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K Peden

Publications and source records attributed to K Peden.

12 recordsLinked to original sources
PubMed1992

Cell-free transmission of Vif mutants of HIV-1.

To determine the phenotype of human immunodeficiency virus type 1 (HIV-1) defective in the production of Vif, mutations were introduced into the vif gene of infectious molecular clones of the LAI, MAL, and ELI strains. Previous results had demonstrated that viruses derived from these wild type clones display different replicative capacities on peripheral blood mononuclear cells (PBMC) and different tropisms for CD4-positive cell lines. Using cell-free infection, Vif mutants of LAI, MAL, and ELI were found to have delayed kinetics and to produce less virus than their corresponding wild type viruses when propagated on most permissive cell lines. An additional mutation in the vpr gene in the LAI strain had no effect on this phenotype. However, on one T cell line, the H9 cell line, two Vif mutants of LAI and a Vif.Vpr double mutant were unable to replicate. Furthermore, Vif mutants from all three strains were only able to establish a productive infection on PBMC by coculture and not by cell-free infection. No defects in the processing of the virion proteins or the release of particles in the Vif mutants were detected.

Amino Acid Sequence↗
PubMed1992

Changes in both gp120 and gp41 can account for increased growth potential and expanded host range of human immunodeficiency virus type 1.

Virus derived from an infectious molecular clone of the ELI strain of human immunodeficiency virus type 1 (HIV-1) replicates well in peripheral blood mononuclear cells and in some CD4-positive cell lines but exhibits a delayed time course of infection in CEM and H9 cells and fails to infect SupT1 and U937 cells. If the virus that emerges from infected H9 cells is used to infect CEM and H9 cells, the time course of infection is accelerated and the virus is able to infect U937 and SupT1 cells. In this study, we used the technique of polymerase chain reaction-single-strand conformation polymorphism to localize changes in both the extracellular gp120 and the transmembrane gp41 components of the envelope gene associated with adaptation to growth in tissue culture cell lines. Specifically, mutations were identified both in a region of gp120 implicated in CD4 binding and in the amino-terminal portion of gp41 adjacent to the region involved in fusion. No changes were found in the V3 loop of gp120, a region previously shown to be involved in viral tropism. When these mutations were introduced into the original molecular clone, they conferred an enhanced replicative capacity on ELI. These results demonstrate that two additional determinants in the HIV-1 envelope protein influence viral tropism and growth in vitro. They also may have important implications for the generation of viruses with increased growth potential and expanded host range seen in the late stages of HIV disease.

Amino Acid Sequence↗
PubMed1991

Changes in growth properties on passage in tissue culture of viruses derived from infectious molecular clones of HIV-1LAI, HIV-1MAL, and HIV-1ELI.

The construction and preliminary biological characterization of three molecular clones of human immunodeficiency virus type 1 (HIV-1) are reported: HIV-1LAI from a French man with AIDS, HIV-1MAL from a Zairian boy with ARC, and HIV-1ELI from a Zairian woman with AIDS. All three sequences were found to code for infectious viruses. Both the host range and the kinetics of infection in CD4+ cells were different for the three viruses. Virus derived from each molecular clone was infectious on peripheral blood mononuclear cells (PBMC), although LAI and ELI displayed more rapid growth kinetics than MAL. The viruses had different tropisms and growth kinetics in six cell lines. LAI was infectious in all of the cell lines and produced high levels of reverse transcriptase activity. MAL and ELI had more restricted tropisms: MAL could only replicate on SupT1, whereas ELI grew on Jurkat and MT-4, was delayed on CEM and H9, and was unable to infect U937 cells. In addition, we observed that both the replicative capacity and the cell tropism of viruses could change after passage through some established cell lines. These results suggest that the genotypes of some viruses in vitro are not stable and that selection for growth can cause the fairly rapid appearance of variants with increased growth potential.

AIDS-Related Complex↗
PubMed1989

The rev gene product of the human immunodeficiency virus affects envelope-specific RNA localization.

By in situ hybridization analysis and immunoprecipitations following transfection of COS cells, we show that the Rev protein of the human immunodeficiency virus is necessary for envelope protein expression, which is correlated with the appearance in the cytoplasm of envelope-specific RNA. In the absence of cotransfection with a plasmid expressing Rev, envelope-specific RNA is retained in the nucleus. Several cis-acting sites in the envelope are involved, one of which is between nucleotides 7330 and 7735 and is required for the response to Rev. Other sequences (nucleotides 5797-7330 and 7735-7989) are involved in the apparent retention of the envelope-specific RNA in the nucleus in the absence of Rev and its response element. Because Rev affects the localization of envelope RNA both in the presence and in the absence of the normal splice sites on the RNA, the mechanism of Rev action is independent of splicing.

Cell Compartmentation↗
PubMed1989

VPX mutants of HIV-2 are infectious in established cell lines but display a severe defect in peripheral blood lymphocytes.

Nucleotide sequence comparison between HIV-1, HIV-2 and SIV has revealed the presence of an open reading frame (ORF) in the central region of the genomes of HIV-2 and SIV that has no counterpart in HIV-1. This new ORF, called vpx, is highly conserved between HIV-2ROD and SIVmac. Using anti-peptide sera to the predicted protein and site-directed mutagenesis, we show that mutations in the vpx ORF eliminate the synthesis of a 16 kd protein in HIV-2 infected cells, confirming that this protein is the product of this gene. Full-length clones of HIV-2 containing these mutations are infectious in two permanent T lymphocytic cell lines and two monocytic cell lines. In contrast, we show that loss of VPX function results in a severe defect in the productive infection of human peripheral blood lymphocytes both in the amount of reverse transcriptase activity produced and in core protein expression. These findings suggest that the VPX protein plays an important role in the in vivo life cycle of the HIV-2/SIV viruses.

Amino Acid Sequence↗
PubMed1989

Method for cloning single-stranded oligonucleotides in a plasmid vector.

A method for cloning single-stranded oligonucleotides in a plasmid vector has been developed. The method relies on ligation of the oligonucleotide into suitable restriction enzyme sites of the cloning vector such that the site at the 5' end has a 5' overhang [for example, a Bgl II site (A decreases GATCT)], and the site at the 3' end has a 3' overhang [for example, a Sac I site (GAGCT decreases C)]. This arrangement allows the oligonucleotide to anneal to the single-stranded ends of the vector and to be covalently joined by T4 DNA ligase. The complementary strand can be synthesized in vitro to generate a double-stranded plasmid, or the partially single-stranded molecule can be used as a target for site-directed mutagenesis. The subsequent transfer of the oligonucleotide to test plasmids or excision for other manipulations, such as band shift experiments to identify protein binding sites, is facilitated by cloning of the oligonucleotide into a polylinker containing multiple restriction enzyme sites. For this purpose, the plasmid vector, pKP59, which is a 2.0 kB derivative of pBR322 lacking "poison sequences" and containing 16 cloning sites, has been the most satisfactory.

Biotechnology↗
PubMed1988

Targeted mutations induced by a single acetylaminofluorene DNA adduct in mammalian cells and bacteria.

Mutagenic specificity of 2-acetylaminofluorene (AAF) has been established in mammalian cells and several strains of bacteria by using a shuttle plasmid vector containing a single N-(deoxyguanosin-8-yl)acetylaminofluorene (C8-dG-AAF) adduct. The nucleotide sequence of the gene conferring tetracycline resistance was modified by conservative codon replacement so as to accommodate the sequence d(CCTTCGCTAC) flanked by two restriction sites, Bsm I and Xho I. The corresponding synthetic oligodeoxynucleotide underwent reaction with 2-(N-acetoxy-N-acetylamino)-fluorene (AAAF), forming a single dG-AAF adduct. This modified oligodeoxynucleotide was hybridized to its complementary strand and ligated between the Bsm I and Xho I sites of the vector. Plasmids containing the C8-dG-AAF adduct were used to transfect simian virus 40-transformed simian kidney (COS-1) cells and to transform several AB strains of Escherichia coli. Colonies containing mutant plasmids were detected by hybridization to 32P-labeled oligodeoxynucleotides. Presence of the single DNA adduct increased the mutation frequency by 8-fold in both COS cells and E. coli. Over 80% of mutations detected in both systems were targeted and represented G.C----C.G or G.C----T.A transversions or single nucleotide deletions. We conclude that modification of a deoxyguanosine residue with AAF preferentially induces mutations targeted at this site when a plasmid containing a single C8-dG-AAF adduct is introduced into mammalian cells or bacteria.

2-Acetylaminofluorene↗
PubMed1983

Biochemical activities of T-antigen proteins encoded by simian virus 40 A gene deletion mutants.

We have analyzed T antigens produced by a set of simian virus 40 (SV40) A gene deletion mutants for ATPase activity and for binding to the SV40 origin of DNA replication. Virus stocks of nonviable SV40 A gene deletion mutants were established in SV40-transformed monkey COS cells. Mutant T antigens were produced in mutant virus-infected CV1 cells. The structures of the mutant T antigens were characterized by immunoprecipitation with monoclonal antibodies directed against distinct regions of the T-antigen molecule. T antigens in crude extracts prepared from cells infected with 10 different mutants were immobilized on polyacrylamide beads with monoclonal antibodies, quantified by Coomassie blue staining, and then assayed directly for T antigen-specific ATPase activity and for binding to the SV40 origin of DNA replication. Our results indicate that the T antigen coding sequences required for origin binding map between 0.54 and 0.35 map units on the SV40 genome. In contrast, sequences closer to the C terminus of T antigen (between 0.24 and 0.20 map units) are required for ATPase activity. The presence of the ATPase activity correlated closely with the ability of the mutant viruses to replicate and to transform nonpermissive cells. The origin binding activity was retained, however, by three mutants that lacked these two functions, indicating that this activity is not sufficient to support either cellular transformation or viral replication. Neither the ATPase activity nor the origin binding activity correlated with the ability of the mutant DNA to activate silent rRNA genes or host cell DNA synthesis.

Adenosine Triphosphatases↗
PubMed1982

Homology between mammalian cell DNA sequences and human herpesvirus genomes detected by a hybridization procedure with high-complexity probe.

Mouse and human DNA used as in vitro-labeled "high-complexity" probes revealed hybridization between specific herpesvirus DNA fragments on Southern transfers and repetitive sequences present at 10(3) to 10(5) copies per mammalian cell genome. Several different sites of major cell-virus sequence homology have been detected in both the herpes simplex virus type 1 and type 2 genomes, and these are located predominantly within the L and S inverted repeat regions and near the center of the L unique region. The hybrids persisted even in relatively stringent conditions, and appear to correlate closely with some of the previously recognized regions of size heterogeneity in the viral genome. Cloned viral DNA fragments from each site hybridized to different sets of discrete bands and dispersed elements within restriction-endonuclease-digested genomic DNA from a variety of vertebrate species. Localized cell-virus homology was also detected in both the human Epstein-Barr virus and cytomegalovirus genomes.

Animals↗
PubMed1979

A study of the organisation of the ribosomal ribonucleic acid gene cluster of Neurospora crassa by means of restriction endonuclease analysis and cloning in bacteriophage lambda.

1. Total Neurospora crassa DNA was restricted with endonucleases and fragments carrying rRNA coding sequences were identified by hybridization with Xenopus laevis ribosomal DNA probes. 2. The repeating unit of the rRNA gene cluster was found to be 8.6 kbp, arranged in a head-to-tail fashion. 3. Digestion with Hind III yielded fragments of 3.4 kbp and 5.2 kbp and both were cloned. 4. Digestion with Eco RI yielded fragments of 2.2 kbp, 3.0 kbp and 3.4 kbp; the 3.0 kbp fragment was cloned. 5. Sequences coding for RNA (S-rRNA)1 of the smaller subribosomal particle were found (at least 90%) in the 2.2 kbp EcoRI subfragment of the 5.2 kbp Hind III fragment. 6. The coding sequences for the major RNA species (L-rRNA) of the larger subribosomal particle were located mainly (at least 95%) in the 3.4 kbp Hind III fragment. 7. For comparison, a Hind III digest of total yeast DNA was cloned and recombinants containing a 6.4 kbp rDNA fragment were isolated.

Animals↗