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A Dolan

Publications and source records attributed to A Dolan.

33 records · Page 2Linked to original sources
PubMed1992

A novel herpes simplex virus gene (UL49A) encodes a putative membrane protein with counterparts in other herpesviruses.

Comparative analysis of DNA sequences located between the coding regions of genes UL49 and UL50 of herpes simplex virus types 1 and 2 (HSV-1 and -2) has revealed a small open reading frame (ORF) of 91 and 87 codons respectively with the characteristics of a genuine protein-coding region. The predicted protein products are clearly related and exhibit features of membrane-inserted proteins, with potential N-proximal signal peptides and C-proximal membrane anchor regions. Counterparts are present in the other sequenced alphaherpesviruses, namely varicella-zoster virus (a previously undescribed gene, 9A) and equine herpesvirus type 1 (gene 10), in the betaherpesvirus human cytomegalovirus (gene UL73) and in the gammaherpesvirus Epstein-Barr virus (gene BLRF1). Therefore, we consider that this ORF represents an additional HSV gene (UL49A) with counterparts in all sequenced alpha-, beta- and gammaherpesviruses.

Amino Acid Sequence↗
PubMed1991

Sequence analysis of the splice junction in the transcript of herpes simplex virus type 1 gene UL15.

Gene UL15 of herpes simplex virus type 1 has been proposed to consist of two coding exons separated by an intron of 3587 base pairs. We have generated a DNA fragment copied from the transcript across the proposed splice junction by successive use of reverse transcription and the polymerase chain reaction, and have sequenced this fragment to determine the precise structure of the splice junction.

Base Sequence↗
PubMed1991

Comparative sequence analysis of the long repeat regions and adjoining parts of the long unique regions in the genomes of herpes simplex viruses types 1 and 2.

We report the determination of the DNA sequence of the long repeat (RL) region and adjacent parts of the long unique (UL) region in the genome of herpes simplex virus type 2 (HSV-2) strain HG52. The DNA sequences and genetic content of the extremities of HSV-2 UL were found to be closely similar to those determined previously for HSV-1. The 5658 bp sequenced at the left end of HSV-2 UL contained coding regions for genes UL1 to UL4 plus part of UL5. The 4355 bp sequenced at the right end of UL contained coding regions for part of gene UL53, and the whole of genes UL54 to UL56. Comparison of the HSV-1 and HSV-2 UL56 sequences led to a correction in the published HSV-1 UL56 reading frame. The HSV-2 RL region, including one copy of the a sequence, was determined to be 9263 bp, with a base composition of 75.4% G+C and with many repetitive sequence elements. In HSV-2 RL, sequences were identified corresponding to HSV-1 genes encoding the immediate early IE110 (ICP0) transcriptional regulator and the ICP34.5 neurovirulence factor; the former HSV-2 gene was proposed to contain two introns, and the latter one intron. Downstream of the HSV-2 immediate early gene, the RL sequence encoding the latency-associated transcripts (LATs) was found to be dissimilar to that in HSV-1; the probable LAT promoter regions, however, showed similarities to HSV-1. Properties of the LAT sequences in both HSV-1 and HSV-2 were consistent with LATs being generated as an intron excised from a longer transcript.

Amino Acid Sequence↗
PubMed1990

Characterization of herpes simplex virus type 2 transcription during latent infection of mouse trigeminal ganglia.

Using a cornea trigeminal ganglion model, we have investigated transcription by herpes simplex virus type 2 (HSV-2) during latency in mice. Latency was verified 2 months postinoculation by reactivation of HSV-2 after explant cocultivation of trigeminal ganglia from the majority of mice (83%). Transcription during latent HSV-2 infection was limited to the repeat regions of the viral genome as determined by in situ hybridization using restriction fragment probes representing 100% of the HSV-2 genome. Further mapping of the positively hybridizing region by using subfragments showed that transcription occurred from approximately 11.5 kb of contiguous DNA fragments. A 1.0-kb PvuI-BamHI fragment within the BamHI F fragment and a 0.3-kb BamHI-SalI fragment and a 3.4-kb SalI-BamHI fragment within the BamHI P fragment hybridized more strongly than other subfragments in in situ hybridization experiments. All positive signals were confined to the nucleus. The RNA that hybridized to the 3.4-kb SalI-BamHI DNA fragment probe by in situ hybridization corresponded to a 2.3-kb transcript on Northern (RNA) blots. Under our conditions for Northern blot hybridization, the 3.4-kb SalI-BamHI probe of HSV-2 hybridized to a limited degree with the latency-associated transcripts of HSV-1. Shorter spliced species of latency-associated transcript RNA, which are seen during HSV-1 latency, have not been detected in latent HSV-2 RNA. However, viral gene expression during HSV-2 latency appears to be very similar to that during HSV-1 latency.

Animals↗
PubMed1988

The complete DNA sequence of the long unique region in the genome of herpes simplex virus type 1.

We have determined the DNA sequence of the long unique region (UL) in the genome of herpes simplex virus type 1 (HSV-1) strain 17. The UL sequence contained 107,943 residues and had a base composition of 66.9% G + C. Together with our previous work, this completes the sequence of HSV-1 DNA, giving a total genome length of 152,260 residues of base composition 68.3% G + C. Genes in the UL region were located by the use of published mapping analyses, transcript structures and sequence data, and by examination of DNA sequence characteristics. Fifty-six genes were identified, accounting for most of the sequence. Some 28 of these are at present of unknown function. The gene layout for UL was found to be very similar to that for the corresponding part of the genome of varicella-zoster virus, the only other completely sequenced alphaherpesvirus, and the amino acid sequences of equivalent proteins showed a range of similarities. In the whole genome of HSV-1 we now recognize 72 genes which encode 70 distinct proteins.

Amino Acid Sequence↗
PubMed1988

Structures of herpes simplex virus type 1 genes required for replication of virus DNA.

Recently, a method has been developed to identify regions in the genome of herpes simplex virus type 1 (HSV-1) which contain genes required for DNA synthesis from an HSV-1 origin of DNA replication, and seven genomic loci have been identified as representing the necessary and sufficient gene set for such replication (C. A. Wu, N. J. Nelson, D. J. McGeoch, and M. D. Challberg, J. Virol. 62:435-443, 1988). Two of the loci represent the well-known genes for DNA polymerase and major DNA-binding protein, but the remainder had little or no previous characterization. In this report we present the DNA sequences of the five newly identified genes and their deduced transcript organizations and encoded amino acid sequences. These genes were designated UL5, UL8, UL9, UL42, and UL52 and were predicted to encode proteins with molecular weights of, respectively, 99,000, 80,000, 94,000, 51,000, and 114,000. All of these genes had clear counterparts in the genome of the related alphaherpesvirus varicella-zoster virus, but only UL5 and UL52 were detectably conserved in the distantly related gammaherpesvirus Epstein-Barr virus, as judged by amino acid sequence similarity. The sequence of the UL5 protein, and of its counterparts in the other viruses, contained a region closely resembling known ATP-binding sites; this could be indicative, for instance, of a helicase or primase activity.

Amino Acid Sequence↗
PubMed1986

DNA sequence of the region in the genome of herpes simplex virus type 1 containing the exonuclease gene and neighbouring genes.

We report the sequence of a 7800 base pair region of herpes simplex virus type 1 DNA, representing approximately 0.16 to 0.20 map units in the genome. This contains sequences transcribed into a leftward oriented set of five 3' coterminal mRNAs, together with two rightward transcribed flanking genes. One of the leftward genes encodes the virus's alkaline exonuclease, but the other gene products are uncharacterized. The amino acid sequence of one encoded protein suggested that it is a membrane embedded species. The DNA sequence is densely utilised, with two predicted out-of-frame overlaps of coding sequences, and probably six occurrences of promoter elements within coding sequences. Homologues of five of the genes were found for the distantly related Epstein-Barr virus, with a similar overall relative arrangement.

Amino Acid Sequence↗
PubMed1986

Complete DNA sequence of the short repeat region in the genome of herpes simplex virus type 1.

We report the complete DNA sequence of the short repeat region in the genome of herpes simplex virus type 1, as 6633 base pairs of composition 79.5% G+C. This contains immediate early gene 3, encoding the IE175 protein, an important transcriptional activator of later virus genes. The IE175 coding region was identified as a 3894 base sequence of 81.5% G+C DNA. The base composition of this gene is thus the most extreme yet determined, and the IE175 predicted amino acid composition is correspondingly biased, most notably with an alanine content of 20.9%. Functionally important regions of the IE175 polypeptide were tentatively identified by comparison with the sequence of the homologous protein from varicella-zoster virus and from locations of ts mutations, and were correlated with properties of the amino acid sequence. Aspects of the evolution of such an extreme composition DNA sequence were discussed.

Amino Acid Sequence↗
PubMed1985

Sequence determination and genetic content of the short unique region in the genome of herpes simplex virus type 1.

We have determined the complete DNA sequence of the short unique region in the genome of herpes simplex virus type 1, strain 17, and have interpreted it in terms of messenger RNAs and encoded proteins. The sequence contains variable regions whose length differs between DNA clones. The clones used for most of the analysis gave a short unique length of 12,979 base-pairs. We consider that this region contains 12 genes, which are expressed by mRNAs which have separate promoters, but may share 3'-termination sites, so that all but two mRNAs belong to one of four 3'-coterminal "families": 79% of the sequence is considered to be polypeptide coding. One pair of genes has an extensive out-of-frame overlap of coding sequences. The proteins encoded in the short unique region include two immediate-early species, two virion surface glycoproteins, and a DNA-binding species. Six of the genes have little or no previous characterization. From the nature of the amino acid sequences predicted for their encoded proteins, we deduce that several of these proteins may be membrane-associated.

Base Sequence↗
PubMed1981

Enhanced mutability associated with a temperature-sensitive mutant of vesicular stomatitis virus.

Temperature-sensitive (ts) mutant tsD1 of vesicular stomatitis virus, New Jersey serotype, is the sole representative of complementation group D. Clones derived from this mutant exhibited three different phenotypes with respect to electrophoretic mobility of the G and N polypeptides of the virion in sodium dodecyl sulfate-polyacrylamide gel. Analysis of non-ts pseudorevertants showed that none of the three phenotypes was associated with the temperature sensitivity of mutant tsD1. Additional phenotypes, some also involving the NS polypeptide, appeared during sequential cloning, indicating that mutations were generated at high frequency during replication of tsD1. Furthermore, mutations altering the electrophoretic mobility of the G, N, NS, and M polypeptides were induced in heterologous viruses multiplying in the same cells as tsD1. These heterologous viruses included another complementing ts mutant of vesicular stomatitis virus New Jersey and ts mutants of vesicular stomatitis virus Indiana and Chandipura virus. Complete or incomplete virions of tsD1 appeared to be equally efficient inducers of mutations in heterologous viruses. Analysis of the progeny of a mixed infection of two complementing ts mutants of vesicular stomatitis virus New Jersey with electrophoretically distinguishable G, N, NS, and M proteins yielded no recombinants and excluded recombination as a factor in the generation of the electrophoretic mobility variants. In vitro translation of total cytoplasmic RNA from BHK cells indicated that post-translational processing was not responsible for the aberrant electrophoretic mobility of the N, NS, and M protein mutants. Aberrant glycosylation could account for three of four G protein mutants, however. Some clones of tsD1 had an N polypeptide which migrated faster in sodium dodecyl sulfate-polyacrylamide gel than did the wild type, suggesting that the polypeptide might be shorter by about 10 amino acids. Determination of the nucleotide sequence to about 200 residues from each terminus of the N gene of one of these clones, a revertant, and the wild-type parent revealed no changes compatible with synthesis of a shorter polypeptide by premature termination or late initiation of translation. The sequence data indicated, however, that the N-protein mutant and its revertant differed from the parental wild type in two of the 399 nucleotides determined. These sequencing results and the phenomenon of enhanced mutability associated with mutant tsD1 reveal that rapid and extensive evolution of the viral genome can occur during the course of normal cytolytic infection of cultured cells.

Animals↗
PubMed1980

Comparisons of nucleotide sequences in the genomes of the New Jersey and Indiana serotypes of vesicular stomatitis virus.

Nucleotide sequences of around 200 residues were determined adjacent to the 3' terminus of the genome RNA of vesicular stomatitis virus, New Jersey serotype, and adjacent to the 3'-terminal polyadenylic acid tract of the N protein mRNA of the same virus. These sequences were compared with the corresponding sequences previously determined for the Indiana serotype of vesicular stomatitis virus. The sequences obtained for the two strains were readily aligned, showing 70.8% homology overall. Examination of the sequences allowed identification of the translation initiation and termination codons for the N mRNA of each serotype. The deduced N-terminal and C-terminal amino acid sequences of the two N polypeptides were each similar, and most of the differences between them consisted of substitution by a clearly homologous amino acid. It was proposed that these nucleotide sequences, within limits imposed by their functions, comprise reasonably representative measures of the extent of sequence homology between the genomes of the two serotypes, and that this is higher than previously estimated, but with little exact homology over extended regions.

Amino Acid Sequence↗
PubMed1980

A comparison of hospital and state agency efficiency in processing medicaid claims in Washington state.

The performance of the Washington State Medicaid agency in processing Medicaid claims was compared with that of hospital providers for one year. We found that the in-hospital processing time was approximately twice that of the Medicaid processing agency. In-agency processing time was found to be significantly related to the size and disposition of a claim, while in-hospital processing time showed a significant relation to hospital dependence on Medicaid reimbursement, the amount of the claim not allowed reimbursement by the Medicaid agency, hospital expense per admission, and the question whether the claim was submitted by the university hospitals. We concluded that lengthy turnaround time for Medicaid reimbursement of hospitals in Washington State was primarily related to hospital speed in submitting claims.

Economics, Hospital↗
PubMed1979

Sequence of 200 nucleotides at the 3'-terminus of the genome RNA of vesicular stomatitis virus.

The sequence of 200 nucleotides at the 3'-terminus of the genome RNA of vesicular stomatitis virus, Indiana serotype, was determined by adding a poly(A) tract to the 3'-terminus of genome RNA, then using the poly(A) as a binding site for a primer to initiate reverse transcription of the RNA, and analysing the complementary DNA sequence by the dideoxynucleoside triphosphate chain termination method. Proceeding 3' to 5', the genome RNA sequence consisted of a sequence complementary to the leader RNA, followed by the sequence AAA, followed by a sequence complementary to the 5'-extremity of N protein mRNA. These results are discussed in terms of leader RNA function, mechanism of transcript processing at the junction between leader RNA and N mRNA, and N mRNA structure.

Base Sequence↗