that filamentous cyanobacteria, those that build chains of cell, utilize a different strategy, that of spatial separation, some cells being involved in nitrogen fixation and others in photosynthesis. The two cell types exchange the end-results of those processes. Thus, it was thought that filamentous cyanobacteria have no need for a circadian clock.

However, it appears that Synechococcus is not the only bacterium to have a clock. Laboratory of Eviatar Nevo in Israel has taken a look at another cyanobacterium, this time a filamentous, chain-forming species, Nostoc linckia, and the work that ensued suggests that a number of other bacteria may possess a circadian clock as well [1,2,3].
Cyanobacteria are some of the oldest organisms on Earth, at least 3.5 billion years old, appearing in the fossil record relatively soon after the split between Eubacteria and Archaea (3.8 billion years ago). For most of the evolutionary history of cyanobacteria, the environment was very harsh, and UV radiation was one of the major factors influencing the evolution of prokaryotes. For most of that evolutionary history, the environment has undergone large changes, not just in oxygen levels, but also in the levels of UV radiation.

Volodymir Dvornik, Eviatar Nevo and collaborators hypothesized that a circadian clock, involved in temporal processing of light (including UV light) may be an important adaptation in all cyanobacteria and have detected the kaiABC cluster in Nostoc. Moreover, they hypothesized that Nostoc living in harsh, exposed environments (on sun-bathed slopes of so-called Evolution Canyons in Israel) would show greater mutation rate and higher nuclotide polymorphisam in the kai genes than Nostoc living on less harsh slopes of the Canyons. This is exactly what they found [1].

Some of the data from that study was intiguing - suggesting gene duplications and horizontal gene transfer of kai genes. So, they followed this up with a study of kai genes in a number of species of cyanobacteria [2] and later in a number of species of Eubacteria and Archea [3]. Here is the tree of kaiC (right) compared to the tree of 16S rRNA genes (left) - with quite amazing overlap:
Their analysis suggests that kaiC is the oldest element of the complex, while the kaiA is the youngest. kaiA occurs only in cyanobacteria, while kaiB, kaiC and the kaiBC complex occur in other types of bacteria and Archaea. There are also two types of kaiC: short and long. The long, double-domain kaiC (dd-kaiC) is found only in photosynthetic bacteria. Likewise, kaiBC cluster is found only in photosynthetic bacteria. Here is the tree of the kaiBC cluster:
Non-photosynthetis bacteria tend to have the short version of kaiC (sd-kaiC), as well as independent kaiB elsewhere in the genome (i.e., not in a cluster with kaiC). Analysis of the trees of kai gene evolution sugests many duplication events, as well as many occurences of gene loss and horizontal tranfer. Curiously, all the horizontal tranfers occured from cyanobacteria, as donors, to other types of bacteria and Archaea as recipients. Here is the proposed evolutionary history of the kai genes:
Thus, a number of bacteria and Archaea posses one, two or three kai genes, sometimes in multiple copies. Does that mean they have functioning circadian clocks?

Bacteria other than cyanobacteria do not have kaiA. Deletion of kaiA in Synechococcus abolishes rhythms. It is not inconceivable that a different gene (and several additional transcription factors besides kaiA are involved in the Synechococcus clock, so there is no lack of potential candidates) may fulfill that role in other microorganisms. Still, Synechococcus is the only prokaryote in which circadian rhythms have been measured and studied (OK, there is a recent exception - but you will have to wait for the next post to hear about it). Is it possible that kai genes in other bacteria have other functions and only in cynobacteria they got exapted for the circadian role? Time and new research will tell.

Previously in this series:
Circadian Clocks in Microorganisms
Clocks in Bacteria I: Synechococcus elongatus
Clocks in Bacteria II: Adaptive Function of Clocks in Cyanobacteria

References:

[1] Volodymyr Dvornyk, Oxana Vinogradova, and Eviatar Nevo, Long-term microclimatic stress causes rapid adaptive radiation of kaiABC clock gene family in a cyanobacterium, Nostoc linckia, from “Evolution Canyons” I and II, Israel, PNAS, February 19, 2002, vol. 99, no. 4, 2082–2087

[2] Volodymyr Dvornyk, Eviatar Nevo, Evidence for Multiple Lateral Transfers of the Circadian Clock Cluster in Filamentous Heterocystic Cyanobacteria Nostocaceae, JMol Evol (2004) 58:341–347

[3] Volodymyr Dvornyk, Oxana Vinogradova, and Eviatar Nevo, Origin and evolution of circadian clock genes in prokaryotes, PNAS, March 4, 2003, vol. 100, no. 5, 2495–2500

Tuesday, April 18, 2006

ClockNews #38

Asleep or awake we retain memory
Sleeping helps to reinforce what we've learned. And brain scans have revealed that cerebral activity associated with learning new information is replayed during sleep. But, in a study published in the open access journal PLoS Biology, Philippe Peigneux and colleagues at the University of Liege demonstrate for the first time that the brain doesn't wait until night to structure information. Day and night, the brain doesn't stop (re)working what we learn.
The science of lost sleep in teens
"Some of our kids are literally sleep-walking through life, with some potentially serious consequences," Millman said. "As clinicians and researchers, we know more now than ever about the biological and behavioral issues that prevent kids from getting enough sleep. But the National Sleep Foundation did something powerful: They asked teens themselves about their sleep. The results are startling and should be a wake-up call to any parent or pediatrician."
Children who sleep less are three times more likely to be overweight
The less a child sleeps, the more likely he or she is to become overweight, according to researchers from Universit Laval's Faculty of Medicine in an article published in the latest edition of the International Journal of Obesity. The risk of becoming overweight is 3.5 times higher in children who get less sleep than in those who sleep a lot, according to researchers Jean-Philippe Chaput, Marc Brunet, and Angelo Tremblay. These results come from data collected among 422 grade school students aged 5 to 10. The scientists measured the weight, height, and waist size of each participant. Information on the children's lifestyle and socioeconomic status was obtained through phone interviews with their parents.
Sleep apnea treatment benefits the heart
Patients with obstructive sleep apnea have enlarged and thickened hearts that pump less effectively, but the heart abnormalities improve with use of a device that helps patients breathe better during sleep, according to a new study in the April 4, 2006, issue of the Journal of the American College of Cardiology.
Low Stairway to Heaven
SAD arises via fluctuation in melatonin, a chemical produced in response to darkness. Those with SAD suffer from depression during the winter, as the ratio of dark to light hours increases. Melatonin produces a certain drowsiness that causes your circadian rhythms to fall out of sync with the day-night cycles of the environment. Further, some research shows that darkness decreases serotonin levels, which negatively affects mood. Certain SAD sufferers find remedy in “light box treatment”—they expose themselves to artificial light for a few hours a day and become less depressed. I like to think of the steps as my own light box treatment—give me a few hours in front of Low and my mood dramatically improves.
Getting enough Zzzzzs? Kids often don’t
You can force a kid to bed, but you can’t make him fall asleep. Especially if he — or she — is a teenager. It’s not adolescent rebellion. It’s adolescent metabolism. They physically cannot fall asleep because their bodies’ internal clocks are on sort of a chronic daylight-saving time overdrive — which worsens through their teen years, ultimately tapering off in their 20s, according to Leigh Heithoff, clinical specialist with BryanLGH Medical Center West’s Department of Sleep Medicine.
What's holding up the sandman for so many of us?
Unfortunately, with the ease of writing and filling a prescription and the mostly good press these new drugs have gotten to date, millions of people are now taking them without first exploring the reasons for their sleep problems and possible nondrug routes to cure them.
Eye cells that don't see, but regulate
As any good high school biology student can tell you, the human eye sees light with special cells called rods and cones. But when George C. Brainard experimented with shining various colors of light into people's eyes, something odd happened: A specific shade of blue light was most effective at shutting down the body's production of melatonin - the "hormone of darkness" that helps regulate sleep and the body's internal clock. Yet that shade of blue is not one of the colors best detected by rods and cones. His conclusion, shared by others conducting studies on blind people and animals: There must be some unknown cells in the eye - some that responded to light but had nothing to do with seeing. Since that experiment at Thomas Jefferson University, reported in 2001, other scientists have indeed found the new cells, as well as the gene that controls them. Only in the last year has a consensus emerged about how the new cells work.
Sleep has become the new obsession
First it was looks, then weight. Now, the new Western obsession is sleep - or a lack of it. But even experts don't agree on how much people really need
Integrating Transcriptomics and Proteomics
An example of time-shifted discord would be that of the mammalian 24-hour circadian clock, in which regulatory proteins such as Period (mPER) exhibit a four- to eight-hour delay between protein and transcript expression.
Aging-Related Sex Dependent Loss of the Circulating Leptin 24-Hour Rhythm in the Rhesus Monkey
The adipocyte-derived hormone leptin plays a pivotal role in the regulation of body weight and energy homeostasis. Many studies have indicated that the circulating levels of leptin show a 24-h rhythm, but the exact cause and nature of this rhythm is still unclear. In the present study we remotely collected blood samples every h from young and old, male and female rhesus monkeys, and examined their 24-h plasma leptin profiles. In both the young males (10-11 yrs) and young females (7-13 yrs) a clear 24-h plasma leptin rhythm was evident, with a peak occurring ~4 h into the night and a nadir occurring ~1 h into the day (lights on from 0700-1900 h). A 24-h plasma leptin rhythm was also observed in the old males (23-30 yrs), even when they were maintained under constant lighting conditions (continuous dim illumination of ~100 lux). In marked contrast, plasma leptin concentrations were relatively constant across the day and night in old perimenopausal and postmenopausal females (17-24 yrs), regardless of the lighting schedule. These data establish that rhesus monkeys, like humans, show a daily nocturnal rise in plasma leptin, and show that the magnitude of this rhythm undergoes a sex-specific aging-dependent attenuation. Furthermore, they suggest that the underlying endocrine mechanism may be driven in part by a circadian clock mechanism.
Wake-Up Call for Sleep Tech
A bad night's sleep is reason for a very big business. Sleeping pills, led by Ambien, rack up more than $2 billion a year in the United States. Then there is the revenue from overnight stays at sleep clinics, over-the-counter pills, a parade of gimmicks and a thriving business for sleep specialists.
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"Sleep is the new sex." So says psychologist Arthur J. Spielman, associate director of the Center for Sleep Disorders Medicine & Research at New York Methodist Hospital in Brooklyn, New York. "People want it, need it, can't get enough of it." The same could be said of profits. Spielman is co-author of The Insomnia Answer (Perigee Books, 2006). He is also developing light-delivering goggles that are supposed to help people reset the circadian rhythms that govern when they nod off and wake up, so they fall asleep faster and stay asleep longer. Sleep is also the new snake oil -- the promise of a good snooze from a book or a bed or a bottle. It's easy pickings.
I'm so tired of being tired
"I'm so tired," said my friend the last time we met for lunch. "The doctor said I have chronic fatigue."
She was not sleeping more than six hours a night, didn't find time to eat well or exercise, and was always achy, so it was not surprising that she felt exhausted. But now there was a label attached to her symptoms that made her feel depressed and alarmed.
CNN Presents Classroom: Sleep: A Dr. Sanjay Gupta Special
Set your VCR to record the CNN Special Classroom Edition: Sleep: A Dr. Sanjay Gupta Special when it airs commercial-free on Monday, April 17, 2006, from approximately 4:10 -- 5:00 a.m. ET on CNN. (A short feature begins at 4:00 a.m. and precedes the program.)
Lighting for the Aging Eye
In the bath, avoid fluorescents, Gilbertson advises. Instead, opt for 100-percent color rendering light bulbs, positioned on either side of your bathroom mirror. Consider installing a dimmer on bathroom lights. Research shows that very low-level regular light, or light in the red spectrum, maximizes night vision while minimizing the disruption of our circadian rhythm, Blitzer says.
Top tips to better sleep
One in three people get less than five hours of sleep a night, according to new research. But Dr John Shneerson, director of the Sleep Centre, Papworth Hospital, Cambridge, says just being aware of some simple tricks can help sleep sufferers achieve a good night's rest. "Sticking to regular bedtimes, helping the body to unwind and avoiding certain foods and drinks in the evening can induce drowsiness and enhance sleep," he says.
Ramelteon Showed Significant Reduction in Time to Fall Asleep With No Evidence of Rebound Insomnia or Withdrawal Effects
Results of a sub-analysis from a phase 3 clinical study showed that Rozerem™ (ramelteon) significantly reduced time to fall asleep in adults with chronic insomnia and showed no evidence of rebound insomnia or withdrawal effects.
Night shift: Late-night work can be bad for your health
According to studies done in the past five years by Harvard University, the National Cancer Institute and the Fred Hutchinson Cancer Research Center in Seattle, women who work the night shift have an increased risk of breast and colorectal cancer. These women have a 60 percent higher risk of breast cancer than women who have never worked nights, the research says. Because of the circadian rhythm -- the 24-hour cycle of sleep and wakefulness -- the body will never be fooled into thinking it's daytime when it's dark out. However, Attarian says there are people who over time can get used to the off-hours. Because of their genetic make-up, Attarian says, some people are just night owls.
Remodeling of astrocytes, a prerequisite for synapse turnover in the adult brain?

A stitch in time, it’s all in the mind
Time slows down in some Kung Fu movie sequences. Jet Li’s foot takes forever to land. Michelle Yeoh’s riposte is glacially slow. This showcases a state-of-the-mind technique called entering the zone: Tai chi masters say this enables aspirants to ‘go faster by going slower.’ While sceptics scoff at such paradoxes, scientists are discovering that, like biofeedback, humans may have more conscious control over their measurement and perception of time than previously thought. Some say this could even lead to chemical cues to shrinking eternity and stretching fleeting moments for those who want to throw away their watch and rock around the clock.
Bed Rest May Not Be Helpful for Threatened Miscarriage
An opinion piece in the March 24 issue of The New York Times highlights a controversial issue in obstetrics: the value of bed rest for threatened miscarriage. Although this intervention is widely prescribed, evidence of its efficacy is limited or absent, and some experts suggest that there may be deleterious effects.
Smart strategies that help you become a beautiful dreamer
Naps can be lifesavers, but if you overdo them, it may be tough to nod off during normal sleeping hours. And you don't want to nap for more than an hour or so at a stretch. "The problem is, when you start getting into two- or three-hour naps, you start resetting your circadian cycle," Dr. Hartse says. (That's your body's internal clock.)

Tuesday, April 11, 2006

REM sleep and paranormal phenomena

Lindsay links to an interesting article in the Washington Post - Near-Death Experiences Linked to Sleep Cycles:
As many as 10 percent of survivors of heart attacks report having a near-death experience -- such as feelings of transcendence, being surrounded by light or floating outside their bodies.

New research announced yesterday suggests a biological explanation for such phenomena: People with near-death experiences are more likely to have different sleep-wake mechanisms in their brains.

In a study comparing 55 people with near-death experiences with 55 people who had no such experiences, neurologist Kevin Nelson of the University of Kentucky found that people who reported such experiences were also more likely to report a phenomenon known as "REM intrusion," where things normally experienced during sleep carry over into wakefulness. REM is an acronym for rapid eye movement, one of the phases of sleep.

Such people wake up but still feel paralyzed or hear sounds that others do not -- as the vestiges of sleep fall away, those experiences disappear. It is not considered a disorder, but merely a variant of the brain's sleep-wake cycle.

Nelson, who published his findings in the journal Neurology, said the extreme fear or feeling of danger brought on by imminent death might trigger the brain mechanism that governs the transition between sleep and wakefulness, leading people to experience various dreamlike phenomena.

The neurologist added that religious and cultural beliefs clearly influenced near-death experiences, and stressed that his findings only spoke to how such a brain mechanism might work, and not why it would work that way.
She also links to the abstract of the paper, a Nature magazine coverage of the connection between near-death experiences and REM sleep and a related article on the connection between sleep paralysis and alien abductions. A year ago, Chris Mooney published a good article on that connection as well:
Our bodies are paralyzed while we undergo REM sleep, and for good reason (lest we act out our dreams and injure ourselves). But in some small number of cases we can actually start to wake up before paralysis wears off, and yet still remain in a dreaming state. What results is hallucination, often of some extremely scary stuff. It appears that humans have always experienced sleep paralysis and sought to explain it, resulting in well known stories of incubi and succubi--demons thought to sexually attack people in their sleep--as well as related tales from other eras and cultures.

Sleepy Americans

Study Shows that Americans are Besieged by Sleeplessness
More and more Americans work and walk around like sleep-deprived zombies, in part due to growing work hours and poor choices made in an environment that is potentially always "on" due to television and the Internet. That's according to a study published last week by the National Academy of Sciences' Institute of Medicine.

The study found that chronic sleep disorders now affect a whopping 50 million to 70 million Americans. Millions more are deprived of sleep on a semi-regular basis. In addition to environment, factors owing to physiology play a role, too. Among other things, more and more Americans are obese, which can interfere with slumber.

The study noted that drug companies are rushing sleep medicines into the sleepless void, targeting the trend as an emerging market. Some 43 million prescriptions for sleep aids were filled last year, and four new drugs will be released over the next year and a half. New sleep centers have sprung up unaccredited throughout the land, tempting Americans. "You can get a sleep study done in a strip mall now without ever meeting with a [qualified] specialist," James Wyatt of the Sleep Disorders Center at Rush University Medical Center in Chicago told the Chicago Tribune.

As noted in the sleep study, the growth in disorders seems to be the product of a failure to deal effectively with environment. That's part of a larger societal trend, say other psychologists. The New York Times ran a piece last week noting that current research shows some 9 percent of Americans suffer from problems related to "high impulsiveness."

Heritability of snoring

Interesting, in today's New York Times:

In the Genes: When the Littlest Family Member Snores, Too
Snoring may be genetic. Children who snore are almost three times as likely as others to have parents who snore. And snoring and sleep-disordered breathing are twice as common in children who test positive for allergies.

Sleep-disordered breathing — snoring is one symptom of it — is associated with poor school performance, cardiovascular troubles and daytime behavioral problems like attention-deficit hyperactivity disorder.

Researchers studied 1-year-old children participating in the Cincinnati Childhood Allergy and Air Pollution Study. Among the 681 children, 105 were habitual snorers — that is, they snored more than three nights a week. The children were also examined for allergies to various foods and other substances using a skin-prick test.

Having a positive allergy test almost doubled the risk for snoring, and having one parent who snored almost tripled the risk. Being African-American more than tripled the risk that a child would be a habitual snorer. The results were published yesterday in the journal Chest.

"If you have a child who snores frequently or loudly," said Dr. Maninder Kalra, an author of the study, "we recommend evaluation by a sleep specialist." Treatment for sleep-disordered breathing in children may involve surgery to remove enlarged tonsils or adenoids, or the use of a breathing device during sleep. Dr. Kalra is an assistant professor of medicine at Cincinnati Children's Hospital Medical Center.

Sleep-disordered breathing can be definitively diagnosed only in a sleep laboratory, and the authors point out that one limitation of their study is that they did not perform this definitive test on each child. Further, the research relied on the reporting of parents, which may not have always been accurate.

Sunday, April 09, 2006

Chossat's Effect in humans and other animals

If you know what Chossat's Effect is, I guess you are a) a physiologist, b) expert in thermoregulation, and c) old. This is term that got expunged from the scientific lexicon a few decades ago, in an effort - correct me if I am wrong on this - spearheaded by the U.S. textbook companies, to replace scientific terminology named after the discoverers (and sometimes even Latin and Greek terms) with bland English neologisms.

But I love Schwann's Cells, Fallopian Tubes (or Mullerian Ducts), Purkinje Fibers, Broca's Area and the amazing Bundle of His! Those terms are memorable, make it easy to sneak in some historical context into teaching science, and have an emotional effect of bringing forth images of ancient scientists working under candlelight, sacrificing their eyesight and health, their social standing and sometimes even their lives, in the feverish hunger for knowledge.

So, what is Chossat's Effect? It comes from a certain 19th century French scientist who was studying the physiology of starvation [1]. The 'modern' term for this effect is "fasting-induced nocturnal hypothernia" (doesn't that sound like something that would prompt the students in the classroom to immediatelly stop paying attention to the teacher and instead pick-up their cell-phones and start text-messaging their friends?).

Actually, this is a very interesting area of research that is very tightly connected to circadian biology. This post is likely to be long, so feel free to skim and just focus on the first part if you are into birds, second part if you are interested in mammals, and the last part if you are into humans.

Birds

All warm-blooded animals (and yes, that includes at least some reptiles, not to mention a few heat-producing plants like stink-cabbage) exhibit a daily rhythm of body temperature. If an animal is active during the day (diurnal) and sleeps during the night, reducing the metabolic rate during the night is a good way to save energy.

Some of the smallest birds, like swifts and hummingbirds, need to feed continuously in order to stay alive. At night, when they are not able to forage (flowers are closed, it's hard to see, and owls are hunting at the time), they drop their metabolic rate, and thus body temperature, quite dramatically. The body temperature gets down as low as the environmental temperature, sometimes daringly close to the freezing point. The total drop can be as large as 40 degrees Celsius in some instances! This is called daily torpor (yup, click on that link - it is an excellent blog post) and the metabolic rate drops as much as 95% [2, 3]. This is like full-scale winter hibernation EVERY DAY!

Chossat's effect does not refer to daily torpor, though. It describes a drop in temperature during the night that is larger than the usual circadian fluctuation, in animals undergoing fasting, e.g., during spells of very bad weather (e.g., hurricanes).

Normal amplitude (daily maximum minus nightly minimum) of body temperature in birds with normal access to food ranges between about 1 and 2 degrees Celsius. For instance, a daily maximum may be 41 degrees and the nightly minimum may be 39 degrees (yes, the birds are much warmer than mammals, which makes them inhospitable to microbes that cause many mammalian diseases), which calculates to 2 degrees of amplitude.

During fasting (or food deprivation in the laboratory), the nightly minima drop down to lower levels than in fed birds. The minimum gets lower and lower with each additional night. Importantly, the daily maxima do not change at all. It is thought that it is advantageous for birds to retain their normal metabolic rates during the day so they can immediately resume foraging once the bad weather subsides. Also, if the bad weather persists for too long, the birds need the daytime metabolic rates in order to fly away [4].

According to John Wingfield's "Emergency Life-History Stage" hypothesis [5], an individual's perception of inclement weather directly affect the levels of stress hormones (e.g., corticosterone). An individual who does not perceive the bad weather to be "too bad", will reduce daytime activity and reduce night-time temperature in order to save energy - this individual has made a decision to sit it out.

On the other hand, an individual who perceives bad weather to be "really bad" (or if it lasts too long) will have higher levels of stress hormones and will attempt to fly away during the day. This is not the same mechanism as the seasonal migration, which is usually a nocturnal flight, i.e., they do not experience Zugunruhe, just stress. Stressed birds do not attempt to escape at night, at which time they have allowed their body temperature to drop by several degrees.

Nocturnal hypothermia has been studied in a large number of species of birds (see, for examples, references # 6-12), but most of the work was performed on pigeons [13-15] and quail [16]. Not all avian species exhibit this response. Laurilla at al. [18] write:
"On the other hand, many large birds that are adapted to long fasting periods as a part of their life histories, e.g. penguins and geese (Cherel et al., 1988; Castellini andRea, 1992), owls (Hohtola et al., 1994) and some raptors (McKechnie andLovegrove, 1999) do not show marked hypothermia during fasting. Some species enter hypothermia upon food restriction only when isolated from conspecifics in a laboratory environment, while in the field they remain normothermic by huddling. These observations have even led some authors to question the usefulness of the concept of hypothermia (Lovegrove andSmith, 2003)."[8]

Here is a graphic example of a fasting-induced nocturnal hypothermia in quail (from[17]). The period between the two triangles is the time (3 days) during which the birds had water but no food. Before and after, birds were fed ad libitum. Below is a graph that shows the difference between the temperature minima during the first, second and third day (left) and night (right) of food deprivation in comparison to the last three days and nights of normal feeding prior to the fasting treatment:
Much of the more recent research is looking at other environmental cues that can modify the Chossat's effect, as well as the involvement of the circadian clock in this time-specific form of thermoreguluation. For instance, some of the ambient cues that affect the response include ambient temperature [16, 20], ambient light [17], photoperiod [18, 19], single vs. repeated fasting [18, 19], caloric food restriction vs. complete food deprivation [13], social situation, e.g., opportunity for huddling [8] and presence of stationary vs. flying predators [19, 20]. Here is an example of an effect of ambient temperature on nocturnal hypothermia in fasted pigeons (from [20]). Lower the ambient temperature, deepeer the Chossat's effect:
Here is the effect of the presence of a predator (from [2]). In the presence of a perched hawk (P), nocturnal hypothermia reached normally low levels. In the presence of the flying hawk (F), temperature did not drop as much. Presumably, the pigeons kept the metabolic rate high enough to be able to fly fast if needed:
As stated above, hypothermia occurs only during the night while the temperature during the days remains normal. However, all the studies are performed either in natural conditions of day and night or in light-dark cycles in the laboratory. In constant darkness, the circadian rhythm of temperature persists and hypothermia is apparent. Moreover, the temperature drops both at the minima during the 'subjective night' and at the maxima during the 'subjective day' (from [17]):
This suggests that light has a direct (or "masking") effect on body temperature during the light-phase of the cycle. But is this effect acting directly on the thermoregulatory centers in the hypothalamus or is it mediated by the circadian clock that drives the rhythm of body temperature? In Japanese quail, the circadian pacemakers are located in the eyes. When the eyes are removed [17], both the daily maxima in the light-phase and the nightly minima during the dark phase drop, suggesting that the effect is mediated via the circadian clock, as the light perceived by the photoreceptors in the pineal gland and in the deep brain is incapable of keeping the daily maxima from dropping:
Mammals

Some small mammals, such as smallest rodents and shrews, exhibit a full-blown daily torpor either normally [21] or in response to fasting [22]. Here is an example of a daily torpor of a mouse-opposum:
In nocturnal animals, which many mammals are, body temperature is high at night when the animals are active and it drops during the day when the animals are sleeping. In rats, fasting induces diurnal hypothermia, i.e., drop of the daily minimum during the day (black circles, compared to pre- and post- treatment values in white symbols) while the nightly maxima remain unaffected [23]:
Chronic caloric food restriction leads to the drop in both the daily minima and nightly maxima of temperature [24].

All the studies until recently have studied responses in relatively small animals (both birds and mammals) with high metabolic rates and high energy needs. But do larger animals, like humans, also exhibit Chossat's effect? After all, the first documented case, that by Chossat himself, was in a dog. This was repeated recently [25]. But even dogs are pretty small compared to humans.

Recently, researchers have addressed this question in a number of species of large mammals, including sheep, goats, horses and yaks [26-29]. Some additional environmental cues were also studied, including the effects of shearing on the circadian temperature rhythm in sheep [30]. Here is a record from a goat:
Notice that, unlike in birds, both the maxima and minima gradually go down.

But, as far as I could find by digging through the literature, nobody has ever performed a similar study in humans. I am assuming that it has been noticed if body temperature drops in fasted humans, but I am not aware of a study systematically addressing this question.

Humans

A few years ago I was teaching one of many sections of an Animal Anatomy and Physiology Course. This course requires students to perform a research project. One group of students studied the effects of fasting on body temperature and blood pressure in humans.

They found 8 subjects, all healthy, athletic, non-drinking, non-smoking students ages 19-23. They were instructed to eat normally during the Day1 of the experiment. They subequently spent 36 hours in a house drinking only water and eating nothing. Every four hours, temperature and pressure were measured. By using kids' digital ear thermometers and manual sphigmomanometers they managed, for the most part, not to awaken the subjects during the night. Here are examples of body temperature of three of the subjects - Night1, followed by Day2 and Night 2:























Here are the pooled data for all eight subjects, starting with Day2 and followed by Night1 and Night2 plotted on top of each other for comparison:
Obviously, body temperature of Night2, after a day of fasting, was lower than that of Night1, after the day of normal feeding. I do not have their raw data any more, but if I remember correctly, the data for blood pressure looked very similar. I heard they had a huge breakfast, courtesy of the young researchers, at the end of the experiment.

So, Chossat's Effect appears to be operating in humans as well. Now, this is cool in itself, and I sure hope that someone with access to good clinical lab repeats this study, but there is something else about these data that really excites me. This finding can be used as a tool for studying something entirely different!

The Hypothesis

One of the first demonstrations that humans have daily rhythms involved the time-of-day dependence of time perception. In other words, our subjective "feel" of the speed of passage of time changes systematically with the time of day. At the same time, it has been known for a couple of centuries now that the subjective time perception is also altered during fever. And we know that circadian clock governs daily rhtyhms of body temperature. So, what affects the time perception: time of day or body temperature? If the time passes faster in the evening than at dawn, is it because of the circadian clock acting on the time-perception brain-centers directly, or because we are warmer at the time (which is also driven by the circadian clock)?

This question has haunted circadian researchers for decades and they have devised ever more elaborate experiments to tease the two hypotheses apart, with no avail - we still do not know. But, if by depriving the subjects of food, we can dissociate clock-time from temperature, perhaps we can address this question after all. If the subjective perception of 1 minute (do not use 1 second or 1 hour - those are durations unsuited for this experiment) is similar between the night after a fed day and the night after the fasting day, then the perception is directly driven by the circadian clock. If, on the other hand, perception of a minute changes systematically between the two nights, then we conclude that it is body temperature that affects subjective time perception. Please, someone do this! And if you do, or even if you just want to replicate the Chossat's Effect in humans, I would appreciate it if you would properly cite this post:

Bora Zivkovic, Chossat's Effect in humans and other animals (April 9, 2006), blog Circadiana, http://circadiana.blogspot.com/2006/04/chossats-effect-in-humans-and-other.html

REFERENCES:

[1] M. Chossat, Sur l'inanition, Paris, 1843

[2] Hiebert, S.M. 1990. Energy costs and temporal organization of torpor in the rufous hummingbird (Selasphorus rufus). Physiological Zoology . 63:1082-1097.

[3] Hiebert, S.M. 1991. Seasonal differences in the response of rufous hummingbirds to food restriction: body mass and the use of torpor. Condor 93:526-537.

[4] Tobias Wang, Carrie C.Y. Hung, David J. Randall, THE COMPARATIVE PHYSIOLOGY OF FOOD DEPRIVATION: From Feast to Famine, Annual Review of Physiology, January 2006, Vol. 68, Pages 223-251

[5] Wingfield, JC; Maney, DL; Breuner, CW; Jacobs, JD; Lynn, S; Ramenofsky, M; Richardson, RD, Ecological bases of hormone-behavior interactions: The "emergency life history stage", American Zoologist [Am. Zool.]. Vol. 38, no. 1, pp. 191-206. 1998.

[6] Tracy A. Maddocks, Fritz Geiser, Energetics, Thermoregulation and Nocturnal Hypothermia in Australian Silvereyes, Condor, Vol. 99, No. 1 (Feb., 1997) , pp. 104-112

[7] Randi Eidsmo Reinertsen and Svein Haftorn, The effect of short-time fasting on metabolism and nocturnal hypothermia in the Willow Tit Parus montanus, Journal of Comparative Physiology B: Biochemical, Systemic, and Environmental Physiology, Volume 154, Number 1 (January 1984): 23 - 28

[8] Barry G. Lovegrove and Gary A. Smith, Is 'nocturnal hypothermia' a valid physiological concept in small birds?: a study on Bronze Mannikins Spermestes cucullatus, Ibis, Volume 145, Issue 4, Page 547 - October 2003

[9] MacMillen RE, Trost CH., Nocturnal hypothermia in the Inca dove, Scardafella inca, Comp Biochem Physiol. 1967 Oct;23(1):243-53.

[10] Colleen T. Downs, Mark Brown, NOCTURNAL HETEROTHERMY AND TORPOR IN THE MALACHITE SUNBIRD (NECTARINIA FAMOSA).

[11] Waite, TA, Nocturnal hypothermia in gray jays Perisoreus canadensis wintering in interior Alaska, ORNIS SCAND. Vol. 22, no. 2, pp. 107-110. 1991.

[12] Cécile Thouzeau, Claude Duchamp, and Yves Handrich, Energy Metabolism and Body Temperature of Barn Owls Fasting in the Cold, Physiological and Biochemical Zoology, volume 72 (1999), pages 170–178

[13] Rashotte ME, Henderson D., Coping with rising food costs in a closed economy: feeding behavior and nocturnal hypothermia in pigeons, J Exp Anal Behav. 1988 Nov;50(3):441-56.

[14] R. Graf, S. Krishna and H. C. Heller, Regulated nocturnal hypothermia induced in pigeons by food deprivation, Am J Physiol Regul Integr Comp Physiol 256: R733-R738, 1989

[15] Michael E. Rashotte, Iuri F. Pastukhov, Eugene L. Poliakov, and Ross P. Henderson, Vigilance states and body temperature during the circadian cycle in fed and fasted pigeons (Columba livia), Am J Physiol Regul Integr Comp Physiol 275: R1690-R1702, 1998

[16] Hohtola E, Hissa R, Pyornila A, Rintamaki H, Saarela S., Nocturnal hypothermia in fasting Japanese quail: the effect of ambient temperature, Physiol Behav. 1991 Mar;49(3):563-7.

[17] Herbert Underwood, Christopher T. Steele and Bora Zivkovic, Effects of Fasting on the Circadian Body Temperature Rhythm of Japanese Quail, Physiology & Behavior, Vol. 66, No. 1, pp. 137–143, 1999

[18] Mirja Laurila, Tiina Pilto, Esa Hohtola, Testing the flexibility of fasting-induced hypometabolism in birds: effect of photoperiod and repeated food deprivations, Journal of Thermal Biology 30 (2005) 131–138

[19] MIRJA LAURILA, THERMOREGULATORY CONSEQUENCES OF STARVATION AND DIGESTION IN BIRDS, PhD Dissertation, Faculty of Science, Department of Biology, University of Oulu, 2005 (http://herkules.oulu.fi/isbn9514277147/isbn9514277147.pdf)

[20] Mirja Laurila, Esa Hohtola, The effect of ambient temperature and simulated predation risk on fasting-induced nocturnal hypothermia of pigeons in outdoor conditions, Journal of Thermal Biology 30 (2005) 392–399

[21] Francisco Bozinovic, Gricelda RuÍz, Arturo CortÉs & Mario Rosenmann, Energetics, thermoregulation and torpor in the Chilean mouse-opossum Thylamys elegans (Didelphidae), Revista Chilena de Historia Natural 78: 199-206, 2005

[22] Lovegrove BG, Raman J, Perrin MR., Daily torpor in elephant shrews (Macroscelidea: Elephantulus spp.) in response to food deprivation, J Comp Physiol [B]. 2001 Feb;171(1):11-21.

[23] Kei Nagashima, Sadamu Nakai, Kenta Matsue, Masahiro Konishi, Mutsumi Tanaka, and Kazuyuki Kanosue, Effects of fasting on thermoregulatory processes and the daily oscillations in rats, Am J Physiol Regul Integr Comp Physiol 284: R1486–R1493, 2003.

[24] Yoda T, Crawshaw LI, Yoshida K, Su L, Hosono T, Shido O, Sakudara S, Fukuda Y & Kanosue K (2000) Effects of food deprivation on daily changes in body temperature and behavioural thermoregulation in rats. Am J Physiol 278: R134-R139.

[25] G. Piccione, G. Caola and R. Refinetti, Daily Rhythms of Blood Pressure, Heart Rate, and Body Temperature in Fed and Fasted Male Dogs, J. Vet. Med. A 52, 377–381 (2005)

[26] Giuseppe Piccione, Giovanni Caola, Roberto Refinetti, Circadian rhythms of body temperature and liver function in fed and food-deprived goats, Comparative Biochemistry and Physiology Part A 134 (2003) 563–572

[27] Piccione, G., Caola, G., Refinetti, R., 2002a. Circadian modulation of starvation-induced hypothermia in sheep and goats. Chronobiol. Int. 19, 531–541.

[28] Piccione, G., Caola, G., Refinetti, R., 2002b. The circadian rhythm of body temperature of the horse. Biol. Rhythm Res. 33, 113–119.

[29] Xing-Tai Han, Ao-Yun Xie, Xi-Chao Bi, Shu-Jie Liu and Ling-Hao Hu, Effects of high altitude and season on fasting heat production in the yak Bos grunniens or Poephagus grunniens, British Journal of Nutrition (2002), 88, 189–197

[30] Giuseppe Piccione, Giovanni Caola, and Roberto Refinetti, Effect of shearing on the core body temperature of three breeds of Mediterranean sheep, Small Ruminant Research 46 (2002) 211–215

Thursday, April 06, 2006

Influence of Light Cycle on Dominance Status and Aggression in Crayfish

Understanding the role of serotonin in depression has led to development of anti-depressant drugs, like Prozac. Much of the research in this area has been performed in Crustaceans: lobsters and crayfish. The opposite behavioral state of depression, something considered a normal state, could possibly best be described as self-confidence.

Self –confidence is expressed differently in different species, but seems to always be tied to high status in a social hierarchy. In crayfish, self-confidence is expressed as aggression. When two individuals meet, they engage in aggressive behavior (Fig. 1, see below).

Outcome of this “fight” determines the social status and leads to long-term changes in the brain, particularly the serotonergic system, associated with either winning (self-confidence) or losing (depression). Thus, experiencing a victory alters the behavior in a way that makes subsequent victories more likely and vice versa (Goessmann et al., 1999; Huber et al., 1997; Issa et al., 1999). Experimental manipulations of the serotonergic system by, for instance, injections of serotonin or Prozac, result in changes in aggressive behavior and social status.

Two standard experimental practices are used in the study of aggression in crustaceans. In one, two or more individuals are placed together in an aquarium and left there for a long period of time (days to weeks). After the initial aggressive encounters, the social status of an individual can be deduced from its control of resources, like food, shelter and mates.

In the other paradigm, two individuals are allowed to fight for a brief period of time (less than an hour), after which they are isolated again and re-tested the next day at the same time of day. Neither of the two approaches is capable of addressing two questions: how fast do the changes in the brain start to occur, and, what if any effect can time of day have on the behavior. Because of this, the existing literature, sometimes implicitly sometimes explicitly, suggests that the rule "once a winner, always a winner" is true, and that the neural changes are fast and induced by a single agonistic encounter.

To address these two questions, Amy Hughes, then an undergraduate student in our department, now an epidemiology graduate student at the University of Minnesota, and I have designed a different experimental procedure. This study began as a project in the Animal Anatomy and Physiology laboratory class in which Amy was my student. However, the initial data were interesting and we easily persuaded Dr.Robert Grossfeld to help support further study as Amy's honors research project. Apart from securing funding, animals, equipment and space, Dr.Grossfeld proved as a valuable resource on crustacean neurobiology and on keeping the research focused and 'on target'.

We kept individual crayfish in social isolation for a month prior to the experiment. They were kept in a light-dark cycle consisting of 12 hours of light and 12 hours of darkness. Then, we matched the individuals by size and tested their aggressive behavior and social status by behavioral observations for about 15 minutes every 3 hours over a period of 24 hours. One set of tests was initiated at “dawn” or lights-on time, which was 8am and ended at 8am on the next day. The other set of tests started at dusk, or lights-off time, which was 8pm and ended at 8pm the following day. We scored the behaviors using the scoring systems modified from standard literature (Karavanich and Attema 1998, see Table 1).

It has been known for quite a long time now that crayfish are nocturnal animals and that the levels of general locomotor activity are much greater during the night than during the day (Page and Larimer 1972). However, no specific behaviors were monitored in such studies. Analysis of our data shows that aggressive behavior is much more intense and frequent during first three hours of night than at other times during the 24-hour cycle (Fig.2). This is somewhat different from the general locomotor activity which tends to be high throughout the night, not concentrated to the early portion of the night.

Expectation that brain changes associated with winning or losing are initiated very fast were met by about half of the tested pairs of animals in each data-set. In these animals, the social status was determined during the first or second time-point and remained stable for the rest of the experiment (Figs 3 and 4).

However, in about a half of the pairs in each data-set, the stable social hierarchy was not achieved during the 24-hour period of the experiment. Levels of aggression and the final outcome varied during this period, suggesting that the brain changes in these individuals did not occur as fast, and that there is considerable plasticity in behavioral states during the first 24 hours of social interactions (Fig. 5).

Interestingly, more switches in social status occurred during the day than during the night. This can be explained in several different ways. For instance, a very high level of aggression may be necessary to trigger the changes in the brain, and such highly aggressive encounters are most likely to occur in the early night. Thus, encounters during the previous day were not intense enough to result in long-term changes in the brain. Further research needs to be done to study the rate at which an experience of victory or loss triggers permanent changes in the brain.

Also, there is no strong evidence in the literature that the two individuals can actually recognize each other. However, they can recognize the social status of their opponents. During the fights, crayfish squirt urine at each other (Zulandt Schneider et al. 2001, also see figure on the right where urine is colored with a fluorescent dye). Chemical signature of the urine was not studied at all so far, but it apparently carries information about the brain-state of the animal.

Since socially dominant animals have higher levels of serotonin in their nervous system, it is likely that the chemical message in the urine is related to serotonin. The most likely candidate, a direct metabolite of serotonin, is melatonin. A recent study has shown that levels of melatonin in these animals are very high in the early night, drop off somewhat during the rest of the night and are practically undetectable during the day (Tilden et al. 2003). Our results are consistent with the notion that urinary melatonin (or its metabolite) may be the signal carrying information about social status, as the most intense fights and most definitive outcomes occurred during the early night. This hypothesis needs to be tested in the future.

This research has been displayed on the poster session of the Undergraduate Research Sympsium at North Carolina State University. It is unlikely that any of the participants in this study will follow up on this work in the near future. Though there is not sufficient data to publish a 'real' paper, we feel that the information should be available online for those who study aggression, social dominance, serotonin, melatonin and circadian rhythms in crustaceans.

The project, as presented by Amy on the poster, is reproduced below. We will appreciate proper attribution in case you follow up on this study. The correct reference is:

Amy Hughes, Bora Zivkovic and Robert Grossfeld, Influence of Light Cycle on Dominance Status and Aggression in Crayfish (April 6, 2006), Circadiana blog; http://circadiana.blogspot.com/2006/04/influence-of-light-cycle-on-dominance.html

Influence of Light Cycle on Dominance Status and Aggression in Crayfish
Amy Hughes, Bora Zivkovic and Robert Grossfeld

INTRODUCTION

Conflicts arise within a population of social animals over the allocation of important resources. Interactions between crayfish determine a social hierarchy both when resources are in dispute and when they are not. Even when no resource except space is contested, crayfish will fight. Several factors determine the outcomes of these contests, including physical attributes of an organism and past experience (Goessmann et al., 1999; Huber et al., 1997; Issa et al., 1999; Zulandt Schneider et al., 2000).

In most previous studies of crustacean aggressive behavior, animals were tested at the same time for consecutive days. In those experiments, winning enhanced further success by heightening aggression, whereas losing decreased subsequent chances for dominance by lowering aggression.

Recognition of the opponent’s attributes plays a role in changes in social status, e.g. detection of the opponent’s relative dominance status and recognition of a prior opponent (Goessmann et al., 1999; Karavanich & Attema, 1998; Zulandt Schneider et al., 2000).

The purpose of this study was to test the hypothesis that the establishment and stability of a dominance hierarchy may be plastic over sequential pairings during the first day, and influenced by time of day.

MATERIALS AND METHODS
  • Forty-four adult male crayfish (Procambarus clarkii) were kept in separate containers with no visual or physical contact for one month on a LD12:12 light cycle (lights on automatically at 8:00 AM and lights off at 8:00 PM). They were fed fish food pellets every 7 days.
  • Pairs of 20-40 g inter-molt males were matched closely by weight (within 1 g).
  • For testing, each pair was placed in a small container [30 cm (L) x 20 cm (W) x 15 cm (D)] filled approximately two-thirds full with fresh water.
  • The same pairs encountered each other for approximately 15 min every 3 h over a 24-h period.
  • One set (11 pairs) was tested first at the time of lights-off (i.e. 8:00 PM).
  • The other set (11 pairs) was tested first at the time of lights-on (i.e. 8:00 AM).
  • The time of initiation of a fight, duration of the fight, number and type of agonistic behaviors, and final “winner” of the encounter were recorded based on visual observation. The total agonistic behavior scores were compared using a one-tailed Student t- test.
Figure 1. Two crayfish in a fight













Table 1. The scoring table of behavior. Modified from Karavanich and Attema 1998. Insert: an example of a meral spread.


Retreat – moving away, turning away: -1

Strike and Rip – using claws unrestrained: +4

Claw Lock – using claws to grasp: +3

Meral Spread – threatening display of claws: +2

Approach – walking towards, turning towards other animal: +1



Figure 2: Agonistic interactions escalate during the early evening following lights off (i.e. 8:00 PM). n=44; p<0.0001.


Figure 3: Behavior scores of crayfish tested first at 8:00 PM
In 7 of 11 pairs, the animal that established dominance at the first or second time point (8:00 PM or 11:00 PM, respectively) remained the more aggressive animal the entire 24 h.
Figure 4: Behavior scores of crayfish tested first at 8:00 AM
In 5 of 11 pairs, the animal that established dominance at the first or second time point (8:00 AM or 11:00 AM, respectively) remained the more aggressive animal the entire 24 h.
Figure 5: In 10 pairs, a stable dominance relationship was not established during the first two time points.
The number of switches in social status was greater during the light phase than during the dark phase (p<0.01). In 4 of 11 pairs (8:00 PM set), dominance switched over the 24 hours:
In 6 of 11 pairs (8:00 AM set), dominance switched over the 24 hours:
CONCLUSIONS

Crayfish agonistic behaviors are most frequent during early evening following lights-off as compared to early morning following lights-on.

In about half of the pairs, the relative levels of aggression (“dominance status”) remained stable after the first or second encounter, whereas in the other pairs it changed at one or more times during the 24 hour testing period, especially during the daytime. The latter results suggest plasticity in social status during the first day that crayfish are paired.

REFERENCES

Balzer I.; Espinola I.R.; Fuentes-Pardo B., Daily variations of immunoreactive melatonin in the visual system of crayfish, Biology of the Cell, Volume 89, Number 8, November 1997, pp. 539-543(5)

Goessmann, C., Hemelrijk, C., and Huber, R. (2000). The formation and maintenance of crayfish hierarchies: Behavioral and self-structuring properties. Behav Ecol Sociobiol. 48:418-428.

Huber, R., Smith, K., Delago, A., Isaksson, K., and Kravitz, E. A. (1997). Serotonin and aggressive motivation in crustaceans: Altering the decision to retreat. Proc. Natl. Acad. Sci. USA. 94: 5939-5942.

Issa, F.A., Adamson, D.J. and Edwards, D.H. (1999). Dominance hierarchy formation in juvenile crayfish Procambarus clarkii. J. Exp. Biol. 202:3497-3506.

Karavanich, C. and Attema, J. (1998). Individual recognition and memory in lobster dominance. An. Behav.. 56:1553-1560.

Page,Terry L. and Larimer, James L. (1972), Entrainment of the circadian locomotor activity rhythm in crayfish: The role of the eyes and caudal photoreceptor, Journal of Comparative Physiology A: Neuroethology, Sensory, Neural, and Behavioral Physiology, Volume 78, Number 2: 107 - 120

Tilden, Andrea R. , Brauch Rebecca, Ball Ryan, Janze Aura M. ,Ghaffari Ali H. , Sweeney Catherine T., Yurek Jamie C. and Cooper Robin L. (2003), Modulatory effects of melatonin on behavior, hemolymph metabolites, and neurotransmitter release in crayfish, Brain Research 992: 252–262

Zulandt Schneider, R. A., Huber, R. and Moore, P.A. (2001), Individual and status recognition in the crayfish, Orconectes rusticus: The effects of urine release on fight dynamics. Behav. 138:137-153.

Wednesday, April 05, 2006

Clocks in Bacteria II: Adaptive Function of Clocks in Cyanobacteria

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. When raised in constant light, they fare even a little better, i.e., multiply faster. Thus, in isolation, clock does not appear to confer adaptive advantage.
However, when the strains are cultured together, two strains grown in the same petri-dish, and exposed to light-dark cycle, the strain whose endogenous period is closer to the period of the environmental cycle "wins" the contest. This suggests that circadian clock confers fitness in rhythmic environments. In constant light, arrhythmic mutants outperform rhythmic strains.
Here is how Johnson describes the experiments (from a book chapter not available online):
"The authors’ laboratory tested the adaptive significance of circadian programs by using competition experiments between different strains of the cyanobacterium Synechococcus elongatus (Ouyang et al., 1998; Woelfle et al., 2004). For asexual microbes such as S. elongatus, differential growth of one strain under competition with other strains is a good measure of reproductive fitness. In pure culture, because the strains grew at about the same rate in constant light and in LD cycles, there did not appear to be a significant advantage or disadvantage in having different circadian periods when the strains were grown individually. The fitness test was to mix different strains together and to grow them in competition to determine whether the composition of the population changes as a function of time. The cultures were diluted at intervals to allow growth to continue. Different period mutants were used to answer the question, ‘‘Does having a period that is similar to the period of the environmental cycle enhance fitness?’’ The circadian phenotypes of the strains used had freerunning periods of about 22 h (B22a, C22a) and 30 h (A30a, C28a). These strains were determined by point mutations in three different clock genes: kaiA (A30a), kaiB (B22a), and kaiC (C22a, C28a). Wild type has a period of about 25 h under these conditions. When each of the strains was mixed with another strain and grown together in competition, a pattern emerged that depended on the frequency of the LD cycle and the circadian period. When grown on a 22-h cycle (LD 11:11), the 22 h-period mutants could overtake wild type in the mixed cultures. On a 30-h cycle (LD 15:15), the 30 h-period mutants could defeat either wild type or the 22 h-period mutants. On a ‘‘normal’’ 24-h cycle (LD 12:12), the wild-type strain could overgrow either mutant (Ouyang et al., 1998). Note that over many cycles, each of these LD conditions have equal amounts of light and dark (which is important, as photosynthetic cyanobacteria derive their energy from light); it is only the frequency of light versus dark that differs among the LD cycles. Figure 1 shows results from the competition between wild type and the mutant strains (Ouyang et al., 1998).

Clearly, the strain whose period most closely matched that of the LD cycle eliminated the competitor. Under a nonselective condition (in this case, constant light), each strain was able to maintain itself in the mixed cultures. Because the mutant strains could defeat the wild-type strain in LD cycles in which the periods are similar to their endogenous periods, the differential effects that were observed are likely to result from the differences in the circadian clock. A genetic test was also performed to demonstrate that the clock gene mutation was specifically responsible for the differential effects in the competition experiment (Ouyang et al., 1998). Because the growth rate of the various cyanobacterial strains in pure culture is not detectably different, these results are most likely an example of ‘‘soft selection’’ where the reduced fitness of one genotype is seen only under competition (Futuyma, 1998).

In a test of the extrinsic versus intrinsic value of the clock system of cyanobacteria, wild type was competed with an apparently arrhythmic strain (CLAb). As shown in Fig. 2, the arrhythmic strain was defeated rapidly by wild type in LD 12:12, but under competition in constant light, the arrhythmic strain grew slightly better than wild type (Woelfle et al., 2004). Taken together, results show that an intact clock system whose freerunning period is consonant with the environment significantly enhances the reproductive fitness of cyanobacteria in rhythmic environments; however, this same clock system provides no adaptive advantage in constant environments and may even be slightly detrimental to this organism. Therefore, the clock system does not appear to confer an intrinsic value for cyanobacteria in constant conditions."
It is telling how many control experiments they had to do in order to eliminate various alternative explanations. They had to show that mutations in clock genes do not have additional effects on the ability of the cell to grow and reproduce. Check. They had to show that clock mutations do not affect the ability of the cells to utilize the food and light energy. Check. They had to show that clock mutations do not affect any conceivable way by which one strain can, perhaps by secreting chemicals, actively disrupt the health of the other strain. Check. And in the end, although they demonstrated that "resonance", i.e., similarity between environmental cycle and the intrinsic period confers some advantage, they still could not state with certainty that this "proves" that the circadian clock has an adaptive function.
Here is Johnson [3] again:
"The original adaptation of circadian clocks was presumably to enhance reproductive fitness in natural environments, which are cyclic (24h) conditions. We can refer to this situation as an adaptation to extrinsic conditions. However, some researchers have proposed that circadian clocks may additionally provide an "intrinsic" adaptive value (Klarsfeld 1998; Paranjpe 2003 and Pittendrigh 1993). That is, circadian pacemakers may have evolved to become an intrinsic part of internal temporal organization and, as such, may have become intertwined with other traits that influence reproductive fitness in addition to their original role for adaptation to environmental cycles. Note that a rigorous evolutionary biologist would no longer consider an intrinsic value for clocks to be an adaptation if their original extrinsic value has been lost. However, if clocks retain extrinsic value and additionally accrue intrinsic value, then they would still be considered an adaptation."
Testing if a trait is an adaptation is a very difficult task. Testing if something as ubiquitous as a circadian clock is an adaptation is even harder. Can you imagine testing if using ATP for energy storage, or using DNA for information storage are adaptations? Are there organisms that do not use these, so we can use them in comparative or competitive studies?

In his book Adaptation and Environment (1990), Robert Brandon came up with five criteria that need to be satisfied in order to determine if a trait is an adaptation (thanks to Robert Skipper for a reminder of this):
"One must have

1. evidence that selection has occurred;
2. an ecological explanation of the fact that some types are better adapted than others;
3. evidence that the trait in question is heritable;
4. information about the structure of the population, including both demic structure and the structure of the selective environment;
5. phylogenetic information concerning what has evolved from what."
The early cyanobacterial studies have shown criterion #3 to be correct. The competitive assay studies started cracking the criterion #2. In the next post on this topic, I will describe some studies that started investigating the criterion #5, with some additional evidence for criteria Nos. 1, 2 and 4. Apparently, we still have a long way to go. Johnson again:

An example from the circadian literature of a ‘‘just-so’’ story that the author has personally promulgated is that of ‘‘temporal separation’’ of photosynthesis and nitrogen fixation in cyanobacteria. In nitrogen-fixing unicellular bacteria, nitrogen fixation is often phased to occur at night. Nitrogen (N2) fixation is inhibited by low levels of oxygen, which poses a dilemma for photosynthetic bacteria because photosynthesis generates oxygen. Mitsui et al. (1986) proposed that the nocturnal phasing of nitrogen fixation was an adaptation to permit N2 fixation to occur when photosynthesis was not evolving oxygen, and the author has repeated this hypothesis in several publications (Johnson et al., 1996, 1998). This hypothesis would predict that cyanobacterial growth in constant light would be slower than in a light/dark (LD) cycle because nitrogen fixation would be inhibited under these conditions and therefore the growing cells might rapidly become starved for metabolically available nitrogen. The problem is that cyanobacteria grow perfectly well in constant light—in fact, they grow faster in constant light than in LD cycles, presumably because of the extra energy they derive from the additional photosynthesis. This result is inconsistent with the ‘‘temporal separation’’ hypothesis. It does not mean that the ‘‘temporal separation’’ hypothesis is incorrect—in fact, the author believes that under appropriate (but as yet untested) conditions of medium, light, and carbon dioxide, the ‘‘temporal separation’’ hypothesis will emerge triumphant. Nevertheless, the point here is that ‘‘temporal separation in cyanobacteria’’ is an example of a ‘‘just-so’’ circadian story that we like to tell without its being rigorously supported by appropriate data. This was the conclusion of Gould and Lewontin (1979) for many investigations in the field of population biology, and this criticism is on target."

[1] YAN OUYANG, CAROL R. ANDERSSON, TAKAO KONDO, SUSAN S. GOLDEN, AND CARL HIRSCHIE JOHNSON, Resonating circadian clocks enhance fitness in cyanobacteria, Proc. Natl. Acad. Sci. USA, Vol. 95, pp. 8660–8664, July 1998

[2] Mark A. Woelfle, Yan Ouyang, Kittiporn Phanvijhitsiri and Carl Hirschie Johnson, The Adaptive Value of Circadian Clocks: An Experimental Assessment in Cyanobacteria, Current Biology, Vol. 14, 1481–1486, August 24, 2004,

[3] Carl Hirschie Johnson, Testing the Adaptive Value of Circadian Systems, Methods in Enzymology, Volume 393 , 2005, Pages 818-837

Monday, April 03, 2006

Ah, Zugunruhe!

I've never ever expected to see the word "Zugunruhe" in New York Times! But here it is. It is one of my most favourite words of all times (right after "elusive"), and is even described pretty accurately:





Zugunruhe brooks no confusion. It has a Germanic certainty, and there can be no doubt what it means, once you know what it means. I confess that I only learned the word this week. If I understand the paper about it by Barbara Helm of the Max Planck Institute for Ornithology in Andechs, Germany, and the late Eberhard Gwinner in the Public Library of Science (www.plos.org), I have often experienced zugunruhe but didn't know it.

The two researchers studied African stonechats. Stonechats are in the thrush family, and many breed in Europe and fly south in winter. The birds that the researchers studied were residents in Africa, and were thought not to have a genetic predisposition to migrate. What the researchers were looking for was evidence of zugunruhe in the resident stonechats, which they raised in the lab at the Max Planck Institute, under a variety of circumstances.

The scientists did not expect to find it in the resident birds. But they did. The stay-at-home stonechats exhibited the same sort of nocturnal restlessness as their migrating relatives. The conclusion: some level of zugunruhe may be common even in birds that don't migrate.
Yup, it is usually translated as "migratory restlesness" and describes a behavior, usually at night, usually in birds, of increased activity, orienting towards the flight destination (e.g., towards the north in spring), practice flights, etc. Since most birds are diurnal (day-active), an increase (or even appearance) of activity during the night is a pretty good behavioral indicator that the animals are experiencing the urge to migrate.

Update: The paper [1] that prompted this article has just been posted online on PLoS: Migratory Restlessness in an Equatorial Nonmigratory Bird

European (migratory) and Kenyan (non-migratory) stonechats were kept in the laboratory and their locomotor activity was monitored continuously. Some of the birds were kept in a constant photoperiod (light/dark 12.25:11.75 h) often seen in Kenya. Other birds were exposed to naturally changing photoperiod in Southern Germany (40 degrees North). In both treatments, both the European and the Kenyan birds showed increased nocturnal activity (zugunruhe). In constant photoperiods, each bird exhibited its own circannual rhythm, independent of the activity of its neighbors. In natural photoperiods, all the birds exhibited nocturnal pre-migratory restlesness at the appropriate season. The activity of the migratory species was much more pronounced, but the non-migrants (who vigorously defend their territories all year round in Kenya) also exhibited substantial levels of nocturnal activity:

From the paper's conclusion:
Our study thus demonstrates common, complex features of Zugunruhe in resident and migrant birds, suggestive of ancestral patterns. However, Zugunruhe programs of African residents are unexpectedly precise, given an estimated divergence from a common ancestor 1 million to 3 million years ago [23,24]. Furthermore, evolutionary rates and heritabilities of migratory traits are reportedly high [8,11,19]. This suggests that Zugunruhe programs of African residents may either be adaptive or maintained by stabilizing selection [29]. Assuming that Zugunruhe indicates time windows during which movements can easily be released or inhibited [15], several selective advantages are conceivable. Persistent Zugunruhe windows could enhance and accelerate adjustments to changing conditions [8,18,20]. Intratropical movements are common in birds and could occur at times in African stonechat populations [9,18,23,28,30]. Southern African stonechat subspecies are thought to be partial altitudinal migrants [31]. The Kenyan population is distinct [24,31] but also inhabits high altitudes. It is conceivable that periodically, altitudinal or other seasonal migrations, for example, related to drought, become necessary. Furthermore, the maintenance of Zugunruhe could be favored by related behaviors, for instance, dispersal [8,17,18,20].

[1] Barbara Helm, Eberhard Gwinner, (2006) Migratory Restlessness in an Equatorial Nonmigratory Bird. PLoS Biol 4(4): e110

Sunday, April 02, 2006

Archives

I have updated the Categories today. They are up-to-date and the links appear to work, though I am toying with the idea of re-organizing them a little bit, perhaps adding a new category "Clocks and Society" to include political, cultural, educational and pseudoscientific aspects of chronobiology.

Update: I have played around with the categories some more. You will find two new categories there:

'Clock Zoo' contains posts that summarize what we know about clocks in particular organisms or groups of organisms.

'Mis-Clock-Ceptions' contains posts that deal with societal aspectes of clocks and sleep, the misperceptions and misunderstandings, as well as psuedoscientific and anti-scientific screeds related to sleep and clocks.

"Cutting Edge Research" has been renamed - "Timely Research", containing posts that review fresh new findings in the literature.

Finally, "Clock Tutorial" has been re-organized. Instead of a chronological listing of posts, it is now organized into topics and sub-topics. This should make it easier for people (especially students and instructors) to find the most relevant posts.

Again, if you are an expert in this field, I'd be glad to have you guest-post here. Write a post about the area of research you know best or about the clocks in your favourite organims and send it to me.

ClockQuotes (Shakespeare)

I wasted time, and now doth time waste me;
For now hath time made me his numbering clock;
My thoughts are minutes.

- William Shakespeare, Richard II

Saturday, April 01, 2006

More on sleep in adolescents

This being the National Sleep Awareness Week and in the heels of the recent study on sleep of adolescents, it is not surprising that this issue is all over the media, including blogs, these days.

I have covered this issue a couple of times last week, e.g., here, here and here. Recently, Lance Mannion wrote an interesting post on the topic, whcih reminded me also of an older post by Ezra Klein in which the commenters voiced all the usual arguments heard in this debate.

There are a couple of more details that I have not touched upon in the previous posts.

First, lack of sleep can lead to obesity and even diabetes, as the circadian clock is tightly connected to the ghrelin/leptin system of hormonal control of hunger, feeding and fat-deposition.

Second, lack of sleep discourages excercise. Put these two pieces of data together, and you get a national epidemic of obesity, not just a bunch of sleep-deprived children.

Third, lack of sleep has a well-documented effect on mood. No, teenagers are not naturally that moody - at least not all of them. They are just barely "functional" (instead of "optimal") and walk through life like zombies because they are operating on 4-8 hours of sleep instead of 9 hours (optimal for teens, it goes down to about 8 for adults). Of course they are moody.

Fourth, chronic sleep deprivation can have long-term consequences, ranging from psychiatric diseases to cancer. Remember that teens in high-school (and college students are faring worse!) are constantly jet-lagged!

There is even a hypothesis floating around that sleep-delay in adolescence may affect the onset of picking up smoking.

Fifth - and I did not think of this although it is obvious - teenagers above a certain age, still in high school, are allowed to drive. If they are driving themselves to school at 6 or 7am, when their circadian clocks think is it 3 or 4am, it is as if they are driving drunk. There is actually a scale devised by one of the sleep researchers that tells which time of the night corresponds to what number of bottles of beer. Driving at 4am (or driving a ship, like Exxon Valdese, or operating a power-plant, like one in Chernobyl) is the equivalent of driving drunk - way over the legal limits. Teenagers driving at 7am are equally "drunk".

One of the reasons for the resistance to healthy inititiatives to change school-start schedules stems from the fact that the world is organized by adults and adults want to have the world run according to schedules that fit their moods and are unwilling to change it - they may not know that teens feel differently, or they defend their preferences nonetheless.

A large proportion of adults in this country still subscribe to barbaric notions that sleep is a shameful activity, a sign of laziness, and that teens need to be tortured in order to "steel" them to grow into "real men". This has roots all the way back to the Puritan so-called "work-ethic" which is really a "no fun for anyone" punitive ethic long ago shown to be physically and emotionally debilitating.

When I was a kid, back in old now-non-existent Yugoslavia, most schools in big urban areas worked in two shifts. All the kids started school at 8am and ended at 1:15pm for one week, then started at 2pm and ended at 7:15pm the next week, and so on...

If a school had, let's say, twelve classes of the seventh grade, six of those would be in the A-shift and the other six in the B-shift. Each shift had its own complete set of teachers, assistants, nurses...everything except the Principal and the school psychologist.

The time between 1:15pm and 2pm was for supplementary classes (either for those who needed extra help, or for those preparing for Math Olympics and such) and clubs. That was also time for kids from two shifts to meet and get to know each other (it is amazing how many kids from opposite shifts started dating each other after the year-end Big Trip to the Coast - me included). There was no such thing as the American hype for high-school competitive sports, which I still find strange and curious after 15 years in this country.

Thus, you get to sleep in for a week (but miss out on afternoon activities), then have to get up relatively early for a week but have the afternoon free to galivant around town. Nobody there understands what's the American fuss over kids being home alone - of course they are home alone, cleaning the house, fixing meals, doing homework and BETTER be getting to school on time!

Teachers were pretty understanding about sleeping types. I do not recall ever having a big test, quiz or exam being given at the extremes of the day (around 8am or around 7pm). As an owl myself, I was much more likely to raise my hand, participate in discussions, or volunteer for oral examinations during the week when I was in school in the afternoon, and that was fine with most of my teachers.

Transportation was not an issue. Most kids lived close enough to their neighborhood school to walk. For those who lived a little farther away - hey, no problem, that's Europe, so Belgrade has a huge and pretty efficient public transportation system. I do not remember ever seeing any of my friends ever being dropped off to school by a parent driving a car! Or being brought to or picked up from school by a parent beyond fourth grade at all - period. And the minimum driving age being 18, nobody drove themselves to school either.

In rural areas, there was no need for two shifts - something like 9am-2:15pm was good enough to accomodate all of the kids.

I do not think that this kind of system can be implemented in the USA. It relies on an efficient public transportation which, with exception of a few oldest East Coast cities, is practically non-existent. American cities have been built for cars.

But some things can be dones. First, swap the starting times so elementary kids go to school first, middle school next and high school last (e.g., around 8am, 8:30am and 9am respectively). Studies show that teens do not go to sleep later if their school starts later. Some cynics claim that is what teens will do.But they do not. Actually, they fall asleep at the same time, thus gaining an additional hour of sleep. Teens are almost adults. The current generation of teens, perhaps because of a closer and tighter contact with their parents than any generation before, is the most serious, mature and responsible generation I have seen. Give them a benefit of the doubt. Just because you were into mischief and hated your parents when you were their age does not mean that today's kids are the same.

Second, start the school day - for all kids every day - with PE (or some kind of excercise), preferably outdoors, as both exposure to daylight and the excercise have been shown to aid in phase-shifting the circadian clock.

Third, let them eat breakfast afterwards (sticking to a meal schedule also helps entrain the clock). Follow up with the electives which kids may be most interested in. By the time they hit math, science and English classes around 11 or so, their bodies are finally fully awake and they can understand what the teacher is saying, and do the tests with a clear mind instead of in a sleepy haze.

Do not permit any caffeine to be sold in schools. Advise parents not to allow TV or any other electronics to be in kids bedrooms. Let them enjoy those activities in the living room. Bedroom is for sleeping, and sleeping alone. A book before bed is fine, but screens just keep them awake even longer.

Finally, rethink all those extra activities you are forcing the teens to do: sports, art, music, etc. In teen's minds, the day does not start with the beginning of school in the morning. We may think that we are at work most of our day. Teens do not - they consider their day to begin at the time schoolday is over. Their day begins in the afternoon. School is something they have to deal with before they can have their day. Realize this and give them time and space to do with their day what they want. Do not push them to do things that you think they'll need to get into Harvard. Let them be - leave them alone. Then they'll go to sleep at a normal time.

Concern for our kids' physical and mental health HAS to trump all other concerns, including economic costs, cultural traditions and adult preferences. We have a problem and we need to do something, informed by science, to fix the problem. Blaming the messenger, proposing to do nothing, and, the worst, blaming the kids, is unacceptable.

Friday, March 31, 2006

Adolescent Sleep on NPR

On today's Talk Of The Nation - Science Friday, Ira Flatow had Dr.Mary Carscadon and Dr.Judith Owens as guests on the show, discussing the latest survey of adolescents and sleep, which I have already covered in a couple of posts last week. In a couple of hours, the podcast will be available here.

The best of recent science-related blogging

Check out the latest editions of science-related blog carnivals:

Tangled Bank (science, nature, medicine and environment)
Grand Rounds (medicine and healthcare)
Carnival of the Green (environment and conservation)
Circus of the Spineless (invertebrates)
I And The Bird (birds and birdwatching)
Animalcules (microorganisms)
Skeptic's Circle (dissecting pseudoscience and medical quackery)
Carnival of Education (education)

Thursday, March 30, 2006

Do sponges have circadian clocks?

Short answer: nobody knows. Nobody has looked yet. Most of the research in biology is, quite rightfully, performed in just a handful of standard models. A sponge is not a standard animal lab model.

Should one expect sponges to have circadian clock? Considering that every animal, plant, fungus and protist, as well as some bacteria have clocks, it would be more surprising if sponges did not have one.

I've been on a lookout, for quite some time now, for any mention in the literature of a possible daily rhythm in sponges. There is not much, but there is some. What is known for sure, is that both adult [1] and larval [2] sponges perceive light, thus they should be capable of entraining to the environmental light-dark cycles.

In the field, sponges release their larvae (spawn) in a manner that suggests that they a) can percieve environmetal light, b) use such information to calculate the time of day, and c) also have a lunar rhythm (either an endogenous circalunar clock entrained by the moon, or exogenous rhythm driven directly by moonlight):
Release started every day of 3 3-d period (12 to 14 October) at about 1400 hrs and lasted until just after sunset (1830 hrs). Ninety percent of the population showed reproductive activity. Exactly one lunar month later (11 to 12 November), a second release of gametes occurred. In the following year the same sequence of events was observed for the original population (2 to 4 October and 1 to 2 November, 1985). In all instances the first gamete release began on the third day after the full moon. These and earlier observations on this phenomenon show a strong correlation between moon phase and the time of gamete release [3].
Another interesting behavior in sponges is called "pumping". Those are the contractions of the whole body of the sponge. Apparently [4], the contractions are slower during the night than during the day, indicating a diurnal, if not a circadian rhythm. Here is a pattern recorded from one sponge in the lab:
Here is the light-to-dark comparison in two individual sponges:
Locomotor activity is the most favored overt rhythm by researchers in chronobiology.

If you did not know this before, sponges can move. Not fast enough to grab your ankle while swimming - more on the order of 6mm per day. This was a serendipitous finding a couple of decades ago, about a mile from where I live now, at UNC-Chapel Hill.

Calhoun Bond, then doing his PhD here (and now teaching at Greensboro College), happened to have an aquarium in his office. One day he looked at it and noticed that a sponge was not in the same place where it was before. So, he got a multi-million-dollar grant needed to buy a Sharpie pen [ ;-) ] and started drawing the position of the sponge on the glass wall of the aquarium. Yup, the sponge sure moved:

















Dr.Bond has since published a couple of papers on the exact mechanim the sponge moves. It does not have a moving "leg" on the bottom. Instead, the whole animal rearranges itself as cells move over each other, pulling the spikules along. I've seen the stop-motion movies and they are impressive.

He has not noticed, though, if the sponge had different speeds during the day as opposed to during the night, but this could be easily done by an undegraduate student in a biology lab. Instead of drawing a mark once per day, draw a mark every 3-4 hours over a period of a couple of days, and the answer will be there. If there is a day/night difference in the sponge locomotion speed in a light-dark cycle, then it would be worth running the sponges through a standard battery of tests, including phase-shifts of the light-dark cycle, exposure to constant dark and constant light, and phase-shifting the rhythm with light pulses. This process could even be automated with a camera which can allow one to monitor the behavior over longer periods of time (e.g,. weeks or months).

The study that most directly tested the effects of light-dark cycle on a behavior of a sponge looked, again, at the timing of spawning. Apparently [7], the sponge releases its larvae 24 hours after the last perceived dawn (i.e., light-to-dark transition) regardless of the light conditions transpiring during those 24 hours. This, in the wild, places the larval release right around the dawn of the next day.

One thing that I am surprised nobody did so far was to see if sponges have core circadian clock genes, like period, timeless, clock and cryptochrome. It is apprently relatively easy technically to do so. I have seen phylogenetic analyses of sequences of clock genes in dozens of, for instance, insect species. It can't be that hard to take a look at a sponge and, if teh clock genes are there, see in which cells and with what temporal dynamics they are expressed.

[1] Werner E.G. Muller, Klaus Wendt, Christopher Geppert, Matthias Wiens, Andreas Reiber, Heinz C. Schroder, Novel photoreception system in sponges? Unique transmission properties of the stalk spicules from the hexactinellid Hyalonema sieboldi, Biosensors and Bioelectronics 21 (2006) 1149–1155

[2] Sally P. Leys and Bernard M. Degnan, Cytological Basis of Photoresponsive Behavior in a Sponge Larva, Biol. Bull. 201: 323-338. (December 2001)

[3] W. F. Hoppe and M. J. M. Reichert, Predictable annual mass release of gametes by the coral reef sponge Neofibularia nolitangere (Porifera: Demospongiae), Marine Biology, Volume 94, Number 2, 277 - 285 (March 1987)

[4] Michael Nickel, Kinetics and rhythm of body contractions in the sponge Tethya wilhelma
(Porifera: Demospongiae), The Journal of Experimental Biology 207, 4515-4524

[5] CALHOUN BOND AND ALBERT K. HARRIS, Locomotion of Sponges and Its Physical Mechanism, THE JOURNAL OF EXPERIMENTAL ZOOLOGY 246:271-284 (1988)

[6] CALHOUN BOND, Continuous Cell Movements Rearrange Anatomical - Structures in Intact Sponges, THE JOURNAL OF EXPERIMENTAL ZOOLOGY 263:284-302 (1992)

[7] Amano, S, Morning release of larvae controlled by the light in an intertidal sponge, Callyspongia ramosa . Biological Bulletin, Marine Biological Laboratory, Woods Hole. Vol. 175, pp. 181-184. (1988).

Tuesday, March 28, 2006

National Sleep Awareness Week


This week (March 27, 2006 - April 2, 2006) is the National Sleep Awareness Week. So, I assume that Circadiana will get a lot of hits this week. Perhaps if you all link to it....(hint, hint LOL)

ClockNews - Adolescent Sleep

Health Journal: Doctors probe why it's hard for many kids to get up (also Night Owls: Disorder may cause teens to sleep less):
"The parents get stigmatized as not having control over their kids when they can't get them to school in time," says James Wyatt, co-director of the sleep-disorders center at Rush University Medical Center in Chicago who is conducting research looking for ways to better diagnose the disorder. "Children themselves get stigmatized as avoiding school or lazy. There's a lot of baggage associated with it."

Technology keeps teens awake, study shows:
An optimal night's sleep for teens is nine hours, said Mary Carskadon, director of the E.P. Bradley Hospital Sleep center at Brown University and the other study author. But researchers found that almost half slept fewer than eight hours on school nights.

Only 40 winks stinks Sleep deprivation hampers youths' growth, learning:
As kids reach adolescence, their internal clocks tend to shift, causing them to naturally feel more alert later at night and to wake up later in the morning. This change can make it difficult for them to fall asleep before 11 p.m. In fact, more than half of high school students stay up past that hour on school nights.

Sleep experts continue to advocate for later school starting times, 9 a.m. or after, a notion that hasn't been embraced by Valley districts.

"Sending students to schools without enough sleep is like sending them to school without breakfast," said Jodi Mindell, associate director of the Sleep Disorders Center at the Children's Hospital of Philadelphia and co-chair of the sleep poll task force. "Sleep serves not only as a restorative function for the adolescents' bodies and brains, but it is also a key time when they process what they've learned during the day."

The science of lost sleep in teens:
"Our results show that the adage 'early to bed, early to rise' presents a real challenge for adolescents," says Carskadon, who directs the Bradley Hospital Sleep and Chronobiology Sleep Laboratory and is a professor of psychiatry and human behavior at Brown Medical School.

Carskadon's work has been instrumental in influencing school start times across the country. Regionally, the North Kingstown School Department in Rhode Island, North Reading Public Schools in Massachusetts, and West Hartford Public Schools in Connecticut are considering school start time changes due, in part, to research on teens and sleep.

In a study published in the November 2005 issue of the journal Sleep, Carskadon found that the "sleep pressure" rate the biological trigger that causes sleepiness slows down in adolescence and is one more explanation for why teens can't fall asleep until later at night. Carskadon's newest finding indicates that, in addition to the changes in their internal clocks, adolescents experience slower sleep pressure, which may contribute to an overall shift in teen sleep cycles to later hours.

New survey sounds the alarm: Nation's kids need more sleep:
At least one of the reasons adolescents don't get enough sleep is not their fault, said Mindell. Hormone changes cause a two-hour shift in circadian rhythm (the body's internal clock), Mindell said. So they are naturally more alert later in the day.

Survey finds most teens are sleep-deprived:
Nature provides at least a partial excuse. When children reach adolescence, their circadian rhythms, or internal clocks, shift, making them more awake at night. Sixth-graders got 8.4 hours on school nights, the survey found. By contrast, seniors in high school slept an average of 6.9 hours on school nights.

The science of lost sleep in teens:
The report indicated that adolescents aged 13 to 22 need nine to 10 hours of sleep each night. It also discussed the hormonal changes that conspire against them. When puberty hits, the body's production of sleep-inducing melatonin is delayed, making an early bedtime biologically impossible for most teens. At the same time, the report notes, external forces such as after-school sports and jobs and early school start times put the squeeze on a full night's sleep.

The result: A "profound negative effect" on mood, school performance and cognitive function. Studies also show that young people between 16 and 29 years of age were the most likely to be involved in crashes caused by the driver falling asleep.
Teens rack up sleep debt:
Most teens miss sleep because of the normal changes of adolescence, compounded by distraction. Sleep specialists speak of circadian rhythms, or the body's internal clock. As children reach their teens, that clock shifts: They are wider awake later at night, and prone to sleep later in the morning. This "phase delay" makes it difficult to fall asleep before 11 p.m.

School schedules, on the other hand, are built around busing needs and plans for daylight sports events, among other things. Most teens must get up around 6:30 or 7 a.m. to make it to school on time.

This leads to epic early-morning battles.
Sleep-Deprived Teens Paying Price:
"In the competition between the natural tendency to stay up late and early school start times, a teen's sleep is what loses out," said Jodi A. Mindell of St. Joseph's University in Philadelphia.
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Some school districts, most notably the Minneapolis public school district, have been trying later start times for high schools, Assuras reports. Researchers have seen some benefits, but in many school districts, conflicts with bus schedules and after-school activities make such changes extremely difficult.

Assuras says, short of getting school start times changed, teens might want to take some advice from experts, who recommend saying goodbye to the entertainment zone in the bedroom, cutting out caffeine after lunchtime, setting up a daily sleep and wake-time routine, and being aware that trying to catch up by sleeping in on weekends throws off your natural body rhythm.
America's Sleep-Deprived Teens Nodding Off at School, Behind the Wheel, New National Sleep Foundation Poll Finds:
As children reach adolescence, their circadian rhythms -– or internal clocks -– tend to shift, causing teens to naturally feel more alert later at night and wake up later in the morning. A trick of nature, this "phase delay" can make it difficult for them to fall asleep before 11 p.m.; more than one-half (54 percent) of high school seniors go to bed at 11 p.m. or later on school nights. However, the survey finds that on a typical school day, adolescents wake up around 6:30 a.m. in order to go to school, leaving many without the sleep they need.

"In the competition between the natural tendency to stay up late and early school start times, a teen's sleep is what loses out," notes Jodi A. Mindell, PhD, co-chair of the poll task force and an NSF vice chair. "Sending students to school without enough sleep is like sending them to school without breakfast. Sleep serves not only a restorative function for adolescents' bodies and brains, but it is also a key time when they process what they've learned during the day." Dr. Mindell is the director of the Graduate Program in Psychology at Saint Joseph's University and associate director of the Sleep Center at The Children's Hospital of Philadelphia.

Just too wired: Why teens don't get enough sleep:
The researchers said that as children reach puberty, their body clocks tended to readjust to start two hours later, so they are more alert at night and sleepier in the early morning. Mindell and Carskadon said schools should adjust their schedules accordingly, and start later. A few have done so, they said, and found that instead of staying up later, students sleep longer.

Studies by Brown, Lifespan scientists are at cutting edge of sleep research:
"Some of our kids are literally sleep-walking through life, with some potentially serious consequences," Millman said. "As clinicians and researchers, we know more now than ever about the biological and behavioral issues that prevent kids from getting enough sleep.

(Also, see my take on this isssue)

Monday, March 27, 2006

Does circadian clock regulate clutch-size in birds? A question of appropriatness of the model animal.

The questions 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 hard to dispute.

Which organisms have been chosen as laboratory models often depends on contingencies of history. Somebody at some point in time had a large supply of a particular species, did some good research on it and everything took off from there. Some species proved untractable and were discarded. Others flourished and were adopted by more and more researchers over time. Some models are really good for studying particular areas of biology. The fruitfly is unparalleled as the organism for genetic studies. However, its development is quite unusual so the findings are difficult to generalize even to other Dipterans, even less to other insects, arthropods or other animals.

What makes a good laboratory animal model?

A good animal model should be one about which there is quite a lot of background information. It should be available in large numbers and it should be rather small in size so a lab can keep large numbers of individuals in a relatively small space. Being social also makes housing easier. A good model animal is also easy to keep in captivity, it is easy to feed and easy to handle without too much danger to the technicians. Ideally, it easily breeds in captivity, has a short generation time and large numbers of progeny.

A brief aside about mammalian models

It is not surprising that early studies in anatomy and physiology utilized domesticated animals. Much of 18th and 19th century research was done in dogs, cats, rabbits, sheep, goats, pigs and even horses. Such animals were easily available, there was a lot of existing knowledge about them, and they were easy to house, feed and handle. Furthermore, one could always "sell" such research as useful for advances in agriculture. However, there are definite drawbacks in using these species as well. They tend to be large, with long generation times and with few progeny. Also, being human companions for thousands of years, people get easily attached to them and the anti-vivisectionist movement was quite strong in the 19th century, especially in England.

Thus, after several decades of effort, several new species were domesticated in order to provide the researchers with more tractable and less controversial animals to work with. These include rats, mice, hamsters, guinea pigs, ground squirrels and ferrets. Much of the research in the 20th century was performed on these species. In the last couple of decades, one of those species gained prominence - the mouse - due to its tractability to genetic techniques. Much of the findings from rodent (including mouse) studies have been found to be generalizable to other rodents, to other mammals (including humans) and to other vertebrates. Much has been learned that proved applicable to endangered species and their reproduction in captivity. Rarely is any work done on rodents these days that as its main aim has the better understanding of the rodents. Mainly, the mouse and the rat are the stand-ins for humans and the research is thought of as biomedical research.

Avian models

The bird models have quite a different history. The readily available species are the domesticated birds, better known as poultry - chicken, quail, duck, turkey, goose, pigeon and the guinea hen. There was never a need to move away from these species, as they are small, social, breed fast and a lot, and are viewed as food (and not as "cute pets") thus they were a less likely target of anti-vivisectionists.

Sure, many biologists studied wild species in the field and in the lab. Even today, much work is done in parrots, European starlings, house sparrows, house finches, crows, etc. But wild species are tough to work with. One has to go out and catch a new batch for each new experiment. Poultry is so much easier to handle and breed in the lab.

The lack of a historical "switch" from one group of species to another had one unfortunate consequence. Research on domesticated species of birds is too easily dismissed as Poultry Science, geared towards increased meat and egg production at farms (what's wrong with that? The findings from such research usually make the life for farm birds better, e.g., less stressful). It is sometimes forgotten that many scientists use poultry species with a different motivation altogether - as a model for wild birds, hopefully generalizable even broader to other vertebrates or even all animals. Many findings from poultry research are now being used to help endangered bird species survive and breed in the wild and in captivity.

Why such a long intro?

Because my lab animal is a domesticated bird, poultry if you wish - the Japanese quail. I will not be unhappy if my research gets picked up by poultry scientists and applied to make the life of farm birds easier, but that is not my main motivation. I am interested in particular aspects of basic science of chronobiology and I found quail to be an excellent model for questions that are difficult or even impossible to do in mammals. I hope that my work is generalizable to wild birds and will help in saving endangered species from extinction. I hope that at least some of my work will be even more broadly generalizable, perhaps to all vertebrates, or even to all of life.

Japanese quail (Coturnix japonica) has been domesticated about 500 years ago in Japan. The name 'Japanese quail' is used to denote the domesticated birds in laboratories and on farms. Their counterpart in the wild, itself not an endangered species, is usually called Asian Migratory Quail, and it appears that there is not that much difference between wild and domesticated populations in many aspects of their biology. With incubation time of 17 days, maturation time of six weeks, and ability to lay almost an egg a day throughout the year, quail is the mouse of the avian biology lab. The chicken genome has been sequenced. Every gene that has beem looked at is between 95 and 100% identical between the chicken and the quail. It appears that the difference between the two species is mainly due to regulatory regions of the genes driving somewhat different trajectoris of embryonic developments, similarly to the difference between humans and chimps.

An important part of my Masters degree research (but not my PhD) was on the mechanisms by which the circadian system controls reproduction - both seasonally (photoperiodism) and daily (the timing of egg-laying). My MS thesis has been published in these two papers [Note: the first one appears not to be available in its entirety online - you can only see the abstract. I have notified the Journal and once this is fixed I will make the appropriate link to the PDF of the whole paper. Update: The paper is now online and can be accessed here].



Circadian control of egg-laying

Circadian system in Japanese quail, and presumably in many other (perhaps all?) species of birds, is a two-oscillator system. It is as if the brain contains two separate circadian clocks, each with its own properties. These two clocks also interact with each other. One of the clocks is easily and directly entrained by the environmental light-dark cycles. It governs the overt daily rhythms of such things as body temperature, feeding activity, heart rate, blood pressure and release of hormones such as melatonin. The other clock appears not to be directly sensitive to light. It seems that it gets its information about the environmental lighting conditions from its interaction with the first clock. This second clock (or second component of the circadian system) also drives rhythms such as activity and body temperature, but more importantly, it drives the circadian rhythms of ovulation and oviposition. In this species, once an egg is laid, the next follicle ovulates about 45 minutes later. It takes anywhere between 24 and 30 hours for an ovulated egg to be laid. Thus, one egg is laid each day.

The two circadian clocks interact in ways that are possible to describe using models borrowed from the physics of oscillations (remember the pendulum from high school?). One of the predictions from the model is that some biological events can happen only when the two oscillators are in a particular phase-relationship with each other. This phase, in regards to ovulation in birds, is sometimes called "the permissive zone". Only if the ovary is ready to ovulate during this zone, ovulation will occur. Otherwise, it will wait until the next day.

In short daylengths, e.g., during the winter, the permissive zone is so narrow (or even non-existent), so that no ovulation happens at all. The bar on top of the graph indicates the duration of the day - white and night - black. The first line is first day, the line below it is the second day, etc. X-axis is 24 hours long. Bluish area shows the times when the first clock drives body temperature to be above the daily mean and drives the animal to be behaviorally active; the white area shows the times when the first clock determines when the quail is asleep and the melatonin levels are high.
As the photoperiod increases in spring, the permissive zone appears (between two dotted lines) and is broad enough that ovulation can happen. In relatively short photoperiods (but above the critical photoperiod for the onset of ovulation), the two clocks are quite tightly coupled. They are almost entrained to each other - they exhibit what is called relative coordination, which means that the two clocks can entrain ("lock") to each other for a few cycles but cannot remain phase-locked indefinitely:
The first egg gets laid at the beginning of the permissive phase. Each day, the second clock tries to escape from the pull of the first clock and to time the egg-laying a little bit later. Finally, the ovulation reaches the end of the permissive phase and the clutch stops. If everything is OK, prolactin will kick in to prevent the hen from laying any more eggs and she can sit down on her eggs and incubate them. If a predator, like a snake, eats the eggs (or a researcher removes the eggs from the cage) there is no rise in prolactin and the quail starts a new clutch all over again, following the same pattern, after one or two days of pause.

A couple of months later, after the bird has succesfully raised a brood of hatchlings, the quail may decide to renest. This is now early summer and the daylength is much longer. The permissive phase is much broader and intrudes even into the night. On the other hand, the coupling between the two clocks is now very weak and the second clock freeruns with its own inherent period which can be anywhere between 26 and 30 hours. The pattern of egg-laying now looks something like this:
Now compare the last two figures. One thing that you will notice is that the clutch consisted of more eggs in shorter photoperiod (spring), than in the long photoperiod (summer). This is something that has been observed in a number of species of birds in the wild. The above figures are schematics. Here are some real data. Every 10-minute period that is black denotes the time when body temperature is above the daily mean. The light bars on top show when the lighs were on (white) and off (black). Circles show times when eggs were laid. On the top is a quail in LD 14:10. In the middle is a quail in LD 18:6. On the bottom are two examples of oviposition patterns during a transition from LD 14:10 to LD 18:6 (all from [1]):

Not so obvious, but the time-difference between two successive eggs in spring is just a little bit longer than 24 hours. In summer, this difference is 26-30 hours. This means that in summer, each follicle has more time to get filled by filtering of blood and each egg has more time to spend in the oviduct and the shell-gland. One should expect that summer eggs will be, on average, larger, heavier and with thicker shell than eggs laid in early spring. Evolutionary theory predicts the existence of a trade-off between egg-number (i.e., clutch-size) and egg-size. It is almost like a switch between r-strategy and K-strategy. In spring, premium is put on quantity and in summer on quality of progeny. The quail literature suggests that the circadian clock is the physiological mechanism underlying this switch in evolutionary strategies.

How generalizable is this finding?

Apart from Japanese quail, few other species have been studied. The sister species, European Migratory Quail (Coturnix coturnix), which is not domesticated, has virtually identical egg-laying patterns. In domestic chickens, it looks very similar, except that the first egg is laid at dawn (as opposed to noon) and the last egg is laid around noon (as opposed to evening). A couple of studies in turkeys also suggest the same mechanism.

Can we generalize this finding to all Gallinaceous birds at least? Sounds reasonable, but I do not know. Is the same mechanism operating in birds from other Orders? Hummingbirds? Owls? Ostriches?

There is an interaction between estrous cycle and circadian cycle in rodents. Sex steroid hormones that are released during ovulation have effects on circadian clocks in several species of birds and mammals (presumably also humans). Does this information make it seem more likely that the quail data are generalizable to all birds?

Every time I ask a friend who studies wild birds at what times the eggs are laid, the answer is "I don't know - we usually find the eggs in the morning". This means that the egg could have been laid at any time between 5pm and 9am - a very broad region. No temporal patterns appear to be known in wild birds. So, if you study wild birds, please let me know at what time of day the eggs are laid. Let's see if the data gathered from poultry are useful for the study of wild species as well.

[1] Bora D. Zivkovic, Herbert Underwood, and Thomas Siopes, Circadian Ovulatory Rhythms in Japanese Quail: Role of Ocular and Extraocular Pacemakers, JOURNAL OF BIOLOGICAL RHYTHMS, Vol. 15 No. 2, April 2000 172-183

Sunday, March 26, 2006

Sleep Schedules in Adolescents

I am glad to see that there is more and more interest in and awareness of sleep research. Just watch Sanjay Gupta on CNN or listen to the recent segment on Weekend America on NPR.

At the same time, I am often alarmed at the levels of ignorance still rampant in the general population, and even more the negative social connotations of sleep as an indicator of laziness.

Nothing pains me more than when I see educators (in comments) revealing such biases in regards to their student in the adolescent years. Why do teachers think that their charges are lazy, irresponsible bums, and persist in such belief even when confronted with clear scientific data demonstrating that sleep phase in adolescents is markedly delayed in comparison to younger and older people?

The shift in sleep-phase of adolescents is one of the best documented and most studied phenomena in human chronobiology. If you dig through my ClockNews category, you'll see that almost every issue has something about adolescent sleep patterns. My first and still most popular post here addresses this phenomenon in some detail (as well as some advice), especially this sweet paper that came out a couple of years ago (follow the references within or search MedLine, Web of Science or Google Scholar for more information).
In short, presumably under the influence of the sudden surge of sex steroid hormones (and my own research gently touches on this), the circadian clock phase-advances in teen years. It persists in this state until one is almost 30 years old. After that, it settles into its adult pattern. Of course, we are talking about human populations - you can surely give me an anecdote about someone who does not follow this pattern. That's fine. Of course there are exceptions, as there is vast genetic (and thus phenotypic) variation in human populations. This does not in any way diminish the findings of population studies.

Everyone, from little children, through teens and young adults to elderly, belongs to one of the 'chronotypes'. You can be a more or less extreme lark (phase-advanced, tend to wake up and fall asleep early), a more or less extreme owl (phase-delayed, tend to wake up and fall asleep late). You can be something in between - some kind of "median" (I don't want to call this normal, because the whole spectrum is normal) chronotype.

Along a different continuum, one can be very rigid (usually the extreme larks find it really difficult to adjust to work schedules that do not fit their clocks), or quite flexible (people who find it easy to work night-shifts or rotating shifts and tend to remain in such jobs long after their colleagues with less flexible clocks have quit).

No matter where you are on these continua, once you hit puberty your clock will phase-delay. If you were an owl to begin with, you will become a more extreme owl for about a dozen years. If you are an extreme lark, you'll be a less extreme lark. In the late 20s, your clock will gradually go back to your baseline chronotype and retain it for the rest of your life.

The important thing to remember is that chronotypes are not social constructs (although work-hours and school-hours are). No amount of bribing or threatening can make an adolescent fall asleep early. Don't blame video games or TV. Even if you take all of these away (and you should that late at night, and replace them with books) and switch off the lights, the poor teen will toss and turn and not fall asleep until midnight or later, thus getting only about 4-6 hours of sleep until it is time to get up and go to school again.

More and more school districts around the country, especially in more enlightened and progressive areas are heeding the science and making a rational decision to follow the science and adjust the school-start times accordingly. Instead of forcing teenagers to wake up at their biological midnight (circa 6am) to go to school, where invariably they sleep through the first two morning classes, more and more schools are adopting the reverse busing schedule: elementary schools first (around 7:50am), middle schools next (around 8:20am) and high schools last (around 8:50am). I hope all schools around the country eventually adopt this schedule and quit torturing the teens and then blaming the teens for sleeping in class and making bad grades.

No matter how much you may wish to think that everything in human behavior originates in culture, biology will trump you every now and then, and then you should better pay attention, especially if the life, health, happiness and educational quality of other people depends on your decisions.

(See more here)

Jet-lag is bad for you long-term, too

Chronic 'jet lag' produces temporal lobe atrophy and spatial cognitive deficits:
Time-zone travelers encounter a pattern of light and darkness, and their endogenous circadian rhythms adapt to the new external time cue until both timing systems synchronize, but the long-term repeated disturbance of synchronization between the two timing systems impairs physiological and psychological health and induces stress. Salivary cortisol levels in cabin crew after repeated exposure to jet lag were significantly higher than after short distance flights, and the higher cortisol levels were associated with cognitive deficits that were dependent on non-semantic stimuli. The present study demonstrates that significant prolonged cortisol elevations produce reduced temporal lobe volume and deficits in spatial learning and memory; these cognitive deficits became apparent after five years of exposure to high cortisol levels.

Hat-tip: Eide Neurolearning Blog

Sunday, March 19, 2006

Some hypotheses about a possible connection between malaria and jet-lag

Malaria Action Day is today, March 19th. Read Tara, Tim and me for more information. You should play basketball today, as part of the Dunk Malaria initiative. You should donate to The Global Fund for the fight against malaria (and send Tim the confirmation e-mail you get, so he can match it up to $300). Post this information on your blog (or e-mail to friends) today. Write a blog-post or journal entry about malaria or something related and I will put together a linkfest on Sunday (on Science And Politics), linking to all bloggers who send me permalinks of their posts on the topic. If you have not written anything recently, but have a good post from the past, send it anyway. The posts need not focus on biology or medicine of malaria - writings on history, geography, economics and politics of this disease are equally welcome.

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 constellation of symptoms popularly known as "jet lag", caused primarily due to mismatch between the timing of circadian clocks of the traveller and the external periodic environment. It is often seen that the jet-lagged individuals who visit their family and friends in areas endemic to malaria have an enhanced susceptibility to malarial infection than the local residents. It would therefore be interesting to explore whether increased susceptibility to malarial infection among the visitors has anything to do with their state of jetlagged.
Indeed an interesting hypothesis. Of course, the travellers may also be less resistant to malaria than the locals, or less likely to have a life-style and behavioral patterns conducive to avoiding the mosquito bites, something that may be "second nature" to the locals. They continue:
Individuals with moderate to severe skin response to mosquito bite are largely protected against mosquito borne malaria because itch alerts an individual to mosquito bite and prepares him/her to take necessary precautions to prevent mosquito bite. Itch in an individual follows a diurnal pattern, and it is about hundred folds higher during midnight than midday. A hundred fold increase in itch sensitivity is viewed as a crucial preventive measure against mosquito bites, as this coincides with the midnight flight activity peak of female Anopheles mosquitoes, when she sucks blood from the host after mating peaks in the evening to raise her progeny. Normally individuals residing in endemic areas have their daily peak of itch sensitivity overlapping with the peak – biting phase of female Anopheles mosquitoes. As a result, they are relatively well protected against malarial infection.
Interesting idea: if you are sensitive to bites at the time when no mosquitoes are flying and are not sensitive to bites at the time when mosquitoes are flying, you may not get to squash that mosquito in time to prevent the Plasmodia to be injected into your bloodstream. Additionally, a jet-lagged individual may experience a peak of body temperature at night. Mosquitoes, among else, home in on the warmth of their victims. Thus, jet-lagged individuals may be warmer than the surrounding locals at midnight and thus more attractive to mosquitoes at that time.
On the other hand individuals visiting endemic areas from different time zones, particularly during the first couple of days are under the state of jet lag, and their peak protective daily behavioural itch sensitivity lies out of phase with the biting peak of female mosquitoes. Therefore, such individuals are at a greater risk for sustaining malaria compared to the residents. Thus from chronobiological perspective one is of the opinion that a person can be protected against malaria by appropriately adjusting circadian clocks regulating itch sensitivity to the periodic environment. We hope that recent developments in circadian biology will help us predict extent of adjustments necessary in a new environment, which can then be of paramount importance for the protection of jet-lagged travelers to endemic regions against malaria. Some protection against malaria in the chronotherapeutic procedures such as melatonin administration, light therapy, scheduled physical exercise, maximum exposure to new environment during vector free times, social interactions, and appropriate food habits, are a few recommended preventive measures for travelers visiting a malaria endemic areas, in addition to malarial antibiotic prophylaxis.
Sounds like good advice, although the administration of melatonin is always an iffy question. However, this hypothesis got my mind all twirling and I came up with some hypotheses of my own. However, it is important to distinguish between different kinds of hypotheses regarding a putative link between jet-lag and malaria. They suggest that jet-lag may:

1) affect the rate/ease of infection with malaria,
2) affect the symptoms of malaria in an infected individual,
3) affect the ability of the body to fight off the infection,
4) affect the effectiveness of treatments, and
5) affect the likelihood that the infected individual will spread the disease to others.

The Kumar/Sharma hypothesis is clearly of the #1 type. I will look more at other types of hypotheses - those that apply to already infected individuals. For that, let's first go quickly through the basic biology of malaria.

Malaria is caused by a protist in the genus Plasmodium. While Plasmodium falciparum is the most common species, three or four other species are also causes of malaria in humans, and dozens of other species cause malaria or malaria-like diseases in other animals, including mammals, birds and reptiles.








Plasmodium is transmitted through bites of several species of mosquito from the genus Anopheles. Once injected into the final host (e.g., human), the plasmodia remain in the skin for several hours, then migrate to lymph nodes, spleen and liver where they undergo several transformations. The final stage - the gametocyte - migrates into the red blood cells. Inside each red blood cell one can find a large number of plasmodia, hiding there from the immune system of the host. The whole life-cycle lasts several days, even weeks to complete.


All the plasmodia burst out of red blood cells simultaneously. Enormous number of plasmodia suddenly released into the blood overwhelms the immune system of the host, allowing the plasmodia to survive unscathed for quite a long time. This time is sufficient for them to invade blood vessels in the skin where, if they are lucky, a mosquito will bite and the plasmodia can invade the mosquito again and search for the next host.


The bursting of red blood cells triggers high fever and sweating. High temperature, high carbon-dioxide, as well as some odors [2] present in the sweat are all highly attractive to mosquitoes, rasing the probability that the host will get bitten. In some species of Plasmodium (like P.falciparum), the bursting of red blood cells occurs every night. In some species of Plasmodium, the resulting fever occurs every two nights and in some every four nights (rarely three), causing, respectively, tertian and quartan fevers. Tertian and quartan malaria are treated by chloroquine, while falciparum malaria is treated by quinine, mefloquine or halofantrine.

Obviously, from the perspective of a Plasmodium, timing is crucial. First, it is important to errupt in synchrony. Yet, hidden inside red blood cells, plasmodia cannot communicate with each other. Second, it is important to time the eruption in such a way as to maximize the probabilty that some of the gametocytes will be picked up by mosquitoes. Thus, it is important for the eruption to occur at the time of day when mosquitoes are most actively foraging for blood.

How do the Plasmodia solve the problem of timing? This is where circadian biology comes in [3,4,5]. Plasmodia residing inside red blood cells use the time-clues generated by the host. More specifically, they key onto the nightly release of melatonin by the pineal gland. Melatonin is practically undetectable in the blood during the day and the concentrations rise steeply in the evening remaining high for the duration of the night (exact patterns differ between vertebrate species), then dropping again at dawn.

Plasmodia have melatonin receptors [3]. Interestingly, unlike melatonin receptors in vertebrates which are nuclear receptors, the receptors in Plasmodia are membrane receptors. Membrane receptors are much faster than nuclear receptors which is important when a biological event has to be timed with precision. However, the plasmodia do not destroy the red blood cell immediately after receiving the melatonin signal - that would be too early in the evening for the timing to be adaptive, as the mosquitoes are still too busy looking for mates and mating at that time. Instead, the plasmodia use their own circadian clocks to measure the exact timing of eruption. In a way, it appears that the host melatonin signal entrains (synchronizes) the clocks in plasmodia, and then the Plasmodium clock determines the phase (exact timing) for the eruption out of red blood cells.

Different species of Anopheles and even geographically distinct populations of the same species have different times of peak foraging (biting) activity. In each geographical region, the local population (or species) of Plasmodium evolved the timing of eruption to match that of the local mosquitoes.

Let's now introduce another player. Apart from the parasite (Plasmodium), the host (a vertebrate, e.g., a human), and the vector (mosquito), one should also consider the predator - insectivorous bats that hunt for mosquitoes. The way that the malaria literature tends to think about timing can schematically be presented like this:
There is an assumption that plasmodium eruption, human fever, mosquito foraging and bat hunting are all synchronous. We have already looked at this from the perspective of the Plasmodium - it is adaptive for the Plasmodium for the three bottom lines to be accurate, i.e, that the parasite, the host and the vector are in synchrony. This also means that this is maladaptive to humans. It is also maladaptive to mosquitoes whose fitness does suffer somewhat if they are loaded with parasites.

On the other hand, it is maladaptive for mosquitoes and plasmodia, and adaptive for humans and bats, if the peak hunting time for bats coincides with the peak foraging time of mosquitoes. More these two events are in sync, more mosquitoes will get eaten, thus less plasmodia will get into a new host and less humans will get infected.

The dynamics of the timing relationship between the four species can be described as an Evolutionary Arms-Race Around The Circadian Clock. While some of the players will try to maximize their fitness by achieving synchrony, the other players maximize their fitness by avoiding synchrony with each other. This can be depicted, for bats and mosquitoes, like this:
In this case, mosquitoes evolve to forage at later times of night, and bats evolve to track the mosquitoes by hunting later at night. This can go on back and forth endlessly. But, and here is a big "but". This model is quite oversimplified as it posits only four players and for each player an absolute loyalty to the other three. But is the real world that simple?

Plasmodium species are pretty host-specific. Species that thrive inside humans, may not thrive or even survive inside the bodies of other animals and vice versa. So, the parasite is pretty loyal to its host. It is also completely dependent on Anopheles - it will most likely not survive inside a different kind of mosquito.

The same mosquito that usually bites a human will happily take a blood meal from another animal. This is actually used as one of the prevention techniques: a village is surrounded by fields full of cattle, sheep, goats, horses, donkeys or camels. The mosquitoes coming out of the woods at night encounter these animals first and get satiated with blood before they ever encounter humans. The animals themselves do not get sick.

Bats are unlikely, in my opinion, to be specialized on Anopheles as their only prey. If there are no mosquitoes around, they will happily hunt other insects (and the tropical regions where malaria is common are swarming with many species of insects!). I think that involvement of bats in the arms-race is the weakest aspect of the hypothesis. Here are four basic types of bat hunting activity that are theoretically possible:
The hypothesis suggests that bats mostly fly around midnight when the mosquitoes are most active, i.e., the bats are winners and mosquitoes loosers in the arms-race (A) . If the peak is at some other point during the night, that would suggest that bats are involved in the arms-race but the mosquitoes are currently winning (B). This may also suggest that bats highly prefer some other type of prey. The bats may be active throughout the night (C) which seems most likely. Finally, the bats may have a bimodal distribution: a lot of hunting early and late at night with a siesta right around midnight (D). This would suggest that mosquitoes have found their best temporal niche in that dangerous world, i.e, although the bats are not involved in the arms-race, the mosquitoes are and are thus winners, without making the bats "loosers" in the process.

What is the real story? I don't know. Obviously, it is possible to monitor patterns of bat activity [6,7], yet it still needs to be done in regions in which malaria is common. Some of the bats studied in the USA follow predominantly pattern C from the figure above, and it is not too far-fetched to hypothesize that all bats everywhere have similar patterns:
What are the Anopheles patterns? While they search for blood around midnight, that is not the only time they are flying around. Most of the early part of night is spent looking for mates, mating and laying eggs [8]. Thus, they are easy pickings for bats at times when they are not actively seeking humans. It appears that becoming diurnal is not a good option for Anopheles in the tropics - perhaps there are more birds there than bats, or the birds are more dangerous? It is not impossible for a mosquito to become diurnal - the mosquito we are used to seeing around here - the Culex - is crepuscular (dawn and dusk) and the Asian tiger mosquito is fully diurnal.
How does jet-lag figure in here? Apart from the hypothesis stated by Kumar and Sharma that itch sensitivity to mosquito bites gets displaced (and what I added - that temperature rhythm is also displaced), jet-lag will have other effects, too. Let's look at possible effects it may have on people who already have malaria (and you'll see why I had to use so much space describing all of the details of the arms-race above!).

Will jet-lag affect the way our body copes with the infection? In a jet-lagged human, there is no clear and sharp rhythm of melatonin release. Some amounts of melatonin are synthetized and secreted at all times of day. This means that the Plasmodium has lost its temporal anchor - there is no signal to use for determination of timing for eruption out of red blood cells. Thus, the gametocytes will errupt at random times - one cell now, another in an hour, another tomorrow. There is no safety in numbers any more - the human immune system is now perfectly capable of dealing with all the plasmodia in the circulation. Of course, the immune system itself may be somewhat compromised in a jet-lagged person.

Will jet-lag affect the way malaria presents its symptoms? The asynchronous eruption of plasmodia also means that there will be no abrupt onset of high fever at midnight. Instead, one may expect a continous low-grade fever. Nightly episodes of high fever are an important symptom of malaria. Will a physician with a patient who exhibits continuous low-grade fever ever suspect malaria? Especially a physician in a country in which there is no malaria and the patient has returned home from the tropical travels and is jet-lagged from a return trip.

Will jet-lag affect the effectiveness of drug treatments? I don't know the details of the way anti-malarial drugs work, so make sure you tell me if I get this all wrong. If the number of plasmodia in the circulation at any time is relatively small, and if the enzymatic destruction of the drug by liver is operating at a constant low rate (instead of with a circadian rhythm of its own), then being jet-lagged should enhance the effectiveness of the drugs, or even allow for the dose to be lowered.

Will jet-lag affect the ability of the patient to be a source of transmittion of the disease to others? With plasmodia erupting at all times of day and with most plasmodia being destroyed by the immune system throughout the day, it is much less likely that any will be present in the skin capillaries at just the right time - at midnight. Also, without a high fever coupled with sweating, the patient is less attractive to the mosquitoes than a malarial patient in the neighboring house who is local and not jet-lagged. Thus, the likelihood of plasmodia being picked up by mosquitoes is even smaller.

To summarize: according to the Kumar/Sharma hypothesis, being jet-lagged increases the chances for contracting malaria. On the other hand, if you already have the disease, it may be good for you to get jet-lagged! As long as you tell your physician that malaria is a serious option so the symptoms are not misinterpreted, you should be better off jet-lagged, allowing your body to fight the disease one plasmodium at a time.

Finally, as a matter of public health policy, how does one get the whole population of malarial patients in one country jet-lagged so as to reduce the transmission rates? Should hospitals induce jet-lag in malaria patients by shifting light-cycles or administering melatonin? How do the pros and cons of such treatment balance? Ah, so many hypotheses, so little data! I hope someone studies this in the future.

One last thing - notice that much of the work described above was performed by researchers outside of USA. Apart from a little bit of cellular physiology, most of the information comes from ecological field-work, and ALL of it is inspired by and informed by evolutionary theory. Not a single gel was run.

Now, I am not dissing molecular biology. Malaria is the only complex parasitic disease in which all players (plasmodium, mosquito and human) have their complete genomes sequenced, and much will be gleaned from such data in terms of designing better anti-malarial drugs, etc. But, as the above research shows, Big (molecular) Biology is not neccessary for findings that have a potential to seriously affect the infection and transmission rates of the disease.


[1] Jet lag and enhanced susceptibility to malaria, C. Jairaj Kumar and Vijay Kumar Sharma, Medical Hypotheses (2006) 66, 671–685

[2] Fooling Anopheles: Scientists Aim to Wipe Out Malaria by Outsmarting a Mosquito's Sense of Smell

[3] Calcium-dependent modulation by melatonin of the circadian rhythm in malarial parasites, Carlos T. Hotta, Marcos L. Gazarini, Flávio H. Beraldo, Fernando P. Varotti, Cristiane Lopes, Regina P. Markus, Tullio Pozzan and Célia R. S. Garcia, NATURE CELL BIOLOGY , VOL 2, JULY 2000, p.468

[4] Melatonin and N-acetyl-serotonin cross the red blood cell membrane and evoke calcium mobilization in malarial parasites, C.T. Hotta, R.P. Markus and C.R.S. Garcia, Braz J Med Biol Res 36(11) 2003

[5] Tertian and Quartan Fevers: Temporal Regulation in Malarial Infection, Célia R. S. Garcia, Regina P. Markus, and Luciana Madeira, JOURNAL OF BIOLOGICAL RHYTHMS, Vol. 16 No. 5, October 2001 436-443

[6] Sampling bats for six or twelve hours in each night? Esberard CEL, Bergallo HG, REVISTA BRASILEIRA DE ZOOLOGIA 22 (4): 1095-1098 DEC 2005

[7] Nightly, seasonal, and yearly patterns of bat activity at night roosts in the Central Appalachians, Agosta SJ, Morton D, Marsh BD, Kuhn KM, JOURNAL OF MAMMALOGY 86 (6): 1210-1219 DEC 2005

[8] Daily oviposition patterns of the African malaria mosquito Anopheles gambiae Giles (Diptera: Culicidae) on different types of aqueous substrates, Leunita A Sumba, Kenneth Okoth, Arop L Deng, John Githure, Bart GJ Knols, John C Beier and Ahmed Hassanali, Journal of Circadian Rhythms 2004, 2:6

Saturday, March 18, 2006

Circadian Rhythms in Human Mating

I remember from an old review that John Palmer did a study on the diurnal pattern of copulation in humans some years ago. You can see the abstract here.

Now, Roberto Reffinetti repeated the study and published it in the online open-source Journal of Circadian Rhythms here.
The two studies agree: The peak copulatory activity in people living in a modern society is around midnight (or, really, around bedtime) with a smaller secondary peak in the morning around wake-time.

Dig through the papers yourself for additional data on workday-weekend differences and the temporal patterns of the female orgasm.

Tuesday, March 14, 2006

Sleep societies

Don't worry too much about the source of this information - the list of sleep societies is correct.

Expecting a baby any day now?

If so, you may want to track the infant's sleep patterns, feeding, diaper-changes, etc. Now made easy with Trixie Tracker. The patterns will make your life more predictable, will let you notice when something goes wrong before it becomes too apparent, and will make childrearing even more fun.

Of course, you can use the software for tracking an adult, yourself included. You can replace baby formula with beer and track your drinking habit. It is quite flexible. Go take a look.

[Note: I just like the software - I do not get anything from advertising it here, and I have only briefly met the author at a blogging conference about a year ago]

Monday, March 13, 2006

What is a 'natural' sleep pattern?

I have mentioned this in my very first post here: in a natural state, humans do not sleep a long consecutive bout throughout the night. The natural condition is bimodal - two bouts of sleep interrupted by a short episode of waking in the middle of the night.

In today's New York Times, there is an article about this:

Sleep Disorder? Wake Up and Smell the Savanna by RICHARD A. FRIEDMAN, M.D.:

------------snip-----------

Many patients tell me they have a sleep problem because they wake up in the middle of the night for a time, typically 45 minutes to an hour, but fall uneventfully back to sleep. Curiously, there seems to be no consequence to this "problem." They are unaffected during the day and have plenty of energy and concentration to go about their lives.

------------snip-----------

The problem, it seems, is not so much with their sleep as it is with a common and mistaken notion about what constitutes a normal night's sleep.

It's a question that Dr. Thomas Wehr at the National Institute of Mental Health asked himself in the early 1990's. He conducted a landmark experiment in which he placed a group of normal volunteers in 14-hour dark periods each day for a month. He let the subjects sleep as much and as long as they wanted during the experiment.

------------snip-----------

By the fourth week, the subjects slept an average of eight hours a night — but not consecutively. Instead, sleep seemed to be concentrated in two blocks. First, subjects tended to lie awake for one to two hours and then fall quickly asleep. Dr. Wehr found that the abrupt onset of sleep was linked to a spike in the hormone melatonin. Melatonin secretion by the brain's pineal gland is switched on by darkness.

After an average of three to five hours of solid sleep, the subjects would awaken and spend an hour or two of peaceful wakefulness before a second three- to five-hour sleep period. Such bimodal sleep has been observed in many other animals and also in humans who live in pre-industrial societies lacking artificial light.

Carol Worthman, an anthropologist at Emory University in Atlanta, has studied the sleep patterns of non-Western populations. From the !Kung hunter-gatherers in Africa to the Swat Pathan herders in Pakistan, Dr. Worthman documented a pattern of communal sleep in which individuals drifted in and out of sleep throughout the night.

She speculates that there may even be an evolutionary advantage to interrupted sleep. "When we lived in open exposed savanna, being solidly asleep leaves us vulnerable to predators."

With artificial light, modern humans have essentially managed to extend their daytime activities late into the night, when all other sensible creatures are busy sleeping.

As a result, we have compressed our natural sleep into artificially short nighttimes, but not all people are so easily tamed by artificial light. Some people, who may just have very strong circadian rhythms, still have this primitive bimodal sleep that they confuse with a sleep disorder.

Add these people to the rest of us who, under the pressures of modern life, often have some trouble falling or staying asleep and there is a large captive audience for drug companies.

Thanks in large part to the meteoric rise in direct-to-consumer advertising, medications like Ambien and Lunesta have become household names and seductive panaceas that millions find hard to resist — even though a majority have no serious sleep problem to repair. If it's any consolation to those of you who are awake in the middle of the night for an hour or so, reading or watching television, you may simply be the most natural sleepers.

I have nothing to add, except I can also give you an image I dug up - the original data from Wehr's experiment. See how the sleep is bimodal during the long winter nights and gets compressed during simulated summer:

ClockNews

Kinder, Gentler Chemotherapy:
"Every drug has an optimal time when it is least toxic and most effective," says Dr. Block. "For cancer treatment, this is determined by several factors, including the biological uniqueness of the particular drug being given, the time when the specific type of cancer cells divide the most, when the normal healthy cells of the patient generally divide the least, the patient’s circadian clock and individual rest-activity cycles, and even the time zone the person resides in."

"We have found that often patients receiving their chemotherapy this way reduce what would have been recurring side effects of nausea, vomiting, diarrhea, and fatigue," explained Dr. Block cofounder and Medical/Scientific Director of the Block Center for Integrative Cancer Care, and Director of Integrative Medicine Program at the University of Illinois College of Medicine at Chicago. This is important because the debilitation caused by chemo can cause patients to reduce or even stop treatments that could otherwise help them win their battle with cancer." In fact, current research shows that up to 1/3 of chemotherapy patients abandon treatments prematurely due to the side effects.



Don't blame the other woman, she says:
Couples often don't consider that their libidos may be on incompatible circadian rhythms, but it's not unusual.


Forest Hill High to test 9 a.m. school-day start:
In fact, recent research finds that teenagers are not unlike narcoleptics at that time in the morning. In lab tests, teenagers fell asleep quickly and into the deep REM sleep state, said Mary Carskadon, the Brown University professor who conducted the study.

Carskadon said teenagers' circadian rhythms — essentially, their internal clocks — along with distractions such as the Internet make it difficult for them to go to bed before 10:30 or 11 p.m. That means they usually don't get enough sleep before early classes.

"It's a double whammy," Carskadon said. "They're not getting enough sleep to recharge their brains, and we're asking their brains to be on duty at the wrong time."

Wednesday, March 08, 2006

Clocks in Bacteria I: Synechococcus elongatus

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 first evolved in an aquatic, unicellular organism. While protists fit the bill quite nicely, having a bacterium with a circadian clock pushed the origin of the clock further back into the past. This made the researchers happy as it supported the notion that the clock was a universal property of life, as well as that it evolved only once in the history of Life on Earth. This also suggested that clocks in all organisms use same or similar intercellular mechanisms for generation of circadian rhythms.

At the time that clocks were discovered in cyanobacteria, only two circadian genes were characterized: period in fruitflies and frequency in Neurospora crassa. The second fly gene, timeless, was diescovered the following year, and the first mammalian gene Clock and the first plant gene Toc were discovered some years later. Thus, at the time, it was still plausible that all of life used the same mechanism for the circadian clock, just as all of life uses ATP for energy storage and DNA for information storage.

However, studying genetics in bacteria is a much quicker and easier task than in the large multicellular eukaryotes. Very soon, the cyanobacterial clock genes were discovered and it turned out that they had no resemblance to fly or mold genes. KaiA, KaiB and KaiC (as they were discovered in Japan, they were named "kaiten", which implies a cycle of events reminiscent of the turning of the heavens) have no homologies with any of the clock genes found in any other group of organisms and the internal logic of the bacterial clock is different from that in plants, fungi and animals, i.e., it is not a typical transcription-translation feedback loop.
The clock in cyanobacteria is better thought of as a relay switch. It turns about 2/3 of the genome on in the morning (and off in the evening) and turns on the remaining 1/3 of the genome at dusk (and off at dawn). Recent findings about bacterial, plant, protist, fungal and animal clocks suggests as many as five separate events of the origin of a circadian clock on Earth - one for each major group of organisms.

Mutations and deletions [1,2 5,6] of either one of the three Kai genes affect the circadian phenotype, either by altering the inherent period of the freerunning rhythm, or by abolishing rhythmicity altogether. Interestingly, Synechococcus cells appear to have a "memory" of the circadian phase in which they find themselves and this memory gets transmitted from parental to daughter cells during cell division. Actually, under certain conditions, cell division is a much more rapid process than a circadian cycle. In other words, Synechococcus may undergo several cell divisions over a period of a single day, yet the colony as a whole keeps its circadian rhythms running all along [2,3].

Next time, I will focus on the contributions of cyanobacteria to the understanding of the origin, evolution and adaptive function of circadian clocks.













References and further reading:

[1] Circadian clock mutants of cyanobacteria by Kondo T, Tsinoremas NF, Golden SS, Johnson CH, Kutsuna S, Ishiura M., Science.266(5188):1233-6 (1994, Nov 18)

[2] Circadian clocks in prokaryotes by Carl Hirschie Johnson, Susan S. Golden, Masahiro Ishiura & Takao Kondo, Molecular Microbiology, Volume 21 Page 5 (July 1996).

[3] Circadian Rhythms in Rapidly Dividing Cyanobacteria by Takao Kondo, Tetsuya Mori, Nadya V. Lebedeva, Setsuyuki Aoki, Masahiro Ishiura and Susan S. Golden, Science, Vol. 275. no. 5297, pp. 224 - 227 (10 January 1997)

[4] Independence of Circadian Timing from Cell Division in Cyanobacteria by Tetsuya Mori and Carl Hirschie Johnson, Journal of Bacteriology, p. 2439-2444, Vol. 183, No. 8 (April 2001)

[5] CYANOBACTERIAL CIRCADIAN CLOCKS — TIMING IS EVERYTHING by Susan S. Golden & Shannon R. Canales, Nature Reviews Microbiology 1, 191-199 (2003)

[6] Circadian rhythms: as time glows by in bacteria by Johnson CH, Nature 430, 23-24 (2004)

Monday, March 06, 2006

So, is Cryptochrome a clock gene in fruitflies, too?

From the press release earlier today:

NYU, Univ. Of London Study Offers Additional Evidence Mammals & Fruit Flies Share Make-Up On Function of Biological Clocks

A study by researchers at New York University and the University of London offers additional evidence that mammals and fruit flies share a common genetic makeup that determines the function of their internal biological clocks. The study appears in the latest issue of Current Biology.

The research team consisted of post-doctoral researcher Ben Collins, Esteban Mazzoni, a graduate student, and Assistant Professor Justin Blau of NYU’s Department of Biology and Professor Ralf Stanewsky of the University of London.

Drosophila fruit flies are commonly used for research on biological, or circadian, clocks because of the relative ease of finding mutants with non-24-hour rhythms and then identifying the genes underlying the altered behavior. These studies in fruit flies have allowed the identification of similar “clock genes” in mammals, which function in a similar manner in mammals as they do in a fly’s clock. However, prior to this study, biologists had concluded that the role of one protein-Cryptochrome (Cry)-was quite different between flies and mammals. In fruit flies, Cry is a circadian photoreceptor, which helps light reset the biological clock with changing seasons, or in jet lag-style experiments (in which light is manipulated to mimic the experience of traveling over multiple time zones) in the lab. In mammals, however, Cry assists in the 24-hour rhythmic expression of clock genes and has nothing to do with re-setting the clock.

The researchers sought to determine additional roles for Cry in fruit flies by testing the rhythmic expression of clock genes in flies with either a mutant version of Cry, or with Cry produced at artificially high levels. In both cases, they found that the clock had stopped - with high levels of clock gene expression when Cry was mutated, and low levels when Cry was over-produced. These results indicated that Cry normally inhibits clock gene expression in many clock cells - just as it does in the mammalian clock.

“In addition to finding a new function for Cryptochrome, the results reinforce that notion that fruit flies provide an excellent model for understanding the human biological clock that drives sleep/wake cycles and many other processes that contribute to our overall health,” said Blau.

The paper itself is not available online yet. If there is something in it that I feel needs to be commented on, I will post it later.

Sleep or Excercise?

What is more important: an additional hour of sleep or an hour of exercise? Dr. Michael Breus answers.

Friday, March 03, 2006

Sleep monitoring under realistic conditions

A new awakening for sleep research

Whether you are having problems to stay awake or falling asleep, sleep science has yet offered little help, due to costly and complicated diagnostics and treatments. Researchers aim to drastically change this with a new way of measuring sleep.

The IST project SENSATION is an ambitious project of 46 partners from 20 different countries, addressing sensing of physiological parameters, core computation, medical and industrial research. The aim is to take sleep research to a whole new level by developing a multipurpose sensing platform consisting of 17 micro sensors and two nano sensors, connected through a local area network.

"The sensors will allow you to sleep at home on, for instance, a mattress with sensors instead of going to a hospital which is much more comfortable and the test becomes more precise," explains Dr Evangelos Bekiaris, project coordinator. Today, you will have to go to a hospital sleep lab for 1-2 nights and have your sleep measured to evaluate your sleep. "These tests are costly and since monitoring sleep cannot be done in your home environment they are not as reliable," says Bekiaris.

The sensors will be integrated into a wide range of materials such as bed and pillow textiles, wrist straps, seat linings and the frames of glasses. Wirelessly integrated through a computer network they will measure your brain activity, heart rate, eye and muscle movements during your waking and sleeping hours. The data will be collected in a body area network, wirelessly transferred to a local area network and then sent to the hospital for analysis, Bekiaris explains. The sensors can also be used for safe monitoring and early warning of people while driving or supervising a critical task, like the operators of nuclear power stations or air traffic controllers, before they fall asleep and cause an accident.

The project is now halfway through its funding period and is already showing a lot of tangible results. The first stage of the project involved data collection, setting up of databases and formulating recommendations for the development of sensors.

"We have developed something which is truly unique, with two extensive databases of sleep data, one with data of normal sleep with 350 participants and another one with sleep data of 400 people monitored while working or driving, crossing the stage between vigilant to sleep," says Bekiaris. "About half of these people were tested in a driving simulator but the other half was tested driving on highways with double command cars. The tests show a significant difference in the persons reactions, as the persons in the simulator were more calm, knowing they were part of a test, whereas the people on the highways were really fighting sleep." It shows that when monitoring people in their daily lives there are significant differences in result, he continues.

The project, spanning such a vast research area, has the potential for a strong impact. According to statistics 25 per cent of the traffic accidents in the UK, or 40 per cent in the US, is related to driver fatigue. The project estimates that the SENSATION sleep platform with its sensors could reduce serious road accidents by 30 per cent and industrial accidents by over 15 per cent.

Although one of the main areas is to develop sensors to measure the waking state of a person, both the collected data from the project and the final results can prove to be useful for further research. "Take falling asleep at workplaces as an example," he says. "Today you have techniques that might alert you as you fall asleep, but what we want is a system that will alert the person already before this happens. In some work environments or while driving it might already be too late if you have started dozing off."

The applications are vast. You could monitor aircraft pilots to make sure they are awake. It could be used to monitor babies and prevent cot death, or in sleep management, to evaluate your own sleep and from this plan shift work according to people's biorhythms, Bekiaris explains.

"We currently have nine sensors ready and plan to present the first sensors and prototypes at the International conference on 'Monitoring sleep and sleepiness - from physiology to new sensors' which will be held in Switzerland 29-30 May 2006," says Bekiaris.

Real-life tests of the prototypes and the entire sleep platform are planned to start by the beginning of next year.

Wednesday, March 01, 2006

Circadian Leaf Movements in Plants

The very first circadian rhythm ever observed was a rhythm of opening and closing of leaves of a mimosa plant. That was a couple of centuries ago (1729, to be exact), reported by astronomer de Mairan. Since then, many researchers, from Charles Darwin, through 19th century botanists Zinn and Hoffer, to 20th century chronobiologist Erwin Bunning, studied this rhythm.

Now, you can see three examples of such movements (check the three plant species on the left sidebar there) on a website that provides the movies. Cool, isn't it?

(hat-tip: Discovering biology in a digital world)

ClockNews

The rhythm of life:
Mention circadian rhythms, and most of us think of jet lag or how tired we were after that all-night party. But researchers say that circadian clocks -- which control a 24-hour cycle first documented by a French scientist in a darkened closet in 1729 -- have profound effects on almost everything that walks, crawls or grows.

Circadian clocks control leaf and petal movements in plants, migratory patterns of birds, the life cycles of insects and biochemical reactions in bacteria. They also have major effects on us.

"We're finding there's no limit to the role these rhythms play," says Jay Dunlap, chairman of genetics at the Dartmouth Medical School, who studies circadian rhythms in fungi. "There's enormously rich biology behind this phenomenon."

The Sleep Racket:

Who's making big bucks off your insomnia?

Over the last year you could have made a pile of money by betting on a little company in the business of ... insomnia. Shares of ResMed, in Poway, Calif., leaped 44%, selling $465 million worth of “sleep-disordered-breathing” equipment--face masks, nasal pillows, humidifiers and so-called continuous positive airway pressure devices. “It’s a monster market; it’s bigger than Ben-Hur,” says Peter C. Farrell, ResMed’s voluble chief executive. You’d have done even better as an original investor in Pacific Sleep Medicine Services, a small chain of sleep centers, mostly in southern California. One of its founders who chipped in an undisclosed amount in 1998 saw his ante jump a hundredfold, says Tom J. Wiedel, Pacific Sleep’s chief financial officer.

Monday, February 27, 2006

Lunar Rhythms in the Antlion

[Note: People who have read my other blog about a year ago are familiar with this story]

When I was a kid I absolutely loved a book called "Il Ciondolino" by Ricardo Vamba - a book in two slim volumes for kids (how times change - try to publish a 200+ page book of dense text for children today!). I later found out that it was translated into English under the title The Prince And His Ants in 1910 (Luigi BERTELLI (M: 1858 or 1860 - 1920) (&ps: VAMBA) The Prince And His Ants [It-?]. Holt.(tr S F WOODRUFF) [1910] * Il Giornalino Di Gran Burrasca [It-?] (tr ?) [?] ) and was even The Nation's Book of the Week on June 2nd 1910.

["Vamba" is the pseudonym of Italian fantasist Luigi
Bertelli. The Prince and His Ants (1910) tells the tale of a boy who becomes an
ant, and a girl who becomes a butterfly. The English translation by one Miss
Woodruff was edited by Vernon Kellogg, an insect authority at Stanford
University. Ninety interior illustrations are scientifically accurate.]

This book is hard to find - don't even bother with Amazon - but my brother was persistent and after several weeks of patient searching he got a copy from Alibris and sent it to me. It is a story of a boy who wakes up one morning transformed into an ant. The book describes his travels and adventures in the world of the small. Of course, he meets a bunch of really cool creatures, like various wasps and bees and moths and honey-ants, etc. But the one I remember the most was the ant-lion.

The antlion is actually quite pretty, yet short-lived, as an adult. But it is the larva that is really cool:

It digs a pit in the send and hides underneath the sand right under the bottom of the pit. When an ant, or some other insect comes by, it falls into the pit and has trouble climbing out of its steep walls again. The ant-lion lunges out of the sand (like a scence from "Tremors") and eats the poor bug:

Now the really cool part: the volume of the pit is bigger when the antlion is hungrier (or so they say at this marvelous website that I highly recommend you browse around). But, hungry or not, the ant-lion digs a bigger pit when the moon is full. Nobody has any idea why that would be so. Here is a photograph of a colony of ant-lions, each with its own little pit:

But here is the coolest part of all. If you take ant-lions out of the field and put them in little sandboxes in the laboratory and isolate them from any cues about the outside world they will still dig bigger pits roughly every four weeks - they have an internal lunar rhythm:

They have, somewhere in their brains, a lunar clock that tells them to dig larger pits whenever the moon is full even if they canot see the moon itself (e.g., on a dark cloudy night). If and when somebody figures out how this little brain works, I'll be sure to tell you all on my blog, but you may have to wait years for it - nobody is even thinking about studying it right now.

Time out of mind

This article, Time out of mind (hat-tip: Inkycircus), is quite good at explaining in lay terms Advanced Sleep Phase Syndrome, describing famous Siffre's experiment (more popular with lay people, I think, as most chronobiologists, me included, regularly forget to mention it when talking about the history of the field), and explaining recent research in subjective time perception.

What really floored me are the comments that reveal that people are mostly still ignorant about biological clocks. Without religious objections that evolution triggers, and with so much coverage in the media, I expected that people will know at least a little bit more. I'll just have to keep blogging, doing my part in educating people about this important aspect of biology.

Thursday, February 23, 2006

Circadian Clocks in Microorganisms

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 easiest to measure. Rodents, as well as large walking insects like cockroaches, will turn running wheels, each revolution triggering a switch that sends a signal to the computer. Songbirds will jump from one perch to another, each perch flipping a switch connected to a computer. Lizards, while walking around the cage will tilt the cage from left to right around an axis - a metal bar on the bottom - which will turn a switch. Plants that exhibit leaf movements (closing at night, opening during the day) were the prime experimental models for a while (e.g., Kalanchoe, mimosa, tobacco).

Monitoring rhythms in other organisms is much harder: it is mighty difficult to make a fish run in a running wheel, or build hopping perches sensitive enough to be triggered by the landing of a butterfly. That was even harder back in the late 1940s and early 1950s when most of this work was done.

It is no suprise that nobody looked at microorganisms back then - it was just technically too hard. The fact is that most of the pioneers in the field came in from vertebrate physiology, ethology or ecology. It is easy for us, large mammals, to forget that we are not among the dominant life-forms on the planet - that title goes to bacteria, in terms of numbers of individuals, in terms of biodiversity, and in terms of total biomass. See if you can find mammals, or even all animals on the Tree of Life (click to enlarge):
Some old papers, mostly parts of Conference Proceedings of various kinds, mention as fact that Bacteria do not have clocks but do not provide any citations. It took me years to dig out three papers (Rogers and Greenbank, 1930, Halberg and Connor, 1961; and Sturtevant, 1973) with relevance to this question and all three are ambiguous about the final verdict. Why is nobody revisiting this with modern molecular techniques?

Being unicellular does not preclude one from having a clock, though, as single-cell Protista and Fungi all have circadian rhythms, which have been studied quite extensively since the 1970s or so (I intend to delve some more in that literature and write some posts on them in the future).

One group of bacteria does have a clock - the unicellular Cyanobacteria (if you are above a certain age, you may remember them under their old name: blue-green algae), in particular those species that do not form chains, e.g., Synechococcus and Nostoc. This was discovered very recently - only ten years ago (Mori et al. 1996). I was two years into my Masters when that paper appeared and I remember the excitement. I will certainly write a post or two on those soon:
There has not yet been a single study of any kind of rhythmicity in Archaea. Most of those microorganisms live in strange places - miles deep under the surface of the earth, in rocks, in ice, on the ocean floors and in the hydrothermal vents. They mostly do not inhabit rhythmic environments, so perhaps they do not need to have clocks - but it would be really nice to know if that is really the case:
Old Faithful, the famous geyser in Yellowstone park contains Archea. As the geyser erupts every 45 minutes or so, the microbes are suddenly exposed to very different environment: light, turbulence, lower temperature. Should we expect them to evolve a 45-minute clock that will help them predict the eruption so they can limit some sensitive biochemical reactions to the quiet periods and switch on the defenses agains light and cold every 45 minutes?

In The Geometry of Biological Time, Arthur T. Winfree suggested an experiment (on Page 580) that it
"... should be possible to demonstrate the effect by bacterial selection experiments in a chemostat. By alternating the nutrient influx from glucose without oxygen, to oxygen without glucose, to alanine and oxygen, cells would be forced into a three-point metabolic cycle." and "... reversing the order of the driving cycle, it should be possible also to select cells whose clocks run backward."
In a later edition (after we learned that cyanobacteria have clocks) he suggested, instead, to use
"one of the species of cyanobacteria that revealed no circadian rhythms in surveys before Mori et al. (1996), and use light as the alternative nutrient".
As of today, nobody has performed such an experiment, although Elowitz and Leibler (2000) came pretty close with a study in which they produced oscillations in Escherichia coli with periods of 3-4 hours, which are slower than the cell-division cycle:
So, if most of Life on Earth is Prokaryotic (Eubacteria and Archaea), and those groups do not have clocks, then clocks are not ubiqutous, are they? In my papers and in my Dissertation I try to hedge a bit by stating that they are found in "organisms that live on or close to the surface of the Earth", thus at least avoiding the deep-oceanic, deep-soil, and parasitic microorganisms (as well as burrowing and cave organisms that may have secondarily lost their clock).

Tuesday, February 21, 2006

Diurnal rhythm of alcohol metabolism

Why is breathalyzer a poor method of measuring blood alcohol levels for purposes of DUI tickets? Ed Brayton explains and links to DUI Blog with additional information.

Also, do not forget that every function in the body exhibits a circadian cycle. Likewise, alcohol metabolism:
This is from an old study, from the times when it was OK to recruit some college freshmen to drink alcoholic beverages in the name of science. This is a record of a diurnal rhythm in alcohol clearance, I believe (I cannot find the original paper I swiped this image from a long time ago).

It shows why we can drink more in the evening than at other times of day. You can save some serious money by downing a single shot at dawn, according to this graph.

So, at what time of day/night did the cops stop you to give you a breathalyzer test?

Sunday, February 19, 2006

Robustness of the Circadian Oscillator

Ricardo Azevedo of Newtons' Binomium wrote a great pair of posts on the robustness of biological systems, using circadian clock as the example.

Check them out: Blind Watchmaker or Swiss Designer? (Part I) and Blind Watchmaker or Swiss Designer? (Part II).

Lithium, Circadian Clocks and Bipolar Disorder

I have previously only touched on the immensely interesting topic of the possible connection between circadian clocks and the Bipolar Disorder. A recent paper prompted me to look into this in a little more detail.

Lithium Affects the Circadian Clock

First, let's go a little bit into the past, the early history of chronobiology. During the 1940s and 1950s, while the field was still in its pioneering spirit and little was known about the circadian clocks, many researchers were using survey (or shot-gun) approaches to the studies of biological rhythms: studying as many organisms as they could get their hands on in order to come up with generalities and evolutionary answers, surgically removing every possible organ or brain region in order to find locations of clocks in various organisms, exposing the organisms to every possible light regimen imaginable in order to study the oscillatory properties of biological clocks, etc.

One of the approaches was to administer to animals every chemical one could find on the lab-shelf to see how it affects the circadian rhythms. This line of work yielded a big surprise - biological clocks are amazingly resistant to pharmacological agents. The few substances that had an effect were hormone melatonin (naturally, as it is the main signaling molecule of the circadian system), heavy water (deuterium oxide) and lithium (a few others were found much later, including sex steroid hormones). Lithium had the same effect - slowing down the clock, i.e., increasing the period - in a number of philogenetically very distant organisms.

Lithium affects the Bipolar Disorder

At the same time, lithium was one of the most prescribed drugs for treating bipolar disorder (at that time usually called "manic-depressive disorder"). Soon enough, people started making the links between effects of lithium on bipolar dissorder and the effects of lithium on the circadian clock. Is the bipolar disorder essentialy a circadian clock disorder?

During periods of depression, the circadian rhythms are phase-advanced (click to enlarge):


Lithium is supposed to phase-delay the phase-advanced rhythms, i.e., bring them back to the normal phase. Here is an actograph of the sleep-wake cycle of a bipolar patient treated with various drugs, including lithium, as well as phase-shifts of the light-dark cycle, over a long period of time - click on the image to enlarge so you can read the text:



This does not appear to be a very efficient treatment by lithium in this particular patient, though.

Lithium Affects Circadian Pacemaker Cells in a dish

Much more recently, it was discovered that each individual pacemaker cell (in the suprachiasmatic nucleus of the hypothalamus) in the mammalian circadian system responds to lithium. In other words, the effects of lithium are not at the system level (e.g., interfering with cell-cell communication), but on the level of the cell. This suggests that lithium may act on a particular clock gene and the search for the gene in question commenced.



To make things easier, the candidate clock-gene target of lithium is likely not to be limited to mammals, or vertebrates, as lithium has the same effects on rhtyhms in other organisms, including the fruitfly Drosophila melanogaster. Thus, it is likely that the target clock gene is one that is shared by the circadian clocks in Invertebrates and Vertebrates, thus somewhat narrowing down the list of candidates.

Molecular Mechanism of Circadian Rhythm Generation in Mammals

Let me now try to explain how the mammalian circadian clock works on the molecular level in as simple way as possible, so the non-scientists reading this can - hopefully - understand. Biologists can follow the links for more detailed information if so inclined. In order to do this, I will first give a super-simple primer on molecular biology (I hope I don't make any stupid mistakes on this part as I type it very fast in order to get to the cool new stuff). This is an oversimplification, so I hope molecular biologists do not chastise me for omitting all the extraneous details, as much as they may be important. This is BIO 101.

We are all composed of billions of cells. All of the genetic material - DNA - is found in the nucleus of each cell. DNA is a very long linear molecule, built like a chain out of many, many links. The links in the chain are the nucleotides, each made of a sugar molecule, a phosphate and a nucleic acid. There are four types of nucleic acids in the DNA: adenine, thymine, cytosine and guanine (A, T, C and G). The order of links with different types of nucleic acids on the DNA chain is the "code".


A gene is a small string on the long DNA chain - a sequence of nucleotides that is transcribed as a unit. Transcription is the formation of an RNA molecule - also a chain - using the DNA as a template. Thus, transcription makes an RNA molecule that is a mirror image of the gene. Wherever in the DNA sequence there was C, in the RNA there will be G, and vice versa. Wherever there was T in the gene sequence, there will be A on the RNA transcript, and vice versa (with a little change here - RNA will have uracil - U - instead of T where appropriate).

Unlike DNA, RNA is capable of exiting the nucleus of the cell and entering the cytoplasm. It goes to a tiny little spherical organelle called the ribosome. There, aided by a bunch of enzymes (which are proteins) and some other types of short chains of RNA, the genetic trasncript gets tranlated into protein. The order of three consecutive nucleotides (a triplet) has a chemical meaning: it is a code for a particular amino-acid. The order of triplets, thus, determines the order of amino-acids placed in the chain.


Once the whole RNA sequence is translated, the chain of amino-acids is further modified by other enzymes - they change its shape, add little molecules to it, etc. These modifications are key to the proper function of the protein. For instance, adding an ion of iron to the hemoglobin makes it possible for this molecule to transport oxygen to every cell in the body. Adding a phosphate group gives the protein extra energy. Adding a short chain of sugars assigns the protein its "zip-code", i.e., tells other proteins in the cell where to take this protein to, so they can shuttle it across the cell along microtubules, to its destination where it will perform its fuction.


Some of the proteins (called "transcription factors") have a specific role to go back into the nucleus, find particular genes (they use particular gene sequences to find and recognize them), and bind to them. The binding has an effect in either stimulating or inhibiting the transcription of that gene into RNA. Thus, the protein of that gene will or will not be synthetized in that particular cell.

Genes involved in the generation of circadian rhythms can be loosely classified into core clock genes and associated clock genes. The core clock genes are almost all transcription factors. Their proteins act by inhibiting or stimulating transcription of other core clock genes (as well as regulating expression of other - downstream - genes that serve as functional outputs of the cell, i.e., telling the body when to relase a hormone and when not, when to sleep, when to wake up, etc.).

If core clock genes were all there is, the circadian cycle would last only a couple of hours, at best. That is how long it takes for all the players to switch on and off each other once. In order to prolong the cycle to be closer to 24 hours, oter genes are associated with the clock. Their protein products act as modifiers - they may add or remove phosphate groups on core clock genes, inhibit or stimulate expression of some of the core clock genes, degrade the core clock proteins either spontaneusly or upon receiving a signal that the retinae have perceived light, etc.

Here is a schematic of the mammalian circadian clock. Genes called Period, Cryptochrome, Clock and Bmal (or MOP) are the core clock genes in the mammals:


It is similar in other organisms, with some changes, and you can also watch a great animation movie here.

How lithium affects the molecular clock?

A couple of years ago, it was proposed that the protein involved in the clock mechanism that is sensitive to lithium is not one of the core clock genes, but one of the accessory genes - namely Glycogen Synthase Kinase 3ß (GSK3), which, in turn, acts on Rev-Erb, which in turn acts on Bmal.

Now, a new paper came out with more evidence that this is so:
Nuclear Receptor Rev-erb{alpha} Is a Critical Lithium-Sensitive Component of the Circadian Clock by Lei Yin, Jing Wang, Peter S. Klein and Mitchell A. Lazar. You can find the press-release and excellent media commentary here, here, here, here, and here.

According to this paper, lithium inhibits GSK3. GSK3 normally protects Rev-Erb from destruction. Rev-Erb normally inhibits expression of the core-clock gene Bmal (and perhaps also Period). Thus, when lithium is present, there is no GSK3 to protect Rev-Erb from being broken down. Without Rev-Erb, Bmal and Period get expressed again.

Perhaps this all means that in the Bipolar Disorder the clock gets "stuck" in some way. Perhaps Rev-Erb accumulates and stops the clock from running. Lithium indirectly aids the distruction of Rev-Erb, thus allowing the circadian cycle to proceed.

As they say:
"These results point to Rev-erb as a lithium-sensitive component of the human clock and therefore a possible target for developing new circadian-disorder drugs. Some patients taking lithium have developed kidney toxicity and other problems. Lazar surmises that new treatments that lead to the destruction of Rev-erb would have the potential of providing another point of entry into the circadian pathway."

Saturday, February 18, 2006

Sleepdoctor


Sleepdoctor is salivating at the prospect of checking out this patient, one of many who claim they never sleep at all - except when monitored in a sleep lab.

He also reports on the new term - Z-pills - that encompasses drugs like Lunesta, Ambien and Sonata.

Thursday, February 16, 2006

Sleep Education

Sleep Education is a new website that answers a lot of questions about sleep, sleep disorders and treatments. Check it out. Hat-tip: Sleepdoctor.

Sex differences, puberty and insomnia

Periods bring on sleepless nights:

Adolescent girls appear to be at greater risk of insomnia after they begin menstruation, a study has found.

This suggests that hormonal changes play a role in developing the sleep disorder, the researchers say in the journal Pediatrics.

Researchers found that among more than 1000 13- to 16-year-olds in the study, nearly 11% had suffered insomnia at some point.

Insomnia, based on formal clinical criteria, was defined as problems falling asleep or staying asleep at least four times a week for a month or longer.

Typically, the study found, the teens started having sleep disturbances around the age of 11.

Before menstruation, girls were about as likely as boys to have insomnia.

But after they began their menstrual periods girls had more than twice the risk of insomnia as boys.

The findings suggest that the hormonal changes that come with menstruation contribute to girls' insomnia risk, according to the authors.

Such a physiological reason is one of two broad explanations for why menstruation would be related to insomnia, says lead author Dr Eric Johnson.

The other possibility is that the physical changes that come with puberty, like breast development, create "social pressures" that contribute to sleep problems, says Johnson, a researcher with RTI International.

But he says menstruation is related specifically to problems with staying asleep and getting enough deep sleep.

These forms of insomnia are more likely to have physiological causes, whereas problems with falling asleep in the first place can often be stress-related.

In addition, girls' higher risk of insomnia was not explained by higher rates of depression, which is often marked by sleep disturbances.

A long lasting problem

Another key finding, Johnson says, is that of all teens who ever suffered insomnia, 88% also had symptoms at the time of the study.

This, he says, signals that the problem is lasting for many teenagers.

"Insomnia seems to be common and chronic among adolescents," Johnson and his colleagues conclude.

Given the consequences of sleep deprivation among teenagers, including blunted mental acuity, poorer school performance, and even poorer physical and emotional health, prevention and treatment may need to become "important priorities", the researchers say.

Therapies for insomnia include lifestyle changes to promote sleep, like getting to bed and rising at regular times each day, cognitive behavioral therapy and sleep medications.

Alternatively, sex steroid hormones may alter the properties of the circadian clock - perhaps decreasing its amplitude along with well-documented delay in phase. As they always say "More research needs to be done"....

Monday, February 13, 2006

Mammalian Clock Genetics - new papers

Here are two new papers, for connoiseurs only:

Rhythmic CLOCK-BMAL1 binding to multiple E-box motifs drives circadian Dbp transcription and chromatin transitions

Mammalian circadian rhythms are based on transcriptional and post-translational feedback loops. Essentially, the activity of the transcription factors BMAL1 (also known as MOP3) and CLOCK is rhythmically counterbalanced by Period (PER) and Cryptochrome (CRY) proteins to govern time of day–dependent gene expression1. Here we show that circadian regulation of the mouse albumin D element–binding protein (Dbp) gene involves rhythmic binding of BMAL1 and CLOCK and marked daily chromatin transitions. Thus, the Dbp transcription cycle is paralleled by binding of BMAL1 and CLOCK to multiple extra- and intragenic E boxes, acetylation of Lys9 of histone H3, trimethylation of Lys4 of histone H3 and a reduction of histone density. In contrast, the antiphasic daily repression cycle is accompanied by dimethylation of Lys9 of histone H3, the binding of heterochromatin protein 1alpha and an increase in histone density. The rhythmic conversion of transcriptionally permissive chromatin to facultative heterochromatin relies on the presence of functional BMAL1-CLOCK binding sites.

Feedback repression is required for mammalian circadian clock function

Direct evidence for the requirement of transcriptional feedback repression in circadian clock function has been elusive. Here, we developed a molecular genetic screen in mammalian cells to identify mutants of the circadian transcriptional activators CLOCK and BMAL1, which were uncoupled from CRYPTOCHROME (CRY)-mediated transcriptional repression. Notably, mutations in the PER-ARNT-SIM domain of CLOCK and the C terminus of BMAL1 resulted in synergistic insensitivity through reduced physical interactions with CRY. Coexpression of these mutant proteins in cultured fibroblasts caused arrhythmic phenotypes in population and single-cell assays. These data demonstrate that CRY-mediated repression of the CLOCK/BMAL1 complex activity is required for maintenance of circadian rhythmicity and provide formal proof that transcriptional feedback is required for mammalian clock function.

Friday, February 10, 2006

Melatonin Not Effective For Insomnias

Melatonin useless for sleeplessness - study

Paris - People who buy melatonin in the belief that it will cure jet lag or other forms of sleeplessness are wasting their money, a study published in Saturday's British Medical Journal (BMJ) says.

Melatonin is a hormone secreted in the pineal gland, a small organ about one centimetre long located at the base of the brain. It is indirectly stimulated by light received through the eyes.

The gland plays a key role in circadian rhythms - the body's state of alertness in response to daylight or darkness - and from this has been born the "alternative" therapy of taking melatonin rather than a sleeping pill to compensate for disrupted sleep.

Researchers at the University of Alberta in Canada reviewed 32 studies in which melatonin was tested on people with secondary sleep disorders (sleep problems associated with medical, neurological or substance misuse) and sleep disorders arising from jet lag or shift-work disorder.

Melatonin was ineffective in treating either kind of disorder, they say.

In the case of secondary sleep disorders, individuals who took melatonin boosted their duration of sleep by just 1.9 percent - less than 10 minutes in an eight-hour spell in bed - and this was so tiny as to be statistically insignificant.

As to whether melatonin is safe, the authors say it appears to be so, at least with short-term use.

Further work, though, is needed to see whether melatonin can be safely used for longer spells.

Related: The Sleep Racket: Who's making big bucks off your insomnia?

Sunday, February 05, 2006

Seasonal Affective Disorder - The Basics

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 Cells (RGCs) located in the retina in each eye. Each of these cells expresses a photopigment melanopsin (the cryptochrome challenger apparently lost the contest about a year ago after several years of frantic research by proponents of both hypotheses).

The axons – nerve processes – from these cells go to and make connections in three parts of the brain. One is the brain center that controls pupillary reflex – when the light is bright the pupils constrict, while in the dark the pupils dilate.

The second is the brain center involved in the control of mood. There is still a lot to work out about this center, but that is probably the place where exposure to light helps alleviate regular, i.e., non-seasonal depression.

The third place where these RGCs project is the suprachiasmatic nucleus (SCN) – the main circadian pacemaker in the mammalian circadian system. The first light of dawn perceived by the eyes tells the SCN that it is day. Likewise, at dusk, the gradual decrease in light intensity perceived by these RGCs signals to the SCN that night is about to start.

Much of the work on seasonal depression (SAD) suggests that it appears in response to the changes in daylength – the photoperiod. While other aspects of the weather, e.g., brightness, temperature, etc., may modulate the response, the basic mechanism appears to be the same way other mammals time their seasonal activities, including breeding, migration, molting and hibernation. Recent studies indicate that other mammals also suffer from winter depresssion, which is triggered by long night and short days (that last link is to a really cool study - perhaps I should write a separate post just on that!).

What is important to keep in mind is that total amount of received light, its intensity and quality, do not matter in photoperiodic response in mammals. What matter is the duration of the night AS PERCEIVED BY THE SCN. One can fool the SCN by, for instance mimicking a long summer day with skeleton photoperiods (a light pulse in the morning and a pulse in the afternoon) – the clock perceives only two pulses of light (a total of a couple of hours of illumination), yet interprets is as a long day.

The output of the SCN, among else, is a projection to the superior cervical ganglia (SCG) in the upper neck region, which are part of the sympathetic (autonomic or vegetative) nervous system. The SCGs, in turn, project their axons onto the pineal gland where release of nor-epinephrine controls the synthesis and secretion of the pineal hormone melatonin. So, whenever the SCN ‘thinks’ it is night, the pineal secretes melatonin into the bloodstream.

During the day, the SCN inhibits the secretion of melatonin. The duration of melatonin secretion is the signal for the duration of the night. This signals is then “read and interpreted” by other parts of the brain that trigger changes in development, morphology, physiology, reproduction and behavior in a seasonally appropriate manner. So, it is the duration of exposure to melatonin, not any direct hormonal activity of melatonin, that is the key to seasonal phenomena.

Here is a schematic of the melatonin profile in the blood of normal people in summer and winter:

Such profiles are very important for fitness (survival and reproduction) in hamsters, sheep, deer and most other mammals. Humans are not so strikingly seasonal – we breed throughout the year – but our distant ancestors certainly were. Some traces of the seasonality of our ancestors can be seen. For instance we crave different foods in different seasons, put on or lose weight seasonally, etc. The best evidence for the human seasonality is the existence of SAD. Just like other mammals, we get slow, grouchy, and in severe cases, clinically depressed during the winter (yes, I know, there are some rare people who are opposite – depressed in summer, but they are seasonal, too, and their SAD is also due to photoperiodic time measurement).

How does exposure to bright light alleviate SAD? Most humans have an inherent freerunning period (tau) of their circadian clock somewhat longer than 24 hours – around 25, actually. Thus, the two figures I drew above are idealized – very few people have profiles exactly like that. We tend to wake up some hours after dawn. We sleep indoors in relatively dark rooms, perhaps under covers, with our eyes closed. The RGCs do not perceive the first light of dawn at the time of dawn but some time afterwards. Thus, the SCN entrains to the environmental light-dark cycle with a slight delay. Most humans are mild “owls” in this respect. And even when we get up, we expose ourselves only to the relatively weak artificial light, or the dim light of a dark and dreary winter morning.

In the evening, most people do not go to bed at dusk, but switch on the lights (curse you, Edison!) and go to bed much later – often around midnight. We phase-delay our clocks with our daily behaviors. Yet, the artificial light is not sufficiently intense to shut down the secretion of melatonin. What you get is something like this – an artificially lengthened night and even longer duration of the melatonin signal than what the actual duration of night warrants:


By exposure to very bright light (a ‘light-box’ that you can buy online) in the morning, we phase-advance our clocks every morning, just enough to place ourselves into a more normal phase. High intensity is needed as the speed and size of phase resetting is dependent on light intensity. This way, we reduce the perceived duration of the night to what it really is (instead of the artificially lengthened night), thus alleviating some of the mood-related effects of short photoperiods.
“Larks” are people whose clocks run with a period at or shorter than 24 hours and who are, thus, somewhat phase-advanced in relation to the environmetal light-dark cycles. The strategy for “larks” is to expose the RGCs to bright light in the evening, thus phase-delaying the clock and, again, reducing the perceived duration of night to the actual duration of night, hopefully eliminating mood-altering effects of long winter nights:
I

Melatonin supplements are often used in treatment of clock-related disorders. Melatonin has been suggested to treat jet-lag, effects of night-work and shift-work (“shift-lag”) and various clock-related insomnias. But beware – melatonin is also a signal of season.

I have not seen a study of this, but here is something that, in theory, can happen. If you are an extreme night owl, i.e., phase-delayed and try to reset your clock by taking melatonin earlier in the evening than your normal (i.e., very late) bed-time, what is going to happen?

Even if you do this in the middle of summer, the melatonin supplement will prolong the nightly melatonin signal (exogenous melatonin in early night + endogenous melatonin during late night). Your brain will interpret this as an abrupt onset of very long winter nights. If you are susceptible to winter depression (and if I remember some studies correctly, owls are more susceptible to SAD than larks), you will artificially trigger SAD in the middle of the summer. So, beware!

Now, you may understand why are people who live in very high latitudes chronically depressed. After all, they are exposed to a continuous night that lasts for several months! One wonders if the reindeer are depressed, too.

What I outlined here is just the very basic mechanism of SAD - the textbook version. There are, as one should expect, many more details, complications and strange data out there. Those are, frankly, outside my domain of expertise. I am a bird kind of guy, after all. So, if you want more details, or medical advice, you will be better off to ask somebody who does research on (and clinical work with) human subjects, or at least on mammals.

ClockQuotes (De Vries)

I write when I'm inspired, and I see to it that I'm inspired at nine o'clock every morning.
- Peter De Vries

No Link Between Lunar Phase and Births/Deliveries

The Claim: Baby Deliveries Are in Sync With the Moon:

Is there any link between childbirth and the lunar cycle? Many ancient cultures looked upon the moon as a sign of fertility, and since Roman times people have blamed full moons for all sorts of human behaviors, hence the word lunacy, from the Latin word for moon.

But as mysterious and alluring as the link between full moons and births may sound, scientific studies suggest that it is more romance than reality.

Over the years, more than a dozen different studies in several countries have looked for a connection, and almost all have found none.

One of the most recent, published last year in The American Journal of Obstetrics and Gynecology, examined about 564,000 births across 62 lunar cycles in North Carolina between 1997 and 2001.

The lunar cycle, the study found, had no predictable influence on deliveries or birth complications at all.

Another study, which appeared much earlier in The New England Journal of Medicine, looked at thousands of births across 51 lunar cycles. It also reached that conclusion.

But scientists have found several factors that do affect workloads in maternity wards.

Most births occur in the summer and in September and October, said Kathleen Capitulo, the director of the Kravis Children's Hospital and Women's Center at Mount Sinai Medical Center.

There are also weekly cycles. Most childbirths occur later in the week, she said, because many women prefer having labor induced before the weekend, full moon or not.

THE BOTTOM LINE: Studies show that workloads in maternity wards are not affected by the full moon.

Saturday, February 04, 2006

Light therapy shines on other conditions

Interesting, but not surprising, though the mechanism may be different in SAD and other disorders. From PsychCentral and APA:

Exposure to bright light–the treatment of choice for seasonal affective disorder, or SAD–may also help people with other mental health conditions including bulimia nervosa, antepartum depression and nonseasonal depression, preliminary research finds.

"The latest news is that light therapy is just as effective as antidepressants in treating nonseasonal depression–it's truly exciting," says Columbia University psychologist Michael Terman, PhD, a SAD researcher who uses both light and medications to treat patients. "The findings almost make me say that it's only by happenstance that light therapy was discovered and developed in the context of SAD."

That said, the literature in the area is still sparse, emphasizes Dan Oren, MD, a veteran SAD researcher at Yale University.

"No one has done any solid head-to-head comparisons that prove that one form of treatment is better than another in treating nonseasonal depression," he notes.

The excitement is the result of several studies that are emerging on the topic, including a meta-analysis in the April 2005 American Journal of Psychiatry (Vol. 162, No. 4, pages 656–662), by University of North Carolina at Chapel Hill psychiatrist Robert Golden, MD, and colleagues concurring that bright light treatment is effective both for SAD and for nonseasonal depression.

"Effect sizes [are] equivalent to those in most antidepressant pharmacotherapy trials," the authors write.

Meanwhile, a 2004 meta-analysis conducted for The Cochrane Collaboration, a not-for-profit organization that prepares systematic reviews of health-care therapies, found that light therapy offered help for nonseasonal depression, especially when administered during the first week of treatment, in the morning and as an adjunct to antidepressants. A revision of that meta-analysis is currently under way, Terman notes, indicating that light therapy plus medications is probably the best approach.

Friday, January 27, 2006

Plant Photoperiodism

TroutGrrrl on the Science And Sarcasm blog wrote a nice post on plant photoperiodism. As an animal kind of person, it's unlikely I would have ever tackled this topic so it is nice to see someone else doing it so I can link. For background information, you may want to check my earlier posts on Seasonality and Photoperiodism.

Wednesday, January 25, 2006

Persistence In Perfusion

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 from the SCN. The mammalian pineal secretes melatonin rhythmically, but only in a animal with an intact SCN. The retina also synthesizes melatonin rhythmically, but only if the SCN is present. The melatonin never exits the eye anyway and the clock (and melatonin) in the retina is thought to regulate only local events, e.g., daily rhythms of rod-cone dominance and disk-shedding.

In non-mammalian vertebrates, SCN (although not as precisely located so far) can also be a pacemaker but it is not the only one. In some species, the pineal gland is the pacemaker (e.g., house sparrow, some lizards). In other species it may be the retina. In some, like the pigeon, both the pineal and the eye are pacemakers - only complete removal of both eyes and the pineal renders the whole animal arrhythmic.

Capability to study a pacemaker in a dish is quite important, as it eliminates from the study all the effects of interactions between multiple clocks or feedback from target organs. The SCN of mammals is easy to culture and much progress has been made in understanding the mammalian pacemaker in vitro.

The pineal of a number of species belonging to all vertebrate classes is also relatively easy to culture. The chicken pineal is so easy to keep in a flow-through setup, that there is a whole industry devoted to the study of cell biology of this organ. People who study the chicken pineal even have their own journal - Journal of Pineal Reearch - and their own Gordon Research Conference (it just ended - I wish I could have gone there).

The retina of the eye is a bit more difficult organ to culture. It is very metabolically active and requires high oxygen levels in the culture media. The eyes of lampreys, fish and frogs have been successfully cultured quite a while ago. Eyes of lizards were cultured first about ten years ago or so. Mammalian eye was a little more difficult to do, but nevertheless, Dr.Gianluca Tosini managed to do it in mice and hamsters a few years back, but he is regarded as Grand Master of in vitro chronobiology. While subsequent studies of these tissues were productive in understanding the vertebrate circadian system, the problem with all of these cultured retinae is that none of them is the main pacemaker in its species. In each case, the pacemaker of the animal was either the SCN or the pineal, and what was cultured was a 'slave oscillator'.

What was needed was a culture of an ocular clock from an animal in which the eye is the main or sole circadian pacemaker. That meant a bird, preferably the Japanese quail. Several of the top people in the field tried to culture an avian retina, but to no avail. One could not detect any melatonin secreted by the cultured tissue. Another one measured whopping levels of melatonin but no rhythm at all. Nothing ever got published on those failed attempts, but such information gets exchanged over beer at the conferences.

Perhaps there is really a need for a Journal of Negative, Inconclusive and Unpublishable Results, to deter people from trying, again and again, experiments that have failed before. On the other hand, past failures are not deterrents to everyone. Some people thrive on challenge. One such person is my lab-mate and friend, Christopher Steele, freshly a PhD, happy in his new job up in New England.

His Dissertation was focused on the eye as a pacemaker in the circadian system of Japanese quail. He was particularly interested in the way the two eyes communicate with each other in order to remain synchronized, and in the neural and hormonal signals going from the eyes to the rest of the system, and from the rest of the system to the eyes.

It would have been great for his work if he could isolate the retina and examine how it responds to various hormones and neurotransmitters, or to light pulses and light-cycles. But it was supposed to be impossible to do! But Chris is a veteran of two wars, not to mention endless melatonin hormone assays - nothing is impossible for him. He got the funding, he got the green light from the PI, he got Dr.Tosini to start a collaboration, and he got to work.

Speak of frustration! There is a reason why all those people before gave up on this problem - it's hard! Over and over and over again, Chris tried and tried, tweaking one little thing at a time, to no avail. A time came when I had a feeling that our advisor was ready to call it quits and was just trying to find a way to suggest that to Chris politely.

But Chris wanted to have another go at it. This time, he decided that all the technical stuff was perfected and doing fine - the method of removing retinae from the eyes, the syringe pumps, the media, the fraction collector, the sterility of the whole setup. Instead, he used his knowledge of biology for a change and decided to supplement the media with precursors of melatonin, either tryptophan or serotonin:
The wells containing retinas perfused with tryptophan-rich media were almost as bad as anything he did before - one cycle, perhaps two, then everything crashes and there is no more melatonin to detect. But with added serotonin, he got this:Ha! It worked. And then it worked again. And again. Of course, this poses all source of new questions. Why did quail retina require supplementation with serotonin while that was not needed for culturing eyes from lampreys, African claw-frogs, green iguanas or hamsters? Would addition of serotonin to flow-through culture also make the quail pineal exhibit melatonin rhythms?

Well, Chris was called up again and spent another year in yet another war. In the meantime, the data just sat there in the corner of the lab, waiting for him to come back. Before he went away, Chris taught me how to use the culture system and I did one run, which did not work, but I knew two days into the experiment why it was not working. Anyway, now I know how to do it and, if anyone ever lets me into a lab again, I intend to use this technique in the future. Once Chris came back, he analyzed the data and the paper is now, finally, out in print.

Now you also understand that the title of this post is a double-entendre. The circadian pacemakers of the quail retina persist in perfusion, but also Chris persisted in trying the perfusion and the persistence paid off.

Monday, January 23, 2006

ClockNews #33

Getting enough sleep

Contrary to the idea that more sleep is better, an editorial in the journal Sleep by Daniel Kripke, a professor of psychiatry at UC San Diego, cites data from Japan and the United States showing that the ideal sleep duration is between 61⁄2 and 71⁄2 hours. Across large numbers of subjects, longevity rates actually decrease as sleep duration shifts beyond this range. Those who slept less than four hours or more than nine or 10 hours were found to have mortality rates greater than those in the middle range.

I wanna be sedated

The insomnia epidemic is now affecting kids
Morning Exercise Provides Top Benefits

When is the best time to exercise? Most experts would say that any time you can find to exercise is the best time. For some people, it’s nearly impossible to find the time to exercise at all, and for others there’s no way they can break a sweat until the evening. But if a.m. exercise may be an option, we’ve got a few reasons why working out in the morning is best…
Darkness unveils vital metabolic fuel switch 5-AMP

Constant darkness throws a molecular switch in mammals that shifts the body's fuel consumption from glucose to fat and induces a state of torpor in mice, a research team led by scientists at The University of Texas Medical School at Houston reports in the Jan. 19 edition of Nature.
Don't be SAD...get out there!

Getting outdoors and then getting active is one of the most effective ways to lessen the symptoms of the winter blues.
The month of no-sun days

It's not the rain that disrupts the body's circadian rhythms, potentially leading to depression; it's the latitude and the amount of daylight someone is exposed to, he said.

Sunday, January 22, 2006

Serotonin, Melatonin, Immunity and Cancer

I love Miss Frizzle from the cartoon "The Magic School Bus". She always says "Make connections, kids, make connections!" Here I'll try to make some tentative connections between two recent papers, both concerning health issues in humans.

The first paper, brought to my attention by Corpus Callosum, a blog I belatedly placed on my blogroll here only today, is titled Commonly Used Antidepressants May Also Affect Human Immune System, which is a high-hype way of presenting a finding that some types of immune cells appear to communicate using serotonin as a signal. To be precise, the dendritic cells, a type of antigen-presenting cell in the immune system, can uptake and relase serotonin, which in turn excites T-cells in a rapid fashion. Thus, manipulation of serotonin by pharmacological agents (as in treatment of depression) may have - as yet unknown - effects on the immune system.

Well, I have a hammer so I see nails everywhere. Whenever I see "serotonin" I wonder if melatonin is also involved. Why? Because the two appear to be connected almost in everything.

First, serotonin is a biochemical precursor of melatonin (you can see the pathway here). Thus, if there is more serotonin now, there can potentially be more melatonin later. If serotonin is lacking now, there will be a lack of melatonin later.

Second, the two substances appear to be ubiquitous throughut the body and their receptors are found apparently everywhere (what are Melatonin receptors doing in the quail ovaries and eggs?).

Third, the two substances almost always have opposite effects. While one stimulates intestinal movement, the other one inhibits it. There are many examples of such antagonism.

And, it has been known for a while now that melatonin enhances immune response. My friend and colleague Chris Moore published several papers on this topic. For instance, in this paper, he showed that exposure to constant light, which supresses melatonin synthesis and release, inhibits both the cellular and the humoral immunity, and that addition of melatonin to drinking water boosts immunity in a dose-dependent manner in quail kept in constant light. In another paper he showed that supression of melatonin by light is not neccessary for additional melatonin to boost the immune response beyond that seen normally. Also, it appears that melatonin enhances immunity via an opiate route. Finally, removing one source of melatonin, the pineal, reduced the immune response, while, strangely, removal of the other source of melatonin, the eyes, did not have an effect.

So, if melatonin boosts immunity, we can expect serotonin to do the opposite, i.e., to supress the immune response. Does that mean that taking Prozac is bad for your immune response? Who knows - it is too early to tell.

The second paper comes by the way of Tara Smith from Aetiology, one of the dozen or so science bloggers who recently joined the Seed group's ScienceBlogs (also added to my blogroll today). She explains it very well in her post, so head over there for more.

In the paper, a series of experiments in nude rats with hepatomas and in rats with transplants of human breast cancer tissue, shows that a) exposure to constant light decreases melatonin, b) both the rat and the human cancer cells express melatonin receptors, c) perfusion with melatonin-rich blood slows down cancer and d) perfusion with melatonin-depleted blood speeds up cancer. Out of several different treatments, one of the types of melatonin-depleted blood came from women working in bright light during night shift.

The effect of melatonin on cancer tissues was direct, via a linoleic acid pathway. But, considering the paper I discussed above, isn't it reasonable to expect that effects of bright light at night will also have an effect on immunity, i.e., the supression of melatonin release would supress immune response and also allow the cancers to form and spread? It is well known, after all, thet night-shift nurses tend to suffer much more, from a variety of diseases including breats cancer, than nurses that always work day-shifts.

Finally, melatonin does not work only directly, as a hormone. It is also a signal of time. A person working on a rotating shift is constantly 'jet-lagged', i.e., all the little clocks in various tissues are out of sync with each other. This in itself, melatonin or no melatonin, should be pretty bad for one's health. After all, in a spectacular series of experiments in 1950s, Dr.Janet Harker showed that cockroaches containing two pacemakers entrained several hours out of phase with each other (e.g., NYC time in the left lobe and New Zealand time in the right lobe) developed intestinal cancer - something rarely seen in insects.

Friday, January 20, 2006

Diversity of insect circadian clocks - the story of the Monarch butterfly

There are pros and cons to the prevalent use of just a dozen or so species as standard laboratory models. On one hand, when a large chunk of the scientific community focuses its energies on a single animal, techniques get standardized, suppliers produce affordable equipment and reagents, experiments are more likely to get replicated by other labs, it is much easier to get funding, and the result is speedy increase in knowledge.

On the other hand, there are drawbacks. One is narrow focus which can breed arrogance. The worst offenders are people who work with rats. They rarely put the word "rat" in the title of the paper, and often it is not even found in the abstract, introduction and discussion of the paper. One has to dig through the materials and methods to find out, although if you know about this, the very fact that the species is not noted in the title is a dead giveaway that it is a paper about rats. Some of the papers dealing with humans also make the same mistake of not pointing out the species in the title.

One of the most important animal laboratory models for the study of genetics and molecular biology is the fruitfly Drosophila melanogaster. For a century now, almost all advances in knowledge in these areas came from fruitfly research first, then this knowledge got applied to other species, e.g., mice and humans.

Last month, a paper came out that highlights both the pros and the cons of the "model" approach. On one hand, all the techniques used in the work were developed by fruitfly researchers and are now standard methods, easily replicable between labs.

On the other hand, it shows how important it is to sometimes move away from the models and take a reality check: is the mechanism described in the model animal generalizable to other animals or is it idiosyncratic to the model. The papers dealing with models, including fruitflies (and of course rats!), often make the implicit claim for generalizibility (helps funding!) without data to support this claim.

The model of the molecular mechanism of the circadian clock has been initially developed in the fruitfly and massive research is still going on in this animal. It is regarded as a reference model in a way - models developed later in mice, bread-mold, Arabidopsis plant, Synechococcus bacterium, etc, are always compared to the fruitfly model to look for similarities and differences. In a sense, it is the 'deafult' model in chronobiology.

This paper took a look at a non-model animal and found out that the fruitfly mechanism does not appear to be even typical of other insects. Steven Reppert and colleages at the University of Massachusets Medical School are studying circadian system in Monarch butterflies (mainly in order to better understand migratory orientation).
In this paper they discover that the Monarch, unlike the fruitfly, has two copies of a clock gene called Cryptochrome (CRY). One copy (CRY1) is very similar to that of Drosophila. The other copy (CRY2), however, is much more similar to the mouse version of the gene.

In the brain pacemakers of fruitflies, CRY is not the core component of the clock but is a blue-light photoreceptor. In the peripheral tissues, the same gene may be a component of the clock (it represses expression of some other clock genes).

In mammals, CRY is not directly photosensitive, but is a core clock gene and a strong repressor of expression of other clock genes.

In Monarchs, as they show in this paper, CRY1 is responsive to light, just like the CRY of fruitflies. The CRY2, though, does not respond to light, but represses expression of other genes, just like the mouse CRY.

The best thing about this paper, though, is that the authors then went on and looked into genebanks of several other insect species and, lo and behold, discovered CRY2 in a few more insects, including moths, honeybees, mosquitoes and flour beetles. Actually, the honeybees and flour beetles appear to have ONLY the mammalian-like version of the gene.

They also plotted the phylogeny of the CRY gene, showing the genealogical relationship between the fruitfly-like and mouse-like versions of CRY, both versions presumably resulting from a gene duplication some time in the past (the apparent precursor, bacterial photolyase, appears as only one copy in E.coli and its function is in DNA repair).
The PERIOD protein does not enter the nucleus in the Chinese silkmoth and the Monarch butterfly. Thus, at least in these two insects, the molecular mechanism of the circadian clock must be different from that of the fruitfly. Presence of the mammalian-like version of the CRY gene, a potent gene repressor, suggests that it may be fulfilling the function of PER in these species. Thus, there appears to be more than one way to run a clock in an insect and the fruitfly mechanism is not as 'standard' at previously thought.

And working with Monarch butterflies must be great fun!

Reference:
Haisun Zhu,1 Quan Yuan,1 Oren Froy, Amy Casselman, and Steven M. Reppert, 2005, The two CRYs of the butterfly.Current Biology, Vol 15, R953-R954, 6 December 2005.

Circadian Rhythms, or Not, in Arctic Reindeer

There are two main hypotheses - not mutually exclusive - for the adaptive value of having a circadian clock. One is the Internal Synchronization hypothesis, stating that the circadian clock serves to synchronize biochemical and physiological processes within the body. The second is the External Synchronization hypothesis, stating that the circadian clock serves to syncronize the physiology and behavior to the natural environment.

The prediction from the Internal Hypothesis is that circadian rhythms in various physiological parameters - for instance body temperature, release of various hormones, cell division - will persist in organisms that live in non-rhythmic environments, e.g., in caves, underground or in the depths of the ocean. Measuring such parameters, especially in the wild, is difficult and expensive, though, so not much work has been done. Work in the laboratory, mostly in fruitflies and hamsters, brings indirect support for this hypothesis.

The predicition from the External Hypothesis is that circadian rhythms of behavior will not persist in organisms that live in arrhythmic environments. This has been shown in a number of fossorial animals in the field.

A research group from Norway has recently published a short paper in Nature (I saw these data on a poster at a meeting in 1999 - just goes to show how long it takes to publish in Nature!), looking at an animal that lives in an environment that is sometimes rhythmic, sometimes not - the Arctic. They have monitored, for a whole year, the gross locomotor activity of 12 reindeer. Six of those were in Svaldbard (78 degrees North) and the other six were of another subspecies in northern Norway (70 degrees North).
In the Arctic, for several months during the winter there is only darkness - it is the long polar night. Likewise, it is one continuous day through the months of summer. However, for a few weeks in spring and again in fall, there is a clear light-dark cycle in the environment.

What the group discovered was that, in both subspecies, there was no detectable rhythm during the one long day of summer. This is consistent with the data in a number of laboratory animals - constant bright light tends to supress circadian rhythmicity. Reindeer, like most ruminants, have ultradian rhythms of activity, i.e., tend to roam and forage in bursts.

During spring and fall, both subspecies entrained to the external light-dark cycle, although the rhythm in Norway deer appeared much more robust. It is unclear if the apparent rhythms in the more Northern population were entrained circadian rhythms or masking effects (i.e., direct effects of light on activity) of the LD cycle.

During the winter, though, the Norway reindeer exhibited a freerunning rhythm of activity, but the Svaldbard deer were again not showing any rhythms. An absence of a freerunning rhythm in constant darkness is a rare finding in animal chronobiology, and the data strongly support the External Synchronization hypothesis.
On the left - Norway deer, on the right - Svaldbard deer. Every black dot is a bout of activity and white dot a bout of inactivity. X-axis is a double-plotted 24-hour day. Y-axis (going from top to bottom) shows one day of the year in each row.

However, people from the same group (mostly Karl-Arne Stokkan) have shown before that Svaldbard reindeer (as well as Svaldbard ptarmigan, a gallinaceous bird, which is also behaviorally arrhythmic in a similar experiment) have no rhythm of melatonin secretion during the long polar night in winter either, something that contradicts the Internal Synchronization hypothesis to some extent. On the other hand, people and seals living at the same latitudes have circadian rhythms in melatonin release.

Circadian pacemakers in the suprachiasmatic nuclei signal time of day using various neural and hormonal mechanisms. One of the mechanisms involves rhythmic stimuulation of melatonin release from the pineal gland. Other hormones may be Arginine Vasopressing, Cortisol, brain peptides, etc. It is possible that melatonin signal acts on brain centers that drive various behaviors, while other neural and humoral signals drive rhythms in biochemistry and physiology of various internal organs. It is, thus, possible that animals in arrhythmic environments have no rhythms in melatonn release or behavior but still retain rhythms in physiology - something that can be tested by, for instance, continuous monitoring of body temperature in the field - hard and expensive, but not impossible to do. If this is the case, that both Internal and External Synchronization hypotheses will be supported.

Circadian clocks are so ubiqutous, it is difficult to come up with a conclusive evidence for their adaptive function. Finding animals, like reindeer, that are not rhythmic in constant natural environments but exhibit rhythms when the environment is rhythmic, add some strength to the notion that the biological clocks are evolved adaptations.

And of course, not being sleepy on the night of December 25th certainly helps Rudolf, Prancer and friends work more efficiently in delivering presents.

Reference:
van Oort BE, Tyler NJ, Gerkema MP, Folkow L, Blix AS, Stokkan KA. Circadian organization in reindeer. Nature. 2005 Dec 22;438(7071):1095-6.

Thursday, January 19, 2006

Sleep And Loneliness

Over at Cognitive Daily (at its new digs on Seed Magazine's new stable of Science Blogs), either Dave or Greta (can't tell which one) comment on an interesting study that suggests that lonely people have less efficient sleep. The study invollved college students without depression and incorporated measurements of sleep quality both in the lab and at home.

They conclude:
Whether loneliness causes poor sleep is not answered by this study, which can only show a correlation between loneliness and inefficient sleep. Perhaps poor sleep causes loneliness, or perhaps some other condition causes both loneliness and poor sleep (though individuals suffering from depression, possibly the most likely culprit, were excluded from this study).
If you have any crazy college sleep/sleep deprivation stories, share them in their comment thread. I'll be reading them over there with great interest.

Perhaps being gregarious exposes one to more germs. On the other hand, it appears that having sex boosts the immune system (from Countess and Blondesense). Perhaps having sex also makes one sleep better, too?

Reference:
Cacioppo, J.T., Hawkley, L.C., Berntson, G.G., Ernst, J.M., Gibbs, A.C., Stickgold, R., & Hobson, J.A. (2002). Do lonely days invade the nights? Potential social modulation of sleep efficiency. Psychological Science, 13(4), 384-387.

Wednesday, January 18, 2006

How Period and Timeless Interact in Fruitflies

A brand new paper is making a splash in the field these days - so much that you can find the press release in three places: here, here and here, this last one being the coolest as it contains a movie and three podcasts!

One of the biggest problems in circadian biology is to account for such a long time - 24 hours - it takes for the whole transcription-translation feedback loop to run its course through a single cycle. Biochemical reactions tend to happen at much shorter time scales. Some mathematical models tried to invent possible mechanisms (with no basis in experimental findings), while molecular biologists, in general, tended to ignore the problem altogether.

Still, I have seen in a few talks over the years some evidence that some circadian clock gene mutations affect only a portion of the cycle. In other words, if a mutation makes the endogenous period in a mutant shorter than that in a wild type, it is not because the whole cycle runs faster, but because one phase of the cycle runs faster. If I remember correctly from various talks, it was almost always the late-afternoon/early-evening phase that got affected.

Now, Young, Saez and Meyer published a paper in Science that sheds some light on the problem. In the process, they also significantly alter the model of the Drosophila circadian clock. You can see the old model in a movie here (see if you can play the movie directly by clicking on this), actually a series of movies produced a couple of years ago. You can see the new model here:
The big difference (let's completely ignore a dozen other molecular players for now) is in the behavior of two core clock proteins: PERIOD and TIMELESS. It was believed, until now, that it takes about six hours for the two proteins to find each other in the cytoplasm and that once they do, they bind to each other (heterodimerize), which is neccessary for their entry into the nucleus where they act to activate expression of some genes and supress expression of some other genes. No need for complicated details now.

However, some very recent studies indicate that the two proteins break off from each other immediatelly before re-entering the nucleus, and they enter the nucleus alone, not as parts of a dimer.

What this new study does is demonstrate that the two proteins, as soon as they are formed, easily find each other and bind to each other, then sit idly in the cell for six hours before breaking off from each other and entering the nucleus. Also, mutations of Tim have no effect, while mutations of Per alter the duration the two proteins sit together as a dimer.

From the press release:
"They discovered that, rather than randomly colliding, the two proteins bind together in the cytoplasm almost immediately and create what Young and Meyer refer to as an "interval timer." Then, six hours after coming together, the complexes rapidly break apart and the proteins move into the nucleus singly, all of them within minutes of each other. "Some switch is thrown at six hours that lets the complex explode. The proteins pop apart and roll into the nucleus," Young says. "Somehow, implanted within the system is a timer, formed by Period and Timeless, that counts off six hours. You have a clock within a clock."
Corpus Callosum comments:
What they found was that the interaction between the two proteins -- somewhat like the resonant frequency of a crystal, used as a timekeeper in an electronic circuit -- acts as a fundamental, but figurative, egg timer within a cell.
It is possible that this is how it works.

One caveat though. The ability of the dimer to stay together for six hours, and the ability of the Per mutations to alter this timing, are not neccessarily the inherent property of the dimer. In other words, it may not have anything to do with resembling properties of a crystal.

They may just as well be the result of interactions between the dimer and other proteins in the cell, some of which may be influenced by the signalling coming from other cells (e.g., from neighboring pacemaker neurons).

In other words, the ability of the dimer to stay put for six hours may be a property of the dimer, or it may be a property of the multicellular system as whole.

Friday, January 13, 2006

New sleep medicine blog

Sleep Disorders is a blog written by an MD who is a sleep specialist.