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Phys Ed Gretchen Reynolds on the science of fitness.

Does exercise influence the body’s internal clock? Few of us may be conscious of it, but our bodies, and in turn our health, are ruled by rhythms. “The heart, the liver, the brain — all are controlled by an endogenous circadian rhythm,” says Christopher Colwell, a professor of psychiatry at the University of California, Los Angeles’s Brain Research Institute, who led a series of new experiments on how exercise affects the body’s internal clock. The studies were conducted in mice, but the findings suggest that exercise does affect our circadian rhythms, and the effect may be most beneficial if the exercise is undertaken midday.

For the study, which appears in the December Journal of Physiology, the researchers gathered several types of mice. Most of the animals were young and healthy. But some had been bred to have a malfunctioning internal clock, or pacemaker, which involves, among other body parts, a cluster of cells inside the brain “whose job it is to tell the time of day,” Dr. Colwell says.

These pacemaker cells receive signals from light sources or darkness that set off a cascade of molecular effects. Certain genes fire, expressing proteins, which are released into the body, where they migrate to the heart, neurons, liver and elsewhere, choreographing those organs to pulse in tune with the rest of the body. We sleep, wake and function physiologically according to the dictates of our body’s internal clock.

But, Dr. Colwell says, that clock can become discombobulated. It is easily confused, for instance, by viewing artificial light in the evening, he says, when the internal clock expects darkness. Aging also worsens the clock’s functioning, he says. “By middle age, most of us start to have trouble falling asleep and staying asleep,” he says. “Then we have trouble staying awake the next day.”

The consequences of clock disruptions extend beyond sleepiness. Recent research has linked out-of-sync circadian rhythm in people to an increased risk for diabetes, obesity, certain types of cancer, memory loss and mood disorders, including depression.

“We believe there are serious potential health consequences” to problems with circadian rhythm, Dr. Colwell says. Which is why he and his colleagues set out to determine whether exercise, which is so potent physiologically, might “fix” a broken clock, and if so, whether exercising in the morning or later in the day is more effective in terms of regulating circadian rhythm.

They began by letting healthy mice run, an activity the animals enjoy. Some of the mice ran whenever they wanted. Others were given access to running wheels only in the early portion of their waking time (mice are active at night) or in the later stages, the equivalent of the afternoon for us.

After several weeks of running, the exercising mice, no matter when they ran, were found to be producing more proteins in their internal-clock cells than the sedentary animals. But the difference was slight in these healthy animals, which all had normal circadian rhythms to start with.

So the scientists turned to mice unable to produce a critical internal clock protein. Signals from these animals’ internal clocks rarely reach the rest of the body.

But after several weeks of running, the animals’ internal clocks were sturdier. Messages now traveled to these animals’ hearts and livers far more frequently than in their sedentary counterparts.

The beneficial effect was especially pronounced in those animals that exercised in the afternoon (or mouse equivalent).

That finding, Dr. Colwell says, “was a pretty big surprise.” He and his colleagues had expected to see the greatest effects from morning exercise, a popular workout time for many athletes.

But the animals that ran later produced more clock proteins and pumped the protein more efficiently to the rest of the body than animals that ran early in their day.

What all of this means for people isn’t clear, Dr. Colwell says. “It is evident that exercise will help to regulate” our bodily clocks and circadian rhythms, he says, especially as we enter middle age.

But whether we should opt for an afternoon jog over one in the morning “is impossible to say yet,” he says.

Late-night exercise, meanwhile, is probably inadvisable, he continues. Unpublished results from his lab show that healthy mice running at the animal equivalent of 11 p.m. or so developed significant disruptions in their circadian rhythm. Among other effects, they slept poorly.

“What we know, right now,” he says, “is that exercise is a good idea” if you wish to sleep well and avoid the physical ailments associated with an aging or clumsy circadian rhythm. And it is possible, although not yet proven, that afternoon sessions may produce more robust results.

“But any exercise is likely to be better than none,” he concludes. “And if you like morning exercise, which I do, great. Keep it up.”