Category Archives: Chronobiology

A couple of months ago I wrote about a study in primates, suggesting that there is a circadian clock in the adrenal gland. This was hyped like a big break-through, but, while that was a good and useful study, it did not show anything surprising, e.g., that the adrenal is a pacemaker, only that it is a peripheral clock, which was known for decades, before the whole paradigm of perihperal clocks matured within the field.
Now, there is a new study, this time in mice, on the same question: How the adrenal ‘clock’ keeps the body in synch.
Again, it is touted as something that will fundamentaly change the field:

The circadian network now revealed for the adrenal gland might serve as a “paradigm for the organization of other physiological rhythms,” the researchers said. The findings might also require scientists to do some rethinking, Oster added. Previous studies using organ cultures found that clock gene rhythms can persist for weeks in the absence of external timing signals, leading to the suggestion that peripheral clocks to a large extent operate independently. In marked contrast, the loss of corticosterone rhythm in clock mutant animals with normal adrenals after 2 days in constant darkness indicates a critical dependence of the adrenal on input from the master clock, Oster said.

The study is good, but there is nothing really new and earth-shattering.
We knew there was a peripheral clock in the adrenal.
We knew that peripheral clocks are autonomous in a dish.
We knew that peripheral clocks get entrained/synchronized by neural and/or hormonal inputs from the central pacemaker (e.g., the SCN in mammals).
We knew that peripheral clocks feed back onto the pacamaker.
We knew that every clock has its own rhythm of sensitivity to its entraining agents (e.g., light, food, hormones, neurotransmitters) – that is why we make Phase-Response Curves.
So, we knew that each clock “gates” its own responses to synchronizers – that is the reigning paradigm in the field, not something new that will have to come out of this particular study.

Interesting, if you are in the field:
The Neurospora Checkpoint Kinase 2: A Regulatory Link Between the Circadian and Cell Cycles
by António M. Pregueiro, Qiuyun Liu, Christopher L. Baker, Jay C. Dunlap, Jennifer J. Loros

The clock gene period-4 (prd-4) in Neurospora was identified by a single allele displaying shortened circadian period and altered temperature compensation. Positional cloning followed by functional tests show that PRD-4 is an ortholog of mammalian checkpoint kinase 2 (Chk2). Expression of prd-4 is regulated by the circadian clock and, reciprocally, PRD-4 physically interacts with the clock component FRQ, promoting its phosphorylation. DNA-damaging agents can reset the clock in a manner that depends on time of day, and this resetting is dependent on PRD-4. Thus, prd-4, the Neurospora Chk2, identifies a molecular link that feeds back conditionally from circadian output to input and the cell cycle.

It has been known for decades that scheduled meals can entrain the circadian clock. In some species (e.g., in some birds), regular timing of feeding entrains the main circadian system of the body in the suprachiasmatic (SCN) area of the hypothalamus, the retina and the pineal. In other species (e.g., rodents), it appears that the food-entrainable oscillator is anatomically and functionally distinct from the main pacemaker in the SCN.
Researchers working on different species discovered different properties and different anatomical locations for the food-entrainable clock. Now, a study from UT Southwestern Medical Center takes yet another look at the location of the food clock in mice, using expression of Period, a canonical clock gene, as the marker for the clock activity:
Timing of Food Consumption Activates Genes in Specific Brain Area:

The researchers put the mice on a 12-hour light/dark cycle, and provided food for four hours in the middle of the light portion. Because mice normally feed at night, this pattern is similar to humans eating at inappropriate times. Dysfunctional eating patterns play a role in human obesity, particularly in the nocturnal eating often seen in obese people, the researchers note.
The mice soon fell into a pattern of searching for food two hours before each feeding time. They also flipped their normal day/night behavior, ignoring the natural cue that day is their usual time to sleep. After several days, the researchers found that the daily activation cycle of Per genes in the SCN was not affected by the abnormal feeding pattern.
However, in a few different areas of the brain, particularly a center called the dorsomedial hypothamalic nucleus or DMH, the Per genes turned on strongly in sync with feeding time after seven days. When the mice subsequently went two days without food, the genes continued to turn on in sync with the expected feeding time.

I wonder what would have happened if instead of fasting, they gave food ad libitum at the end of the experiment. Also, what would have happened if either the whole experiment or that last 2-day bit was performed in constant darkness?
The paper is coming out on August 8 in PNAS. If there is something in the paper that the press release did not get right, I’ll be sure to tell you at that time.

You and I, as well as all of our mammalian brethren, have just a few photopigments, i.e., colored molecules that change shape when exposed to light and subsequently trigger cascades of biochemical reactions leading to changes in electrical properties of sensory neurons, which lead to modulation of neurotransmitter release, which propagates the information from one neuron to the next until it is integrated and interpreted somewhere in the brain – we see the light!
More under the fold….

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This is so basic that I even teach it in Intro Bio:

Wherever the master clock may be located (SCN, pineal or retina) in any particular species, its main function is to coordinate the timing of peripheral circadian clocks which are found in every single cell in the body. Genes that code for proteins that are important for the function of a particular tissue (e.g., liver enzymes in liver cells, neurotransmitters in nerve cells, etc.) show a daily rhythm in gene expression. As a result, all biochemical, physiological and behavioral functions exhibit daily (circadian) rhythms, e.g., body temperature, blood pressure, sleep, cognitive abilities, etc.

And here is a little bit more detail:

What does a peripheral clock in a cell do? It acts as a relay – turning on and off batteries of genes in a tissue-specific way. So, for instance, in a liver cell, there will be three categories of genes:
First, genes that liver does not use (needed for muscle contraction or gas exchange, for instance, in other organs) are not expressed at all.
Second, genes involved in general cell metabolism (e.g., genes that code for proteins that are involved in transcription, translation or DNA repair) are expressed at high levels constituitively – there is no variation in levels over time.
Finally, there are genes that are expressed with a circadian pattern. Expression of these genes is under the control of the circadian clock in the liver cell. Which genes are those? Those that code for proteins which serve a liver-specific function, e.g., various enzymes used in biosynthesis, detoxification etc.
Are all those genes expressed at the same time? No! They are expressed in several “batteries” – some in the morning, some in the afternoon, some at night, etc. Thus, for instance, alcohol dehydrogenase (together with hundreds of other genes) is expressed in the late evening and early night – allowing one to drink more alcohol than in the morning. Importantly – most of the genes are not switched completely on and off – they are just expressed a little more or a little less over the 24-hour period.
What this all implies is that there is no down-time for the liver. It always does something, only that “something” changes over time. The same goes for every other cell-type in the body.

But now, Michael Hastings et al. have gone a step further. They have shown not just that key tissue-specific genes cycle, but also that the gene products – the proteins – also cycle:

The new research used state of the art proteomic analysis to examine clock-controlled changes in the livers of normal mice and mice with genetically impaired body clocks.
Dr Hastings went on: “We discovered that around one fifth of liver enzymes show circadian rhythms, which means that the metabolic capabilities of the liver changes dramatically between day and night as different groups of proteins and enzymes are turned on and off in sequence. This is brought about by a new level of chemical co-ordination that we were never aware of, involving sophisticated modifications of proteins and their time-dependent synthesis.

Nice to see the story getting more complete. Rhythmicity of gene expression is in itself not sufficient. Sometimes there are cycles in transcription but not translation, sometimes the other way round. It’s nice to know that both processes show circadian rhythms in at least one studied tissue, the liver.