Original reverse transcription polymerase chain reaction method to obtain the full-length cDNA of rice tungro spherical virus

A two-step reverse transcription reaction combined with long PCR was developed in order to obtain the full-length cDNA from the 12.2 kbp genomic RNA of rice tungro spherical virus. A first step reverse transcription, performed at 45 degrees C using a reverse transcriptase deprived of RNase H activity, allowed the synthesis of a nearly full-length cDNA of 11.7 kbp. A second step reaction, carried out at 65 degrees C using a thermostable polymerase, was necessary to destabilise secondary structures present at the 5' extremity of the RNA template which hampered the reverse transcription reaction in this region. The full-length cDNA obtained by the two-step reverse transcription was amplified successfully by long PCR and subsequently cloned into a plasmid vector. The cloned cDNA showed toxicity and proved to be unstable when amplified in E. coli.

Detection of episomal banana streak badnavirus by IC-PCR

A polymerase chain reaction (PCR) based strategy to detect episomal banana streak badnavirus (BSV) in banana and plantain plants that carry integrated BSV sequences was developed. Antisera used in immuno-capture polymerase chain reaction (IC-PCR) are capable of binding a large number of BSV serotypes. The primers used for PCR are capable of annealing to and amplifying across the aspartic protease-reverse transcriptase domain boundaries of both episomal and integrated BSV sequences and result in similar or identical sequence size fragments from either template. However, we show that under the conditions selected for IC-PCR, nuclear, mitochondrial or chloroplast genomic sequences are not amplified and thus only captured episomal BSV is amplified. IC-PCR is suitable for the large-scale screening of Musa for episomal BSV which is necessary for germplasm movement.

Evidence that badnavirus infection in Musa can originate from integrated pararetroviral sequences

When some virus- and disease-free Musa spp. (banana and plantain) are propagated by tissue culture, the resulting plants develop infections with banana streak badnavirus (BSV), a pararetrovirus. In sharp contrast to the virion DNA recovered from natural infections, the virion DNA from tissue culture-associated infections of different Musa spp. was highly similar if not identical. Although BSV does not employ integration during the infection cycle, BSV DNA was found to be integrated into the Musa genome. While one integration consisted of a partial BSV genome, a second contained more than one complete genome that was almost identical to BSV recovered from tissue culture-derived plants. The arrangement of this integrated BSV DNA suggests that it can yield an infectious episomal genome via homologous recombination. This report documents the first instance of integrated DNA of a nonintegrating virus giving rise to an episomal viral infection and identifies tissue culture as a possible trigger for the infection, raising the question of whether similar activatable viral sequences exist in the genomes of other plants and animals.

Integration of banana streak badnavirus into the Musa genome: molecular and cytogenetic evidence

Breeding and tissue culture of certain cultivars of bananas (Musa) have led to high levels of banana streak badnavirus (BSV) infection in progeny from symptomless parents. BSV DNA hybridized to genomic DNA of one such parent, Obino l'Ewai, suggesting integration of viral sequences. Sequencing of clones of Obino l'Ewai genomic DNA revealed an interface between BSV and Musa sequences and a complex BSV integrant. In situ hybridization revealed two different BSV sequence locations in Obino l'Ewai chromosomes and a complex arrangement of BSV and Musa sequences was shown by probing stretched DNA fibers. This is the first report of integrated sequences that possibly lead to a plant pararetrovirus episomal infection by a mechanism differing markedly from animal retroviral systems.

Cloning and sequence analysis of banana streak virus DNA

Banana streak virus (BSV), a member of the Badnavirus group of plant viruses, causes severe problems in banana cultivation, reducing fruit yield and restricting plant breeding and the movement of germplasm. Current detection methods are relatively insensitive. In order to develop a PCR-based diagnostic method that is both reliable and sensitive, the genome of a Nigerian isolate of BSV has been sequenced and shown to comprise 7389 bp and to be organized in a manner characteristic of badnaviruses. Comparison of this sequence with those of other badnaviruses showed that BSV is a distinct virus. PCR with primers based on sequence data indicated that BSV sequences are present in the banana genome.

[Cloning and sequencing analysis of rice stripe virus genome segment 4 of Chinese isolate Y]

The cDNA fragment covering full-length sequence of RStV RNA4 of Yunnan isolate in China was obtained by RT-PCR. The PCR-derived fragment was then cloned into vector pCRII. The cloned cDNA was sequenced. Comparison of the nucleotide and deduced amino acid sequences with those of the Japanese isolate T was made. The results showed that at the nucleotides level, vORF, vcORF and the intergenic region had 94.9%, 94.1% and 86.1% identity respectively, the 5'-untranslational region was exactly the same as that of Japanese isolate T, while the 3'-terminal sequence had 96.1% identity, differing by two nucleotides; at the amino acid level, vORF and vcORF had 99.4% and 98.3% identity respectively. Therefore, as well as being exactly the same size for the two isolates, the amino acid sequences of the coding regions and the 5'- and 3'-terminal sequences were well conserved. Our results indicated that the Chinese isolate is closely related to the Japanese isolate T.

Mechanisms of protection induced by attenuated simian immunodeficiency virus. II. Lymphocyte depletion does not abrogate protection

To determine the role that cellular immune responses play in the protection conferred by vaccination with attenuated SIVmac32H (pC8), we have attempted to deplete macaques of their CD8+ cells prior to challenge with wild-type SIVmac32H (pJ5). In two of four pC8-infected macaques, N109 and N112, a transient partial depletion of CD8+ cells by antibody treatment was achieved. On the day of challenge peripheral CD2+CD4-CD8+ cell counts were reduced by 92 and 95%, respectively, in animals N109 and N112 and their lymph nodes revealed a 46 and 58% reduction, respectively, in CD2+CD4-CD8+ cells. Two other pC8-immunized macaques, N110 and N111, treated in the same way, did not show significant depletion of CD8+ cells. None of these four pC8-immunized animals became infected when challenged with 50 MID50 of pJ5. Treatment of a further four pC8-infected and protected macaques and two naive control animals with Campath-1H antibody successfully depleted peripheral CD3+ cell counts by >99% in all treated animals. Campath-1H depletion resulted in enhanced, longer lasting lymphoid depletion. Yet subsequent challenge with 20 MID50 of pJ5 still failed to infect the pC8-immunized animals. All eight of the naive controls, including two Campath-1H-treated animals, became infected following challenge. In summary, partial depletion of circulating CD8+ cells or total lymphocytes prior to challenge failed to abrogate the protection conferred by vaccination with pC8.

Variation in coat protein genes among five geographically different isolates of rice tungro spherical virus

The variation in the sequence of the coat protein genes of four isolates of rice tungro spherical virus from different countries, Malaysia, Thailand, India and Bangladesh, was compared with an isolate from the Philippines. The evidence from RT-PCR, Southern blot hybridization and sequences of the coat protein genes indicated that the isolates appeared to fall into two groups. One comprised the Philippine and Malaysian isolates (about 95% sequence similarity) and the other the Bangladeshi and Indian isolates, the sequences of which differed by about 15% from that of the Philippine isolate. The Thai isolate seemed to be a mixture of these two subgroups.

Rice tungro spherical virus polyprotein processing: identification of a virus-encoded protease and mutational analysis of putative cleavage sites

Rice tungro spherical virus encodes a large polyprotein containing motifs with sequence similarity to viral serine-like proteases and RNA polymerases. Polyclonal antisera raised against domains of the putative protease and polymerase in fusion with glutathione S-transferase detected a protein of about 35 kDa and, in very low amounts, a protein of about 70 kDa, respectively, in extracts from infected plants. In in vitro transcription/translation systems and in Escherichia coli we demonstrated a proteolytic activity in the C-terminal region of the polyprotein. This protease rapidly cleaved its polyprotein precursors in vitro. Mutating a potential cleavage site located N-terminal to the protease domain, Gln2526-Asp2527, diminished processing. The transversion mutation at the putative C-terminal cleavage site of the protease, at Gln2852-Ala2853, led to a delayed and partial processing.

In Situ Studies of the Interaction of Dislocations with Point Defects during Annealing of Ion Implanted Si/SiGe/Si (001) Heterostructures

: Strained layer heterostructures provide ideal systems with which to study the dynamics of dislocation motion via in situ transmission electron microscopy, as the geometry, strain state, and kinetics can be characterized and directly controlled. We discuss how these structures are used to study dislocation-point defect interactions, emphasizing the experimental requirements necessary for quantification of dislocation motion. Following ion implantation, different concentrations and types of point defects are introduced within the SiGe epilayer depending on the implantation species, energy, and current density. By annealing samples in situ in the transmission electron microscope (TEM) following implantation, we can directly observe dislocation motion and quantify the effect of dislocation-point defect interactions on dislocation velocities. We find that dislocation motion is impeded if the implantation dose peak lies within the epilayer, as dislocations pin at point defect atmospheres. Shallow BF2 implantation into the sample capping layer results in more complicated behavior. For low current density implants, dislocation velocities may be dramatically increased; at higher current densities the magnitude of this increase is significantly smaller. Implantation of different ions separately implicates fluorine as the species responsible for the observed increases in dislocation velocities, presumably due to an electrical effect on the rate of dislocation kink nucleation.

Applications of Ion Microscopy and In Situ Electron Microscopy to the Study of Electronic Materials and Devices

: We discuss the application of ion microscopy and in situ electron microscopy to the study of electronic and optical materials and devices. We demonstrate how the combination of in situ transmission electron microscopy and focused ion beam microscopy provides new avenues for the study for such structures, enabling extension of these techniques to the study of dopant distributions, nanoscale stresses, three-dimensional structural and chemical reconstruction, and real-time evolution of defect microstructure. We also discuss in situ applications of thermal, mechanical, electrical, and optical stresses during transmission electron microscopy imaging.

Genetic variation of rice tungro bacilliform virus in the Philippines

Restriction fragment length polymorphisms (RFLPs) were found in 27 full genome length clones from a glasshouse isolate of rice tungro bacilliform pararetrovirus (RTBV) from the International Rice Research Institute (IRRI), the Philippines and from clones from 5 field isolates from different parts of the Philippines. There was much less variation between the IRRI clones than between the field isolate clones. The RFLPs were due to single base changes and represented about 10% of the potential sites. Sequencing across the region between nt 7772 and 7989 confirmed that the field isolates differed from the published sequence more than did the IRRI clones. The most common substitutions were G > A, A > G and T > C. Sequence heterogeneity was also noted in PCR products from RTBV DNA from the isolates. These observations are discussed in relation to the quasispecies population concept of viruses.

Evaluation of a candidate human immunodeficiency virus type 1 (HIV-1) vaccine in macaques: effect of vaccination with HIV-1 gp120 on subsequent challenge with heterologous simian immunodeficiency virus-HIV-1 chimeric virus

Human immunodeficiency virus type 1 (HIV-1) envelope vaccines can now be evaluated for efficacy in macaques by challenging with chimeric viruses in which the env, tat and rev genes of simian immunodeficiency virus (SIV) have been replaced by those of HIV-1. Most experiments have so far been conducted using gp120 molecules derived from T-cell-adapted LAI or MN strains of HIV-1, which predominantly use the CXCR-4 co-receptor. These vaccines protect against infection by apathogenic chimeric virus carrying the same envelope sequences. In the experiment described here, four macaques were vaccinated with W61D gp120 derived from a low passage Dutch isolate and capable of inhibiting the binding of MIP1beta to the co-receptor CCR-5. This vaccine was potent, inducing high titres of binding and neutralizing antibodies against the homologous HIV-1 and tenfold lower titres against a heterologous challenge virus (SHIV(SF33)) in which the env, tat and rev genes of SIV had been replaced by those of a San Francisco isolate, HIV-1(SF33). Despite strong immune responses to the vaccine there was no evidence that it protected against challenge with this chimeric virus. The antigenic divergence between vaccine and challenge virus or the increased virulence of the challenge virus may be responsible for the inability of this vaccine to protect against infection by SHIV(SF33).

Comparison of sequences of RNAs 3 and 4 of rice stripe virus from China with those of Japanese isolates

The sequences were determined of RNAs 3 and 4 of a Chinese isolate (Y) of rice stripe tenuivirus (RStV) and were compared with those of two RStV isolates (M and T) from Japan. Both RNAs of the Y isolate were longer than those of the M and T isolates. There was almost complete conservation in the 5' and 3' non-coding regions for each RNA between the isolates. The analogous ambisense coding regions for each isolate were exactly the same size and the sequences were highly conserved. The major differences were in the intergenic regions, the sizes of which accounted for the differences in size of each RNA of the three isolates. There were no obvious patterns of differences in comparisons of the two RNA over the three isolates. The significance of the similarities and differences in sequences of isolates of RStV separated by more than 3500 km is discussed.

Metastatic bone disease presenting as trochanteric bursitis

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Sequences of the three coat protein genes of a Malaysian isolate of rice tungro spherical virus reveal a close relationship to the Philippine isolate

Coat protein genes CP1, CP2 and CP3 of an isolate (MaP1) of rice tungro spherical virus (RTSV) from Malaysia were isolated, cloned and sequenced. Comparative analysis indicated that MaP1 isolate is closely related to the Philippine isolate.

Comparison of ELISA and RT-PCR for the detection of beet yellows closterovirus in plants and aphids

A reverse-transcription polymerase chain reaction (RT-PCR) was developed to detect beet yellows closterovirus (BYV) in plants and single aphids using primers spanning the conserved regions of the published sequences of the coat protein gene and open reading frames 7 and 8. Three total RNA extraction procedures were examined and all were found to produce RNA of sufficient quality for RT-PCR, although the RNA extraction kit supplied by Flowgen was found to be the most versatile for the extraction of BYV from individual aphids. When 60 aphids, which had fed on virus infected sugar beet were tested by RT-PCR, 55% of individuals were found to contain BYV. Two groups of 36 individual aphids were tested by TAS-ELISA using a specific BYV monoclonal antibody; 53% gave positive absorbance values when a substrate amplification system was used, but none was found to contain virus when the system was replaced with the substrate p-nitrophenyl phosphate. An immunocapture RT-PCR method was shown to detect BYV regardless of whether the RNA had been extracted from the trapped particles or the reverse transcription and PCR mixtures were added to the wells containing intact particles. The RT-PCR method is now used to determine the numbers of BYV carrying aphids migrating into sugar-beet crops.

Mechanisms of protection induced by attenuated simian immunodeficiency virus. IV. Protection against challenge with virus grown in autologous simian cells

Attenuated simian immunodeficiency virus (SIV) induces potent protection against infection with wild-type virus, but the mechanism of this immunity remains obscure. Allogeneic antibodies, which arise within animals as a result of SIV infection, might protect against challenge with exogenous SIV grown in allogeneic cells. To test this hypothesis, eight macaques were infected with attenuated SIV and subsequently challenged with wild-type SIV grown in autologous cells or heterologous cells. The results clearly demonstrated that animals infected with attenuated SIV are protected against wild-type SIV grown in autologous or heterologous cells. Thus, the hypothesis that live attenuated SIV protects by the induction of allogeneic antibodies is not tenable.

Analysis of gram negative recolonization of the neuropathic bladder among patients with spinal cord injuries

Over a 4 year period, 119 acute spinal cord injury (SCI) patients were enrolled in this study. The 101 males and 18 females had a mean age of 35.9 years (range 16-87). Sixty-two patients were tetraplegic and 57 were paraplegic. All patients had a urine specimen taken for culture, colony count and sensitivity once weekly while they were receiving intermittent catheterization. Of these, 22 patients (18.5%), none of whom had underlying genito-urinary (GU) pathology, developed recolonization by an organism of the same species and genus previously cultured. All 22 reached sterile-urine between colonizations after being treated with antibiotics for at least 7 days. The 16 males and six females had a mean age of 35.1 years (range 17-79). Sixteen were tetraplegic and six were paraplegic. Plasmid analysis (PA) was used to determine whether these recolonizations were from the same or from a different strain. In those instances where the bacteria harbored no plasmids or where the results of plasmid analysis were otherwise inconclusive, bacteria were also compared using restriction fragment length polymorphism (RFLP) analysis. Recolonization was caused primarily by E. coli and K. pneumoniae. While there was no significant difference between the two organisms with respect to the number of days when sterile urine occurred to the time when recolonization was observed, there were significant differences seen in both organisms with regard to the time lapse from one colonization to the next: the average number of days to recolonization with an identical organism was 10.3 days, whereas with a different strain it was 15.9 days (P < 0.04). When a different organism was cultured between the recolonizations, the mean recolonization interval was 17.9 days. When no intervening organism occurred, the interval was 9.5 days (P < 0.005). Both intervals measured the days from the first sterile urine after the first colonization to the next colonization. These data indicate the proclivity for two common Gram negative normal bowel inhabitants to recolonize the neuropathic bladder of spinal cord injured patients even after adequate treatment. PA and RFLP provide a means of discriminating between relapses by the same organism versus recurrences by a different organism of the same species and genus. Those with the same identity tend to recur sooner than those of different identities and may be suspected when relapse occurs within two weeks of cessation of 7 day course of antibiotics. While an intervening organism may delay the relapse (or recurrence), it does not prevent it and identical organisms can reappear even after adequate therapeutic regimens. Since none of the patients in this study had GU pathology, recolonization by an identical strain (relapse) does not necessarily warrant an extensive investigation for disease within the GU tract.