Biophysical and biochemical properties of an unusual birnavirus pathogenic for rotifers

A cytoplasmic dsRNA virus, rotifer birnavirus (RBV), has recently been isolated from the rotifer Brachionus plicatilis and is associated with a high mortality rate. Histologically, the viral lesions consist of characteristic inclusions, particularly amorphous dense bodies containing occluded particles. Purified virions are about 59 nm in diameter, single-shelled and display four capsomers per edge. The purified virions have a buoyant density of 1.290 (full particles) and 1.250 (empty particles) in CsCl gradients. Four major structural polypeptides of MrS 60K, 52K, 33K and 27K were detected by SDS-PAGE. The genome is composed of two linear segments of dsRNA with MrS of 2.45 x 10(6) and 2.31 x 10(6); additionally, small circular ssRNA molecules were detected by electrophoresis in overloaded agarose gels, but their significance is currently unknown. Except for this last feature and the structural instability of purified virions under freeze storage, all the other biochemical and biophysical characters indicate that RBV is a member of the Birnaviridae family with, for the moment, a unique position in this group.

Two new formulas for triangulation number T

The present paper reports two new formulas for calculating triangulation number T. T = L2/l2 and T = 1.45 r2/l2, where L is the distance between pentons, l the distance between any two adjacent capsomeres, r the radius of viral nucleocapsid. The formulas have been verified and applied. It is worth noticing that the triangulation number, viral size and distance between capsomeres are fully connected by the formula r/the square root of Tl = 0.83, and the capsid parameters of all icosahedral viruses are unified in one constant, 0.83.

Structural homology among four nodaviruses as deduced by sequencing and X-ray crystallography

The genomic RNA2s of nodaviruses encode a single gene, that of protein alpha, the precursor of virion proteins beta and gamma. We compared the sequences of the RNA2s of the nodaviruses, black beetle virus (BBV), flock house virus, boolarra virus and nodamura virus, with the objective of identifying homologies in the primary and secondary structure of these RNAs and in the structure of their encoded protein. The sequences of the four RNAs were found to be similar, so that homologous regions relating to translation and RNA replication were readily identified. However, the overall, secondary structures in solution, deduced from calculations of optimal Watson-Crick base-pairing configurations, were very different for the four RNAs. We conclude that a particular, overall, secondary structure in solution within host cells is not required for virus viability. The partially refined X-ray structure of BBV (R = 26.4% for the current model) was used as a framework for comparing the structure of the encoded proteins of the four viruses. Mapping of the four protein sequences onto the BBV capsid showed many amino acid differences on the outer surface, indicating that the exteriors of the four virions are substantially different. Mapping in the beta-barrel region showed an intermediate level of differences, indicating that some freedom in choice of amino acid residues is possible there although the basic framework of the capsids is evidently conserved. Mapping onto the interior surface of the BBV capsid showed a high degree of conservation of amino acid residues, particularly near the protein cleavage site, implying that that region is nearly identical in all four virions and has an essential role in virion maturation, and also suggests that all four capsid interior surfaces have similar surfaces exposed to the viral RNA. Apart from a small portion of the C promoter, the amino terminus of the BBV protein (residues 1 to 60) is crystallographically disordered and the amino acid residues in that region are not well conserved. The disordered portion of the BBV protein clearly projects from the capsid inner surface into the interior of the virion, the region occupied by the viral RNA. In all four viruses, residues 1 to 60 had a high proportion of basic residues, suggesting a virus-specific interaction of the amino terminus with the virion RNA.

Purification and biochemical characterization of chicken anaemia agent

Chicken anaemia agent (CAA) was purified using differential centrifugation and successive cycles of equilibrium density gradient centrifugation using sucrose and CsCl. The purification method was dependent on the use of an antigen-detecting ELISA based on a CAA-specific monoclonal antibody. Virus particles banded at a density of 1.33 to 1.34 g/ml in CsCl and measured 23.5 +/- 0.8 nm in diameter. Purified preparations contained one major polypeptide (Mr 50,000) and a single-stranded, circular DNA (2.3 kb). CAA shares some of the biochemical characteristics possessed by porcine circovirus and the virus associated with psittacine beak and feather disease.

Further analysis on the structural proteins of infectious pancreatic necrosis virus

The structural proteins of infectious pancreatic necrosis virus (IPNV) have been analyzed. Two-dimensional gel electrophoresis showed that IPNV proteins are slightly acidic with apparent pIs ranging from 5.8 to 6.6. To identify the IPNV surface-located proteins, purified virus was labelled either with fluorescein isothiocyanate (FITC) or with Na 125I. After analysis by SDS-PAGE, only the major viral protein, VP2, was labelled by either procedure. The accessibility of VP2 to these reagents suggests that this protein is externally located. In addition, using Concanavalin A conjugated with FITC and IPNV labelling with 3H-mannose, evidence is present that VP2 contains carbohydrate residues.

Acid helix-turn activator motif

A common sequence/structural motif pattern has been identified within the steroid/thyroid hormone receptors and other transcriptional activators using a new massively parallel symbolic learning assistant computer system. The pattern appears nearly diagnostic of transcription activation, including relative activation strength, among nuclear and DNA-binding prokaryotic proteins. In cases where mutation/deletion/chimeric studies have identified the activation domain, the pattern matches within that domain. These facts and the nature of the pattern itself strongly support the idea that the patterned domain is directly involved in a protein-protein transcription activation interaction.

Protein fingerprinting: a novel virus identification system

Viral proteins separated by one-dimensional SDS-PAGE produce protein binding patterns (fingerprints) which are unique for different viruses. We have applied this concept successfully for the development of a practical and objective virus identification system which is applicable to most viruses. The method is simple, specific, and, unlike the currently available methods, free from all virus-specific reagents. Interference by host protein bands in SDS-PAGE preparations of virus-infected cell lysates was eliminated consistently by treating virus infected cell cultures with optimum concentration of NaCl for selective inhibition of host protein synthesis. The method utilizes the comparison of protein fingerprints of 'unknown' viruses with protein fingerprints of reference viruses stored in a computer data base, using pattern recognition software. All 113 'unknown' virus strains were correctly identified to the genus level by the protein fingerprint method, when compared with the conventional virus identification methods.

Fatal infection of silvered leaf monkeys with a virus-like infectious agent (VLIA) derived from a patient with AIDS

Four silvered leaf monkeys, inoculated with a virus-like infectious agent (VLIA) derived from transformed NIH/3T3 cells (sb51) transfected with Kaposi's sarcoma DNA of an AIDS patient, showed wasting syndromes and died in 7-9 months. Two monkeys had a transient lymphadenopathy in earlier stages. Two moribund animals showed lymphopenia. Although 3 of the VLIA inoculated monkeys had persistent low grade fever early in the infection, the animals became afebrile in the later stages. One VLIA inoculated animal had a prominent antibody response, which occurred 7 months after VLIA inoculation. The other 3 monkeys had a transient or poor antibody response in the later stages. These 3 animals revealed periodic VLIA antigenemia during the course of the experiment. A control monkey was killed 8 months after the last VLIA inoculated monkey succumbed and showed neither an antibody response nor evidence of antigenemia. VLIA-specific DNA could be directly detected in necropsy tissues of all 4 monkeys inoculated with VLIA using the polymerase chain reaction method. VLIA infection was identified in all 4 spleens, 2 of 4 livers, 1 of 2 kidneys, and all 3 brains tested from these 4 animals, but not in the tissues from the control monkey. The necropsy examination of the 4 VLIA inoculated animals revealed no opportunistic infections, acute inflammatory lesions, malignancy or cause of death other than VLIA infection. We believe that the VLIA caused a fatal systemic infection in these monkeys.

Computer simulation of the variable agarose fiber dimensions on the basis of mobility data derived from gel electrophoresis and using the Ogston theory

Agarose gel electrophoresis of viruses and proteins was evaluated for estimating fiber dynamics of agarose by computer simulation based on the extended Ogston theory. By introducing functions, in place of previously used constant parameters, into the equations derived from the Ogston theory it was demonstrated that the effective fiber properties are variable as a function of both gel concentration and the size of the particle passing through the gel. This variability accounts for the curvature of plots of log(mobility) vs gel concentration in agarose gel electrophoresis as well as for the apparent dichotomy between fiber properties obtained from the electrophoresis of either viruses or proteins. Specifically, computer simulation based on the electrophoretic mobility values of five viruses and seven proteins by use of an eight (gel-specific) parameter model yielded functions relating gel concentration and/or particle size with electrophoretic mobility of particles, the retardation coefficient, K'R, and effective fiber radius, length, and volume. The simulations give further insights into, as well as mathematical basis for, a number of previously made assumptions (such as variation of agarose fiber structure with gel concentration, variation of fiber volume with particle size, continuity of the K'R vs radius plot from 0 to 45 nm), thus demonstrating the continued usefulness of the Ogston model. The mathematical model provides the elements for an improved method for the determination of particle size, charge, and potentially shape by agarose gel electrophoresis, and can be regarded as the basis for future elaboration of a computer program for the routine determination of these parameters.

Use of protein A in the serum-in-agar diffusion method in immune electron microscopy for detection of virus particles in cell culture

A modified technique using protein A in the serum-in-agar (SIA) method for immune electron microscopy (IEM) was presented. Grids coated with staphylococcal protein A were floated on samples mounted on agar containing 2% antiserum and incubated at 37 C, for 60 min. After washing and staining, the grids were observed in an electron microscope. The effects of protein A on virus detection were evaluated using poliovirus and bovine rotavirus infected cell culture fluids. The results showed that the technique using protein A (PA-SIA) had at least 10-fold higher sensitivity for virus detection than the original SIA. The optimal concentration of protein A was 1 to 10 micrograms/ml for coating the grids to trap virus particles. The PA-SIA method was also compared with immunosorbent electron microscopy (ISEM). The former showed higher or at least the same sensitivity and some advantages in detecting antigen-antibody reaction than the latter method. These results indicate that our PA-SIA method may be superior to other IEM techniques presented previously for the detection and identification of viruses.

[Solubilization of glycoproteins from enveloped viruses by detergents]

The effects of some known ionic and nonionic detergents as well as that of a novel nonionic detergent MESK on various enveloped viruses were investigated. It was found that nonionic detergens (MESK, Triton X-100, octyl-beta-D-glucopyranoside) selectively solubilize glycoproteins of enveloped viruses. The most mild selective action is exerted by the nonionic detergent MESK. Using this detergent, pure preparations of glycoproteins of influenza, parainfluenza, equine Venezuela encephalomyelitis, rabies, vesicular stomatitis and herpes viruses were obtained. The procedure of isolation of purified glycoproteins includes incubation of viral suspensions with MESK, removal of subviral structures by centrifugation and purification of glycoproteins from detergent admixtures by dialysis. Purified glycoproteins retain their native structure and a high biological activity and immunogenicity. MESK seems to be due a perspective tool in the production of subunit vaccines.

Microbial diagnosis by nucleic acid sandwich hybridization

Sandwich hybridization is a three-component nucleic acid hybridization method suitable for the identification of microbes. In this method, one specific DNA fragment on solid support acts as catching reagent, and the second reagent is a labeled probe. The labeling of the support is mediated by a specimen nucleic acid homologous to both reagents. Because the specimen is kept in solution, relatively crude specimens not requiring elaborate pretreatments can be tested without background problems. The utility of the method in microbial diagnosis (adenovirus, cytomegalovirus, and Chlamydia trachomatis) has been demonstrated. Increased sensitivity and nonradioactive detection methods will no doubt further extend the applicability of the sandwich hybridization method.

Nucleic acid hybridization in the diagnosis of viral infections

Recombinant DNA technology, including molecular cloning and nucleic acid hybridization, is now being applied to problems in clinical virology. Although viral isolation in cell culture remains the most sensitive and specific diagnostic test for many viruses, for some viruses, isolation in cell culture is lengthy or difficult or has not yet been achieved. Utilization of hybridization techniques has already resulted in important new information concerning the pathogenesis of a number of viruses, such as Epstein-Barr virus, hepatitis B virus, and human papillomavirus. In addition, time to diagnosis for viruses such as cytomegalovirus, Epstein-Barr virus, and varicella-zoster virus can be significantly shortened to 36 to 48 hours, a great improvement over standard isolation with obvious importance for patient management. Hybridization techniques have also been applied to screening of antiviral agents. Although results of studies to date have been encouraging, significant problems remain to be solved before these techniques can be applied in a routine diagnostic laboratory. First, more sensitive assays must be developed. One approach is the generation of probes with higher specific activities. Synthesis of single-stranded probes using recombinant M13 bacteriophage as a template results in probes of higher specific activities that also cannot re-anneal to themselves because they are not complementary. Thus, more probe is available to anneal to sample DNA. Synthesis of cRNA probes that form more stable hybrids with DNA is another approach that is receiving attention. A second problem is reagent safety and stability. The most sensitive and commonly used label in the studies reviewed in this article has been 32P. With its half-life of 2 weeks, potential hazards to personnel, and disposal problems, it is probably not suitable for clinical laboratories. A major step in the development of nonradioactive, stable probes has been synthesis of biotinylated nucleotide analogues that can be efficiently incorporated into DNA or RNA. Biotinylated probes are stable for 1 to 2 years at -20 degrees C, and their use obviates the need for autoradiography, thus shortening reaction times. In addition, very high concentrations of probes can be used without the background problems encountered with radiolabels. To date, biotinylated probes have been significantly less sensitive than those labeled with 32P, but continued efforts to improve sensitivity have yielded promising results.(ABSTRACT TRUNCATED AT 400 WORDS)

High-performance liquid chromatography of DNA restriction fragments

High-performance liquid chromatography on Nucleogen-DEAE 4000-10 has been applied to several problems of the isolation of DNA restriction fragments. Large amounts of DNA fragments of high purity are necessary for biophysical studies and for molecular hybridization in basic research, as well as in medical diagnosis. The influence of various parameters, such as buffer, pH, eluting salt, gradient slope, flow-rate and the addition of urea on the resolution of fragments by high-performance liquid chromatography were studied on an analytical scale, and the optimal conditions were then used for the large-scale preparation of milligram amounts. The best resolution of fragments between 25 and 1500 base pairs was obtained with a linear gradient from 500 mM to 1200 mM sodium chloride in 6 M urea -30 mM sodium phosphate (pH 6.0). Quantitative data are given for the purity and recovery of the sample, and the capacity and lifetime of the column. The following applications of high-performance liquid chromatography of restriction fragments are described: preparation of 2 mg of fragments, separation of 1 mg of DNA insert from 7 mg of its plasmid vector, and analysis of DNA-RNA hybrids.

[Physicochemical and biological properties of the agents isolated from a patient with amyotrophic leukospongiosis and monkeys with experimentally reproduced disease]

The paper describes isolation from the brain of a patient who died of amyotrophic leukospongiosis (ALSP) and from squirrel monkeys with experimentally induced disease of heretofore unknown agents whose reproduction in continuous cell lines (HEp-2, CV-1, Vero) was accompanied by a significant increase in the mitotic activity of cells and adsorption of human 0(1) and M. rhesus erythrocytes. The blood sera from patients with ALSP and a monkey with experimental disease were found to contain a factor specifically inhibiting the hemadsorption phenomenon and the increase of the mitotic activity in the infected cell cultures. Investigations of the properties of the isolates showed them to have a buoyant density of 1.18 g/cm3 in a 20-60% sucrose gradient, to incorporate radioactive precursors of RNA and protein synthesis, and to be highly resistant to the effect of some physical and chemical factors. The data obtained suggest that the isolates differ from all the presently known conventional viruses but have some similarity with etiological agents of slow infections and may be classified as unconventional viruses.

Evidence for sequence heterogeneity among the double-stranded RNA segments of Penicillium chrysogenum mycovirus

We have examined the dsRNA segments of the multipartite virus from Penicillium chrysogenum (ATCC 9480). A fourth RNA segment has been detected recently and, in the present work, we separated the four RNA segments and looked for possible homologies among them by thermal denaturation and electron microscopical heteroduplex studies. Differences were found between the differential melting profiles of the separated RNA segments, and no extensive regions of homology were detected among the various RNA segments by heteroduplex analyses. The results suggest that each RNA segment contains unique sequences. A comparison of the lengths of the RNA segments determined by electron microscopy with those determined by gel electrophoresis suggests that one of the segments has a distinct tertiary structure.

Comparative studies of United Kingdom isolates of swine vesicular disease virus

The characteristics of four United Kingdom isolates of swine vesicular disease (SVD) virus from 1981 to 1982 have been compared with those of an isolate obtained from the first outbreak of swine vesicular disease diagnosed in the United Kingdom in 1972. When the virus structural proteins were examined by polyacrylamide gel electrophoresis the four isolates from 1981-82 all had the same polypeptide pattern, which was different from that of the 1972 isolate. Immunodiffusion tests with the 1972 isolate and one 1982 isolate did not reveal any antigenic difference between the viruses but minor antigenic differences were shown by cross-neutralisation tests between the 1972 isolate and the four isolates from 1981-82. In experimentally infected pigs the 1972 isolate produced typical SVD lesions whereas the four more recent SVD viruses produced only very mild clinical disease. Clinical lesions scored numerically were four- to 10- and five- to 11-fold higher at seven and 14 days after infection for pigs infected with the 1972 isolate than with the four isolates from 1981-82. The serum of pigs infected with the 1972 isolate contained significantly higher levels of neutralising antibody than those of pigs infected with more recent isolates. The antibody titres of pigs with only primary lesions ranged from log10 1.9 to 2.8 and one clinically normal pig had a titre of log10 2.4 at 14 days after infection. Attention is drawn to the implication of these findings for SVD control policies based only on the recognition and reporting of clinical disease.

Interferon induction by viruses. IX. Antagonistic activities of virus particles modulated interferon production

Cells generally responded to viral inducers of interferon (IFN) by generating a dose (multiplicity of infection)-response (interferon-yield) curve which showed a good fit to a model in which the fraction of interferon-yielders corresponded to the fraction of cells infected with one or more particles. These were defined as interferon-inducing particles (IFPs). The IFN-producing capacity of cells infected with these particles was modulated upon coinfection with a second type of virus particle, those with the capacity to suppress IFN production. These were termed interferon induction-suppressing particles (ISPs). In cells coinfected with IFP and ISP the latter were dominant phenotypically. In some systems ISP activity was expressed by IFP when the latter were present at two or more particles per cell. The existence of virus particles with antagonistic activities for interferon induction provides a mechanism for regulating the production of IFN and hence the potential outcome of a virus infection.

Denaturation and renaturation of Penicillium chrysogenum mycophage double-stranded ribonucleic acid in tetraalkylammonium salt solutions

The base composition dependence of double-stranded ribonucleic acid (RNA) melting was studied by observing the structure and widths of melting transitions for Penicillium chrysogenum mycophage RNA as well as differences in melting temperatures of two RNAs of different base composition. Double-stranded RNA melting is independent of base compositions in 3.5 M Et4NCl and 4.6 M Me4NCl, where the melting temperatures are 25 and 92 degrees C, respectively. Double-stranded RNA renaturation rate constants are reported in Et4NCl solutions. The nucleation rate constant is about 10 times lower than that for double-stranded deoxyribonucleic acid. Analyses of renaturation kinetics results lead to the conclusion that each of the three similar but separable RNA segments of Penicillium chrysogenum mycophage is unique.

Affinity chromatography of cells and cell membranes

This article attempts to introduce the concept of cellular affinity chromatography as it departs from molecular affinity chromatography. Special emphasis is placed on the selectio of a solid support as well as on the role of lectins as affinity ligands. Our major goal was to bring to light the basic principles involved, multiple options of ligands and matrices, and different techniques, which may be applied to separate the complex cell population as well as cell membranes. It is hoped that further developments in the field, especially in the selection of proper experimental conditions, ligands and matrix material may provide better results. We have tried to identify some of the potential problems which should be considered before these approaches can be used on a routine basis. Although the review deals primarily with the affinity chromatography of cells and cell membranes, examples are presented for diverse systems such as cell organelles, viruses and phages. A table summarizing the use of cellular affinity chromatography is included. It lists more than 80 examples covering the literature up to December, 1979.

Codon catalog usage and the genome hypothesis

Frequencies for each of the 61 amino acid codons have been determined in every published mRNA sequence of 50 or more codons. The frequencies are shown for each kind of genome and for each individual gene. A surprising consistency of choices exists among genes of the same or similar genomes. Thus each genome, or kind of genome, appears to possess a "system" for choosing between codons. Frameshift genes, however, have widely different choice strategies from normal genes. Our work indicates that the main factors distinguishing between mRNA sequences relate to choices among degenerate bases. These systematic third base choices can therefore be used to establish a new kind of genetic distance, which reflects differences in coding strategy. The choice patterns we find seem compatible with the idea that the genome and not the individual gene is the unit of selection. Each gene in a genome tends to conform to its species' usage of the codon catalog; this is our genome hypothesis.

[Physicochemical characteristics of the Penicillium-bacterial virus type 5 and its nucleic acid]

Physico-chemical characteristics of PBV-5 virus and its nucleic acid were studied. Morphologically, the virus is a rectilinear polyhedron 270 A in diameter, without a process. The sedimentation constant of a virus particle is 117S, the buoyant density of the virus in cesium chloride density is 1.437 g/cm3. As shown by qualitative reactions with orcinol and diphenylamine, the virus contains DNA. The viral DNA preparation in CsCl gradient solution showed the buoyant density 1.719 g/cm3. Electron microscope examination of a PBV-5 DNA preparation showed the nucleic acid molecules to be single-stranded rings.

Detection and discrimination of individual viruses by flow cytometry

A new flow cytometer with a very small observation volume has been developed to detect individual viruses with good resolution, and has been used to discriminate between two types of viral particles based on differences in their light scattering. Measurements of light scattering and fluorescence made with such an instrument can provide a basis for quantitative analysis and sorting of viruses and other particles in the micron and submicron size range.

Double-stranded ribonucleic acid in viruses of Penicillium citrinum

The nucleic acid content of two viral populations in a strain of Penicillium citrinum is shown to be double-stranded ribonucleic acid, resolved through polyacrylamide gel electrophoresis into 10 size groups ranging from 1.17 to 3.98 megadaltons.

Chick muscle in tissue culture: the ubiquity of viral infection

In chick skeletal muscle fibers cultured from embryos of commercially obtained "normal" eggs we have demonstrated numerous C-particles and large amounts of avian leucosis/sarcoma envelope antigen, especially when cultured in the presence of dinitrophenol. C-particles were present in t-tubules, which were possible intracellular viaducts of infection or dissemination and perhaps were the loci of receptors of viral invasion of the cytoplasm and sites of egress. The abundant lace-like membraneous proliferations, probably of t-tubules, usually had C-particles adjacent to or within them and perhaps were virus-provoked. Questioned is the validity of using cultured muscle, or extract, of embryos from ordinary chicken eggs for analysing normal biological phenomena--or conversely, is viral influence "normal" in chick development?

Polypeptide composition of spleen necrosis virus, a reticuloendotheliosis virus

The polypeptide composition of virions of spleen necrosis virus, a reticuloendotheliosis virus, was determined using electrophoresis on sodium dodecyl sulfate-containing, 10 percent polyacrylamide gels. Ten polypeptides were resolved. Four of these were present in minor and somewhat variable amounts. Two proteins, gp71 and gp22, contained D-glucosamine and were located on the outer surface of the lipid envelope, as demonstrated by lactoperoxidase-catalyzed iodination and by bromelain digestion. The results suggest that two of the minor proteins, p36 and p26, were also located on the outer surface, although they lacked D-glucosamine. Treatment of the virus with 0.25 percent Nonidet P-40 and 1 percent dithiothreitol produced a subparticle with a buoyant density of approximately 1.31 g/cm-3. This particle was relatively enriched with polypeptides p77, p62, and p50 and contained small amounts of three other polypeptides.

A classification of virus groups based on the size of the particle in relation to genome size

For 59 different viruses, when the amount of nucleic acid in the particle is related either to the dry weight of the particle or to the particle volume, two classes of virus groups emerge--those with enveloped or those with geometrical particles. The enveloped viruses have particles with the following properties: (i) about 40 X 10-6 daltons of anhydrous weight per 10-6 daltons of nucleic acid; (ii) a particle volume of about 2 X 10-5 nm3 per 10-6 daltons of nucleic acid; (iii) a limiting lipoprotein membrane. These properties are qualitatively and quantitatively close to those of prokaryotic cells. The geometric viruses have particles with roughly one-tenth the anhydrous mass per unit of nucleic acid and one twenty-fifth the particle volume per unit of nucleic acid. They do not possess a limiting lipoprotein membrane.