1. Defective Interfering RNAs DI RNAs are formed by deletion and recombination during viral RNA replication They require helper virus to replicate and to be packaged into DI particles They must retain all cis-acting signals required for replication and packaging Most DI RNAs are not translated They interfere with the replication of helper virus by competing with it for resources Because they interfere, they may serve to ameliorate the symptoms of viral infection Amelioration has been shown in model systems, but no convincing evidence for amelioration of any natural infection by DIs has been produced

7. Viroids Viroids are small (~300 nt) circular RNA molecules that are infectious and commonly cause disease in plants They are not translated and are not packaged into protein- containing particles Transmission is commonly inadvertent, occurring during horticulture Replication of the RNA is effected by host polymerases, usually RNA Polymerase II Some viroids are capable of self-cleavage and self-ligation to form the circular RNA genome. Others use cellular enzymes

11. Hepatitis Delta Hepatitis is commonly called a virus and abbreviated HDV, although technically it is a satellite of hepatitis B virus that is related to viroids HDV requires HBV as a helper and exacerbates the symptoms of HBV infection It can establish a chronic infection if HBV becomes chronic The HDV genome of 1.7 kb is a covalently closed circular RNA molecule The genome is effectively a viroid into which has been inserted a single gene encoding the hepatitis antigen Replication of the genome is carried out in the nucleus by host RNA Polymerase II, and antigen is required The HDV core is composed of two forms of antigen and the RNA; budding to produce virions uses helper HBV surface glycoproteins

16. Editing of Hepatitis d Antigen S-HDAg is 195 aa in length and terminates at a UAG codon Editing occurs to change this codon to UGG during infection Editing occurs by deamination of A S-HDAg is required for RNA replication The edited mRNA is translated into L-HDAg of 214 aa L-HDAg suppresses RNA replication Both L-HDAg and S-HDAg are present in the core of HDV The envelope proteins of HBV are used to assemble HDV virions

17. Prion Diseases Prion diseases, also called transmissible spongiform encephalopathies, are slowly progressing but uniformly fatal neurological diseases They are characterized by alterations in the metabolism of a brain protein called the prion protein The normal function of the prion protein is not known The nature of the infectious agent remains controversial but a favored hypothesis is that an altered form of the prion protein is itself the infectious agent

18. Human TSEs Human TSEs may occur sporadically, may be inherited, or may be acquired by infection (the infectious agent is often called the scrapie agent) Sporadic TSE, usually a form of CJD, occurs at a frequency of about one per million Inherited or familial TSEs are always associated with mutations in the prion protein, and the probability of developing TSE may approach 100% in the case of some mutations Sporadic or familial TSEs are usually transmissible once they arise

20. Human Prion Diseases Although all human TSEs are characterized by changes in the metabolism of the prion protein, the symptoms differ, in part because different areas of the brain are affected. CJD is characterized by dementia and ataxia. It may occur sporadically, may be contracted iatrogenically, or may be familial. Kuru is characterized by progressive ataxia leading to total incapacitation. It was spread by canabilism. nvCJD is characterized by psychiartric symptoms, usually depression. Onset of symptoms occurs much earlier in life than CJD. It is thought to be contracted by consumption of beef from cattle infected with BSE. FFI is characterized by intractable insomnia. It is usually an inherited disease but sporadic cases have been reported. GSS is characterized by cerebellar disorders and a decline in cognitive ability. It is an inherited disease.

21. Two Victims of Kuru Among the Fore People

22. Spongiform Encephalophy In Creutzfeld-Jacob Disease A and B illustrate two different forms of vacuolar degeneration of the gray matter C illustrates astrocytic gliosis

27. Conversion of PrP c to PrP sc The conversion of PrP c to PrP sc involves a transition from helices to beta-sheet and the acquisition of partial resistance to protease. Mouse studies have shown that a neuron must express PrP c before is is susceptible to being killed by exposure to the scrapie agent (PrP sc ?). Such a conversion will occur in vitro when PrP c is exposed to PrP sc, which appears to act as a seed to induce the conversion of PrP c. Why neurons die upon exposure to the scrapie agent is not known, nor is the nature of the toxic substance that leads to neuronal death understood (is it PrP sc ?).

28. The Importance of the Prion Protein for TSE Disease Mice that do not express the prion protein do not develop TSE upon infection with the scrapie agent Mice that overexpress the prion protein are more sensitive to the development of TSE and may even develop TSE spontaneously There is a species barrier to infection by scrapie derived from another animal because of differences in the sequence of the prion protein in different animals Mice that express, for example, the hamster prion protein are more easily infected by scrapie from hamsters than scrapie from mice, and vice versa

29. The Protein Only Hypothesis The protein only hypothesis proposes that the infectious agent that transmits TSE is PrP sc. In this model, PrP sc is a seed that induces the formation of more of itself. The seed may arise spontaneously or by infection with PrP sc. Mutations in the prion protein make formation of the seed more probable. Biochemical studies of the scrapie agent have found nothing other than PrP sc in purified preparations, but because of the very low specific infectivity of such preparations, contamination by a virus or other infectious agent cannot be rigorously excluded. Transmission of ingested PrP sc to the brain might require replication of the agent in lymph nodes followed by invasion of peripheral nerves.

30. The Protein Only Hypothesis (con) One of the major criticisms of this hypothesis is that multiple strains of scrapie exist that cause different symptoms, but there is only one prion protein. How can one protein assume multiple conformations that breed true and why should different symptoms be produced? There have been shown to be at least two different strains of scrapie whose PrP sc can be distinguished on the basis of their structure, and that breed true. The conversion to the two different structural forms can be demonstrated in vitro. Thus, it is possible that multiple conformational states do in fact exist that can act as a seed to induce the formation of more of themselves.

37. Chronic Wasting Disease A TSE of deer and elk Found in the western U.S. and Canada In areas of Wisconsin 3% of the white tailed deer are infected There have occurred 5 unusual cases of CJD in the U.S. Victims were age 30 or younger Two were hunters and one was the daughter of a hunter and regularly ate deer or elk The disease was different from BSE Has been known for at least 35 years

39. Prions in Fungi If prions are defined as Proteins that have two or more conformational forms One form of which is soluble Other forms aggregate and can induce conversion of the soluble form to the aggregated form Then prions have been found in yeast The prion form of protein represents loss of function Once it appears the prion form is dominant but reversible by treating with denaturants It occurs spontaneously at low frequency