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Hypothesised in 1982 by Dr. Stanley B. Prusiner of UCSF, prions are a class of infectious agents composed of nothing but protein. Dr. Prusiner was awarded the Nobel Prize in physiology or medicine in 1997 for the discovery. Though their exact mechanisms of action and reproduction are still unknown, it is now commonly accepted that they are responsible for a number of previously known but little-understood diseases including scrapie (a disease of sheep), Kuru (a disease common among a New Guinean tribe who practiced funerary cannibalism), Creutzfeldt-Jakob Disease (a neurological disorder), and Bovine Spongiform Encephalopathy ("Mad Cow Disease").

The word is derived from a combination of the words "proteinaceous infectious particle". It refers to the hypothesis (widely discounted when first proposed) that infectious agents causing such diseases consisted only of protein, with no nucleic acids. All pathogens known prior to that time (bacteria, viruses, etc.) contain nucleic acids, which enable reproduction. The prion hypothesis was developed to explain why the mysterious infectious agent causing Creutzfeldt-Jakob Disease resisted ultraviolet radiation (which breaks down nucleic acids) but responded to agents that disrupt proteins.

A breakthrough occurred when researchers discovered that the infectious agent consisted mainly of a protein called PRP. This protein is found in the membranes of normal cells (its precise function is not known), but the infectious agent was distinguished by an altered shape. It is hypothesized that the distorted protein binds to normal proteins of the same type and somehow induces them to change their shape as well, producing a chain reaction that both propagates the disease and generates new infectious material. Since the original hypothesis was proposed, a gene for the PRP protein has been isolated, the mutation that causes the variant shape has been identified and successfully cloned, and studies using genetically altered mice have bolstered the prion hypothesis. The evidence in support of the hypothesis is quite strong now, but not incontrovertible.

Prions appear to be most infectious when in direct contact with affected tissues. For example, Creutzfeldt-Jakob Disease has been transmitted to patients taking injections of growth hormone harvested from human pituitary glands, and from instruments used for brain surgery (prions can survive the "autoclave" sterilization process used for most surgical instruments). It is also believed that dietary consumption of affected animals can cause prions to accumulate slowly, especially when cannibalism or similar practices allow the proteins to accumulate over more than one generation. Though the risk is not yet proven, modern farming practices now disallow the use of rendered ruminant proteins in ruminant feed as a precaution.

Not all prions are dangerous; in fact they are found naturally in many (perhaps all) plants and animals. Because of this, scientists reasoned that the deformed proteins must give some sort of evolutionary advantage to their host. This was proved to be the case when studying a specific type of moss covering forest floors. Normally viruses can travel from an infected moss section to an uninfected moss section when the areas grow close enough for the outer cells to touch. However prions were discovered in the infected moss, which appeared to travel part way in to the sides of the uninfected moss. This caused cells on the edges of the moss to die, creating a barrier of dead cells which viruses are unable to cross, preventing contamination. Prions have also been speculatively linked to the differentiation process, which causes embyronic cells to specialize into specific tissues (such as muscle or blood cells).

The reason prions are not detected by the immune system is that their "safe" form is already present from birth in the body. The only distinction the "dangerous" prions have is that they are folded slightly differently. Prions infect the nerve lining of neural cells, froming an aggregate which ultimately destroys nerve cells. Depending on the area of the brain which they infect the symptons can be different. For example infecting the cerebellum causes impairment of movement. Infecting the cerebral cortex results in a decrease in memory and mental agility.

These diseases are now believed to be caused by prions: