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A prion is an infectious agent that is composed primarily, if not entirely of misfolded protein. Humans and other mammals make cellular prion protein (that we call cellular prion related protein, or PrPC) whose function is thought to be for copper binding or signal transduction. When cellular prion protein misfolds (either sporadically or due to the introduction of exogenous prions), the structure changes into one very resistant to unfolding/breakdown. The misfolded prion protein is referred to as PrPTSE (or often PrPSc). PrPTSE aggregates into fibrils and amyloid plaques, and it is the accumulation of PrPTSE in the brain (and subsequent damage done to the brain tissue) that ultimately causes death.

Sure. Kuru was one of diseases that initally led to the discovery of prions. That was present in the Fore tribe in Papua New Guinea, and was believed to be transmitted because the tribe members ate the brains of their dead out of respect. CJD can present sporadically or as variant CJD (from eating BSE infected beef), and there is fatal familial insomnia and Gerstmann–Sträussler–Scheinker syndrome, which are both very rare genetic prion diseases that run in some families. There are also prion diseases in other mammals: scrapie in sheep and goats, chronic wasting disease (CWD) in cervids (deer, elk, moose), bovine spongiform encephalopathy (BSE) in cattle, and a couple other uncommon ones like transmissible mink encephalopathy.

To be perfectly blunt, reading Laura Manuelidis' papers is like reading the diary of a girl who has been told 1200 times by her crush that he's not interested, and she still believes it will happen. Sure, she could end up proving us all wrong, but there is an ENORMOUS amount of evidence to the contrary. Now, where detractors of the prion theory (like Laura, and some others) make an argument that does make sense is within the theory of strain differences. Prion strains are defined as isolates that yield distinct disease phenotypes within a group of identical host organisms (viz. clinical symptoms, incubation times, histopathological profiles). These phenotypic differences persist upon serial transmission of disease. The PrPTSE associated with different strains can exhibit distinct biophysical properties such as migration patterns in Western blotting following PK digestion and protein secondary structure. The prevailing hypothesis is that strain properties are enciphered in the structure of PrPTSE. The difficulty of incorporating the existence and diversity of strains within the protein-only hypothesis for prions has led some to posit a role for a separate informational molecule that occurs alongside PrPTSE.

You are correct. They have not been found to contain any genetic material, making them unlike any infectious agent ever known.

Philosophically, because they are so foreign. Bacteria and viruses, while capable of killing us, are LIKE us. They contain DNA/RNA just as we do. Thus agents that destroy DNA and/or RNA can harm them just as they can harm us. A prion, however, is like an alien species. It goes against everything we understand about classical infectious agents. It is not alive, but can be transported, can persist outside of the host, is very hard to degrade, and can initiate diseases that are invariably fatal. That makes them way scary.