Biological clocks

The Siberian hamster is a peculiar little creature. It has figured out a unique way to hide from its predators in the harsh Arctic landscape – it changes its fur color from brown in summer to white in winter to make it easier for it to hide from all the animals that want to eat it. How does it know when to change? It uses something we are all probably familiar with – biological clocks.

But have you ever pondered whether there really is a ticking clock in your body? True enough, the body does keep track of its own time – but probably not in the way most people think. Mankind has long suspected the presence of some sort of biological clock system. Yet only by looking at the biological clock through the eyes of science, more particularly, through molecular biology and genetic engineering, have we seen the ingenious way Nature has designed body clocks to anticipate daily changes of day and night.

It’s a pretty well-known fact that the Earth revolves around the sun in more or less a predictable manner. Every day, our planet rotates on its axis, causing us inhabitants to experience day and night. As a result, we end up patterning our lives to the 24-hour day and to the subsequent changes in season also caused by the Earth’s revolution around the sun. Because of this, we sleep at roughly the same time each night, bears hibernate in winter and bats hunt at night. All these actions are controlled by biological clocks present in all these animals.

Biological clocks are more commonly known as circadian clocks or circadian rhythms. The word circadian comes from the Latin words circa, meaning "around," and diem, meaning "day." Evolution favored the existence of these circadian rhythms because with it, an animal would know when it is most advantageous for it to look for grub, or when to hide from its predators; plants know when it can use light to make its own food. Those equipped with circadian systems are better able to cope with their environment, thus gaining higher chances of surviving and reproducing to pass on its traits to the next generation.

The circadian rhythm is an active cycle. Every single day, it takes in some sort of input from the animal’s surroundings to synchronize itself, to make sure that its timekeeping is as accurate as possible. Scientists call this input a zeitgeber, German for "time giver." It refers to any sort of environmental cue that tells your body what time it is. The most important of these zeitgebers is light; another is temperature. The presence of light is detected by the eye, more specifically, special proteins in the retina called melanopsin and rhodopsin, and this message is passed on to the master timekeeper in the brain.

Apart from the input system used to register these zeitgebers, other major components of the animal circadian system include a master timekeeper and a way for the timekeeper to communicate the message of time to the rest of the body.

The center of the circadian system in humans is a pair of small bunches of brain cells located near the hypothalamus called the suprachiasmatic nuclei or SCN. It is what is called the circadian pacemaker – the master clock in your body. Containing roughly between 16,000 and 20,000 brain cells (called neurons) each, it tells the rest of your body what time it is.

The idea of the SCN as the circadian pacemaker was first verified in studies using laboratory mice in the early ’90s. Anybody who has ever owned a pet mouse knows that they like to run in their exercise wheels more at night than during the day. Applying this information, scientists attached sensors to exercise wheels in mouse cages to monitor when they run. Monitoring this activity, 24 hours a day, seven days a week, had led them to establish a normal mouse activity pattern. This pattern of activity repeats itself every 24 hours.

They then destroyed the SCNs of these mice and measured their activity patterns again. These mice then exhibited arrhythmia, the complete loss of their original 24-hour activity rhythm. Moreover, transplanting healthy SCN to these mice caused them to reacquire their 24-hour activity rhythm.

Since the SCN is the master timekeeper, it is of utmost importance that it keeps the correct time. The SCN does something no different from what the average person, who is always unsure of the correct time, would do – it carries several clocks. In the case of the SCN, around 20,000 clocks – each one of the neurons that compose the SCN keeps its own time through a cellular clock. These neurons then send messages to each other to make sure that the SCN generates a single, consolidated output.

The third major component of the circadian system is also the least studied. Output pathways from your circadian pacemaker to the rest of the body are assumed to be quite complex. Scientists think that the SCN uses various ways to send the message of time to the rest of the body. One of these uses small molecules called neurotransmitters to send messages to different glands that secrete hormones into the blood. Eventually, all of these output pathways get the message of time to the different organs that need it.

Though these general components are present in all circadian rhythms, it is important to note that they have different effects on different organisms. To exemplify just how the circadian rhythm has varying effects on different organisms, let’s look at something that we can all relate to – sleep. Many animals sleep, and the average total sleep time varies with each organism. At one end of the spectrum, bats sleep almost 20 hours per day; on the opposite end, giraffes sleep for just about two hours. In one way or another, these sleep patterns are affected by the organism’s own circadian rhythms. (An interesting tidbit on sleep you may not know about is that the ways animals sleep vary as well. Bats sleep upside down, rats sleep intermittently, dolphins sleep with only half of their brains at a time, and cattle can sleep standing up – often with their eyes wide open!)

Even with organisms of the same species, like humans, the fact that each of us has exactly the same type of circadian rhythm does not stop us from manifesting different time-dependent activities. Some of us classify ourselves as morning persons; others, evening persons. The circadian rhythm does not limit what kind of activities we do throughout the day. Rather, it is used more as a guide to help the body anticipate what we’re likely to do next.

A common misconception about biological clocks is that there is only one clock inside the body. Actually, clock mechanisms are present in many different cells in the body. Cellular clocks, similar to those in the neurons of the SCN, are present in many major organs in the body like the liver, heart and lungs. Each of these organs keeps its own clock for its own purpose. For example, the liver knows when to secrete bile in time to digest your dinner.

My sister and I went to California to visit our folks this last summer break. The trip led me to experience first-hand one of the more modern effects on human circadian rhythms – jet lag. Only in the past century has man been able to travel through 15 time zones in half a day. This ability was not one that evolution anticipated. Because of this, it takes a long time for us to reset our biological clocks. Apart from the obvious disruption in regular sleep-wake patterns, other effects of jet lag can be changes in your eating patterns, indigestion, headaches and a general feeling of weakness. All these symptoms are probably because of the desynchrony between your SCN’s clock and the clocks present in the various organs of the body.

Say you went from San Francisco, California to Manila. By the time you get here, your SCN automatically knows that it is on Manila time. On the other hand, the rest of your body still thinks it’s on San Francisco time. Though your SCN knows its lunchtime in Manila and you’re supposed to be eating, as far as your liver knows, it’s already 9 p.m. and you’re about to go to bed. It takes several days for the rest of the body to get accustomed to the actual time. Studies in "jet-lagged" mice have shown that liver cells take as much as 14 days to adjust themselves to the correct time. Cells in your major organs take such a long time to change because they have to receive signals from the SCN before they can change. With this, it’s no wonder drinking espresso shots to keep myself awake in class caused my tummy to feel fuzzy! I eventually restored my regular body rhythm after several days.

At the heart of any clock, whether it be biological or mechanical, is a mechanism which can produce a reliable oscillation – a repetitive motion or occurrence of some sort that can be used to measure time accurately. For mechanical clocks such as watches, oscillation is achieved by the hands of the clock. The second hand moves around the clock once every minute, the minute hand every hour, and the hour hand completes a full cycle every 12 hours.

Cellular clocks, on the other hand, cycle proteins. Studies on these core clock components have been more extensively studied in the humble fruit fly Drosophila melanogaster than any other animal. In their cells, two proteins called Period and Timeless accumulate in the cell through the course of late afternoon and night. Both of these proteins are only stable inside the cell if they are paired together. Otherwise, either gets destroyed. At some point, these pairs accumulate enough numbers to stop the production of individual Period and Timeless components, thereby preventing more pairs from piling up inside the cell.

When dawn comes, Timeless proteins get destroyed by another protein, the light-sensitive Chryptochrome. With the absence of Timeless, the Period protein gets destroyed as well. Because Period-Timeless pairs are no longer present in the cell, it can now re-accumulate these pairs when nighttime comes. This whole cycle takes roughly around 24 hours and is what scientists call a delayed negative feedback loop. The cell takes note of the time of day by checking the amount of these proteins in the cell.

Going back to the cute Siberian hamster, how does it know when to change color? Apparently, it knows what season it is because of the changes in the amount of daylight. In the Arctic, the difference in the amount of daylight in summer and winter is much more pronounced than it is here. Daylight in the summer can last as long as six months. When cells in its body notice that daylight has been present for quite a long time, it knows that it is summer and thus, its coat color becomes brown. Conversely, a long period of darkness indicates winter and triggers the hamster to change its coat color to white.

If anything, the study of circadian rhythms has led us to understanding that time matters. Even the simplest actions we take for granted may be affected by our body clocks. This is why in scientific laboratories around the world, when one makes observations is as important as the observations themselves. Scientists studying all sorts of topics always consider time-dependent factors such as age and feeding time when designing their experiments. As much as possible, many of these factors are kept constant for the entire duration of the study.

The Laboratory of Molecular and Cell Biology, one of several laboratories in the National Institute of Molecular Biology and Biotechnology in UP Diliman, maintains a room filled with mice used for their various experiments on developmental biology. To make sure that all their mice have roughly the same circadian rhythms, they keep a strict light-dark cycle in their mouse room. Lights are turned on every morning at 8 a.m. and turned off at 8 p.m. at night. Lab members always feed the mice at 4 p.m., and all observations regarding mouse behavior are done during the same time everyday.

The discovery of clock genes has led scientists to ask – what can we use this new information for? For instance, can this information be used to treat insomniacs? Not quite yet, but initial studies done in humans have determined that some sleep problems may be due to broken cellular clock components. Familial advanced sleep phase syndrome (or FASPS) is an inherited disease characterized by individuals who cannot help but sleep and wake up very early. This disease has been linked to mutations in a clock component called human Period 2 – one of several human versions of the Period gene in the fruit fly. Maybe in the future we can somehow fix this protein to restore normal sleep patterns to these people.

One of the most promising applications of this information may be in cancer therapy. Certain clock components have been linked to the regulation of cell division. Hopefully, one day, we can use this information to stop cancer cells from proliferating – by fooling them into thinking that it is not time to divide yet. Nowadays, studies have also shown that taking anti-cancer medication at specific times of day makes them more effective in treating cancer.

The possible applications of information derived from studies with circadian rhythms are wide and varied. Who knows what other activities are controlled by the interesting and complex nature of biological timekeeping.

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References:

Harmer SL, Panda S, Kay SA. 2001. Molecular Bases of Circadian Rhythms. Annual Review of Cell and Developmental Biology. 17:215-253.

King DP, Takahashi JS. 2000. Molecular Genetics of Circadian Rhythms in Mammals. Annual Review of Neuroscience 23:713-742.

Konopka RJ, Benzer S. 1971. Clock Mutants of Drosophila Melanogaster. PNAS USA 68:2112-2116.

Lowery PL, Takahashi JS. 2004. Mammalian Circadian Biology: Elucidating Genome-Wide Levels of Temporal Organization. Annual Review of Genomics and Human Genetics. 5:407-441.

Panda S, Hogenesch JB, Kay SA. 2002. Circadian rhythms from flies to human. Nature 417:329-335.

Ralph MR, Foster RG, Davis FC, Menaker M. 1990. Transplanted suprachiasmatic nucleus determines circadian period. Science 247:975—978.

Reghunandanan V, Reghunandanan R. 2006. Neurotransmitters of the suprachiasmatic nuclei. Journal of Circadian Rhythms 4:2.

Rosbash M, Takahashi JS. 2000. Clockwork Genes: Discoveries in Biological Time. Howard Hughes Medical Institute Holiday Lectures on Science.

Siegel LJ. 2006. The Time of Our Lives. http://learn.genetics.utah.edu/features/clockgenes/

Takahashi JS. 2004. Finding New Clock Components: Past and Future. Journal of Biological Rhythms 19:339-347.

Time Matters: Biological Clocks. 2006. HHMI Biointeractive Exhibit. www.hhmi.org/biointeractive/ museum/exhibit00/00.html.

Yu Q, Jacquier AC, Citri Y, Hamblen M, Hall JC, Rosbash M. 1987. Molecular mapping of point mutations that stop or speed up biological clocks in Drosophila melanogaster. PNAS 84:784-788.

Special thanks to Dr. Cynthia Saloma for information regarding mouse room maintenance.

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Cherry Mae G. Ignacio, 20, is currently a senior at the University of the Philippines, Diliman taking up BS Molecular Biology and Biotechnology. She initially did research on biological clocks as part of her undergraduate seminar class – MBB 196. A self-confessed bookworm and dog-lover, she plans to pursue graduate studies after college to become a full-fledged researcher. Her present research project involves characterizing toxin genes from marine snails. You can reach her through e-mail at [email protected].