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Rat Brain Tissue Sections

The rat brain has served as an excellent model for elucidating the complex anatomy and physiological mechanisms of the human brain. As a result, a significant amount of information on brain diseases, such as dementia and Parkinson's disease, has been determined from investigations using rat brains. Brain tissue has been mapped into dozens of major and hundreds of minor regions that are anatomically and functionally distinct. Individual brain cells segregate into specialized areas by expressing a wide spectrum of specific housekeeping proteins, enzymes, transporters, and receptors. This digital image gallery explores many regions of the rat brain as observed with immunofluorescence in coronal, horizontal, and sagittal thick sections using laser scanning confocal microscopy.

Amygdala - The amygdala is a subcortical nuclear complex that plays a critical role in the coordination of emotional states and their physical expression. It is considered part of the limbic system and is located near the base of the cerebral hemispheres. Studies indicate that the amygdala is particularly involved with the emotional experience of fear and anxiety, which can be produced in humans when this region of the brain is electrically stimulated. Experimental investigations with laboratory animals have also demonstrated that impairment of the amygdala results in placidity and tameness.

Blood Vessels - Blood vessels are located on the surface of the brain and deeply seated in its tissues. These vessels enter the skull through the small openings known as foramina. Two primary sets of vessels provide blood to the brain: the right and left internal carotid arteries and vertebral arteries. At the base of the brain, the vertebral arteries are joined together into the basilar artery, which connects to the carotid arteries in a vascular loop called the circle of Willis.

Cerebellum - In humans, the cerebellum comprises only about one-tenth of the total volume of the brain, but more than 50 percent of all its neurons are located in the structure. Cerebellar neurons are highly organized, and although various regions of the structure receive input from different sources and project to various motor systems, they appear to carry out comparable types of activity. This activity involves integrating and evaluating information regarding intent and action so that adjustment may be made in the motor systems to correct for any disparities between the two during the course of a movement.

Cerebral Cortex - The cerebral cortex is the outer mantle of the brain that in humans is highly folded. Due to this folding, numerous fissures and crests (termed sulci and gyri) can be seen along the surface of the human brain. The cerebral cortices of other animals, however, do not necessarily have the same appearance as the human cortex. Rat brains, for example, exhibit almost entirely smooth cortices, and the brains of cats exhibit only a small number of convolutions compared to human brains.

Dentate Gyrus - The strata of the dentate gyrus include molecular, granule cell, and polymorphic layers, though the rest of the hippocampal formation features a pyramidal layer in place of the granule cell stratum. The granule cells of the dentate gyrus primarily receive input from the entorhinal cortex, a part of the limbic association cortex that accepts signals from higher-order association areas of the cerebral cortex and other areas of the limbic association cortex. In turn, the axons of granule cells (termed mossy fibers) project to the pyramidal cells located in the CA3 section of the hippocampus.

Hippocampus - The hippocampus is closely associated with two other structures of the brain, the dentate gyrus and the subiculum. Together the structures comprise an assembly known as the hippocampal formation that in humans lies deep within the parahippocampal gyrus. The hippocampus and other components of the hippocampal formation are morphologically simpler than the neocortex that overlies them. The structures exhibit a laminar organization, but unlike the neocortex, are each composed of three primary cell layers rather than six.

Hypothalamus - Input to the hypothalamus arrives via both circulatory and neural routes. Chemical, hormonal, and certain physical information, such as body temperature, are received by the hypothalamus from the blood as it circulates through the brain structure. The hypothalamus obtains other types of data from the medulla oblongata and the midbrain. Signals based on information acquired by receptors that comprise part of the autonomic nervous system are sent to the hypothalamus from projection neurons located in the nucleus solitarus of the medulla.

Lateral Ventricle - The lateral ventricles have a complex C-shape that features several projections into different parts of the brain. The anterior horn of each lateral ventricle projects into the frontal lobe of the brain, while the posterior and inferior horns respectively extend into the occipital and temporal lobes. The area of a lateral ventricle where the three horns meet is called the atrium. Most of the cerebrospinal fluid entering into the ventricular system is secreted by the choroid plexus in the walls of the lateral ventricles.

Longitudinal Fissure - The longitudinal fissure is a deep grove in the brain that divides the right and left cerebral hemispheres from each other. Sometimes the cleft is alternatively known as the interhemispheric fissure. Division of the cerebrum by the longitudinal fissure is incomplete. Located at the base of the cleft is a fibrous band of white matter called the corpus callosum that connects analogous regions on opposite sides of the brain. Communication between the hemispheres is carried via the corpus callosum.

Medulla Oblongata - A number of functional centers that regulate autonomic activities of the body, such as respiration, circulation, and digestion, are found in the medulla oblongata. The brain stem structure also is important as a relay between the spinal cord and the rest of the brain, and it plays a role in the regulation of motion and the sleep-wake cycle. Some of the activities associated with the medulla are influenced by other parts of the brain stem as well. The central core of the brain stem is the reticular formation, which can affect the excitability of neurons and thereby govern states of arousal.

Pons - As the major nerve fiber tract that links the two halves of the cerebellum, the pons plays an important role in the coordination of movement of the right and left sides of the body. The horseshoe-shaped structure is also involved in information integration and transfer, respiration, control of eye movement and head muscles, taste, and states of arousal. Nuclei located where the pons and midbrain meet have been of particular interest in studies of the rapid eye movement (REM) stage of the sleep cycle. These nuclei and neighboring structures in the brain stem appear to instigate REM and dreaming.

Striatum - The vast majority of cells in the striatum are medium-spiny projection neurons, and some simple staining techniques seem to suggest that the structure is homogenous. Yet, in reality, the striatum is heterogenous in both composition and function. Neurotransmitters and neuromodulators are not evenly distributed throughout the striatum, but are concentrated in patches. These patches, often termed striosomes, are interspersed in a matrix of material that is histochemically distinct from them.

Thalamus - Unlike other regions of the diencephalon, the thalamus does not appear to play a notable role in cyclical behaviors. Instead, the thalamus functions in motor control by being the primary recipient of motor information transmitted by the cerebrum. The thalamus is also a receiver of all auditory, somatosensory, and visual sensory signals from diverse areas of the brain, acting as the final gateway impulses must pass on their way to higher brain centers where additional interpretation and integration take place.

Third Ventricle - The ventricular system is comprised of several cavities and the narrow channels that connect them to one another. The third ventricle is a narrow slit-like cavity positioned vertically in the brain. The anterior, posterior, dorsolateral, and ventrolateral walls that demarcate the third ventricle are formed by the lamina terminalis, the epithalamus, the thalamus, and the hypothalamus, respectively. In 70 to 80 percent of humans, the two thalami of the brain are connected across the third ventricle by the massa intermedia, a band of gray matter.


Contributing Authors

Nathan S. Claxton, Shannon H. Neaves, and Michael W. Davidson - National High Magnetic Field Laboratory, 1800 East Paul Dirac Dr., The Florida State University, Tallahassee, Florida, 32310.

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