Viroids: structure and function

Measuring intramolecular connectivity in long RNA molecules using two-dimensional DNA patch-probe arrays

We describe a DNA-array-based method to infer intramolecular connections in a population of RNA molecules in vitro. First we add DNA oligonucleotide "patches" that perturb the RNA connections, and then we use a microarray containing a complete set of DNA oligonucleotide "probes" to record where perturbations occur. The pattern of perturbations reveals couplings between regions of the RNA sequence, from which we infer connections as well as their prevalences in the population, without reference to folding models. We validate this patch-probe method using the 1058-nucleotide RNA genome of satellite tobacco mosaic virus (STMV), which has been shown to have multiple long-range connections. Our results not only indicate long-range connections that agree with previous structures but also reveal the prevalence of competing connections. Together, these results suggest that multiple structures with different connectivity coexist in solution. Furthermore, we show that the prevalence of certain connections changes when pseudouridine, an important component of natural and synthetic RNAs, is substituted for uridine in STMV RNA, and that the connectivity of STMV minus strands is qualitatively distinct from that of plus strands. Finally, we use a simplified version of the method to validate a predicted 317-nucleotide connection within the 3569-nucleotide RNA genome of bacteriophage MS2.

Unlocking the potential of circular RNA vaccines: a bioinformatics and computational biology perspective

Bioinformatics has significantly advanced RNA-based therapeutics, particularly circular RNAs (circRNAs), which outperform mRNA vaccines, by offering superior stability, sustained expression, and enhanced immunogenicity due to their covalently closed structure. This review highlights how bioinformatics and computational biology optimise circRNA vaccine design, elucidates internal ribosome entry sites (IRES) selection, open reading frame (ORF) optimisation, codon usage, RNA secondary structure prediction, and delivery system development. While circRNA vaccines may not always surpass traditional vaccines in stability, their production efficiency and therapeutic efficacy can be enhanced through computational strategies. The discussion also addresses challenges and future prospects, emphasizing the need for innovative solutions to overcome current limitations and advance circRNA vaccine applications.

Circular RNAs and their associations with breast cancer subtypes

Circular RNAs (circRNAs) are highly stable forms of non-coding RNAs with diverse biological functions. They are implicated in modulation of gene expression thus affecting various cellular and disease processes. Based on existing bioinformatics approaches, we developed a comprehensive workflow called Circ-Seq to identify and report expressed circRNAs. Circ-Seq also provides informative genomic annotation along circRNA fused junctions thus allowing prioritization of circRNA candidates. We applied Circ-Seq first to RNA-sequence data from breast cancer cell lines and validated one of the large circRNAs identified. Circ-Seq was then applied to a larger cohort of breast cancer samples (n = 885) provided by The Cancer Genome Atlas (TCGA), including tumors and normal-adjacent tissue samples. Notably, circRNA results reveal that normal-adjacent tissues in estrogen receptor positive (ER+) subtype have relatively higher numbers of circRNAs than tumor samples in TCGA. Similar phenomenon of high circRNA numbers were observed in normal breast-mammary tissues from the Genotype-Tissue Expression (GTEx) project. Finally, we observed that number of circRNAs in normal-adjacent samples of ER+ subtype is inversely correlated to the risk-of-relapse proliferation (ROR-P) score for proliferating genes, suggesting that circRNA frequency may be a marker for cell proliferation in breast cancer. The Circ-Seq workflow will function for both single and multi-threaded compute environments. We believe that Circ-Seq will be a valuable tool to identify circRNAs useful in the diagnosis and treatment of other cancers and complex diseases.

CircNet: a database of circular RNAs derived from transcriptome sequencing data

Circular RNAs (circRNAs) represent a new type of regulatory noncoding RNA that only recently has been identified and cataloged. Emerging evidence indicates that circRNAs exert a new layer of post-transcriptional regulation of gene expression. In this study, we utilized transcriptome sequencing datasets to systematically identify the expression of circRNAs (including known and newly identified ones by our pipeline) in 464 RNA-seq samples, and then constructed the CircNet database (http://circnet.mbc.nctu.edu.tw/) that provides the following resources: (i) novel circRNAs, (ii) integrated miRNA-target networks, (iii) expression profiles of circRNA isoforms, (iv) genomic annotations of circRNA isoforms (e.g. 282 948 exon positions), and (v) sequences of circRNA isoforms. The CircNet database is to our knowledge the first public database that provides tissue-specific circRNA expression profiles and circRNA–miRNA-gene regulatory networks. It not only extends the most up to date catalog of circRNAs but also provides a thorough expression analysis of both previously reported and novel circRNAs. Furthermore, it generates an integrated regulatory network that illustrates the regulation between circRNAs, miRNAs and genes.

Cell-free circularization of viroid progeny RNA by an RNA ligase from wheat germ

Linear, potato spindle tuber viroid RNA has been used as a substrate for an RNA ligase purified from wheat germ. Linear viroid molecules are efficiently converted to circular molecules (circles) which are indistinguishable by electrophoretic mobility and two-dimensional oligonucleotide pattern from viroid circles extracted from infected plants. In light of recent evidence for multimeric viroid replication intermediates, cleavage followed by RNA ligation by a cellular enzyme may (i) be a normal step in the viroid life cycle and (ii) may also reflect cellular events.

Are viroids escaped introns?

A complex of considerable stability is possible between the 5' end of U1 RNA and a specific nucleotide sequence of the potato spindle tuber viroid complement. Because base-pairing between the 5' end of U1 RNA and the ends of introns is believed by some to be responsible for the precise alignment and correct excision of introns, the U1-related sequence may represent the two ends of a presumed intron ancestor of the viroid complement after circularization.

Properties of a cell-free system for synthesis of citrus exocortis viroid

Partially purified nuclei from citrus exocortis viroid (CEV)-infected Gynura aurantiaca are able to synthesize linear and circular viroid molecules. Pretreatment of the nuclei with actinomycin D or deoxyribonuclease did not affect viroid synthesis, whereas the synthesis of other cellular RNAs was severely reduced. These observations support the essential role of CEV complementary RNA sequences in viroid replication. However, when alpha-amanitin was included in this in vitro synthesis system, CEV replication was markedly reduced by concentrations of 10 nM or greater. Taken together, these data support the proposition that viroid synthesis is catalyzed by a DNA-dependent RNA polymerase acting on a RNA template.

RNA intermediates in potato spindle tuber viroid replication

Two double-stranded RNA intermediates of viroid replication have been isolated from potato spindle tuber viroid (PSTV)-infected tomato tissue and characterized by polyacrylamide gel electrophoresis and DNA-RNA hybridization techniques. These replicative intermediates contain monomeric circular or linear PSTV strands complexed with a multimeric complementary RNA strand. Synchronous synthesis of single-stranded PSTV is accompained by a simultaneous marked increase in double-stranded PSTV RNA; thus, in vivo precursors of the characterized double-stranded PSTV RNAs seem to be involved in PSTV replication. A "rolling circle" model for viroid replication on a circular PSTV template can accommodate the double-stranded PSTV RNA species characterized.

Molecular cloning and characterization of potato spindle tuber viroid cDNA sequences

Double-stranded cDNA has been synthesized from a polyadenylylated potato spindle tuber viroid (PSTV) template and inserted in the Pst I endonuclease site of plasmid pBR322 by using the oligo(dC).oligo(dG)-tailing procedure. Tetracycline-resistant ampicillin-sensitive transformants contained sequences complementary to PSTV [(32)P]cDNA, and one recombinant clone (pDC-29) contains a 460-base-pair insert. This cloned double-stranded PSTV cDNA contains the cleavage sites for six restriction endonucleases predicted by the published primary sequence of PSTV as well as one additional site each for Ava I, Hae III, Hpa II, and Sma I. The additional Ava I, Hpa II, and Sma I sites are explained by the presence of a second C-C-C-G-G-G sequence in the cloned double-stranded cDNA. The largest fragment released by Hae III digestion contains approximately 360 base pairs. These results suggest that we have cloned almost the entire sequence of PSTV, but the sequence cloned differs slightly from that published. Hybridization probes derived from pDC-29 insert have allowed detection and preliminary characterization of RNA molecules having the same size as PSTV but the opposite polarity. This RNA is present during PSTV replication in infected tomato cells.

Studies on encapsidated viroid-like RNA I. Characterization of velvet tobacco mottle virus

Velvet tobacco mottle virus (VTMoV) isolated from Nicotiana velutina growing wild in arid Central Australia was transmitted by inoculation to a limited number of plant species of which N. clevelandii was the most convenient experimental host. The virus was also transmitted from field-grown plants toN. velutina and N. clevelandii by the mirid Cyropeltis nicotianae. VTMoV preparations purified by clarification with organic solvents and differential centrifugation contained polyhedral particles about 30 nm in diameter sedimenting as a single component at about 115 S. The particles were shown to be located in the nucleus, cytoplasm, and vacuoles of infected plant cells. Virus dissociated in the presence of mercaptoethanol and sodium dodecyl sulfate (SDS) separated into one major and two minor polypeptides with estimated molecular weights of 33,000, 36,000 and 31,000, respectively. Single-stranded RNA isolated from VTMoV by extraction with phenol was separated into five components with apparent molecular weights of 1.5 x 10(6), 0.63 x 10(6), 0.25 x 10(6), 0.16 x 10(6), and 0.12 x 10(6) referred to as RNAs 1, 1a, 1b, 2, and 3, respectively. It appears that RNAs 1a and 1b are breakdown products of RNA 1, as shown elsewhere, and electron microscopic examination of the other species showed that whereas RNAs 1 and 3 are linear molecules, RNA 2 is circular. The similarity of RNAs 2 and 3 to the RNA of viroids is discussed. VTMoV has been compared with several RNA plant viruses with small polyhedral particles. Only solanum nodiflorum mottle virus appears to share some of its unique features and the two have been shown to be antigenically related.

RNA folding pathway functional intermediates: their prediction and analysis

The massively parallel genetic algorithm (GA) for RNA structure prediction uses the concepts of mutation, recombination, and survival of the fittest to evolve a population of thousands of possible RNA structures toward a solution structure. As described below, the properties of the algorithm are ideally suited to use in the prediction of possible folding pathways and functional intermediates of RNA molecules given their sequences. Utilizing Stem Trace, an interactive visualization tool for RNA structure comparison, analysis of not only the solution ensembles developed by the algorithm, but also the stages of development of each of these solutions, can give strong insight into these folding pathways. The GA allows the incorporation of information from biological experiments, making it possible to test the influence of particular interactions between structural elements on the dynamics of the folding pathway. These methods are used to reveal the folding pathways of the potato spindle tuber viroid (PSTVd) and the host killing mechanism of Escherichia coli plasmid R1, both of which are successfully explored through the combination of the GA and Stem Trace. We also present novel intermediate folds of each molecule, which appear to be phylogenetically supported, as determined by use of the methods described below.

Compilation and analysis of viroid and viroid-like RNA sequences

We have created a catalogue comprising all viroid and viroid-like RNA sequences which to our knowledge have been either published or were available from on-line sequence libraries as of October 1, 1995. In the development of this catalogue nomenclature ambiguities were removed, the likely ancestral sequence of most species was determined and the most stable secondary structures of these sequences were predicted using the MulFold package. Only viroids of PSTVd-type possessed a rod-like secondary structure, while most other viroids adopted branched secondary structures. Several viroids have predicted secondary structures that include either a Y or cruciform structure reminiscent of the tRNA-like end of virus genomes at an extremity. However, it remains unknown whether or not these predicted structures are adopted in solution, and if they serve a particular function in vivo. Additional information such as the position of the self-catalytic domains are included in the catalogue. An analysis of the data compilated in the catalogue is included. The catalogue will be available on the world wide web (http://www.callistro.si.usherb.ca/jpperra), on computer disk and in printed form. It should provide an excellent reference point for further studies.

Subviral pathogens of plants: the viroids

Research during the last 15 years has conclusively shown that viroids are not only fundamentally different from viruses at the molecular level, but that they are most likely not directly related to viruses in an evolutionary sense. Today, viroids are among the most thoroughly studied biological macromolecules. Their molecular structures have been elucidated to a large extent, but much needs to be learned regarding the correlation between molecular structure and biological function. The availability of the tools of recombinant DNA technology in viroid research promises rapid progress in these areas of inquiry.

Viroids and virusoids are related to group I introns

Group I introns are found in nuclear rRNA genes, mitochondrial mRNA and rRNA genes, and chloroplast tRNA genes. The hallmarks of this intron class are a 16-nucleotide consensus sequence and three sets of complementary sequences. The viroids (circular pathogenic plant RNAs) and the virusoids (plant satellite RNAs) also contain the consensus sequence and the three sets of complementary bases. Pairing of the complementary bases would generate a viroid structure resembling a group I intron, which might be stabilized in vivo through interactions with proteins. The Tetrahymena self-splicing rRNA intron further has sequences homologous with regions of potato spindle tuber viroid associated with the severity of viroid symptoms.

The electrophoretic analysis of low molecular weight nucleic acids from Crohn's disease tissues in the search for an unconventional small infectious agent. Brief report

A small unconventional, viroid-like aetiological agent might initiate Crohn's disease (CD). Electrophoresis of radiolabelled low molecular weight nucleic acids from mesenteric lymph nodes and leucocytes did not distinguish CD-specific sequences compatible with a viroid-like agent.

Relationship of viroids and certain other plant pathogenic nucleic acids to group I and II introns

The nucleotide sequences of viroids contain features believed to be essential for the splicing of group I introns. Common sequence elements include a 16-nucleotide consensus sequence and three pairs of short sequences arranged in the same sequential order in both types of RNAs. The calculated probability of finding sequences resembling the 16-nucleotide consensus sequence in random nucleotide chains showed that at low fidelity (up to 5 mismatched nucleotides), the number of such sequences in viroids, plant viral satellite RNAs, plant viral RNAs and one plant viral DNA, group I introns and flanking exons does not significantly differ from the number expected at random. As the degree of fidelity is increased, the number in both introns and viroids, but not in exons or the other plant pathogens examined, greatly exceeds that expected in random chains. These findings suggest that viroids may have evolved from group I introns and/or that processing of viroid oligomers to monomers may have structural requirements similar to those of group I introns. The nucleotide sequences of viroids do not show close homology with two conserved regions of group II introns, the 14-base pair consensus region and the 5' terminal segment. However, close homology does exist between the conserved sequence of the 3' terminal segment of group II introns and viroids thus suggesting a possible evolutionary or functional relationship.

Viroid processing: a model involving the central conserved region and hairpin I

A model is proposed for the processing of oligomeric viroid replication intermediates into monomeric, circular progeny viroids. The model identifies a thermodynamically extremely stable base-paired configuration that partially or completely dimeric, as well as higher, viroid oligomers can assume and postulates that this structure, which involves structural features common to all viroids (the central conserved region and secondary hairpin I), is essential for precise cleavage and ligation. The model explains why recombinant plasmids containing tandem repeats of two or more viroid sequence equivalents are highly infectious when inoculated into viroid-susceptible plants, why certain plasmids containing partially duplicated viroid-specific inserts are less infectious, and why plasmids containing monomeric inserts are noninfectious or at best marginally infectious. The model also accounts for the fact that vector-derived sequences on either or both sides of the viroid sequence(s) of a restriction fragment are precisely excised and are lacking in progeny viroids.

What's new in hepatitis delta virus?

Seven years of clinical and laboratory research have provided us with a rather good knowledge of the infectious agent that causes hepatitis delta. This agent is a small RNA containing virus (hepatitis delta virus), which is functionally incomplete and needs the help of hepatitis B virus for infection and replication. It is unique also in respect to its RNA, which is smaller than the RNA of every other known RNA virus, but larger than the RNA of the viroids of higher plants. Animal experiments as well as clinical studies showed that hepatitis delta virus infection can be transmitted either simultaneously with hepatitis B, leading to a clinical picture which usually resembles that of hepatitis B alone, or as superinfection of a chronic HBsAg-carrier. The latter often leads to severe, and sometimes fatal, acute hepatitis, followed by chronic liver disease in as many as 30-40% of cases. The hepatitis delta virus is distributed world-wide, showing a high endemicity in Italy and some Arab countries, but also in certain risk groups such as intravenous drug addicts and haemophilics. Further epidemiological studies will probably reveal other foci where the hepatitis delta virus is endemic; especially in Africa, areas of high endemicity of hepatitis delta virus are suspected. Extensive research on delta agent is continuing: further clinical studies, using the highly sensitive method of DNA-RNA-hybridization for the detection of hepatitis delta virus RNA, will tell us more about the role of this virus in acute and chronic hepatitis, and future biochemical and biological research may be expected to increase our insight into the still enigmatic cooperation of the hepatitis delta virus and hepatitis B viruses.

Conformational transitions in viroids and virusoids: comparison of results from energy minimization algorithm and from experimental data

Viroids are single-stranded circular RNA molecules of 240 to 400 nucleotides which are pathogens of certain higher plants and replicate autonomously in the host cell. Virusoids are similar to viroids in respect to size and circularity but replicate only as genomic part of a plant virus. Their structure and structural transitions have been investigated by thermo-dynamic, kinetic and hydrodynamic methods. The special features of the sequences of these RNAs, which are the basis for their secondary structures and structural flexibility, are investigated with theoretical methods. A set of thermodynamic parameters for helix growth and loop formation is selected from the literature to calculate secondary structures and structural transitions of single-stranded RNAs. Appropriate modifications of the chosen parameter set are discussed. For calculations we used either Tinoco-plots and the model of "cooperative helices" or the Zuker-program based on the exact algorithm of Nussinov et al, or both. Calculations were done for viroids and virusoids. As both are single-stranded, circular RNAs we had to modify the Zuker-program as described in the appendix. Calculations are done for different viroids, i.e. potato spindle tuber, citrus exocortis, chrysanthemum stunt, coconut cadang-cadang, and avocado sunblotch, and for two virusoids, i.e. the circular RNAs of Solanum nodiflorum mottle virus, and velvet tobacco mottle virus. For viroids the calculations confirm our earlier theoretical and experimental results about the extended native structure and the highly cooperative transition into a branched structure. Virusoids show less base pairing, branching in the native secondary structure, and only low cooperativity during denaturation. They resemble more closely the properties of random sequences with length, G:C content, and circularity as in viroids but statistical sequences. The comparison of viroids, virusoids, and circular RNA or random sequences confirms the uniqueness of viroid structure.

Yeast mitochondria contain a linear RNA strand complementary to the circular intronic bI1 RNA of cytochrome b

bI1 RNA (excised from the first intron of the long form of the cytochrome b gene of Saccharomyces cerevisiae mitochondria) hybridizes with the two strands of a Bg/II-MboI DNA segment from this region. This fraction is resistant to digestions by DNase I and RNase T1 and disappears completely upon alkali hydrolysis. Strand-specific labeling of an intronic DNA fragment, cloned in pBR322 plasmid, was accomplished through the use of a T4 DNA polymerase. The purity of the probes was demonstrated by cloning an exon-intron fragment and labeling it by the same procedure; mRNA and pre-mRNA bands hybridized only with the transcribed DNA strand whereas bI1 RNA hybridized with the two strands under the stringent washing conditions employed (tm + 20 degrees C). Several experimental results argue against the possibility that the observation of two complementary bI1 RNA strands results from a partial self-complementarity of the RNA. A pre-mRNA intermediate from a box8 (G5046) mutant, still containing this intron, hybridizes only with the transcribed DNA strand of the pure intronic probe. The amount of the non-sense bI1 RNA strand is very low, in cells from two wild-type strains, relative to the sense RNA strand during the early stages of growth on glucose. It increases as the cells are released from glucose repression. bI1 RNA is resistant to RNase. Very little self-complementarity is seen by computer analysis of the sequence. Purified bI1 RNA is seen by electron microscopy under non-denaturing conditions as a mixture of double-stranded circular and linear molecules thus confirming the existence of the two complementary strands. The disappearance of all material following alkali hydrolysis demonstrates that these are indeed two RNA strands. Under fully denaturing conditions a mixture of single-stranded circular and linear molecules is seen as reported previously (Cell, 19, 321-329, 1980). We conclude that yeast mitochondria contain the two complementary bI1 RNA strands, one circular and the other linear. Considering a largely asymmetrical transcription of the mitochondrial genome in yeast and assuming that circularization of some intronic RNAs is part of RNA processing, we do not believe that the two strands are each a mixture of linear and circular molecules. The ratio of non-sense to sense bI1 RNA in a cytoplasmic petite mutant, A1B1, also varies according to growth conditions.(ABSTRACT TRUNCATED AT 400 WORDS)

Multicopy single-stranded DNA isolated from a gram-negative bacterium, Myxococcus xanthus

A gram-negative bacterium, Myxococcus xanthus, was found to contain 500 to 700 copies per chromosome of a short single-stranded linear DNA fragment. When this DNA (multicopy single-stranded DNA; msDNA) labeled at the 5' end with kinase was used as a probe against total chromosomal blots, it hybridized to unique high molecular weight bands, which were cloned and sequenced. Labeling of msDNA was also possible using the Klenow fragment of DNA polymerase I as well as terminal deoxynucleotidyl transferase, permitting direct sequencing. The 5' end of msDNA was found to be primed by a short RNA segment. The DNA portion of msDNA consisted of 163 bases. Exact correspondence was seen between the msDNA sequence and the sequence of a chromosomal clone. An elaborate secondary structure is postulated for the msDNA sequence. A similar satellite DNA was also found in another myxobacterium, Stigmatella aurantiaca.

Large-scale purification of viroid RNA using Cs2SO4 gradient centrifugation and high-performance liquid chromatography

A procedure for the purification of viroid RNA from tomato plants is described which yields up to a milligram of viroid RNA of gel electrophoretic homogeneity within 2 days. This technique is at least three times as fast as previous methods and is generally applicable to other RNA species. Plant material was homogenized and phenol extracted. In a Cs2SO4 density gradient, viroid RNA together with low-molecular-weight RNA, was separated from large single-stranded RNA, DNA, polysaccharides, polyphenols, and other compounds. The separation is based on the differences in the buoyant density and on the selective precipitation of large single-stranded RNA in Cs2SO4. Further purification of viroid RNA was achieved by HPLC over a weak anion exchanger linked to silica gel of optimized pore size. The elution was carried out by a salt gradient with complete exclusion of divalent metal ions. The procedures were applied to whole plants, leaves, stems, roots, cells, and protoplasts. The yields of nucleic acids at the different steps of purification are given for leaves, stems, and roots.

Molecular cloning and characterization of a complete DNA copy of potato spindle tuber viroid RNA

Double-stranded cDNA has been synthesized from RNA of a severe strain of potato spindle tuber viroid using a synthetic oligodeoxyribonucleotide as a primer. Upon cloning in bacteriophage M13mp9, two recombinant phages were selected to construct a pBR322-derived plasmid containing a complete viroid DNA copy. Elucidation of the nucleotide sequence revealed four differences with the previously established sequence of another PSTV strain, three of which were base exchanges and one a deletion.

Nuclear DNA from uninfected or potato spindle tuber viroid-infected tomato plants contains no detectable sequences complementary to cloned double-stranded viroid cDNA

High molecular weight tomato nuclear DNA was isolated from uninfected and potato spindle tuber viroid (PSTV)-infected tomato leaves. Restriction digests were fractionated on agarose gels, denatured and transferred to diazobenzyloxymethylpaper, and hybridized to 32P-labeled cloned double-stranded PSTV cDNA. No hybridization to DNA from either uninfected or infected tissue could be detected under conditions that permitted detection of cloned double-stranded PSTV cDNA at a concentration equivalent to one-fifth copy of PSTV-related DNA per haploid tomato genome. Hybridization of tomato DNA to 32P-labeled cloned soybean 18S and 28S ribosomal DNA sequences showed that the restricted nuclear DNA was suitable for hybridization to probes containing homologous sequences. Our results indicate that neither PSTV nor its complementary strand is transcribed from nuclear DNA but do not rule out the possibility of sequence homology between host DNA and a small portion of PSTV or its complement.

Scrapie agent contains a hydrophobic protein

The scrapie agent causes a degenerative nervous system disorder of sheep and goats. Considerable evidence indicates that the scrapie agent contains a protein that is necessary for infectivity [Prusiner, S. B., Groth, D. F., Cochran, S. P., Masiarz, F. R., McKinley, M. P. & Martinez, H. M. (1980) Biochemistry 19, 4883-4891], but direct demonstration of a protein moiety has been hampered by lack of sufficiently purified preparations. Employing preparations of the scrapie agent enriched 100- to 1000-fold with respect to protein, we found that digestion by proteinase K destroyed more than 99.9% of the infectivity. Diethylpyrocarbonate, which chemically modifies amino acid residues in proteins with high efficiency, also inactivated the scrapie agent in these purified preparations. Reductions of infectivity by proteinase K and diethylpyrocarbonate were not observed with less purified preparations. The agent bound to phenyl-Sepharose could not be eluted with 8.5 M ethylene glycol; however, a combination of ethylene glycol and detergents did release the agent. These observations provide good evidence for a protein and for hydrophobic domains within the scrapie agent. Whether the protein required for infectivity is the same protein responsible for the hydrophobic properties of the scrapie agent remains to be established.

Sensitive and Rapid Diagnosis of Potato Spindle Tuber Viroid Disease by Nucleic Acid Hybridization

A sensitive and reliable new method for the detection of potato spindle tuber viroid in potato tubers has been developed. The method is based on hybridization of highly radioactive recombinant DNA to viroid RNA that has been attached to a solid support. The method can be automated and permits the rapid testing of large numbers of tubers.

Thiocyanate and hydroxyl ions inactivate the scrapie agent

To probe the macromolecular structure of the scrapie agent and explore conditions for monomerization, the stability of the agent in low concentrations of inorganic ions was determined. A reduction by a factor of 10(5) in scrapie titer was found on exposure of the agent to 1 M KSCN or 0.3 M NaOH. In addition to the inactivation by thiocyanate ions, other chaotropic ions such as guanidinium and trichloroacetate inactivate the scrapie agent. Removal of thiocyanate ions by dialysis or glass permeation chromatography prevented the reduction in scrapie agent infectivity. Addition of equimolar amounts of (NH4)2SO4, a nonchaotrope, to preparations containing 1 M KSCN also prevented the loss of scrapie infectivity. In contrast, neutralization of the alkali-treated fractions with HCl did not restore infectivity. Acidification of partially purified fractions did not cause inactivation of the agent but did result in precipitation of the infectious agent. Inactivation by relatively low concentrations of chaotropic ions is consistent with many observations, all of which suggest that the scrapie agent contains a protein component that is essential for the maintenance of infectivity. Thus, it is unlikely that the agent is composed only of a "naked" nucleic acid. Certainly, if the agent were a naked nucleic acid, its lability in alkali virtually eliminates the possibility that it is composed of a single-stranded molecule of DNA.

delta Agent: association of delta antigen with hepatitis B surface antigen and RNA in serum of delta-infected chimpanzees

The hepatitis B virus-associated beta antigen was found in the serum of experimentally infected chimpanzee as an internal component of a discrete subpopulation of hepatitis B surface antigen (HBsAg) particles. The 35- to 37-nm particles banded in CsCl at 1.24-1.25 g/cm3 and sedimented with a mobility intermediate between that of the hepatitis B virion and that of the 22-nm form of HBsAg. The particles contained only indistinct internal structure by electron microscopy and were not unique to delta agent infection, similar particles without delta-antigen activity being observed in the preinfection serum of HBsAg carrier chimpanzees. A small RNA (Mr, 5 X 10(5)) was temporally associated with delta antigen in the serum of infected chimpanzees and copurified with the delta-antigen-associated particles. This RNA is smaller than the genomes of known RNA viruses but larger than the viroids of higher plants.