Category Archives: Clock Zoo

Persistence In Perfusion

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

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How eyes talk to each other?

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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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Clock Tutorial #9: Circadian Organization In Japanese Quail

Circadian Organization In Japanese QuailGoing into more and more detail, here is a February 11, 2005 post about the current knowledge about the circadian organization in my favourite animal – the Japanese quail.

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Clock Tutorial #8: Circadian Organization In Non-Mammalian Vertebrates

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Circadian Organization In Non-Mammalian Vertebrates This post was originally written on February 11, 2005. Moving from relatively simple mammalian model to more complex systems.

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Clock Tutorial #7: Circadian Organization in Mammals

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Circadian Organization in Mammals This February 06, 2005 post describes the basic elements of the circadian system in mammals.

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Daily rhythm in predator-avoidance in tadpoles

A nice new study on ecological aspects of circadian rhythms:

To a tiny tadpole, life boils down to two basic missions: eat, and avoid being eaten. But there’s a trade-off. The more a tadpole eats, the faster it grows big enough to transform into a frog; yet finding food requires being active, which ups the odds of becoming someone else’s dinner.
Scientists have known that prey adjust their activity levels in response to predation risk, but new research by a University of Michigan graduate student shows that internal factors, such as biorhythms, temper their responses.
Michael Fraker, a doctoral student in the laboratory of ecology and evolutionary biology professor Earl Werner, will present his results Aug. 10 at a meeting of the Ecological Society of America in Memphis, Tenn.
Fraker studied tadpoles of the green frog (Rana clamitans), which normally feed more at night, to see whether their responses to predatory dragonfly larvae differed with time of day.
“Green frog tadpoles, like many other aquatic animals, assess predation risk indirectly by sensing chemicals released by their predators into the water,” Fraker said. Typically, the tadpoles respond to such cues by swimming down to the bottom, seeking shelter and remaining still. In his experiments, Fraker exposed tadpoles in a tank to the chemical signatures of dragonfly larvae for one hour during the day and one hour at night. Then he recorded their swimming and feeding activity during and after exposure. Both during the day and at night, the tadpoles initially responded similarly to the chemical cues, showing the typical plunge in activity. But at night they returned to feeding more quickly than during the day.
“My interpretation of these results is that green frog tadpoles behave more conservatively in response to a predator chemical cue during the day because predation risk may still be fairly high and the tadpoles are going to feed very little anyway. That means the growth rate-to-predation risk ratio is low. At night, the ratio is higher because that’s when the tadpoles do most of their feeding. This favors a quicker return to their pre-cue activity levels.”
Considering biorhythmic activity patterns in predator-prey studies is something of a new slant, Fraker said. “The main implication of my results is that prey behavior can be influenced by both external factors—the chemical cues released by the predators—and internal factors such as circadian rhythms. This is important for understanding the mechanisms of prey behavior, which need to be identified in order to make long-term predictions about the effects of prey behavior in ecological communities.”

The work will be presented at a meeting, thus no paper is available yet. Still, one needs to be careful here – different responses during the day and night may be entirely due to effects of light or darkness without modulation by the circadian clock. Thus, they show a diurnal, not circadian, rhythm in this behavior. A real test would be to repeat the experiment in constant light conditions (e.g., constant dim light or constant dark).

Postscript to Pittendrigh’s Pet Project – Phototaxis, Photoperiodism and Precise Projectile Parabolas of Pilobolus on Pasture Poop

We have recently covered interesting reproductive adaptations in mammals, birds, insects, flatworms, plants and protists. For the time being (until I lose inspiration) I’ll try to leave cephalopod sex to the experts and the pretty flower sex to the chimp crew.
In the meantime, I want to cover another Kingdom – the mysterious world of Fungi. And what follows is not just a cute example of a wonderfully evolved reproductive strategy, and not just a way to couple together my two passions – clocks and sex – but also (at the very end), an opportunity to post some of my own hypotheses online.

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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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Biological Clocks in Protista

Writing a chronobiology blog for a year and a half now has been quite a learning experience for me. I did not know how much I did not know (I am aware that most of my readers know even less, but still….). Thus, when I wrote about clocks in birds I was on my territory – this is the stuff I know first-hand and have probably read every paper in the field. The same goes for topics touching on seasonality and photoperiodism as my MS Thesis was on this topic. I feel equally at home when discussing evolution of clocks. I am also familiar with the clocks in some, but not all, arthropods. And that is all fine and well….but, my readers are anthropocentric. They want more posts about humans – both clocks and sleep – something I knew very little about. So, I have learned a lot over the past year and a half by digging through the literature and books on the subject. I was also forced to learn more about the molecular machinery of the circadian clock as most newsworthy (thus bloggable) new papers are on the clock genetics.
I know almost nothing about clocks in plants, fungi or fish, for instance, but I intend to learn – both for my own sake and for the sake of my blog readers. Actually, I started digging through the literature taxon by taxon some while ago, pretty much on two tracks: one covering the Invertebrates (like this and this), the other on microorganisms.
It is interesting to see how much I have regurgitated textbook dogma and conference hallway “truths” in my initial post on the clocks in microorganisms, only to have to contradict myself once I actually delved into the literature and learned for myself (see the series here: one, two, three, four and five).
I bet the same thing is going to happen next, as I am embarking on the literature on the clocks in Protista. I wish I could have a copy of Cellular and Molecular Bases of Biological Clocks: Models and Mechanisms for Circadian Timekeeping by Leland N. Edmunds, an excellent book that contains a lot of infromation on the clocks in protists. However, it is expensive, and although it is on my amazon wish list, I doubt anyone will splurge on it for me.
chlamy5.jpgSo, over the next couple of months, expect a series of posts on the clocks in protists. From the old textbooks and conference lore, I believe that one of the first (if not THE first) circadian mutation was discovered in the Chlamydomonas, belonging to the group of green algae (recently moved into the Kingdom Plantae, but I will treat it as a Protist for the purposes of my series) which was an important laboratory model early in the development of the field.
Euglena.JPGPeople like Leland Edmunds have worked out a lot of cell biology of clocks in the Paramecium (Ciliata) and Euglena (Flagellates).
acetabularia.jpgThe most astonishing results came from some 1950s studies in the Acetabularia, another green alga, in which rhythms persisted in the absence of the cell nucleus. The studies were repeated in early 1990s, yet to this day there is no good explanation of the findings – I am looking forward to reviewing that part!
Starting on my literature search, I discovered that some work was also done on Rhodophyta (red algae), e.g., this and this.
gonyalax.jpegMost of the work in protists, however, was performed on Lingulodinium polyedrum, much better known by its old name Gonyaulax polyedra. It was initially studied by one of the pioneers of chronobiology, J.Woodland Hastings. ‘Woody’, as he is known, had many graduate students who, after leaving his lab, took Gonyaulax with them and did further research for many years. Several very important findings, with implicaitons for the whole field of chronobiology, came out of that research on Gonyaulax.
Unfortunately, the way science funding is going these days, when even fruitfly researchers are complaining, little to no research is currently done on clocks in protista – all those researchers have moved to mice and rats in order to get their work funded. I hope this situation changes in the future. Protists are such a huge and diverse group of organisms, they are bound to keep many cool secrets we should try to uncover.

Clocks, cell cycle and cancer

This is in the bread-mold Neurospora crassa. It is unlikely to be universal. I expect to see the connection in some protists and fungi, perhaps in some animals. I am not so sure about plants, and I am pretty sure it is not like this in Cyanobacteria in which the cycle of cell division is independent from circadian timing:
Novel connection found between biological clock and cancer

Hanover, NH–Dartmouth Medical School geneticists have discovered that DNA damage resets the cellular circadian clock, suggesting links among circadian timing, the cycle of cell division, and the propensity for cancer.
——-snip———
One gene (period-4) was identified over 25 years ago by a mutation that affects two clock properties, shortening the circadian period and altering temperature compensation. For this study, the researchers cloned the gene based on its position in the genome, and found it was an important cell cycle regulator. When they eliminated the gene from the genome, the clock was normal, indicating that the mutation interfered in some way with the clock, rather than supplying something that the clock normally needs to run.
Biochemically, the mutation results in a premature modification of the well understood clock protein, frequency (FRQ). The investigators demonstrated that this was a direct result of action by an enzyme, called in mammals checkpoint kinase-2 (CHK2), whose normal role is exclusively in regulating the cell division cycle. CHK2 physically interacts with FRQ; the mutation makes this interaction much stronger. However, a mutant enzyme that has lost its activity has no effect on the clock.
Normally CHK2 is involved in the signal response pathway that begins when DNA is damaged and results in a temporary stoppage of cell division until the damage is fixed. The researchers found that the resetting effect of DNA damage requires the period-4 clock protein, and that period-4 is the homolog, the Neurospora version, of the mammalian checkpoint kinase.
Moreover, the clock regulates expression of the period-4 gene. This closes a loop connecting the clock to period-4 and period-4 to the clock and the cell cycle. The clock normally modulates expression of this gene that encodes an important cell cycle regulator, and that cell cycle regulator in turn affects not only the cell cycle but also the clock.
Recent evidence in mammalian cells shows that other cell cycle regulators physically interact with clock proteins. Loss of at least one clock protein (mammalian period-2) is known to increase cancer susceptibility. The coordination of the clock and cell division through cell cycle checkpoints, supports the clock’s “integral role in basic cell biology,” conclude the researchers.” Their work can help advance understanding of cancer origins as well as the timing of anti-cancer treatment.

Daily Rhythms in Cnidaria

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The origin and early evolution of circadian clocks are far from clear. It is now widely believed that the clocks in cyanobacteria and the clocks in Eukarya evolved independently from each other. It is also possible that some Archaea possess clock – at least they have clock genes, thought to have arived there by lateral transfer from cyanobacteria.[continued under the fold]

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Chestnut Tree Circadian Clock Stops In Winter

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chestnuttree.jpgThe persistence of circadian rhythmicity during long bouts of hibernation in mammals has been a somewhat controversial topic in the literature. While some studies suggest that circadian clock is active during hibernation, other studies dispute this. Apparently, the truth is somewhere in-between – it differs between species:

Not all hibernating animals retain apparent circadian rhythmicity during the hibernation season. Whereas some species, such as bats and golden-mantled ground squirrels, maintain circadian rhythmicity in Tb throughout the hibernation season when held in constant conditions, other species, such as European hamsters, Syrian hamsters, and hedgehogs, lose circadian rhythmicity in Tb.

The outputs of the clock measured in these studies range from body temperature abd brain temperature, to timing of waking, to metabolic and behavioral parameters. But, to my knowledge, nobody has yet looked if the circadian pattern of expression of “core clock gene” persists during hibernation.
Thus, it was really interesting to see a study on the state of hibernation in a completely different kind of organism – a tree. About a year ago, a group from Spain, did exactly what was needed – they measured the levels of expression of circadian clock genes in the chestnut tree.
They measured the expression of clock genes both during naturally occuring winter dormancy and in the laboratory experiments involving chilling of seedlings combining with exposure to different photoperiods. In both cases, the core molecular mechanism of the circadian clock stopped entirely if the temperature and photoperiod both indicated ‘winter’, and was revived by warming-up the seedlings or the onset of spring.
Circadian clocks exhibit temperature independence, i.e., the period of the rhythm is not affected by temperature, within relatively broad limits. Apparently, the winter temperatures are outside the lower limit in the chestnut tree. Furthermore, it appears that the chestnut actively stops the clock with the onset of winter.
How can we interpret these data?
Overwintering is the stage in which all energetically expensive processes are minimized or shut down. However, workings of the clock itself are not very energetically expensive, so this is an unlikely reason for the elimination of rhythmicity during winter.
Second interpretation would be that, as the tree shuts down all its processes, there is nothing for the clock to regulate any more. There is also no feedback from the rest of metabolism into the clock. Thus, circadian rhythmicity fades as a by-product of overall dormancy of the plant.
Third, the clock itself may be a part of the mechanism that keeps everything else down. In other words, a clock stopped at (for instance – this is a random choice of phase) midnight will keep giving the midnight signal to the rest of the plant for months on end, keeping all the other processes at their normal midnight level (which may be very low). Thus, the clock may be central to the overal mechanism of hibernation in trees – i.e., the autumnal stopping of the clock is an evolved adaptation.