Transcription of Rous sarcoma proviruses in rat cells is determined by chromosomal position effects that fluctuate and can operate over long distances.

Most Rous sarcoma proviruses integrated in rat DNA are inactive. The active minority are not necessarily a consequence of long terminal repeat mutations and their transcription can fluctuate in parallel with previously demonstrated transitions in chromatin configuration. Transcriptional alternations cannot be attributed to variations in positive or negative factors that operate independently of the site of provirus integration. Moreover, distinct proviruses in the same cell can be differentially expressed and flanking cellular elements can act over several kilobases to inhibit provirus transcription. We postulate that position-dependent fluctuations in proviral repression can be mediated by trans-acting factors, and DNA transfections indicate that initiation and maintenance of this phenomenon are separable entities. Provirus activity presumably reflects otherwise inapparent cell controls that affect chromatin structure over long distances.

Direct sequence determination of the influenza B HA-1 gene after PCR amplification of clinical specimens from an infected volunteer.

When clinical isolates of influenza A and B viruses are propagated in embryonated hens' eggs or tissue culture cells, different selective pressures in vitro result in specific amino acid substitutions in the haemagglutinin (HA) gene. A proportion of such viruses which lose a potential glycosylation site near the receptor binding region of the HA at amino acid positions 196-198 appear to have reduced virulence. Direct polymerase chain reaction (PCR) amplifications of cDNA and subsequent nucleotide sequence analysis of part of the HA-1 gene of the original infecting influenza B strain and the nasal wash material from an infected volunteer were performed. The nucleotide sequences of the viral HA-1 from the nasopharynx of the infected volunteer were the same as that of the original infecting strain. Antigenic analysis of both the original infecting virus and the viruses isolated from sequential samples collected from the volunteer, all of which were cultivated on Madin-Darby Canine Kidney (MDCK) cells and in embryonated hens' eggs, revealed variation in the HA of viruses only after egg adaptation. In particular, we describe the use of direct nucleotide sequencing techniques without the use of cloning strategies in order to determine the sequence of the HA-1 gene after direct PCR amplification of clinical nasal wash material.

Electrophoretic analysis of nucleic acids isolated from scrapie-infected hamster brain.

The purpose of this study was to investigate previous reports of a scrapie-specific 1.2 kb single-stranded DNA observed in alkaline agarose electrophoresis gels. Protocols were developed to be as consistent as possible with those used previously. Partial subcellular fractionation was applied to the brains of hamsters clinically affected by the 263K strain of scrapie. Nucleic acids were then isolated, and compared electrophoretically to nucleic acids isolated from equivalent fractions, made from the brains of hamsters inoculated with normal brain. Several modifications to the protocols were suggested. Results obtained by using these modifications were compared to results obtained using the original protocols. Scrapie-specific DNA was not observed in a total of eleven consecutive experiments. Thus, these results do not support the hypothesis that the agents of transmissible spongiform encephalopathy contain a single-stranded 1.2 kb DNA species as previously described.

Sequence analysis of proviral HIV RT amplified directly by a semi-quantitative technique from AZT treated patients.

To minimise possible arbitrary selective effects of culturing HIV, proviral RT DNA was isolated directly from PBMCs of four patients treated for 6-14 months with AZT. RT DNA was amplified by PCR and sequenced directly without further in vitro manipulation. Eighteen changes additional to those 4 or 5 changes previously shown by genetic reconstruction experiments [Kellam et al.: Proceedings of the National Academy of Sciences of the United States of America 89:1934-1938, 1992] were found in the 14 different sequences analysed. Substitutions clustered in two defined areas of the RT, from amino acids 60 to 70 and from 180 to 220. Mutations were observed at each of the two areas independently or at both sites simultaneously. Amino acid changes in RT from patients harbouring resistant strains of HIV-1 were found in positions 60 (Val), 62 (Ala), 93 (Gly), 100 (Phe), 161 (Pro), 173 (Asn), 177 (Glu), 180 (Ile), 181 (Tyr), 182 (Leu), 186 (Asp), 194 (Gln), 196 (Glu), 200 (Ile), 209 (Val), 210 (Trp), 211 (Lys), and 214 (Phe) in addition to those described previously. It was anticipated that multiple proviral DNAs would be present in a single clinical sample. Therefore end point dilution PCR methodology was used, which allowed sequence analysis of separate proviral DNA molecules from the patients' proviral DNA. Even in patients who had received AZT for more than 10 months wild-type "AZT-sensitive" RTs co-existed with mutated "AZT-resistant" RTs in the same patient sample.

Control of expression of an integrated Rous sarcoma provirus in rat cells: role of 5' genomic duplications reveals unexpected patterns of gene transcription and its regulation.

Rat cells transformed by Rous sarcoma virus frequently contain duplications of viral (and sometimes cellular) DNA 5' to the integrated provirus, suggesting that such rearrangements favor provirus expression. In one cell line, A11, the duplication includes the viral src gene and proviral sequences that flank it. We examined three possible roles for this structure. Since the proviral v-src gene transformed recipient cells upon DNA transfer and was the major template for v-src transcription in A11 cells, the presence of v-src in the duplication is presumably not necessary for transformation. Since the size and structure of transcripts from the proviral v-src gene in A11 cells were conventional, the duplication does not facilitate transformation by providing a novel transcriptional strategy. Thus, we favor the concept that the duplication either attenuates a negative effect of flanking elements at the host chromosome integration site or augments the positive regulation of conventional provirus expression or both. Gene transfer and transcription analyses with both genomic and cloned DNA showed that the mechanisms of such regulatory phenomena are complex. Identical sequences in the provirus and the 5' duplication displayed different patterns of expression in A11 cells that could be disrupted in segments of cloned DNA. Among the elements that influenced such expression were sequences from the gag-pol region of the provirus.

Sequence analysis of an HIV-1 isolate which displays unusually high-level AZT resistance in vitro.

Multiple mutations in the reverse transcriptase (RT) gene were observed in a drug-resistant isolate of human immunodeficiency virus type 1 (HIV1) from an individual having prolonged (greater than 2 years) zidovudine (AZT) therapy. The virus replicated in PBMC's in the presence of very high concentrations of AZT (125 microM). Drug-sensitive strains were curtailed by 0.01 microM AZT. Eleven defined mutations were observed as compared with published sequences of RT for eight strains of HIV1. Eight of these mutations were found in the domain involved in nucleotide recognition and enzyme function. Only one of the mutations, giving a Thr--Tyr change at amino acid 215, matched those previously ascribed (67, 70, 215, and 219) to the generation of high-level resistance to AZT. Therefore additional amino acid changes may have significance in the emergence of super-resistant viruses.