The clock in the SCN, through its neurological connections, has a circadian influence not only on sleep, but also on temperature control, hormone secretion and other functions. The multisynaptic processing of the SCN output allows circadian rhythm and other controlling influences to be coordinated through integration with other inputs at each stage. Removal of the SCN causes a loss of most of these rhythms, but does not prevent sleep from taking place or temperature from being controlled.

In normal circumstances these functions have a constant relationship, but they can become desynchronized. This may occur even if the SCN is working normally, if there are unusual environmental situations, such as time zone changes, which can disturb their coordination. The potential for this internal desynchronization varies between the various circadian rhythms. Loss of function of the SCN increases the duration of sleep, indicating that the SCN has a wakefulness maintaining effect and tends to counteract the homeostatic drive to sleep.

Individual circadian rhythms
The most important SCN-related circadian rhythms concern cell growth and proliferation, autonomic and immune function, sleep, temperature and endocrine secretion.

Cell growth and proliferation
The genetic control of clock function and circadian rhythms through protein production is closely linked with a diurnal variation in cell growth and proliferation in many tissues. The clock genes for instance control the production of a rate limiting enzyme in haem synthesis. Regeneration of liver cells varies diurnally, and division of the squamous cells of the skin is most rapid at night.

Several tissues such as the liver and kidneys have local pacemakers which are capable of sustaining a circadian rhythm for several days independently of the SCN. These local pacemakers represent an inherent circadian rhythm which may be present in all cells of the body, and which feed back to the main circadian rhythm controller in the SCN, and are also controlled through changes in autonomic innervationand melatonin. Circadian cell growth and proliferation cycles may be relevant to the development of malignancy.

Autonomic and immune function
Several autonomic functions, including bronchoconstriction, heart rate and renal function, have a circadian rhythm, and several aspects of immune function have a similar pattern. Parasympathetic activity has a circadian rhythm with a peak at 4.00 am and a nadir in the late afternoon, whereas sympathetic activity is more related to the sleep–wake state.

Motor and feeding behaviour
Motor activity and feeding behaviour have a circadian pattern which is closely related to the sleep–wake rhythms, but is also controlled by, for instance, orexins and leptin.

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