Suprachiasmatic nucleus
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The suprachiasmatic nucleus (SCN) is a nucleus in the hypothalamus and is so named because it resides immediately above the optic chaism (OX). It consists of two nuclei each of which lies on either side of the hemisphere separated by the third ventricle (3V). Its principal function is to create the circadian rhythm, which regulates the body functions over the 24-hour period. It consists of various cell types, principally ventrolatral (vlSCN) and dorsomedial (dmSCN) types. The vlSCN neurons possess ability for light-induced gene expression. If light is turned on during the night, vlSCN catches this information and relays it throughout the SCN, the process called entrainment. The dmSCN neurons are believed to make endogeneous 24-hour rhythm that can persist under constant darkness. Melanopsin-containing ganglion cells in the retina have a direct connection to suprachiasmatic nucleus via the retino-hypothalamic tract (RHT). The SCN sends information to other hypothalamic nuclei and the pineal gland to modulate body temperature and hormone production such as cortisol and melatonin. Rats with damage to the SCN sleep "erratically" (i.e. they do not show night-day rhythm).
The suprachiasmatic nucleus is one of four nuclei that receive nerve signals from the retina, the other three being the lateral geniculate nucleus (aka LGN), superior colliculus, and the pretectum. The LGN is responsible for passing information about color, contrast, shape, and movement on to the visual cortices. The superior colliculus is responsible for controlling the movement and orientation of the eyeball itself. The pretectum is responsible for controlling the size of the pupil.
Gene Expression
The circadian rhythm in the SCN is generated by the gene expression cycle in the nucleus. Two so-called clock gene are involved, PER and TIM genes which are made into PER and TIM proteins that inhibit their own transcription. This negative feedback mechanism gives a 24-hour rhythm in the expression of the clock genes. The genes encode various transcription factors which trigger expression of other proteins.
Electrophysiology
The firing rate of the spontaneous action potentials in the SCN gets modulated with 24-hour period as well. During the mid-day the firing rate reaches the maximum (above 7 Hz at room temperature) and during the night it goes near zero or at a rate below 4 Hz with irregular patterns. How the gene expression cycle (so-called the core clock) connects to the neural firing remains unknown.
Calcium Dynamics
Two contradictory reports exist about circardian variation of the cell calcium content. However, both reports agree the resting calcium level is slightly higher during the day compared to night.