Category Archives: Chronobiology

How eyes talk to each other?

How eyes talk to each other?One of the important questions in the study of circadian organization is the way multiple clocks in the body communicate with each other in order to produce unified rhythmic output.

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Quail: How many clocks?

Quail:  How many clocks?One of the assumptions in the study of circadian organization is that, at the level of molecules and cells, all vertebrate (and perhaps all animal) clocks work in roughly the same way. The diversity of circadian properties is understood to be a higher-level property of interacting multicelular and multi-organ circadian systems: how the clocks receive environmental information, how the multiple pacemakers communicate and synchronize with each other, how they convey the temporal information to the peripheral clocks in all the other cells in the body, and how perpheral clocks generate observable rhythms in biochemistry, physiology and behavior.

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Ah, Zugunruhe!

Ah, Zugunruhe! How birds know when and where to migrate (from April 03, 2006)

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Circadian Rhythms, or Not, in Arctic Reindeer

Blogging on Peer-Reviewed Research

Circadian Rhythms, or Not, in Arctic ReindeerA January 20, 2006 post placing a cool physiological/behavioral study into an evolutionary context.

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How do bats in a cave know if it is dark outside yet? Guest post by Anne Marie Hodge.

As traveling is not conducive to vigorous blogging (apart from posting travelogue pictures), I have asked a couple of friends to write guest posts here. The first to step up to the plate is Anne Marie who put together her passion for bats and my passion for biological clocks and wrote this fascinating post:

Blogging on Peer-Reviewed Research

Casinos on the infamous Vegas “strip” spare no expenses when it comes to extravagant decorations and architecture. You can find everything from indoor gondola rides to full-sized pirate ships that are sunk in mock-battles multiple times each day. One thing that you might notice, however, is that these massive, opulent buildings almost always lack windows in the rooms where major gambling activity takes place. The massive interior rooms echo with the bells of slot machines and the soft buzz of cards being dealt at hundreds of tables all throughout the day and night, and after several hours inside one of these caverns of opulence it is easy to forget what time of day it is supposed to be. That, of course, is the point: if you aren’t able to keep track of the passing hours by subtle cues such as the angle of the sun, casino managers hope that it will keep you (and your money) around for longer periods of time.
Fortunately, whether you are a high-rolling VIP showing off your Rolex or a more budget-minded tourist playing the quarter slots with your trusty plastic Aquatech strapped to your wrist, chances are you have some way to tell time even when you are sequestered from typical environmental day length clues. Other mammals, however, don’t have the luxury of mechanical time instruments. If even a few hours inside a windowless casino is enough to distort our natural perception of time, how do other mammals manage to keep regular daily rhythms?
Obviously, most mammals do not hang out in windowless casinos, and thus are able maintain circadian rhythms using external cues such as day length and temperature. Bora recently gave an excellent primer on mammalian circadian clocks, definitely check out that post for detailed information on how these rhythms are regulated.
Light cycles are crucial for proper circadian clock calibration, but some animals live in large, isolated places that lack both sunlight and slot machines. The most notable cave mammals are bats, the winged wonders of the mammal world. The idea that all bats are caves-dwellers is actually a misconception. Many bat species roost in trees, buildings, or “bat houses” put out by helpful humans in areas where natural forest roots have been destroyed. Studies have shown that day length is the most common factor regulating bats’ daily activity cycles. Foraging strategies and diet specialization seem to have an impact on what time of night specific species emerge from their roosts. Insectivorous species often begin foraging a bit before true sunset, in spite of exposing themselves to increased predation risk, in order to take advantage of the peaks in insect activity at dusk (Jones and Rydell 1994). Fruit eating bats can afford to sleep in a little, because their “prey” isn’t likely to go anywhere between dusk and full darkness, so it’s not worth risking increased predation by diurnal or crepuscular predators. Thus, being able to detect the rising and setting of the sun is crucial for these bats to regulate their activity cycles.
While many common species of bats never even venture into caves, some species do indeed roost in large caves that are entirely devoid of light. Without being able to see when the sun rises and sets, how do these little guys maintain regular circadian rhythms?
bat.JPGThe most extensive studies of the circadian rhythms of cave bats have focused on Hipposideros speoris, Schneider’s roundleaf bat, which is native to India and Sri Lanka. Back in the 1980s, a group from Madurai Kamaraj University did some fascinating work to determine how these bats are able to tell when it is time to leave the cave for foraging each night (Marimuthu et al. 1981). Within the cave roost, bats are isolated from both light and temperature fluctuations, so the researchers sought another explanation for how they calibrate their circadian clocks. They did this by capturing some of the bats within a large colony of H. speoris, then putting them in holding cages inside the original cave, to observe their activity patterns in situ without ever letting them access a chamber of the cave that could give them external light or noise cues.
So, what did the Cave Cage experiment tell us? Surprisingly, it appears that social interactions are the key. The bats were observed to become mildly active within the cave well before the sun went down, and they spent some time grooming and flitting around within the roost chamber. Some of those bats ventured in between the roost chamber and into an outer portion of the cave, “sampling” the light. Once adequate darkness set in, all of the bats (not just the “samplers,” left the cave to forage. The caged bats also increased their activity in sync with the rest of the colony, even though they were unable to “sample” the outer chambers. The researchers concluded that the bats’ circadian rhythms were entrained by social cues. Bats could have been responding to the noise of the wingbeats of the first bats to leave the cage, or there could have been active vocal signaling. Pheromones could also come into play, if specific hormones are released by “samplers” as they prepare to leave for foraging, signaling the rest of the colony that it is time to leave.
One question that immediately crossed my mind was how the bats know when to start stirring around in the first place, It seems probable that the nightly emergence “sets” their clocks so that they’re properly entrained to wake up slightly before sunset, using hormones such as melatonin to control the length of their sleep cycle. These are largely tropical bats, so day length does not vary much throughout the year, allowing them to have a fairly constant interval of sleep in between returning from foraging in the morning and waking up in the evening.
The group also observed activity patterns of captive bats kept inside a cave after exterminating all of the other bats that roosted there (not the most conscientious field method, but not quite as terrible as it sounds: it was a small bachelor roost and only two bats were killed). They found that bats that were isolated from conspecifics displayed “free run” activity cycles that were significantly less than 24 hours long. Thus, it appears that the bats use social cues from other colony members to time their outflight.
There is no information on whether the same individuals are “samplers” each night, although that would be a fascinating study. While social cues do appear to play a large factor in determining the circadian rhythms of H.speoris colonies, sunlight is still a factor: the “samplers” couldn’t determine the time of day without sunlight available for sampling. The researchers did a follow-up study a few years later that shows that both light and conspecific communication are necessary to maintain accurate cycles. This time, they illuminated a cave around the clock (Marimuthu and Chandrashekaran 1983). Being exposed to constant light, with conspecifics resulted in free run cycles longer than 24 hours, as opposed to the shortened cycles displayed by isolated bats in constant darkness, showing that light cues facilitated by social communication appear to entrain the circadian clocks of these bats.
So, it appears that some bats depend upon social cues to help regulate their circadian clocks, with a few individuals in the colony serving as light “samplers” and alerting the other bats when it is time to emerge for nightly foraging. They still depend upon light cues for regulation, but the significant factor is that only a few actually see the light levels before emerging each evening, the rest rely upon social cues to tell them when it’s dinner time and entrain their internal clocks.
1. Image credit: Phil Richardson
References:
Jones, and Rydell. 1994. Foraging strategy and predation risk as factors influencing emergence time in echolocating bats. Phil. Trans. R. Soc. Lond. B. 345: 445-455.
Marimuthu, G.S. and M.K. Chandrashekaran. 1983. Continuous light inside a cave abolishes the social synchronization of the circadian rhythm in a bat. Behavioral Ecology and Sociobiology. 12: 321-323.
Marimuthu, G., S. Rajan, and M.K. Chandrashekaran. 1981. Social entrainment of the circadian rhythm in the flight activity o fthe microchiropteran bat Hipposideros speoris. Behavioral Ecology and Sociobiology, 8: 147-150.

Persistence In Perfusion

Blogging on Peer-Reviewed Research

Persistence In PerfusionThis post, from January 25, 2006, describes part of the Doctoral work of my lab-buddy Chris.

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What makes a memorable poster, or, when should you water your flowers?

What makes a memorable poster, or, when should you water your flowers?Being out of the lab, out of science, and out of funding for a while also means that I have not been at a scientific conference for a few years now, not even my favourite meeting of the Society for Research on Biological Rhythms. I have missed the last two meetings (and I really miss them – they are a blast!).
But it is funny how, many years later, one still remembers some posters from poster sessions. What makes a poster so memorable?

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Farrell Prize in Sleep Medicine

From the Harvard Division of Sleep Medicine:

To honor the distinguished career of Professor Richard Kronauer, we will again award the Richard E Kronauer Prize for Excellence in Biomathematical Modeling. This is presented to a graduate student or post-doctoral fellow who has made significant contributions to Modeling Circadian Rhythmicity, Sleep Regulation or Neurobehavioral Function. If you would like to be considered for this prize or would like to nominate someone, please send a recent abstract or paper as well as a current C.V. to ebklerman@hms.harvard.edu before April 27 2008.
The award will be presented in Boston in June 2008 at the Farrell Day festivities (http://sleep.med.harvard.edu/what-we-do/farrell-prize-in-sleep-medicine) at which Drs. Kronauer and Borbely will be honored. The recipient will receive a cash award plus travel to the ceremony.

Everything You Always Wanted To Know About Sleep (But Were Too Afraid To Ask)

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This post is perhaps not my best post, but is, by far, my most popular ever. Sick and tired of politics after the 2004 election I decided to start a science-only blog – Circadiana. After a couple of days of fiddling with the templae, on January 8, 2005, I posted the very first post, this one, at 2:53 AM and went to bed. When I woke up I was astonished as the Sitemeter was going wild! This post was linked by BoingBoing and later that day, by Andrew Sullivan. It has been linked by people ever since, as recently as a couple of days ago, although the post is a year and a half old. Interestingly, it is not linked so much by science or medical bloggers, but much more by people who write about gizmos and gadgets or popular culture on LiveJournal, Xanga and MySpace, as well as people putting the link on their del.icio.us and stumbleupon lists. In order to redirect traffic away from Circadiana and to here, I am reposting it today, under the fold.
Update: This post is now on Digg and Totalfark. I urge the new readers to look around the site – just click on the little SB logo in the upper left corner. Also, several points made briefly in this post are elaborated further over on Circadiana, as well as here – just browse my Sleep category.

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Mel-Mel-Mel: it’s easy to remember in snowshoe hares

It has been almost three years since I promised to write a post detailing the photoperiodic response in mammals. (Birds are more complicated).
Now Shelley gives a good example – the snowshoe hare which changes color annually: it is dark in summer and white in winter. It is pretty easy to remember – it’s all the Mel-something molecules involved. So, here is a very simplified, but essentially correct description of how this happens:
Light is detected by the photo-pigment melanopsin in the retinal ganglion cells of the eye. The cells send a signal to the clock (in the suprachiasmatic nucleus, SCN).
SCN sends a signal to the pineal gland. During the night, when it is dark, the pineal gland responds to the SCN signal by synthetizing and releasing the hormone melatonin into the bloodstream. The duration of the melatonin release is an indicator of the length of the night: long night = winter, short night = summer.
Melatonin receptors are found in the SCN, in some other places in the brain, and in some other places in the body. In the snowshoe hare, one of the targets of melatonin is the hypothalamo-pituitary system that controls the deposition of the pigment melanin into the hair follicles.
Thus, in summer, melanin gets deposited into the hair follicles and the hair that grows out of them is dark. At the onset of winter, when the clock starts detecting the shortening of the day (i.e., lengthening of the night-time melatonin signal), melanin is supressed and the dark hair is replaced with white hair (and more of it) instead.

See you at the SRBR meeting!

SRBR08splash.gif
The 11th Biennial Meeting of the Society for Research on Biological Rhythms will be held in Sandestin, FL on May 17th-21st, 2008. And I’ll be there. This meeting occurs every two years (on even-numbered years, the International Congress and the Gordon Conference are in odd-numbered years). I attended three or four of these when it was down on Amelia Island, FL. Then I skipped the one in Whistler, Canada, four years ago as I had no money to go, and the one in Sandestin two years ago as I was out of science. But I’ll be going back – with a mission: to explain Open Access to my colleagues, to get them to publish with PLoS, to get them to read my blog, to catch up with my field and to do some blog-interviews with the interesting people there. So, if you are chronobiologist and you’ll be there, please find me and say Hi.

New and Exciting in PLoS Computational Biology

I found two articles interesting to me in today’s issue of PLoS Computational Biology – the first one about becoming a good scientist, the other on circadian rhythms:
On the Process of Becoming a Great Scientist:

In the vein of promoting further debate and discussion, I provide here a different and perhaps deeper look at what makes a successful scientist. While I can’t claim to have the reputation of Hamming, I grew up in a family of well-known scientists, and have had plenty of chances to observe the trajectories of scientific careers over my lifetime. Based on that experience, I propose the following as a somewhat distinct set of guidelines for doing the best research:

Modeling an Evolutionary Conserved Circadian Cis-Element:

Life on earth is subject to daily light/dark and temperature cycles that reflect the earth rotation about its own axis. Under such conditions, organisms ranging from bacteria to human have evolved molecularly geared circadian clocks that resonate with the environmental cycles. These clocks serve as internal timing devices to coordinate physiological and behavioral processes as diverse as detoxification, activity and rest cycles, or blood pressure. In insects and vertebrates, the clock circuitry uses interlocked negative feedback loops which are implemented by transcription factors, among which the heterodimeric activators CLOCK and CYCLE play a key role. The specific DNA elements recognized by this factor are known to involve E-box motifs, but the low information content of this sequence makes it a poor predictor of the targets of CLOCK/CYCLE on a genome-wide scale. Here, we use comparative genomics to build a more specific model for a CLOCK-controlled cis-element that extends the canonical E-boxes to a more complex dimeric element. We use functional data from Drosophila and mouse circadian experiments to test the validity and assess the performance of the model. Finally, we provide a phylogenetic analysis of the cis-elements across insect and vertebrates that emphasizes the ancient link between CLOCK/CYCLE and the modeled enhancer. These results indicate that comparative genomics provides powerful means to decipher the complexity of the circadian cis-regulatory code.

Genetics and Biochemistry of Sleep

Keystone sleep/circadian meeting. Jay Dunlap, Emmanuel Mignot and Amita Seghal are organizing a Keystone meeting on Genetics and Biochemistry of Sleep in Lake Tahoe, March 7-12 (click here to see large):
amita%20sleep%20flyer%20small.jpg

Clocks and Migratory Orientation in Monarch Butterflies

Blogging on Peer-Reviewed Research

I had no time to read this in detail and write a really decent overview here, perhaps I will do it later, but for now, here are the links and key excerpts from a pair of exciting new papers in PLoS Biology and PLoS ONE, which describe the patterns of expression of a second type of cryptochrome gene in Monarch butterflies.
This cryptochrome (Cry) is more similar to the vertebrate Cry than the insect Cry, also present in this butterfly. The temporal and spatial patterns of expression of the two types of Cry suggest that they may be involved in the transfer of time-information from the circadian clock to the brain center involved in spatial orientation during long-distance migration.
The PLoS Biology paper looks at these patterns of expression, while the PLoS ONE paper identifies a whole host of genes potentially implicated in migratory behavior, including the Cry2. Here is the PLoS Biology paper:
Cryptochromes Define a Novel Circadian Clock Mechanism in Monarch Butterflies That May Underlie Sun Compass Navigation:

During their spectacular fall migration, eastern North American monarch butterflies (Danaus plexippus) use a time-compensated sun compass to help them navigate to their overwintering sites in central Mexico. The circadian clock plays a critical role in monarch butterfly migration by providing the timing component to time-compensated sun compass orientation. Here we characterize a novel molecular clock mechanism in monarchs by focusing on the functions of two CRYPTOCHROME (CRY) proteins. In the monarch clock, CRY1, a Drosophila-like protein, functions as a blue-light photoreceptor for photic entrainment, whereas CRY2, a vertebrate-like protein, functions within the clockwork as the major transcriptional repressor of the self-sustaining feedback loop. An oscillating CRY2-positive neural pathway was also discovered in the monarch brain that may communicate circadian information directly from the circadian clock to the central complex, which is the likely site of the sun compass. The monarch clock may be the prototype of a clock mechanism shared by other invertebrates that express both CRY proteins, and its elucidation will help crack the code of sun compass orientation.

Here is the editorial synopsis:
In Monarchs, Cry2 Is King of the Clock:

Back in the brain, the authors showed that Cry2 was also found in a few dozen cells in brain regions previously linked to time-keeping in the butterfly, and this Cry2 underwent circadian oscillation in these cells, but not in many other cells that were not involved in time keeping. By taking samples periodically over many hours, they found that nuclear localization of Cry2 coincided with maximal transcriptional repression of the clockwork, in keeping with its central role of regulating the feedback cycle. This is a novel demonstration of nuclear translocation of a clock protein outside flies.
Finally, the authors investigated Cry2’s activity in the central complex, the brain structure that is believed to house the navigational compass of the monarch. Monarchs integrate information on the position of the sun and the direction of polarized light to find their way from all over North America to the Mexican highlands, where they spend the winter. Cry2, but not the other clock proteins, was detected in parts of the central complex where it undergoes strong circadian cycling. Some cells containing Cry2 linked up with the clock cells, while others projected toward the optic lobe and elsewhere in the brain.
Along with highlighting the central importance of Cry2 in the inner workings of the monarch’s clock, the results in this study suggest that part of the remarkable navigational ability of the butterfly relies on its ability to integrate temporal information from the clock with spatial information from its visual system. This allows the monarch to correct its course as light shifts across the sky over the course of the day. Other cues used for charting its path remain to be elucidated.

This is the PLoS ONE paper:
Chasing Migration Genes: A Brain Expressed Sequence Tag Resource for Summer and Migratory Monarch Butterflies (Danaus plexippus):

North American monarch butterflies (Danaus plexippus) undergo a spectacular fall migration. In contrast to summer butterflies, migrants are juvenile hormone (JH) deficient, which leads to reproductive diapause and increased longevity. Migrants also utilize time-compensated sun compass orientation to help them navigate to their overwintering grounds. Here, we describe a brain expressed sequence tag (EST) resource to identify genes involved in migratory behaviors. A brain EST library was constructed from summer and migrating butterflies. Of 9,484 unique sequences, 6068 had positive hits with the non-redundant protein database; the EST database likely represents ~52% of the gene-encoding potential of the monarch genome. The brain transcriptome was cataloged using Gene Ontology and compared to Drosophila. Monarch genes were well represented, including those implicated in behavior. Three genes involved in increased JH activity (allatotropin, juvenile hormone acid methyltransfersase, and takeout) were upregulated in summer butterflies, compared to migrants. The locomotion-relevant turtle gene was marginally upregulated in migrants, while the foraging and single-minded genes were not differentially regulated. Many of the genes important for the monarch circadian clock mechanism (involved in sun compass orientation) were in the EST resource, including the newly identified cryptochrome 2. The EST database also revealed a novel Na+/K+ ATPase allele predicted to be more resistant to the toxic effects of milkweed than that reported previously. Potential genetic markers were identified from 3,486 EST contigs and included 1599 double-hit single nucleotide polymorphisms (SNPs) and 98 microsatellite polymorphisms. These data provide a template of the brain transcriptome for the monarch butterfly. Our “snap-shot” analysis of the differential regulation of candidate genes between summer and migratory butterflies suggests that unbiased, comprehensive transcriptional profiling will inform the molecular basis of migration. The identified SNPs and microsatellite polymorphisms can be used as genetic markers to address questions of population and subspecies structure.

Here is an article written after the press release, which, as such articles usually do, greatly overstates the extent of the findings:
Clocking monarch migration:

In previous work, Reppert and his team showed that pigment-producing genes in the monarch eye communicate with the butterfly’s circadian clock. As part of the new study, Reppert and his team also found, in an area of the monarch brain called the central complex, a definitive molecular and cellular link between the circadian clock and the monarch’s ability to navigate using the sun. Briscoe said that Reppert’s study was “really going to overturn a lot of views we had about the specific components of circadian clocks.”

The spatial and temporal patterns of expression make Cry2 the most serious candidate for the connection between the clock and the Sun-compass orientation mechanism. Much work, both at the molecular and at higher levels of organization needs to be done to figure out the exact mechanism by which this animal, during migration, compensates for the Sun’s movement across the sky during the day, and thus does not stray off course. Cry2 appears to be a good molecular “handle” for such studies.
For background, see my older post on the initial discovery of Cry2 in Monarch butterflies by the same team.

Pilobolus, Antlion and the Vertebrate Eyes

On Pilobolous:
When I first wrote my post on Pilobolus (here and here) I really wanted to do something extra, which I could not do at the time. If you scroll down that post, you will see I reprinted the Figure 1 from the Uebelmesser paper. What I wanted to do was find (and I asked around for something like that) the exact times of dawn and dusk at the site where Uebelmesser did her work and thus be able to figure out the dates when the tests were done and the exact phase-relationship between the dawn and the time when Pilobolus shoots its spores.
Now, I see that such a chart exists (via) and I can, if I find time and energy, do it one of these days. Then, I can do the same thing for the Chapel Hill coordinates, go out to a nearby farm, and repeat the experiment myself.
On Antlions:
I knew, when I wrote my post on antlions (here and here) that they had endogenous circalunar rhythms. But today, I also learned that:
– antlions secrete a toxin that paralyses their prey
– the antlion toxin is produced by its bacterial endosymbiont Enterobacter aerogenes
– the normal function of that toxin in the bacterial cell is as a chaperonin, i.e., a protein that makes sure that other proteins are folded correctly into their normal 3D shapes
– the Enterobacter aerogenes toxin is very similar to a protein made by Escherichia coli
– the Enterobacter aerogenes toxin is 1000 times more toxic to cockroaches than the E.coli one
– neither of the proteins is toxic to mice (and presumably to us).
One learns something new and cool every day.
On Vertebrate Eyes:
Eye is a very important organ in my own specialty, so I was surprised to see how much new I learned by reading this eye-opening post by PZ. Bookmarked for future use in teaching….

Daylight Savings Time worse than previously thought

I am sure I have ranted about the negative effects of DST here and back on Circadiana, but the latest study – The Human Circadian Clock’s Seasonal Adjustment Is Disrupted by Daylight Saving Time (pdf) (press releases: ScienceDaily, EurekAlert) by Thomas Kantermann, Myriam Juda, Martha Merrow and Till Roenneberg shows that the effects are much more long-lasting and serious than previously thought. It is not “just one hour” and “you get used to it in a couple of days”. Apparently it takes weeks for the circadian system to adjust, and in some people it never does. In this day and age of around-the-clock life, global communications, telecommuting, etc., the clock-shifting twice a year has outlived its usefulness and should go the way of the dodo. The research also shows why studies of photoperiodism is not some arcane field, but has real-world applications.

Oxytocin and Childbirth. Or not.

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When teaching human or animal physiology, it is very easy to come up with examples of ubiqutous negative feedback loops. On the other hand, there are very few physiological processes that can serve as examples of positive feedback. These include opening of the ion channels during the action potential, the blood clotting cascade, emptying of the urinary bladder, copulation, breastfeeding and childbirth. The last two (and perhaps the last three!) involve the hormone oxytocin. The childbirth, at least in humans, is a canonical example and the standard story goes roughly like this:

When the baby is ready to go out (and there’s no stopping it at this point!), it releases a hormone that triggers the first contraction of the uterus. The contraction of the uterus pushes the baby out a little. That movement of the baby stretches the wall of the uterus. The wall of the uterus contains stretch receptors which send signals to the brain. In response to the signal, the brain (actually the posterior portion of the pituitary gland, which is an outgrowth of the brain) releases hormone oxytocin. Oxytocin gets into the bloodstream and reaches the uterus triggering the next contraction which, in turn, moves the baby which further stretches the wall of the uterus, which results in more release of oxytocin…and so on, until the baby is expelled, when everything returns to normal.

As usual, introductory textbook material lags by a few years (or decades) behind the current state of scientific understanding. And a brand new paper just added a new monkeywrench into the story. Oxytocin in the Circadian Timing of Birth by Jeffrey Roizen, Christina E. Luedke, Erik D. Herzog and Louis J. Muglia was published last Tuesday night and I have been poring over it since then. It is a very short paper, yet there is so much there to think about! Oh, and of course I was going to comment on a paper by Erik Herzog – you knew that was coming! Not just that he is my friend, but he also tends to ask all the questions I consider interesting in my field, including questions I wanted to answer myself while I was still in the lab (so I live vicariously though his papers and blog about every one of them).
Unfortunately, I have not found time yet to write a Clock Tutorial on the fascinating topic of embryonic development of the circadian system in mammals and the transfer of circadian time from mother to fetus – a link to it would have worked wonderfully here – so I’ll have to make shortcuts, but I hope that the gist of the paper will be clear anyway.

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Postdocs in some really good circadian labs

A post-doctoral position is available in the laboratory of Dr. Tosini to investigate the cellular and molecular mechanisms that control circadian rhythms in the mammalian retina [Tosini et al., (2007) Faseb J.; Sakamoto et al., (2004). J. Neuroscience 24: 9693-9697; Fukuhara et al., (2004) J. Neuroscience 24:1803-1811; Tosini G., Menaker, M. (1996) Science, 272: 419-421).The position is funded by a grant from the National Institute of Health.
The work will focus on the characterization of newly developed transgenic mice using physiological (ERG), molecular (Q-PCR and Laser Capture Microdissection) and bioluminescence recording from the whole retina or single photoreceptors. Previous experience in the circadian field and with retinal tissue is a plus, but not necessary.
The Neuroscience Institute at Morehouse School of Medicine is equipped with state-of-the-art equipments for research in Neuroscience and in particular on circadian rhythms and sleep disorders.
Gianluca Tosini, Ph.D.
Professor and Director
Circadian Rhythms and Sleep Disorders Program
Neuroscience Institute
Morehouse School of Medicine
720 Westview Dr. Atlanta, GA
Postdoctoral Research position available to study the control of circadian rhythms by sustained attention. Emphasis is on the ACh projection from the basal forebrain to the suprachiasmatic nucleus and the control of circadian rhythms. Ph.D. in Biopsychology, Neuroscience, or related fields is preferred. Familiarity with chronobiology and/or control of behavior through operant conditioning will be helpful. Primary responsibilities: designing and coordinating experiments to study the control of daily rhythms by a task that requires high, sustained attention; microdialysis; stereotaxic surgery; histology; managing students that will also work on this project. Salary commensurate with experience; health insurance provided. Length of appointment could be 3 yrs. Please send resume and contacts for recommendations to: Dr. Theresa M. Lee, University of Michigan, Dept of Psychology, 530 Church St, Ann Arbor, MI 48109-1043. Review of applications will begin Sept 1, 2007 and continue until the position is filled. Start date is negotiable.
Theresa M.Lee, Ph.D.
Professor, Psychology & Neuroscience Program
Chair, Department of Psychology
University of Michigan
530 Church St
Ann Arbor, MI 48109-1043

Endocrine rhythms

Circadian clocks: regulators of endocrine and metabolic rhythms by Michael Hastings, John S O’Neill and Elizabeth S Maywood is a new and excellent review of the interaction between the clocks and hormones in mammals, focusing at the molecular level. The pre-print PDF of the article is freely available on the Journal of Endocrinology site.

Phase-Response Curves to Melatonin

NBM found an excellent online article (which I have seen before but I forgot) depicting Phase-Response Curves (PRC) to injections of melatonin in humans, rodents and lizards.
melatonin%20PRCs.gif
Note how the shape is roughly opposite to that of a PRC to light pulses, i.e., at phases at which light elicits phase-delays, melatonin produces advances and vice versa:
melatonin-light-PRC%20small.jpg
The lizard PRC was actually constructed in our lab, about ten years before I joined. The article, though, gives the wrong reference to this:
Underwood, H. and M. Harless (1985). “Entrainment of the circadian activity rhythm of a lizard to melatonin injections.” Physiology & Behavior 35(2): 267-70.
In that paper, lizards were entrained by daily melatonin injections. The PRC was reported in a different paper the following year:
H Underwood (1986) Circadian Rhythms in Lizards: Phase Response Curve for Melatonin, Journal of Pineal Research 3 (2), 187-196.
Update: an alert reader sends a better figure, taken from this freely available recent paper:
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Deceptive Metaphor of the Biological Clock

Deceptive Metaphor of the Biological ClockSometimes a metaphor used in science is useful for research but not so useful when it comes to popular perceptions. And sometimes even scientists come under the spell of the metaphor. One of those unfortunate two-faced metaphors is the metaphor of the Biological Clock.

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

 Does circadian clock regulate clutch-size in birds? A question of appropriatness of the model animal.This post from March 27, 2006 starts with some of my old research and poses a new hypothesis.

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Clock Tutorial #3c – Darwin On Time

Darwin On Time This post is a modification from two papers written for two different classes in History of Science, back in 1995 and 1998. It is a part of a four-post series on Darwin and clocks. I first posted it here on December 02, 2004 and then again here on January 06, 2005:

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ClockTutorial #3b – Whence Clocks?

ClockTutorial #3b - Whence Clocks?This post about the origin, evolution and adaptive fucntion of biological clocks originated as a paper for a class, in 1999 I believe. I reprinted it here in December 2004, as a third part of a four-part post. Later, I reposted it here.

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ClockTutorial #3a – Clock Evolution

ClockTutorial #3a - Clock EvolutionThis post, originally published on January 16, 2005, was modified from one of my written prelims questions from early 2000.

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The Amplitude Problem

Blogging on Peer-Reviewed Research

If you are one of the few of my readers who actually slogged through my Clock Tutorials, especially the difficult series on Entrainment and Phase Response Curves, you got to appreciate the usefulness of the oscillator theory from physics in its application to the study of biological clocks. Use of physics models in the study of biological rhythms, pioneered by Colin Pittendrigh, is an immensely useful tool in the understanding of the process of entrainment to environmental cycles.
Yet, as I warned several times, a Clock is a metaphor and, as such, has to be treated with thought and caution. Is the physics model always applicable? Is it sometimes deceptive? How much does it oversimplify the behavior out in the natural environment?
The few tests of the theory conducted in the field demonstrate that the models of entrainment (the PRCs) work quite well, though not always perfectly. Use of Limit Cycles (something that is, IMHO, too complex for me to try to explain on a blog) is also useful. The theory appears to work quite well in regard to period and phase, but the effects of amplitude of the oscillation are not as well tested, although a number of studies, especially regarding photoperiodism in non-mammalian vertebrates and invertebrates, suggests that the amplitude is an important parameter of a biological rhythm.
oscillation.jpg
The main problem with the amplitude is that it is not clear if the measured amplitude of the overt rhythms (e.g., activity, body temperature, melatonin release, etc.) faithfully reflects the amplitude of the underlying oscillator. It is not even certain that the amplitude of the expression of core clock genes and proteins is the equivalent of the amplitude of the idealized physical system.
In a recent paper (provisional PDF) in the Journal of Circadian Rhythms (an Open Access journal, where you can also comment on the papers, just like on PLoS ONE), Daniel Kripke, Jeffrey Elliott, Shawn Youngstedt and Katharine Rex, using that most difficult laboratory model of all – the human – tried to kill two birds with one stone: test if the physical oscillatory models apply for the amplitude of circadian clocks and test if the amplitude of the overt rhythms is a good reflection of the amplitude of the underlying biological oscillator. The medical implicaitons of their work, no matter what the results, is quite obvious as well.
It is well known that the amplitude of overt rhythms (activity, sleep-wake cycle, temperature, melatonin, cortisol, etc.) gets a little smaller with advanced age in humans. Measuring simultaneously several overt rhythms (always a good thing!) while constructing a Phase-Response Curve to light pulses in two groups – young and old people – they excpected, from theory, to see a change in the shape and size of the PRC. According to theory, an oscillator with a higher amplitude (young) would be more difficult to shift, i.e., the size of phase-shifts would be smaller than in the old cohort (for some odd reason – typo perhaps? – they state they expected the opposite, i.e., smaller shifts in the older group).
If they got positive results, i.e., if the size of phase-shifts differed between the two age groups, they would have demonstrated that a) physical model of oscillatons applies to biological clocks in respect to amplitude, and b) that the amplitude of overt rhythms faithfully reflects the amplitude of the underlying biological oscillator.
But, their results were negative, i.e., there was no difference in the size of phase-shifts between young and old cohorts (or, for that matter, between women and men), though the phase of all rhythms (except temperature and the offset of melatonin metabolites in the urine – likely due to the slower metabolism itself) was advanced and the PRCs, as expected, moved somewhat to the left to reflect this.
This unfortunate result suggests one (or both) of the two possibilities:
– Oscillator models borrowed from physics do not apply to biology in regard to amplitude, or
– Amplitude of overt rhythms does not reflect the amplitude of the underlying oscillator
As they say, more work needs to be done.

Persistence In Perfusion

Persistence In PerfusionThis post, from January 25, 2006, describes part of the Doctoral work of my lab-buddy Chris.

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The Mighty Ant-Lion

The Mighty Ant-LionFirst written on March 04, 2005 for Science And Politics, then reposted on February 27, 2006 on Circadiana, a post about a childrens’ book and what I learned about it since.

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What makes a memorable poster, or, when should you water your flowers?

What makes a memorable poster, or, when should you water your flowers?Being out of the lab, out of science, and out of funding for a while also means that I have not been at a scientific conference for a few years now, not even my favourite meeting of the Society for Research on Biological Rhythms. I have missed the last two meetings (and I really miss them – they are a blast!).
But it is funny how, many years later, one still remembers some posters from poster sessions. What makes a poster so memorable?

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

Some hypotheses about a possible connection between malaria and jet-lagHypotheses leading to more hypotheses (from March 19, 2006 – the Malaria Day):

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Chossat’s Effect in humans and other animals

Chossat's Effect in humans and other animalsThis April 09, 2006 post places another paper of ours (Reference #17) within a broader context of physiology, behavior, ecology and evolution.
The paper was a result of a “communal” experiment in the lab, i.e., it was not included in anyone’s Thesis. My advisor designed it and started the experiment with the first couple of birds. When I joined the lab, I did the experiment in an additional number of animals. When Chris joined the lab, he took over the project and did the rest of the lab work, including bringin in the idea for an additional experiment that was included, and some of the analysis. We all talked about it in our lab meetings for a long time. In the end, the boss did most of the analysis and all of the writing, so the order of authors faithfully reflects the relative contributions to the work.
What is not mentioned in the post below is an additional observation – that return of the food after the fasting period induced a phase-shift of the circadian system, so we also generated a Phase-Response Curve, suggesting that food-entrainable pacemaker in quail is, unlike in mammals, not separate from the light-entrainable system.
Finally, at the end of the post, I show some unpublished data – a rare event in science blogging.

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Seasonal Affective Disorder – The Basics

Seasonal Affective Disorder - The BasicsThis is an appropriate time of year for this post (February 05, 2006)…

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Circadian Rhythms, or Not, in Arctic Reindeer

Circadian Rhythms, or Not, in Arctic ReindeerA January 20, 2006 post placing a cool physiological/behavioral study into an evolutionary context.

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Does Tryptophan from turkey meat make you sleepy?

Does Tryptophan from turkey meat make you sleepy?Well, it’s Thanksgiving tomorrow night so it’s time to republish this post from last year, just in time for the ageless debate: does eating turkey meat make you sleepy? Some people say Yes, some people say No, and the debate can escalate into a big fight. The truth is – we do not know.
But for this hypothesis to be true, several things need to happen. In this post I look at the evidence for each of the those several things. Unfortunately, nobody has put all the elements together yet, and certainly not in a human. I am wondering…is there a simple easily-controlled experiment that people can do on Thursday night, then report to one collecting place (e.g., a blog) where someone can do the statistics on the data and finally lay the debate to rest? Any ideas?
Also, I will add the comments that the post originally received and I hope for new comments from people with relevant expertise. Is Trp Hxlse really a rate-limiting enzyme? If so, why gavaging chickens and rats with Try increases plasma melatonin? Is it different in humans? You tell me!
(originally posted on November 25, 2005)

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Lithium, Circadian Clocks and Bipolar Disorder

Lithium, Circadian Clocks and Bipolar DisorderYou probably realize by now that my expertise is in clocks and calendars of birds, but blogging audience forces me to occasionally look into human clocks from a medical perspective. Reprinted below the fold are three old Circadiana posts about the connection between circadian clocks and the bipolar disorder, the third one being the longest and most involved. Here are the links to the original posts if you want to check the comments (especially the first comment on the third post):
January 18, 2005: Clocks and Bipolar Disorder
August 16, 2005: Bipolar? Avoid night shift
February 19, 2006: Lithium, Circadian Clocks and Bipolar Disorder

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Clock Genetics – A Short History

Clock Genetics - A Short HistoryA short post from April 17, 2005 that is a good starting reference for more detailed posts covering recent research in clock genetics (click on spider-clock icon to see the original).

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Cortisol necessary for circadian rhythm of cell division

Cortisol necessary for circadian rhythm of cell divisionA new paper just came out today on PLoS-Biology: Glucocorticoids Play a Key Role in Circadian Cell Cycle Rhythms. The paper is long and complicated, with many control experiments, etc, so I will just give you a very brief summary of the main finding.

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The Clock Metaphor

The Clock Metaphor
Chad wrote a neat history of (or should we say ‘evolution of’) clocks, as in “timekeeping instruments”. He points out the biological clocks are “…sort of messy application, from the standpoint of physics…” and he is right – for us biologists, messier the better. We wallow in mess, cherish ambiguity and relish in complexity. Anyway, he is talking about real clocks – things made by people to keep time. And he starts with a simple definition of what a clock is:

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Is sunshine good for you?

“Is sunshine good for you?” is the latest Ask a ScienceBlogger question and Nick Anthis did a great job answering it – focusing on the circadian aspects of the need for sunlight – in his response here. Excellent and quite correct, if I may say so, (and I had trouble commenting on his blog, so I’ll put it here) except perhaps the details of the Viagra paper.

Everything Important Cycles

Blogging on Peer-Reviewed Research

Microarrays have been used in the study of circadian expression of mammalian genes since 2002 and the consensus was built from those studies that approximately 15% of all the genes expressed in a cell are expressed in a circadian manner. I always felt it was more, much more.
I am no molecular biologist, but I have run a few gels in my life. The biggest problem was to find a control gene – one that does not cycle – to make the comparisons to. Actin, which is often used in such studies as control, cycled in our samples. In the end, we settled on one of the subunits of the ribosome as we could not detect a rhythm in its expression. The operative word is “could not detect”. My sampling rate was every 3 hours over a 24-hour period, so it is possible that we could have missed circadian expression of a gene that has multiple peaks, or a single very narrow peak, or a very low amplitude of cycling (it still worked as a control in our case, for different reasons). Thus, my feeling is that everything or almost everything that is expressed in a cell will be expressed in a rhythmic pattern.
If you have heard me talk about clocks (e.g., in the classroom), or have read some of my Clock Tutorials, you know that I tend to say something like “All the genes that code for proteins that are important for the core function of a cell type are expressed in a circadian fashion”. So, genes important for liver function will cycle in the liver cells, genes important for muscle function will cycle in muscle cells, etc.
But I omit to note that all such genes that are important for the function of the cell type are all the genes that are expressed in that cell. The genes not used by that cell are not expressed. But I could not go straight out and say “all the genes that are expressed in a cell are expressed in a circadian pattern”, because I had no data to support such a notion. Until yesterday.
What happened yesterday?

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Sleep Genes are not the same as ‘Genes for sleep’

Back in the late 1990s, when people first started using various differential screens, etc. looking for elusive “genes for sleep”, I wrote in my written prelims (and reprinted it on my blog several years later):

Now the sleep researchers are jumping on the bandwagon of molecular techniques. They are screening for differences in gene expression between sleeping and awake humans (or rats or mice), searching quite openly for the “genes for sleep”. Every time they “fish out” a gene, it turns out to be Protein kinase A, a dopamine receptor, or something similar with a general function in the brain. Don’t they understand that sleep (like hibernation) is an emergent property of a multicellular brain? Unlike in the clock field, a single neuron does not carry the function – it does not sleep. Only whole (or halves of) brains can be asleep or awake. The sleep “mechanism” is not a molecular mechanism but a result of a particular pattern of neural connectivity and activity.

And, lo an behold, all the genes that affect sleep (the duration or quality of it, not timing which is guided by the circadian clock), turned out to be those “maintanance” molecules, involved in general, day-to-day activity of neurons. Most geneticists have since moved away from such a simplistic, bean-bag genetics notion of sleep and started studying sleep from a much more integrative perspective. But some persist. The newest discovery of a “sleep-gene” is just like what I predicted, a general-maintanance molecule – an ion channel:
Second Sleep Gene Identified:

A gene that controls the flow of potassium into cells is required to maintain normal sleep in fruit flies, according to researchers at the University of Wisconsin School of Medicine and Public Health (SMPH). Hyperkinetic (Hk) is the second gene identified by the SMPH group to have a profound effect on sleep in flies.
The finding supports growing evidence that potassium channels–found in humans and fruit flies alike–play a critical role in generating sleep.
“Without potassium channels, you don’t get slow waves, the oscillations shown by groups of neurons across the brain that are the hallmark of deep sleep,” says Chiara Cirelli, SMPH psychiatry professor and senior author on the latest study, which appeared in the May 16, 2007, Journal of Neuroscience.

Very cool and important for the advancement of our understanding of sleep, but surely not a “gene for sleep”.

Carolus Linnaeus’ Floral Clocks

When it’s someone’s birthday it is nice to give presents, or a flower. Perhaps a whole boquet of roses. But if the birthday is a really big round number, like 300, and the birthday boy is the one who actually gave names to many of those flowers, it gets a little tougher. Perhaps you may try to do something really difficult and build, actually plant, a Flower Clock. After all, it was Carl von Linne, aka Carolus Linnaeus, today’s birthday celebrator, who invented the flower clock. He drew it like this, but he never actully built one:
flower%20clock%20linnaeus.jpg
The first one to make (and write down) an observation that some plants (in that case, a tropical Tamarind tree) raise their leaves during the day and let them droop down during the night, was Androsthenes, an officer who accompanied Alexander the Great. In the first century, Pliny the Elder made a similar observation, repeated in the thirteenth century by Albertus Magnus.
In 1729, Jean Jacque d’Ortous de Mairan, an astronomer, not a botanist, reported an experiment – considered to be the first true chronobiologial experiment in history – in which he observed the spontaneous daily rise and nightly fall of leaves of Mimosa pudica kept in a closet in the dark. The experiment was repeated with some improvements by Duhamel de Monceau and by Zinn, both in 1759.
Another Swede, Arrhenius argued that a mysterious cosmic Factor X triggered the movements. Charles Darwin published an entire book on the Movement of Plants, arguing that the plant itself generates the daily rhythms. The most famous botanist of the 19th century, Pfeffer, started out favouring the “external hypothesis”, but Darwin’s experiments forced him to change his mind later in his career and accept the “internal” source of such rhythmic movements. In the early 20th century, Erwin Bunning was the first to really thoroughly study circadian rhythms in plants. For the rest of the century, animal research took over and though there has been some progress recently, the understanding of clocks in plants still lags behind that of Drosophila and the mouse.
But it was Carolus Linnaeus back in the 18th century who, fond of personifying plants (mostly in regard to sex) named this phenomenon “sleep” in plants. Soon, he switched his focus from movements of leaves to the daily opening and closing of flowers and performed a broad study of the times of day when each flower species opened and closed:

Linnaeus observed over a number of years that certain plants constantly opened and closed their flowers at particular times of the day, these times varying from species to species. Hence one could deduce the approximate time of day according to which species had opened or closed their flowers. Arranged in sequence of flowering over the day they constituted a kind of floral clock or horologium florae, as Linnaeus called it in his Philosophia Botanica (1751, pages 274-276). A detailed and extended account of this in English will be found in F.W.Oliver’s translation of Anton Kerner’s The Natural History of Plants, 1895, vol.2, pages 215-218. As many of the indicator plants are wildflowers and the opening/closing times depend on latitude, the complexities of planting a floral clock make it an impractical proposition.

While it is not easy to make a functioning flower clock, people have done it. There is one in his hometown of Uppsala, for instance. It has been made in the classroom (pdf) and one can pretty easily find locally useful lists of plants to try to build one.
flowerclocklarge.jpg

Linnaeus; in writings titled Philosophia Botanica wrote about 3 types of flowers:
1. Meteorici, A category which changes their opening and closing times according to the weather conditions.
2. Tropici, Flowers which change their opening and closing specifically to the length of the day.
3. Aequinoctales, Most important here to this story, are the flowers having fixed times for opening and closing, regardless of weather or season.

It is only those last ones that could be used for buildiing Floral Clocks, while the first two groups were important for the studies of vernalization and photoperiodism in plants in the early 20th century.
flower%20clock%20schematic.JPG
You can find some more detail of the flower clock history here. And the idea of a flower clock was also picked up by artists of various kinds:

Linnaeus’s idea for a collection of flowers that opened or closed at a particular time of day was taken up by the French composer Jean Fran aix in his composition L’horloge de flore (The Flower Clock), a concerto for solo oboe and orchestra.
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A floral clock features in the fictional city of Quirm, in Soul Music, one of the books in Terry Pratchett’s Discworld series.

Is That Your Jet-Lag Treatment Showing or are you just Happy To See Me?

Blogging on Peer-Reviewed Research

If this gets more widely known (and, with this post, I am trying to help it become so), you can just imagine the jokes about the new challenges to the aviation industry and the renewed popularity of the Mile High Club, or the cartoons utilizing the phallic shape of airplanes!
Hamsters on Viagra Have Less Jet Lag, Research Shows (also Viagra helps jet-lagged hamsters, maybe humans, too: study and Viagra ‘improves jet lag’):

Hamsters given Pfizer Inc.’s Viagra adapted more quickly to changes in their internal clocks, scientists said.
Hamsters given sildenafil, the chemical name of the drug sold as Viagra, adapted more easily to altered patterns of light exposure to simulate changes caused by air travel across time zones. Long-haul travel desynchronizes the body’s alignment to the day-night cycle, leading to the disorientation of jet lag.
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The researchers synchronized the hamsters to a 24-hour day by simulating light-dark cycles. Once the hamsters adjusted to a cycle, they shifted the light-dark phases forward six hours. One group of hamsters was given saline; the other was given Viagra. The hamsters given Viagra got used to the change 4 days faster, on average, than their counterparts given a placebo. Viagra eased the transition that mimicked crossing the international dateline from west to east, known as phase advancing, and had no effect on a transition that mimicked westward travel.

There should be a rule in journalism making sure that no article about Viagra ever contains the words “harder” and “screw”, especially close to each other. Oooops!

“All animals, including humans, have a harder time with phase advancing,” said Colwell in a telephone interview today. “Humans are unique in our ability to screw up our timing system — you know, jet lag, shift work, staying up too late playing video games, or whatever.”

OK, now seriously…what does the study say?

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Chronobiology primer

Far too gene-centered for my taste, but an excellent chronobiology primer (pdf) nonetheless.

Flirting under Moonlight on a Hot Summer Night, or, The Secret Night-Life of Fruitflies

Blogging on Peer-Reviewed Research

As we mentioned just the other day, studying animal behavior is tough as “animals do whatever they darned please“. Thus, making sure that everything is controlled for in an experimental setup is of paramount importance. Furthermore, for the studies to be replicable in other labs, it is always a good idea for experimental setups to be standardized. Even that is often not enough. I do not have access to Science but you may all recall a paper from several years ago in which two labs tried to simultaneously perform exactly the same experiment in mice, using all the standard equipment, exactly the same protocols, the same strain bought from the same supplier on the same date, the same mouse-feed, perhaps even the same colors of technicians’ uniforms and yet, they got some very different data!
The circadian behavior is, fortunately, not chaotic, but quite predictable, robust and easily replicable between labs in a number of standard model organisms. Part of the success of the Drosophila research program in chronobiology comes from the fact that for decades all the labs used exactly the same experimental apparatus, this one, produced by Trikinetics (Waltham, Massachusetts) and Carolina Biologicals (Burlington, North Carolina):
drosophila%20apparatus.jpg
This is a series of glass tubes, each containing a single insect. An infrared beam crosses the middle of each tube and each time the fly breaks the beam, by walking or flying up and down the tube, the computer registers one “pen deflection”. All of those are subsequently put together into a form of an actograph, which is the standard format for the visual presentation of chronobiological data, which can be further statistically analyzed.
The early fruitfly work was done mainly in Drosophila pseudoobscura. Most of the subsequent work on fruitfly genetics used D.melanogaster instead. Recently, some researchers started using the same setup to do comparative studies of other Drosophila species. Many fruitfly clock labs have hundreds, even thousands, of such setups, each contained inside a “black box” which is essentially an environmental chamber in which the temperature and pressure are kept constant, noise is kept low and constant (“white noise”), and the lights are carefully controlled – exact timing of lights-on and lights-off as well as the light intensity and spectrum.
In such a setup, with a square-wave profile of light (abrupt on and off switches), every decent D.melanogaster in the world shows this kind of activity profile:
fruitfly%20crepuscular.JPG
The activity is bimodal: there is a morning peak (thought to be associated with foraging in the wild) and an evening peak (thought to be associated with courtship and mating in the wild).
The importance of standardization is difficult to overemphasize – without it we would not be able to detect many of the subtler mutants, and all the data would be considered less trustworthy. Yet, there is something about standardization that is a negative – it is highly artificial. By controlling absolutely everything and making the setup as simple as possible, it becomes very un-representative of the natural environment of the animal. Thus, the measured behavior is also likely to be quite un-natural.
Unlike in the lab, the fruitflies out in nature do not live alone – they congregate with other members of the species. Unlike in a ‘black box’, the temperature fluctuates during the day and night in the real world. Also unlike the lab, the intensity and spectrum of light change gradually during the duration of the day while the nights are not pitch-black: there are stars and the Moon providing some low-level illumination as well. Thus, after decades of standardized work, it is ripe time to start investigating how the recorded behaviors match up with the reality of natural behavior in fruitflies.
Three recent papers address these questions by modifying the experimental conditions in one way or another, introducing additional environmental cues that are usually missing in the standard apparatus (and if you want to know what they found, follow me under the fold):

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A Pacemaker is a Network

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This is going to be a challenging post to write for several reasons. How do I explain that a paper that does not show too much new stuff is actually a seminal paper? How do I condense a 12-page Cell paper describing a gazillion experiments without spending too much time on details of each experiment (as much as I’d love to do exactly that)? How do I review it calmly and critically without gushing all over it and waxing poetically about its authors? How do I put it in proper theoretical and historical perspective without unnecessarily insulting someone? I’ll give it a try and we’ll see how it turns out (if you follow me under the fold).
Clock Genes – a brief history of discovery
Late 1990s were a period of amazing activity and rate of discovery in chronobiology, specifically in molecular basis of circadian rhythms. Sure, a few mutations resulting in period changes or arrhythmicity were known before, notably period in fruitflies, frequency in the fungus Neurospora crassa, the tau mutation in hamsters and some unidentified mutations in a couple of Protista.
But in 1995, as the molecular techniques came of age, flood-gates opened and new clock genes were discovered almost every week (or so it appeared).

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Big Circadian Changes at UVA

One chronobiological pioneer is leaving and another one is coming in. Gene Block is going to UCLA and Joe Takahashi is leaving Northwestern (What are Fred Turek and others going to do there without him? What happens to the Howard Hughes institute?) and coming in to head the new Center for Circadian and Systems Biology. A very interesting game of musical chairs. Stay tuned.

Three labs simultaneously discover a new clock gene!

Thus reports The Scientist:

Researchers from three different labs have identified a new circadian gene in the mouse, according to two papers in Science and one paper in Cell published online this week. Mutagenesis screens revealed that mutations in a protein called FBXL3 lengthen the mouse circadian period by several hours, and biochemical analyses showed that FBXL3 is necessary for degradation of key circadian clock proteins.

I’ll probably have something more to say once I get hold of the actual papers.
In a perfect world, the three groups would have done Open Notebook science, found each other, collaborated, minimized waste of parallel work, and ended with a kick-ass monster paper in PLoS-Biology that would get cited hundreds of times within a year. Ah well….

Oh, how I wish I could go there…

Cold Spring Harbor 72nd Symposium: Clocks & Rhythms, May 30 – June 4, 2007. Abstract deadline is way past due, but just to go and be there (and blog from there) would be super-awesome.

Rotating shifts shorten lives

This is the first study I know that directly tested this – the effects of rotating shifts on longevity – in humans, though some studies of night-shift nurses have shown large increases in breast cancers, stomach ulcers and heart diseases, and similar studies have been done in various rodents and fruitflies:
Working in shifts shortens life span: Study:

A study of 3,912-day workers and 4,623 shift workers of the Southeastern Central Railway in Nagpur showed the former lived 3.94 years longer than their counterparts on shift duties, said the study by Atanu Kumar Pati of The School of Life Sciences in Pt Ravishankar Shukla University, Raipur.
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Shift work affects the circadian rhythm, the 24-hour cycle in the physiological processes of humans that leads to several sleep-related and social problems.
Circadian rhythms are important in determining the sleeping and feeding patterns of all animals, including humans. Brain wave activity, hormone production, cell regeneration and other biological activities are linked to this daily cycle.
Pati and his colleague K Venu Achari analysed a database of dates of death, retirement and death of each worker and published their findings in the latest issue of “current science”.
They also studied data on deaths due to all causes of 594 railway employees, including 282 day workers and 312 shift workers, over a span of 25 years. The cause of death was not documented in the database. An analysis of the data showed that day workers tend to live 3.94 years longer than counterparts working in shifts.
All day workers performed duty between 9 am and 6 pm with an hour-long lunch break from 1 pm and included those on office job and doing miscellaneous duties, the study said.
Those coming for shift duties worked in a rotating system consisting of a day shift (8 am to 4 pm), first night (4 pm to midnight) and second night (midnight to 8 am).
They worked in each shift continuously for six days and had a single day break before resumption of the next shift. The shift workers included running staff, gangmen and those doing miscellaneous jobs.
“The longevity of each worker was computed from the dates of birth, retirement and death,” Pati said. The researchers cited a number of animal studies that documented the life-shortening effects of weekly shifting of light-dark cycles.
It has been argued that these effects could be mediated through disruption of the circadian rhythm. Lighting schedule manipulation has also been reported to produce detrimental effects on the lifespan of insects.