Publications
| Title | Abstract | Year(sorted ascending) Filter | PMID Filter |
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| infectivity of chimeric viroid transcripts reveals the presence of alternative processing sites in potato spindle tuber viroid. | in an investigation of viroid replication and pathogenesis, we have assessed the effect of sequence duplication of the upper central conserved region (ccr) of the molecule on the infectivity of rnas transcribed in vitro from partial dimers of wild-type and mutant viroid cdnas. in one set of experiments, the relative infectivities of one monomeric potato spindle tuber viroid (pstv) and five oligomeric sp6 transcripts [pstv or pstv-tasv (tomato apical stunt viroid) chimeras] were compared. with on ... | 1989 | 2728347 |
| nonradioactive, photobiotin-labelled dna probes for routine diagnosis of viroids in plant extracts. | avocado sunblotch viroid (asbv), coconut cadang cadang viroid (cccv), chrysanthemum stunt viroid (csv) and potato spindle tuber viroid (pstv) were detected in plant extracts by dot-blot hybridization using nonradioactive photobiotin-labelled nucleic acid probes. recombinant dna probes, containing full-length monomer viroid inserts in the plasmid vectors psp64 or puc9, were biotinylated with photobiotin and used as sonicated double-stranded dna fragments. using fresh leaf material, a general meth ... | 1989 | 2654169 |
| a microscale procedure for isolating and sequencing the viroid rna present in one gram of infected leaf tissue. | a microscale procedure for the isolation and purification of viroid rna from one gram of viroid-infected leaf tissue and for its subsequent sequencing at the cdna level is described using potato spindle tuber viroid (pstv) as model system. total nucleic acids are phenol-extracted and salt-fractionated with 2 m licl. the viroid-containing fraction is then subjected to bidirectional polyacrylamide gel electrophoresis. this removes all co-fractionated cellular rnas from the circular viroid rna whic ... | 1989 | 2723017 |
| biotinylated rna probes for the detection of potato spindle tuber viroid (pstv) in plants. | diseases caused by potato spindle tuber viroid (pstv) are of significant agronomic importance, and early detection is vital. the objective of this paper was to synthesize biotinylated rna probes in order to develop a specific, sensitive, and reliable assay system for detection of pstv in infected plants. rna probes were prepared by in vitro transcription of cloned pstv, and were labelled with either biotin-11-utp or [32p]utp. partially purified total rnas from healthy and from pstv-infected plan ... | 1989 | 2723019 |
| characterisation of synthetic dna probe detecting potato spindle tuber viroid. | chemically synthesized dna fragments complementary to selected regions of the potato spindle tuber viroid (pstv) genome were cloned into escherichia coli plasmid puc9. one of the recombinant plasmids (pibb4) with a 87 bp insert representing the central region of the pstv genome (nucleotides 88 to 174) was used after labelling by nick translation for detecting pstv by dot-blot hybridization. the molecular probe was almost as sensitive as the one carrying the full genomic pstv copy (pav401), detec ... | 1989 | 2668314 |
| interactions between citrus exocortis and potato spindle tuber viroids in plants of gynura aurantiaca and lycopersicon esculentum. | plants of gynura aurantiaca and tomato (lycopersicon esculentum) were inoculated with severe strains of citrus exocortis viroid (cev) and potato spindle tuber viroid (pstv). the progeny of both viroids was analyzed by two systems of page which allowed discrimination between cev and pstv on the basis of their different sizes. when inoculated separately to g. aurantiaca cev and pstv induced severe and very mild symptoms, respectively, with cev accumulating to a higher level than pstv, whereas when ... | 1989 | 2722468 |
| 32p- and biotin-labelled in vitro transcribed crna probes for the detection of potato spindle tuber viroid and chrysanthemum stunt viroid. | replacing nick-translated dna probes by in vitro transcribed complementary rna (crna) probes considerably increased the sensitivity of dot-blot detection tests of potato spindle tuber viroid and chrysanthemum stunt viroid. as compared to the limit of detection of 5-10 pg of viroid obtained with 32p-labelled dna probes, crna probes allow the detection of less than 1 pg of pure viroid. when labelled with biotin by incorporation of biotin-labelled ribonucleotides, the crna probes have a limit of de ... | 1990 | 1691524 |
| detection of potato spindle tuber viroid (pstv) in dormant potato tubers by concatameric cdna probe. | the 32p-labelled concatameric insert cut out from a plasmid pspav6.2(+), containing 6.2 copies of a full-length pstv, was used to detect pstv in dormant potato tubers by dot-blot hybridisation assay. the concatameric insert probe was 4 times more sensitive than the monomeric one. this allowed the detection of 0.5 pg of viroid rna. the sensitivity makes th eoligomeric cdna probe a useful alternative to cdna probes. | 1990 | 2086594 |
| a new strain of potato spindle tuber viroid (pstvd-n) exhibits major sequence differences as compared to all other pstvd strains sequenced so far. | 1990 | 2103469 | |
| parallel algorithms for finding a near-maximum independent set of a circle graph. | a parallel algorithm for finding a near-maximum independent set in a circle graph is presented. an independent set in a graph is a set of vertices, no two of which are adjacent. a maximum independent set is an independent set whose cardinality is the largest among all independent sets of a graph. the algorithm is modified for predicting the secondary structure in ribonucleic acids (rna). the proposed system, composed of an n neural network array (where n is the number of edges in the circle grap ... | 1990 | 18282845 |
| comparison of nonradioactive cdna probes for detection of potato spindle tuber viroid by dot-blot hybridization assay. | six nonradioactive cdna probes were compared for their sensitivities for detecting potato spindle tuber viroid (pstvd) by dot-blot hybridization assay. three biotinylated pstvd cdna probes, labeled by photoactivation with photobiotin, by nick translation or by random priming with biotinylated deoxyribonucleotides, were all capable of detecting 20 pg of purified pstvd by a colorimetric assay and 2-20 pg by a chemiluminescent assay. digoxigenin-labeled probe was able to detect 200 pg of purified p ... | 1991 | 1816253 |
| coat protein of potyviruses. 7. amino acid sequence of peanut stripe virus. | the amino acid sequence of the 287-residue coat protein of peanut stripe virus (pstv) was determined from the sequences of overlapping peptide fragments. results indicated that the amino terminus was blocked by an acetyl group, as has previously been found for the coat protein of johnsongrass mosaic potyvirus. comparison of the pstv sequence with coat proteins of 20 distinct potyviruses gave sequence identities of 47-57%, except for zucchini yellow mosaic virus (zymv), passionfruit woodiness vir ... | 1991 | 1863222 |
| development and application of a nonradioactive nucleic acid hybridization system for simultaneous detection of four potato pathogens. | cdna clones of potato virus x (pvxcp strain), potato virus y (pvyo strain), potato leaf roll virus (plrv) and potato spindle tuber viroid (pstv) were used separately or combined for the detection of the corresponding rnas in extracts of infected plants. a general method for the rapid preparation of rna extracts without use of organic solvents (i.e. phenol) was developed for this purpose. plant extracts from a range of field, artificially inoculated germplasm genotypes, micro-propagated and proto ... | 1991 | 2016393 |
| formation of a thermodynamically metastable structure containing hairpin ii is critical for infectivity of potato spindle tuber viroid rna. | the functional relevance of a hairpin ii-containing structure of viroid rna was studied by site-directed mutagenesis, thermodynamic calculations, experimental denaturation curves and infectivity tests. hairpin ii is formed during thermal denaturation of circular viroids or as part of a metastable structure during synthesis of viroid replication intermediates. in potato spindle tuber viroid (pstvd), eight single-site mutations were generated in the segments which form hairpin ii. from the mutated ... | 1991 | 2001685 |
| effects of random mutagenesis upon potato spindle tuber viroid replication and symptom expression. | a combination of random chemical mutagenesis plus temperature gradient gel electrophoresis was used to isolate a collection of 57 potato spindle tuber viroid (pstv) cdnas containing mutations distributed throughout the entire 359 nucleotide genome. although the presence of multiple mutations was often associated with a loss of cdna infectivity, infectious pstv cdnas containing as many as four unlinked alterations could be isolated. several mutations in the pathogenicity domain and left terminal ... | 1991 | 1926773 |
| the antigen of hepatitis delta virus: examination of in vitro rna-binding specificity. | the only known protein of hepatitis delta virus (hdv), the delta antigen, is found both within virus particles and within the nucleus of the infected cell, where it has one or more roles essential for rna genome replication. others have demonstrated that the antigen has the ability, in vitro, to specifically bind hdv rna species. we report a further examination of this phenomenon, using partially purified recombinant protein, expressed as a fusion with the staphylococcal protein a. from northwes ... | 1991 | 1906549 |
| ribonuclease t1 generates circular rna molecules from viroid-specific rna transcripts by cleavage and intramolecular ligation. | a 406 nucleotide long potato spindle tuber viroid (pstvd)-specific linear rna transcript was synthesized in vitro and subjected to limited digestion with ribonuclease (rnase) t1. under certain conditions this guanosine-specific endoribonuclease proved to be capable of processing the longer-than-unit-length, precursor-like viroid rna transcript by cleaving out a linear 358 nucleotide long product and ligating that to a circular rna molecule. the new finding that rnase t1 acts as an rna processing ... | 1991 | 1709278 |
| sequence analysis of five new field isolates demonstrates that the chain length of potato spindle tuber viroid (pstvd) is not strictly conserved but as variable as in other viroids. | the sequence analysis of five new field isolates of potato spindle tuber viroid (pstvd) of different virulence revealed that the length of their rna chain is not strictly conserved to 359 nucleotides (nts), as one could have inferred from the previously sequenced pstvd strains. it was now found that the chain length is strain-specific like in the case of practically all other viroids, and that it may vary, so far, between 356 and 360 nts. taking our previously sequenced and least virulent mild s ... | 1992 | 1623184 |
| rna progeny of an infectious two-base deletion cdna mutant of potato spindle tuber viroid (pstv) acquire two nucleotides in planta. | deletion mutations were generated in four structural domains of a potato spindle tuber viroid (pstv) complementary dna (cdna) clone. deletions of 3 to 5 nucleotides at the central conserved domain (ccggg, positions 94 to 98), variable domain (gccg, positions 146 to 149) and pathogenicity domain (cga, positions 286 to 288) abolished infectivity of dimeric or trimeric cdna constructs, or their in vitro transcripts. by contrast, a clone (st4) with a deletion of two nucleotides (uu, positions 339 an ... | 1992 | 1546455 |
| base-pair probability profiles of rna secondary structures. | dynamic programming algorithms are able to predict optimal and suboptimal secondary structures of rna. these suboptimal or alternative secondary structures are important for the biological function of rna. the distribution of secondary structures present in solution is governed by the thermodynamic equilibrium between the different structures. an algorithm is presented which approximates the total partition function by a boltzmann-weighted summation of optimal and suboptimal secondary structures ... | 1992 | 1498695 |
| strains of bean common mosaic virus consist of at least two distinct potyviruses. | bean common mosaic virus (bcmv) consists of a large number of pathotypes and strains which have largely been identified by their characteristic interactions with a selected number of differential bean cultivars. the relationships among these strains and other potyviruses that infect legumes are complex, with indications that bcmv, blackeye cowpea mosaic virus (blcmv) and azuki bean mosaic virus (azmv) may be strains of the one virus. using high performance liquid chromatographic peptide profiles ... | 1992 | 1450767 |
| serological and biological relationships among viruses in the bean common mosaic virus subgroup. | bean common mosaic virus (bcmv), blackeye cowpea mosaic virus (b1cmv), cowpea aphid-borne mosaic virus (cabmv), azuki bean mosaic virus (azmv), and peanut stripe virus (pstv) are five species of the genus potyvirus, family potyviridae which are seed-transmitted in beans or cowpeas. eighteen isolates of bcmv, five isolates of b1cmv, four isolates of cabmv, and one isolate each of azmv, and pstv were compared serologically using a panel of 13 monoclonal antibodies (mabs) raised against bcmv, b1cmv ... | 1992 | 1450766 |
| highly sensitive digoxigenin-labelled dna probe for the detection of potato spindle tuber viroid. | a molecular probe pspav6.2(+), with concatameric insert representing 6.2-times repeated copy of potato spindle tuber viroid (pstv) rna, was labelled with digoxigenin and used to detect pstv by dot-blot hybridization assay. the probe was highly sensitive and specific, detecting as little as 2.5 pg of pstv rna. both severe and mild pstv strains were detectable in 64-512-times diluted crude extracts from infected tomato leaves, and potato leaves, sprouts, and seeds. for extraction of plant tissue t ... | 1992 | 1430068 |
| [determination of potato spindle tumor viroid and chrysanthenum stund viroid using biotinylated olideoxyribonucleotides]. | a 26 base long oligodeoxyribonucleotide complementary to a common rna sequence of potato spindle tuber viroid (pstv) and chrysantemum stunt viroid (csv) was synthesized. the 3'-end biotinylated one was used for the detection of pstv and csv rna immobilized on nitrocellulose filters by nucleic acid hybridization. visualization of hybridization results was performed by two ways, either by streptavidin-alkaline phosphatase conjugate or streptavidine and biotinylated alkaline phosphatase. it was pos ... | 1992 | 1406609 |
| structural requirements for viroid processing by rnase t1. | viroids are replicated via a rolling circle-like mechanism in which (+) strand oligomeric intermediates have to be cleaved enzymatically to unit-length molecules followed by ligation to mature circles. a transcript of potato spindle tuber viroid, which is still infectious, consists of a monomeric molecule with only 22 additional nucleotides, thus doubling part of the central conserved region of viroids. it was shown that this transcript can be cleaved and ligated in vitro to circles by rnase t1. ... | 1992 | 1404386 |
| pear blister canker viroid is a member of the apple scar skin subgroup (apscaviroids) and also has sequence homology with viroids from other subgroups. | the sequence of pear blister canker viroid (pbcvd), the putative causal agent of pear blister canker (pbc) disease, has been determined. pbcvd consists of a single-stranded circular rna of 315 nucleotide residues which assumes a branched conformation when it is folded in the model of lowest free energy. pbcvd has highest sequence similarity with grapevine 1b viroid (52.4%), but also contains sequences related to regions present in viroids that belong to different subgroups, suggesting that pbcvd ... | 1992 | 1383394 |
| a viroid from nematanthus wettsteinii plants closely related to the columnea latent viroid. | a viroid was isolated from symptomless nematanthus wettsteinii plants using the return-page method for analysis of low m(r) nucleic acids. the rna was transmitted to tomato, three cultivars of potato, and scopolia sinensis plants by mechanical inoculation or by grafting. infected solanaceous plants developed symptoms similar to those caused by potato spindle tuber viroid (pstvd). the nematanthus viroid consists of 372 nucleotides, 214 g+c, 158 a+u, with a g+c/a+u ratio of 1.35. one of seven cdna ... | 1992 | 1279098 |
| generation of viroid conformational isomers that are stable to incubation with magnesium ions and in a nuclear extract from tomato plants. | we identified conditions for heating and quick cooling viroid rnas in the presence of salt which lead to the production of conformational isomers stable to incubation for at least 45 minutes at 30 degrees in the presence of magnesium ions. elution in 0.3 m nacl allowed the purification of an electrophoretically slow form of an in vitro transcript carrying a complete copy of the potato spindle tuber viroid rna sequence. slow forms of this transcript and of kinase-labeled linear viroid rna persist ... | 1992 | 1282703 |
| processing of linear longer-than-unit-length potato spindle tuber viroid rnas into infectious monomeric circular molecules by a g-specific endoribonuclease. | different cdna constructs were used for the in vitro synthesis of rna transcripts that contain a complete monomeric unit of the potato spindle tuber viroid (pstvd) plus an additional repeat of a part of the circular rna genome. these permutated linear longer-than-unit-length pstvd rnas were incubated with the g-specific endoribonuclease rnase t1 which generated monomeric circular pstvd rna molecules that were infectious when mechanically inoculated to tomato plants. besides the correct monomeric ... | 1992 | 1381536 |
| coat protein properties suggest that azuki bean mosaic virus, blackeye cowpea mosaic virus, peanut stripe virus, and three isolates from soybean are all strains of the same potyvirus. | the interrelationship of a number of potyviruses infecting legumes has been investigated by comparing molecular properties of their coat proteins. comparison of the coat proteins by the techniques of amino acid analysis and page was inadequate to distinguish strains from distinct potyviruses. however, high-performance liquid chromatographic peptide profiles of tryptic digests of coat proteins of these legume-infecting potyviruses enabled such assignments to be made. these data indicate that amin ... | 1992 | 1500273 |
| analysis of the virulence modulating region of potato spindle tuber viroid (pstvd) by site-directed mutagenesis. | a series of nucleotide substitutions (g46----c; c47----a; c315----u; u317----c) were introduced into the virulence modulating region of the intermediate strain of potato spindle tuber viroid (pstvd) in order to examine their effect upon viroid infectivity and pathogenicity with the presence of all four mutations resulting in the sequence of a previously reported severe strain of pstvd. eight of the resulting mutant cdnas were characterized for infectivity and symptom induction in tomato, and the ... | 1992 | 1546460 |
| a method combining immunocapture and pcr amplification in a microtiter plate for the detection of plant viruses and subviral pathogens. | a method for the detection of rna viral and subviral plant pathogens was developed that combines pathogen partial purification by solid-phase adsorbed antibodies, reverse transcriptional-polymerase chain reaction (rt-pcr) and quantitation of the amplified products by fluorescence. the reverse transcription of the rna is performed directly on the retained material without any previous thermal or chemical disruption of the virus particles. the whole procedure can be carried out in a microtiter pla ... | 1993 | 8113346 |
| primary and secondary structure of a 360-nucleotide isolate of potato spindle tuber viroid. | full-length complementary dnas (cdna) of a mild (kf5) and a severe (s-pstvd) isolate of potato spindle tuber viroid (pstvd) were constructed. dna sequencing of four kf5 cdna clones (m3, m4, m5, and m7) revealed that kf5 is comprised of 360 nucleotides. by comparison, all three cdna clones (s2, s9, and s10) of s-pstvd possess 359 nucleotides. sequence microheterogeneity was observed among the kf5 cdna clones. clone m5 differs from mild pstvd isolate kf6 by a u-to-a transversion at position 303 fo ... | 1993 | 8435045 |
| mechanism of viroid pathogenesis: differential activation of the interferon-induced, double-stranded rna-activated, m(r) 68,000 protein kinase by viroid strains of varying pathogenicity. | purified potato spindle tuber viroid (pstvd) was added to an in vitro assay system containing purified interferon-induced, dsrna-activated protein kinase (p68). viroid rna activated (phosphorylated) the enzyme, although with less efficiency than did the synthetic, perfectly matched poly i-poly c. in binding experiments, rna transcripts of the intermediate strain of pstvd were shown to specifically bind to a p68-antibody complex. activation of the enzyme by a strain of pstvd that results in sever ... | 1993 | 7505621 |
| rna-directed rna polymerase from tomato leaves. i. purification and physical properties. | an rna-directed rna polymerase (rdrp, ec 2.7.7.48) from tomato leaf tissue was purified to electrophoretic homogeneity. a terminal transferase activity that was found to cofractionate with rdrp from deae-sepharose and dna-cellulose columns was removed by chromatography on a mono q column. the highly purified rdrp exhibits a specific activity of 500 nmol x mg-1 x 30 min-1, which corresponds to a 100,000-fold enrichment of the enzyme. in buffer containing 50% glycerol, its activity decreased by ab ... | 1993 | 7685022 |
| cloning of the capsid protein gene from a blotch isolate of peanut stripe virus. | the 3' terminal 1,367 nucleotides (nts) of a blotch isolate of the potyvirus, peanut stripe virus (pstv), were cloned and sequenced. this region included the 861 nts (287 amino acids) of the pstv capsid protein (cp). the amino acid sequence of the predicted proteinase cleavage site was identified. this region shared limited homology with other potyvirus proteinase cleavage sites. the viral cp gene sequence was followed by 254 nucleotides of 3' nontranslated sequence and a poly-a tail. based on c ... | 1993 | 7916587 |
| [design of a universal biotin-containing oligonucleotide diagnostic kit for detecting viroid plant diseases]. | a non-radioactive diagnosticum for plant viroid diseases has been designed, based on hybridization of a biotin-labeled 26-member oligonucleotide probe with the viroid rna site identical for potato spindle tuber viroid and chrysanthemum stunt viroid. the biotin label has been introduced into the synthetic oligonucleotide probe by the high-yield acylation of the oligonucleotide aminoalkylamide with the biotin imidazolide or n-hydroxysuccinimide ester. hybridization techniques have been elaborated ... | 1993 | 8250981 |
| antisense dna inhibits infection of potato spindle tuber viroid. | the effect of oligodeoxyribonucleotides complementary to the region of the so-called pathogenicity domain (nucleotides 42-78) of the upper rna strand of potato spindle tuber viroid (pstvd) (severe) on viroid infection was investigated. the oligonucleotides were allowed to form hybrids with pstvd in the infection mixtures before inoculation. infectivity tests were performed using intact plants and plant protoplasts. it was found that the dna oligonucleotides caused significant reduction of viroid ... | 1993 | 8258371 |
| chemiluminescent detection of potato and pome fruit viroids by digoxigenin-labeled dot blot and tissue blot hybridization. | a chemiluminescent molecular hybridization protocol was compared to 32p autoradiography for detecting potato spindle tuber viroid (pstvd) and apple scar skin group viroids (assvd). labeled crna probes for pstvd and assvd were synthesized by sp6 rna polymerase transcription using digoxigenin-11-utp or alpha-[32p]utp. dot blot hybridization of purified viroids and sap extracts from infected plants showed that chemiluminescent detection using digoxigenin-labeled probes was as sensitive as autoradio ... | 1993 | 8366166 |
| multiple pathways of reversion in viroids for conservation of structural elements. | from site-directed mutagenesis of potato spindle tuber viroid (pstvd) it had been concluded earlier that the formation of a thermodynamically metastable structure containing hairpin ii (hp ii) is critical for infectivity. in order to differentiate between structural and sequence effects, in the present work base pairs in hp ii were exchanged by site-directed double mutations without significant alterations in the native rod-like structure of pstvd. the mutants were viable and genetically stable ... | 1993 | 8491201 |
| inhibition of potato spindle tuber viroid (pstvd) infection with dna oligonucleotides. | the effects of dna oligonucleotides complementary to potato spindle tuber viroid (pstvd) on viroid infection were investigated. the oligonucleotides were used to form hybrids with pstvd in the infection mixture. a 75% reduction of viroid infection was found when an oligonucleotide complementary to nucleotides 79-110 of pstvd was hybridized with pstvd at a molar ratio of approximately 5000:1, respectively. a total inhibition of pstvd infection was observed using an oligonucleotide complementary t ... | 1993 | 8504180 |
| photosynthetically active suspension cultures of potato spindle tuber viroid infected tomato cells as tools for studying viroid - host cell interaction. | photosynthetically active callus and cell suspension cultures were established from uninfected lycopersicon peruvianum plants and from uninfected and potato spindle tuber viroid (pstvd) infected plants of lycopersicon esculentum cv. rutgers. viroid infection was maintained in photoheterotrophic culture on media containing 3% sucrose, but during continuous photo-mixotrophic culture in low sucrose media (1% sucrose), the level of pstvd accumulation decreased. photoautotrophic cell suspensions coul ... | 1993 | 24201870 |
| rna-directed de novo methylation of genomic sequences in plants. | one monomeric and three oligomeric potato spindle tuber viroid (pstvd) cdna units were introduced into the tobacco genome via the agrobacterium-mediated leaf-disc transformation. southern analysis of the integrates revealed that only their pstvd-specific sequences become fully methylated, whereas the flanking t-dna and the genomic plant dna remain unaltered. viroid cdna methylation could only be observed after autonomous viroid rna-rna replication had taken place in these plants. these findings ... | 1994 | 8313476 |
| nucleotide sequence and genome organization of peanut stripe potyvirus. | a blotch isolate of peanut stripe virus (pstv) was cloned, sequenced and compared with other full-length potyvirus sequences. the viral genome was 10059 nucleotides (nt) in length excluding the poly(a) tail. two potential aug start codons were identified in the 5' non-translated region. analysis of in vitro translation products from transcripts containing the first 600 nt of the pstv genome indicated that the first aug (nt 134 to 136) was preferred over the second aug (nt 146 to 148) for initiat ... | 1994 | 8077957 |
| inhibition of viroid infection by antisense rna expression in transgenic plants. | complex formation between different antisense rnas directed against either plus-strand or minus-strand sequences of the potato spindle tuber viroid (pstvd) was studied using temperature-gradient gel electrophoresis and immunochemical detection with an antibody specific for double-stranded rna. short minus-strand sequences were directed against the upper central conserved region (uccr) of plus-strand viroid replication intermediates, a plus-strand corresponding to the left half of the rod-like se ... | 1994 | 7695839 |
| capsid protein properties of cowpea aphid-borne mosaic virus and blackeye cowpea mosaic virus confirm the existence of two major subgroups of aphid-transmitted, legume-infecting potyviruses. | a study of the capsid proteins of different legume-infecting potyviruses using specific monoclonal antibodies on immunoblots of crude extracts from infected plants revealed that cowpea aphid-borne mosaic virus (camv) and blackeye cowpea mosaic virus (bicmv) have coat protein m(r) values of 32k and 35k, respectively. immunoblot comparisons of bicmv, peanut stripe mosaic virus (pstv), bean common mosaic virus (bcmv) and azuki bean mosaic virus (azmv) revealed equal reactivity of their 35k coat pro ... | 1994 | 7996147 |
| analysis of the population structure of three phenotypically different pstvd isolates. | phenotypically dissimilar greenhouse isolates from a polish collection of potato spindle tuber viroid (pstvd) were analysed. partially purified pstvd genomic rnas from severe, intermediate and mild isolates was reverse transcribed and the resulting cdnas enzymatically amplified. abutting-primer pcr (ab-p pcr) technology was used to obtain, in a single step, infectious full-length pstvd cdna monomers and these were sequenced. the mild isolate was found to be composed of a unique molecular variant ... | 1994 | 7998831 |
| detection of avocado sunblotch viroid in chloroplasts of avocado leaves by in situ hybridization. | in situ hybridization experiments were carried out to detect avocado sunblotch viroid (asbvd) in foliar tissue of avocado, using a digoxigenin-labelled rna probe complementary to the asbvd-rna in sections of aldehyde-fixed, lrgold-embedded leaf samples. detection of the probe was made through anti-digoxigenin antibody and protein-a colloidal gold (20 nm). seventy to 80% of the signals came from chloroplast while the cytoplasm and vacuole were labelled with ca. 10% of the gold particles. this is ... | 1994 | 7998844 |
| cloning and sequence analysis of the coat protein genes of an australian strain of peanut mottle and an indonesian 'blotch' strain of peanut stripe potyviruses. | we have analysed the coat protein gene sequences of two potyviruses infecting peanut. the 3' terminal 1247 nucleotides (nt) of an australian strain of peanut mottle virus (pemov-au) and the 3' terminal 1388 nt of an indonesian 'blotch' strain of peanut stripe virus (pstv-ib) were cloned and sequenced. those regions included the 861 and 864 nt encoding the respective putative coat proteins as well as the 285 and 253 nt, respectively of 3' non-coding sequences. comparison of the nucleotide sequenc ... | 1994 | 7999143 |
| cowpea aphid borne mosaic virus-morocco and south african passiflora virus are strains of the same potyvirus. | high performance liquid chromatography (hplc) profiles of tryptic peptides and partial amino acid sequence analysis have been employed to establish the taxonomic status of the moroccan isolate of cowpea aphid-borne mosaic virus (cabmv). some previous reports have suggested cabmv to be very closely related to blackeye cowpea mosaic virus (b1cmv) while other reports have concluded that this relationship is distant. in this report a tryptic digest of the coat protein of cabmv-morocco was compared w ... | 1994 | 8002788 |
| replication of avocado sunblotch viroid: evidence for a symmetric pathway with two rolling circles and hammerhead ribozyme processing. | the structure of a series of rnas extracted from avocado infected by the 247-nt avocado sunblotch viroid (asbvd) was investigated. the identification of multistranded complexes containing circular asbvd rnas of (+) and (-) polarity suggests that replication of asbvd proceeds through a symmetric pathway with two rolling circles where these two circular rnas are the templates. this is in contrast to the replication of potato spindle tuber viroid and probably of most of its related viroids, which p ... | 1994 | 7809126 |
| multimeric non-radioactive crna probes improve detection of potato spindle tuber viroid (pstvd). | experimental data showed that multimeric, complementary rna (crna) probes, labelled with non-radioactive digoxigenin (dig), improved sensitivity of detection of the potato spindle tuber viroid (pstvd) rna by 2- to 30-fold as compared with corresponding multimeric cdna probes. the degree of pstvd detectability improvement depended upon the type of alkaline phosphatase substrate (colorimetric vs. chemiluminescent) used. use of hexameric dig-labelled crna probes in combination with chemiluminescent ... | 1994 | 7822462 |
| digoxigenin-labelled molecular probe for the simultaneous detection of three potato pathogens: potato spindle tuber viroid (pstvd), potato virus y (pvy), and potato leafroll virus (plrv). | a molecular probe, p3pot, was constructed of pstvd, pvy, plrv cdna fragments introduced into puc18 vector. sequencing of the inserts revealed that cloned fragments covered conservative parts of pathogenic genomes. dot-blot hybridization of digoxigenin-labelled construct to crude extracts from plants infected with different potato viruses proved high sensitivity and specificity of the p3pot probe. this makes p3pot probe an useful tool for the routine testing, and selection of virus-free potatoes. | 1994 | 7732766 |
| gel dependence of electrophoretic mobilities of double-stranded and viroid rna and estimation of the contour length of a viroid by gel electrophoresis. | double-stranded (ds) rna normally exhibits a lower electrophoretic mobility than dsdna having the same number of base pairs. this has been attributed to its net charge density that is lower than that of b-form dna. but we show here that dsrna runs faster than corresponding dna in gels containing either > or = 2.5% agarose or > or = 8% acrylamide with high crosslinking (19:1 acrylamide:n,n'-methylenebisacrylamide). however, the relative mobility of dsrna as compared with dna, extrapolated to 0% g ... | 1994 | 7720685 |
| agrobacterium-mediated inoculation of pstvd cdnas onto tomato reveals the biological effect of apparently lethal mutations. | potato spindle tuber viroid (pstvd) mutants which contain alterations in the terminal loops of the rod-like native structure have previously been reported from our laboratory. pstvd-p contains mutations at positions 2, 4, and 6 in the left terminal loop; pstvd-r+, a sequence permutation of pstvd-r, contains the same mutations at positions 177 and 178 in the right terminal loop as pstvd-r and contains in addition a 1-nucleotide g insertion at position 176. pstvd-p, pstvd-r, and pstv-r+ were nonin ... | 1994 | 7513926 |
| interdependence of pathogenicity and replicability with potato spindle tuber viroid. | after the unexpected appearance of lethal symptoms on tomato plants infected with the pstvd strain intermediate di, viroids were isolated and sequenced. it was found that a new strain, named rg 1, had been generated spontaneously in our greenhouse. in a different series of plant passages two new strains, named qf a and qf b, were detected which coexisted with the wild-type strain di. strains qf a and qf b showed intermediate symptoms when inoculated separately. in order to confirm the working hy ... | 1995 | 7747485 |
| nucleotide sequence of a hop stunt viroid variant isolated from citrus growing in taiwan. | the 303 nucleotide sequence of hsvd-citrus(t), a hop stunt viroid (hsvd) variant present in etrog citron growing in taiwan, was determined from cdnas amplified by the polymerase chain reaction. hsvd-citrus(t) is very similar to several hsvd isolates previously recovered from citrus or cucumber, and exhibits microsequence heterogeneity at positions 154 and 181. phylogenetic analysis using maximum parsimony grouped hsvd-citrus(t) with seven other isolates from citrus and cucumber in a large cluste ... | 1995 | 7732666 |
| suppression of potato spindle tuber viroid replication and symptom expression by mutations which stabilize the pathogenicity domain. | nucleotides within the pathogenicity domain of potato spindle tuber viroid (pstvd) are known to play an important role in regulating symptom expression, but the underlying molecular mechanism is unknown. in order to determine more precisely how structural features within the pathogenicity domain regulate symptom expression, we have characterized a series of mutations that progressively stabilize premelting region 1 and the rest of the "virulence modulating" region. the structural effects of thes ... | 1995 | 7747427 |
| only one of four possible secondary structures of the central conserved region of potato spindle tuber viroid is a substrate for processing in a potato nuclear extract. | the influence of rna secondary structure on the substrate activity of a longer-than-unit length transcript for processing to circular viroids was studied in a nuclear extract from potato suspension cells. the nuclear extract was prepared according to a modified procedure for a plant transcription extract. the transcript of the potato spindle tuber viroid (pstvd) consists of a monomeric molecule with 17 additional nucleotides, thus doubling most of the central conserved region of viroids of the p ... | 1995 | 7501442 |
| role of the variable domain in modulating potato spindle tuber viroid replication. | potato spindle tuber viroid (pstvd) is believed to undergo a series of specific structural transitions during replication. the variable domain of pstvd is known to contain sequences that are important for replication/accumulation as well as one of three "premelting regions" which control breakdown of the native structure in vitro. we have examined the structural and biological effects of five single and two double nucleotide substitutions within premelting region 3 in an effort to isolate temper ... | 1996 | 8623553 |
| the cdna sequence and infectious transcripts of peanut stripe virus. | a full-length cdna clone of the blotch isolate of the peanut stripe potyvirus (pstv) rna genome was constructed downstream from the bacteriophage sp6 rna polymerase promoter. the full-length pstv cdna clone (pstvsf9) was sequenced and compared to the previously published sequence of pstv-b. in vitro-synthesized pstv transcripts capped with m7gpppg were infectious in nicotiana benthamiana plants, and the progeny virus was aphid transmissible. to confirm the origin of infection, a mutant pstv (pst ... | 1996 | 8666291 |
| description of rna folding by "simulated annealing". | an algorithm is proposed which describes the thermodynamically as well as the kinetically controlled folding process of rna. the algorithm, based on a special monte carlo procedure known as "simulated annealing", takes into account the probabilities for opening and closing of single base-pairs. thus, the algorithm is able to reach structures and structure distributions near the global minimum of structure space, and is not restricted by the tendency to halt in local minima. three types of struct ... | 1996 | 8568872 |
| mexican papita viroid: putative ancestor of crop viroids. | the potato spindle tuber disease was first observed early in the 20th century in the northeastern united states and shown, in 1971, to be incited by a viroid, potato spindle tuber viroid (pstvd). no wild-plant pstvd reservoirs have been identified; thus, the initial source of pstvd infecting potatoes has remained a mystery. several variants of a novel viroid, designated mexican papita viroid (mpvd), have now been isolated from solanum cardiophyllum lindl. (papita güera, cimantli) plants growing ... | 1996 | 8790341 |
| identification and molecular properties of a 306 nucleotide viroid associated with apple dimple fruit disease. | a new viroid associated with an apple fruit disorder similar to, but more severe than, the dapple apple disease induced in some varieties by apple scar skin viroid (assvd) has been found. the new viroid, tentatively termed apple dimple fruit viroid (adfvd), is a circular rna of 306 nucleotides which adopts a quasi-rod-like conformation of minimum free energy. it contains the core nucleotides of the central conserved region (ccr) of the assvd group as well as the terminal conserved region (tcr) p ... | 1996 | 8922478 |
| a single nucleotide substitution converts potato spindle tuber viroid (pstvd) from a noninfectious to an infectious rna for nicotiana tabacum. | mechanical inoculation of nicotiana tabacum with the pstvd isolate kf 440-2 from the host plant tomato resulted in the de novo emergence, replication, and accumulation of a new "tobacco variant," designated pstvd nt. it produces no symptoms in tobacco but, like pstv kf 440-2, severe ones in tomato. the sequence analysis of pstvd nt revealed a single nucleotide substitution from c-->u at position 259. autonomous viroid replication was also induced in tobacco by genomic integration of oligomeric c ... | 1996 | 8955038 |
| rna structural features responsible for potato spindle tuber viroid pathogenicity. | the native structure of potato spindle tuber viroid (pstvd) contains a series of short double helices and small internal loops that are organized into five structural domains. nucleotides within the pathogenicity domain are known to play a critical role in modulating pstvd symptom expression, and it has been suggested that disruption of a comparatively unstable "premelting region" within the pathogenicity domain may be required for disease induction. we have used a combination of quantitative bi ... | 1996 | 8806495 |
| a viroid from solanum pseudocapsicum closely related to the tomato apical stunt viroid. | a viroid was isolated from symptomless solanum pseudocapsicum cultivar (cv) 'new patterson' plants using the bidirectional page method for analysis of small circular rna molecules. the viroid was transmitted to tomato by mechanical inoculation. infected tomato plants developed symptoms similar to those caused by potato spindle tuber viroid (pstvd). cloning and sequencing revealed that the viroid from solanum pseudocapsicum is closely related to the tomato apical stunt viroid (tasvd). therefore, ... | 1996 | 8856021 |
| secondary structure probing of potato spindle tuber viroid (pstvd) and sequence comparison with other small pathogenic rna replicons provides evidence for central non-canonical base-pairs, large a-rich loops, and a terminal branch. | using pcr and in vitro transcription, linear (non-circular) unit-length (+)strand rna molecules of a lethal pstvd variant were produced which are able to initiate typical disease symptoms when inoculated into tomato. non-denaturing gel electrophoresis shows that these transcripts can adopt the same two conformations as circular pstvd molecules, namely a fast migrating rod-like and a slowly migrating cruciform structure. the rod-like conformer of two end-labelled transcripts was probed with nucle ... | 1996 | 8876645 |
| the molecular structure of iresine viroid, a new viroid species from iresine herbstii ('beefsteak plant'). | a viroid was isolated from iresine herbstii plants using the bidirectional page method for analysis of small circular rna molecules. the viroid was transmitted to viroid-free iresine herbstii plants of the cultivar 'aureoreticulata' by mechanical inoculation. infected plants did not develop any symptoms. the new viroid species has been named iresine viroid (irvd). it is a member of the potato spindle tuber viroid group and consists of 370 nucleotides, 227 g+c, 143 a+u (gc content, 61.4%). the mo ... | 1996 | 8887500 |
| a viroid from brunfelsia undulata closely related to the columnea latent viroid. | a viroid was isolated from symptomless brunfelsia undulata plants using the bidirectional page method for analysis of small circular rna molecules. the viroid was transmitted to tomato by mechanical inoculation. infected tomato plants developed symptoms similar to those caused by intermediate strains of potato spindle tuber viroid (pstvd). cloning and sequencing revealed that the viroid from brunfelsia undulata is closely related to the columnea latent viroid (clvd). therefore, the new viroid se ... | 1996 | 8920818 |
| classification of rna secondary structures using the techniques of cluster analysis. | an rna molecule has a lot of suboptimal secondary structures. some of these suboptimal structures are very similar and some are entirely different. in some cases, the free energy of these suboptimal structures does not differ much from that of the optimal structure. in order to characterize this relationship more clearly, we defined a metric among the secondary structures by the unweighted pair group method, using the arithmetic average and extended this metric to the sets of secondary structure ... | 1996 | 8959113 |
| use of intramolecular chimeras to map molecular determinants of symptom severity of potato spindle tuber viroid (pstvd). | nucleotide sequence comparison shows that sequence variations are mostly clustered in the p (pathogenicity) and v (variable) domains of the potato spindle tuber viroid (pstvd) molecule. although these comparisons suggest the p domain as the primary determinant of pstvd symptom severity, the potential contribution of the v domain has never been analysed in detail. to investigate the relationship between the structure of these domains and pathogenicity, six intraspecific chimeric pstvd variants we ... | 1996 | 8973522 |
| the genetic stability of potato spindle tuber viroid (pstvd) molecular variants. | rna viruses propagate as a population of genetically related entities composing a quasi-species. specific representatives are the result of both a high mutation rate during replication and competition between the continuously arising sequence variants. similar to other rna pathogens, potato spindle tuber viroid (pstvd) propagates as a population of similar but nonidentical sequences. the sequence of progeny molecules derived from cloned molecular variants of pstvd were studied after one and six ... | 1997 | 8990400 |
| destabilization of potato spindle tuber viroid by mutations in the left terminal loop. | infectivity studies with highly infectious rna inocula generated by ribozyme cleavage were used to compare the biological properties of three apparently nonviable mutants of potato spindle tuber viroid (pstvd). one of these mutants (pstvd-p) contains three nucleotide substitutions in the left terminal loop, and mechanical inoculation of tomato seedlings with rna transcripts at levels equivalent to 10(3)-10(5) times the id50 for pstvd-intermediate failed to result in systemic infection. viable pr ... | 1997 | 9191908 |
| evidence for heterologous encapsidation of potato spindle tuber viroid in particles of potato leafroll virus. | the aphid myzus persicae (sulz.) was shown to transmit potato spindle tuber viroid (pstvd) to potato clone dto-33 from source plants doubly infected with potato leafroll virus (plrv) and pstvd. transmission was of the persistent type and did not occur when the insects were allowed to feed on singly infected plants. only low levels of pstvd were associated with purified plrv virions, but its resistance to digestion with micrococcal nuclease indicates that the viroid rna is encapsidated within the ... | 1997 | 9191909 |
| detection and tissue distribution of potato spindle tuber viroid in infected tomato plants by tissue print hybridization. | potato spindle tuber viroid (pstvd) was detected in two cultivars of tomato (lycopersicon esculentum mill.) by tissue print hybridization of cross-sections of stem and rhachis, using a 35s-labeled pstvd rna probe. pstvd was detectable in the viroid-sensitive and symptom-developing cv "rutgers" 2 weeks p.i., and in the viroid-tolerant and practically symptomless cv "goldkugel" 3 weeks p.i. in both tomato cultivars, pstvd accumulated in the upper parts of the plants newly grown after inoculation. ... | 1997 | 9267443 |
| viroid processing: switch from cleavage to ligation is driven by a change from a tetraloop to a loop e conformation. | a longer-than-unit-length transcript of potato spindle tuber viroid is correctly processed in a potato nuclear extract only if the central conserved region is folded into a multi-helix junction containing at least one gnra tetraloop-hairpin. the cleavage-ligation site between g95 and g96 was mapped with s1 nuclease and primer extension. the structural motifs involved in the processing mechanism were analysed by uv crosslinking, chemical mapping, phylogenetic comparison and thermodynamic calculat ... | 1997 | 9034342 |
| ribozyme-mediated high resistance against potato spindle tuber viroid in transgenic potatoes. | a hammerhead ribozyme [r(-)] targeting the minus strand rna of potato spindle tuber viroid (pstvd) and a mutated nonfunctional ribozyme [mr(-)] were designed, cloned, and transcribed. as predicted, both monomer and dimer transcripts of the active r(-) ribozyme gene could cleave the pstvd minus strand dimer rna into three fragments of 77, 338, and 359 bases in vitro at 25 and 50 degrees c. the tandem dimer genes of r(-) and mr(-) were subcloned separately into the plant expression vector prok2. t ... | 1997 | 9144155 |
| transgenic potato expressing a double-stranded rna-specific ribonuclease is resistant to potato spindle tuber viroid. | we have produced transgenic potato lines expressing the yeast-derived double-stranded rna-specific ribonuclease pac1. five lines of pac1 potato (solanum tuberosum l., cultivar russet burbank) challenged with potato spindle tuber viroid (pstvd) suppressed pstvd infection and accumulation. all of the progeny potato tubers produced by resistant plants were also free of pstvd. because the pac1 gene product digested pstvd in vitro, double-stranded regions in pstvd molecule and/or replicative intermed ... | 1997 | 9359114 |
| cell-to-cell movement of potato spindle tuber viroid. | viroids are non-translatable, autonomously replicating circular rnas that infect only plants. an important component of the viroid infection process is cell-to-cell movement; however, there is virtually no information available about the pathways and mechanisms of this process. in this study, potato spindle tuber viroid (pstvd) has been used as a model system to investigate the mechanism of viroid cell-to-cell transport. infectious rna transcripts were produced from pstvd cdna clones in vitro, l ... | 1997 | 9375403 |
| precisely full length, circularizable, complementary rna: an infectious form of potato spindle tuber viroid. | the replication of many viral and subviral pathogens as well as the amplification of certain cellular genes proceeds via a rolling circle mechanism. for potato spindle tuber (pstvd) and related viroids, the possible role of a circular (-)strand rna as a template for synthesis of (+)strand progeny is unclear. infected plants appear to contain only multimeric linear (-)strand rnas, and attempts to initiate infection with multimeric (-)pstvd rnas generally have failed. to examine critically the inf ... | 1998 | 9601006 |
| a mixture of synthetic oligonucleotide probes labeled with biotin for the sensitive detection of potato spindle tuber viroid. | five kinds of synthetic oligonucleotide probes labeled with biotin (bio) were designed for the detection of potato spindle tuber viroid (pstvd), and their sensitivities were compared with that of a digoxigenin (dig)- or bio-labeled cdna probe. although each oligonucleotide probe alone was less sensitive than the dig-cdna probe, sensitivity was increased by using a mixture of two or all of the five oligonucleotide probes. the sensitivity of a psmix1-5 probe, which was a mixture of five oligonucle ... | 1998 | 9626955 |
| specific rna self-cleavage in coconut cadang cadang viroid: potential for a role in rolling circle replication. | the rolling circle replication of the small, single-stranded viroid rnas requires a specific processing reaction to produce monomeric rnas that are ligated into the final circular form. for avocado sunblotch viroid, peach latent mosaic viroid, and chrysanthemum chlorotic mottle viroid, the hammerhead self-cleavage reaction is considered to provide this processing reaction. we have searched for a similar type of reaction in the 246-nt coconut cadang cadang viroid, the smallest viroid of the 24-me ... | 1998 | 9630248 |
| the dimerization domain of potato spindle tuber viroid, a possible hallmark for infectious rna. | covalently closed circular (+) rna of the potato spindle tuber viroid (pstvd) can efficiently dimerize noncovalently upon heating and slow cooling in the presence of monovalent cations or mg2+. in vitro transcription of subgenomic fragments reveals that the ability to dimerize resides in the "upper strand" of its self-complementary rod-like structure. nuclease probing of these fragments, namely, molecules spanning either the upper or the lower strand of pstvd, confirms the existence of the previ ... | 1998 | 9760245 |
| correlation between bending of the vm region and pathogenicity of different potato spindle tuber viroid strains. | only 40 of the 359 nucleotides of potato spindle tuber viroid (pstvd) represent the virulence-modulating (vm) region. minor sequence variations in this domain distinguish mild from severe and even necrotic strains. our recent hypothesis (owens ra et al., 1996, virology 222:144-158) that these differences result in varying degrees of bending of this part of the molecule could be tested experimentally. by in vitro transcription and partial double-strand formation, three types of model rnas were pr ... | 1998 | 9769103 |
| sequences of the coat protein gene of five peanut stripe virus (pstv) strains from thailand and their evolutionary relationship with other bean common mosaic virus sequences. | the coat protein gene and part of the 3' non-coding region of five strains of peanut stripe virus (pstv) from thailand have been cloned and sequenced. phylogenetic comparisons of these strains, known as t1, t3, t5, t6 and t7, and related sequences showed that these strains are indeed strains of pstv. further, pstv strains appear to be related to each other according to their geographic origin. that is, the thai strains are more closely related to each other than they are to strains from the usa ... | 1998 | 9787652 |
| potyvirus aphid transmission requires helper component and homologous coat protein for maximal efficiency. | aphid transmission of potyviruses depends on the presence of specific sequence domains in two virus encoded proteins, the coat protein (cp) and helper component-proteinase (hc-pro). aphid transmissable peanut stripe virus (pstv), like most potyviruses, has an asp-ala-gly (dag) motif in the amino-terminal part of the cp. peanut mottle virus (pemov) was determined to be highly aphid transmissible but has a unique asp-ala-ala-ala (daaa) motif. to determine if the daaa motif could functionally repla ... | 1998 | 9856099 |
| a simple, rapid method of nucleic acid extraction without tissue homogenization for detecting viroids by hybridization and rt-pcr. | a simple, rapid method of nucleic acid extraction on a microcentrifuge tube scale for detecting viroids is presented. five distinct citrus viroids (cvds), chrysanthemum stunt viroid (csvd), hop stunt viroid (hsvd), hop latent viroid (hlvd) and potato spindle tuber viroid (pstvd) were detected in their natural host plants by hybridization using crna probes and reverse transcription-polymerase chain reaction (rt-pcr). nucleic acids (na) were liberated from tissues by incubation in a buffer contain ... | 1999 | 10029324 |
| heavy de novo methylation at symmetrical and non-symmetrical sites is a hallmark of rna-directed dna methylation. | previous analysis of potato spindle tuber viroid (pstvd) rna-infected tobacco plants has suggested that an rna-dna interaction could trigger de novo methylation of pstvd transgene sequences. using the genomic sequencing technique, the methylation pattern associated with the rna-directed dna methylation process has been characterized. three different pstvd transgene constructs all showed a similar pattern of methylation. most of the cytosines at symmetrical as well as non-symmetrical positions ap ... | 1999 | 10075993 |
| rapid generation of genetic heterogeneity in progenies from individual cdna clones of peach latent mosaic viroid in its natural host. | viroids, small single-stranded circular rnas endowed with autonomous replication, are unique systems to conduct evolutionary studies of complete rna genomes. the primary structure of 36 progeny variants of peach latent mosaic viroid (plmvd), evolved from inoculations of the peach indicator gf-305 with four individual plmvd cdnas differing in their pathogenicity, has been determined. most progeny variants had unique sequences, revealing that the extremely heterogeneous character of plmvd natural ... | 1999 | 10466824 |
| sensitive detection of potato spindle tuber and temperate fruit tree viroids by reverse transcription-polymerase chain reaction-probe capture hybridization. | a rapid and sensitive assay for the specific detection of plant viroids using reverse transcription-polymerase chain reaction (rt-pcr) -probe capture hybridization (rt-pcr-enzyme-linked immunosorbent assay (elisa)) was developed. the assay was applied successfully for the detection of potato spindle tuber viroid, peach latent mosaic viroid, or apple scar skin viroid from viroid infected leaf tissue. clarified sap extract from infected leaf tissue was treated first with genereleaser polymeric mat ... | 1999 | 10471024 |
| rna movies: visualizing rna secondary structure spaces. | rna movies is a system for the visualization of rna secondary structure spaces. its input is a script consisting of primary and secondary structure information. from this script, the system fully automatically generates animated graphical structure representations. in this way, it creates the impression of an rna molecule exploring its own two-dimensional structure space. | 1999 | 10068690 |
| formation of metastable rna structures by sequential folding during transcription: time-resolved structural analysis of potato spindle tuber viroid (-)-stranded rna by temperature-gradient gel electrophoresis. | a model of functional elements critical for replication and infectivity of the potato spindle tuber viroid (pstvd) was proposed earlier: a thermodynamically metastable structure containing a specific hairpin (hp ii) in the (-)-strand replication intermediate is essential for template activity during (+)-strand synthesis. we present here a detailed kinetic analysis on how pstvd (-)-strands fold during synthesis by sequential folding into a variety of metastable structures that rearrange only slow ... | 1999 | 10199573 |
| tomato chlorotic dwarf viroid: an evolutionary link in the origin of pospiviroids. | over 40 isolates of potato spindle tuber viroid (pstvd) have been reported from potato, other solanum species and greenhouse tomato. these isolates have sequence similarities in the range 95-99%. a viroid which caused chlorotic leaves and severe dwarfing of plants in greenhouse tomato crops was detected. the viroid was found to hybridize readily with pstvd probes. it migrated faster than pstvd in return-polyacrylamide gel electrophoresis and was not amplified in rt-pcr by a primer pair based on ... | 1999 | 10580043 |
| a dna target of 30 bp is sufficient for rna-directed dna methylation. | in higher plants, rna-dna interactions can trigger de novo methylation of genomic sequences via a process that is termed rna-directed dna methylation (rddm). in potato spindle tuber viroid (pstvd)-infected tobacco plants, this process can potentially lead to methylation of all c residues at symmetrical and nonsymmetrical sites within chromosomal inserts that consist of multimers of the 359-bp-long pstvd cdna. using pstvd cdna subfragments, we found that genomic targets with as few as 30 nt of se ... | 2000 | 10668798 |
| characterization of a tomato protein kinase gene induced by infection by potato spindle tuber viroid. | viroids--covalently closed, circular rna molecules in the size range of 250 to 450 nucleotides-are the smallest known infectious agents and cause a number of diseases of crop plants. viroids do not encode proteins and replicate within the nucleus without a helper virus. in many cases, viroid infection results in symptoms of stunting, epinasty, and vein clearing. in our study of the molecular basis of the response of tomato cv. rutgers to infection by potato spindle tuber viroid (pstvd), we have ... | 2000 | 10975647 |
| the variability of hop latent viroid as induced upon heat treatment. | we have previously shown that heat treatment of hop plants infected by hop latent viroid (hlvd) reduces viroid levels. here we investigate whether such heat treatment leads to the accumulation of sequence variability in hlvd. we observed a negligible level of mutated variants in hlvd under standard cultivation conditions. in contrast, the heat treatment of hop led to hlvd degradation and, simultaneously, to a significant increase in sequence variations, as judged from temperature gradient-gel el ... | 2001 | 11531412 |
| a novel usage of random primers for multiplex rt-pcr detection of virus and viroid in aphids, leaves, and tubers. | a multiplex reverse transcription polymerase chain reaction (m-rt-pcr) was developed for the simultaneous detection of five potato viruses and a viroid. the synthesis of cdnas used for amplification was primed by hexanucleotides (random primers, rp). an rna extraction procedure employing dnase i, is routinely used to isolate potato viruses and viroid (potato virus s, pvs; potato leafroll virus, plrv; potato virus x, pvx; potato virus a and y, pva, pvy; and potato spindle tuber viroid, pstvd) fro ... | 2001 | 11164484 |
| use of a vector based on potato virus x in a whole plant assay to demonstrate nuclear targeting of potato spindle tuber viroid. | potato spindle tuber viroid (pstvd) is a covalently closed circular rna molecule of 359 nucleotides that replicates within the nucleus of host cells. to determine how this small, highly structured rna enters the nucleus, we have developed a virus-based, whole plant in vivo assay that uses green fluorescent protein (gfp) as the reporter molecule. the coding region of gfp was interrupted by insertion of an intron derived from the intervening sequence 2 of the potato st-ls1 gene. a cdna copy of the ... | 2001 | 11369895 |
| replicating potato spindle tuber viroid rna is accompanied by short rna fragments that are characteristic of post-transcriptional gene silencing. | the low molecular weight fraction of tomato plants inoculated with potato spindle tuber viroid (pstvd) contains a population of short pstvd-specific rnas of either polarity. the main constituents were rnas of 22 and 23 nt representing different domains of the viroid genome. the occurrence of such distinct rna species indicated that the nuclear replicating pstvd rna induces post-transcriptional gene silencing. the short rnas were slightly more abundant at 30 days post-inoculation than at later st ... | 2001 | 11376158 |