Detection of adeno-associated virus (AAV)-specific nucleotide sequences in DNA isolated from latently infected Detroit 6 cells.

Detroit 6 cells exposed to 250 TCID₅₀/cell of adeno-associated virus (AAV)-2 retained the ability to produce AAV antigens and infectious virus upon subsequent exposure to helper adenovirus type 2 for many passages. The increased rate of annealing of ³²P-labeled AAV-DNA in the presence of cellular DNA from two such latently infected clones indicated the presence of three to five AAV genome equivalents per diploid amount of cell DNA.     

Physical and gene mapping of cauliflower (Brassica oleracea) mitochondrial DNA

Summary A physical map of the mitochondrial DNA isolated from B. oleracea (cauliflower) inflorescences was constructed with the restriction endonucleases Sall, Kpnl and Bgll. Physical mapping was made using the multi enzyme method with either unlabeled or labeled DNA fragments isolated by preparative electrophoresis and a clone bank prepared by inserting incomplete Sall restriction digests of mitochondrial DNA into a cosmid vector.The different mapping studies led to a circular map, about 217 kb in size, containing the entire sequence complexity of the genome. The 26S and 18S – 5S ribosomal RNA genes appeared to be separated by about 75 kb in this map. However, the particular cross-hybridization between several restriction fragments and the sequential diversity of some cosmids indicated that intra molecular recombination may occur naturally in higher plant mitochondria. Namely, one recombinational event resulted in the ribosomal RNA genes mapping closer together.Abbreviations mtDNA mitochondrial DNA - kb kilobasepairs - rRNA ribosomal RNA - LGT agarose low gelling temperature agarose     

DNA sequences of chromosome 21-specific YAC detect the t(8;21) breakpoint of acute myelogenous leukemia.

The t(8;21)(q22;q22) is a nonrandom translocation specifically marking blasts of acute myelogenous leukemia (AML) with undifferentiated phenotype. The breakpoint on chromosome 21 involved by this rearrangement has been precisely localized relative to cloned DNA markers by physical and genetic linkage analysis enabling the use of positional cloning for its isolation. Yeast artificial chromosome (YAC) clones for loci proximal (D21S65) and distal (ERG) to the (21q22) breakpoint have been developed and their chromosome 21 origin and location relative to the breakpoint has been established. By using in situ hybridization analysis, a 240 kb YAC clone for the D21S65 locus clearly identified both derivative chromosomes of the (8;21) translocation in metaphase spreads of leukemia blasts with the rearrangement. The characterization of the DNA sequences contained in this 240 kb YAC can reveal the functional consequences of their derangement in leukemia with abnormalities of the (21q22) region.     

Enzyme-linked immunoassay for detection of PCR-amplified DNA of legionellae in bronchoalveolar fluid.

A nonradioactive method is described that detects 10 to 100 legionellae in 1 ml of bronchoalveolar lavage fluid. DNA is purified by a proteinase K-phenol protocol or with a commercial DNA preparation kit and amplified by PCR with amplimers specific for the 16S rRNA gene of Legionella pneumophila. The upstream primer is 5' biotinylated. The amplification product is immobilized on streptavidin-coated microtiter plates. Because of the high binding capacity, no removal of nonincorporated biotin from the PCR product is required. After alkaline denaturation, the single-stranded PCR product is hybridized with a 5' digoxigenin-labeled probing oligomer. The amplification product is then detected by using peroxidase-labeled anti-digoxigenin antibodies in a luminescence or colorimetric reaction. The assay detects as few as 10 legionellae in 1-ml bronchoalveolar lavage fluid specimens. It is specific for medically relevant Legionella species, including Legionella pneumophila, L. bozemanii, and L. longbeachae. Of over 250 clinical specimens examined, 8 were positive for legionellae by both culture and the PCR assay. Six further specimens were culture negative but PCR positive for legionellae; of these, five specimens were from patients receiving high-dose erythromycin therapy for suspected or previously diagnosed legionella pneumonia. None of the remaining 240 specimens that were culture negative for legionellae yielded a positive PCR test, although a total of over 30 different bacterial species were cultured from these specimens. The PCR assay therefore appears to exhibit high sensitivity and specificity and thus could prove suitable for use in the routine microbiological diagnostic laboratory.     

Distribution of specific DNA sequences among pathogenic and commensal Neisseria species.

Several traits, including pili and the outer membrane proteins P.II and H.8, have been associated with pathogenic Neisseria species. We examined several Neisseria species for DNA sequence homology to cloned pilin, P.II, and H.8 genes. Strains of Neisseria gonorrhoeae and N. meningitidis showed hybridization to all of these genes. Commensal strains showed little hybridization to any of these genes. Strains of N. lactamica and N. cinerea showed intermediate patterns of hybridization. Generally, organisms that expressed a given trait showed DNA homology to the corresponding cloned gene. However, we observed pili on some commensal strains that did not show hybridization to the cloned gonococcal pilin gene.     

Cloning and comparative mapping of recently evolved human chromosome 22-specific alpha satellite DNA

We have isolated and characterized a new alphoid probe, named p190.22. Its chromosomal location was investigated using fluorescence in situ hybridization. Under high stringency conditions p190.22 recognizes specifically the centromere of chromosome 22. A chromosome 22-specific alphoid subset has been previously reported in the literature (p22/12.1). The partial sequence and the genomic organization comparison strongly suggests that they recognize distinct subsets both specific for chromosome 22. The comparative mapping of probes p190.22 and p22/12.1 on chimpanzee (PTR and PPA) and gorilla (GGO) chromosomes was investigated. The two probes showed different hybridization results. p190.22, in particular, did not show any hybridization signal in these three species, suggesting a recent evolution.     

Evaluation of the Gen-Probe DNA probe for the detection of legionellae in culture.

A commercial DNA probe kit designed to detect rRNA from legionellae was evaluated for its ability to correctly discriminate between legionellae and non-legionellae taken from culture plates. The probe kit, made by the Gen-Probe Corp. (San Diego, Calif.), was radiolabeled with 125I, and probe bacterial RNA hybridization, detected in a simple one-tube system hybridization assay, was quantitated with a gamma counter. A total of 156 Legionella sp. strains were tested, of which 125 were Legionella pneumophila and the remainder were strains from 21 other Legionella spp. A total of 106 gram-negative non-legionellae, isolated from human respiratory tract (81%) and other body site (19%) specimens, were also tested; 14 genera and 28 species were represented. The probe easily distinguished all of the legionellae from the non-legionellae. The average legionellae/non-legionellae hybridization ratio was 42:1, and the lowest ratio was 2:1; a minor modification in the procedure increased the lowest ratio to 5:1. In addition to correctly identifying all Legionella species, the probe was able to separate some of the various species of Legionella. L. pneumophila strains hybridized more completely to the probe than did the other Legionella spp.; L. wadsworthii and L. oakridgensis hybridized only about 25% of the probe relative to L. pneumophila. Some strains of phenotypically identified L. pneumophila had much lower hybridization to the probe than other members of the species and may represent a new Legionella species. The simplicity of the technique and specificity of the probe make it a good candidate for confirming the identity of legionellae in culture.     

Genetic mapping of telomeric DNA sequences in the maize pathogen Cochliobolus heterostrophus

Numerous polymorphic bands were observed when genomic DNA of Cochliobolus heterostrophus was cut with restriction enzymes and hybridized with a telomere-specific probe. Bal31 digestion demonstrated that the majority of the bands were from the chromosome termini and thus constitute telomeres. However, numerous hybridizing sequences in the strain B30.A3.R.45 were Bal31 exonuclease-insensitive and thus located at least 600 bases internal to the chromosome ends. Segregation analysis of the polymorphic bands identified nine telomeres; seven were linked to other markers and thus permitted the proper orientation of linkage groups with respect to their chromosome ends. Three internal, telomere-homologous sequences, at least one of which may be subtelomeric, were also mapped. Received: 8 May / 22 June 1998     

Radiation hybrids for mapping and cloning DNA sequences of distal 16p

Three hundred fifteen radiation hybrids (RH) were isolated using a monochromosomal cell hybrid containing chromosome 16 only. A panel of 18 RH, which showed breakpoints among four markers (3.15, 26.6, 3HVR, and 5HVR) mapping in the distal portion of 16p, were selected and characterized for the retention of nine additional DNA sequences already localized in this region, and for one centromeric sequence. One or more breakpoints were identified in nine of the 12 intervals defined by the 13 single-copy sequences used. This panel of RH represents a tool for the construction of a detailed physical map of the distal part of 16p and for cloning sequences located in the proximity of disease genes. Three inter-Alu DNA sequences, amplified from one of these RH containing the autosomal dominant polycystic kidney disease (PKD1) gene, were cloned and mapped in the panel. Sequencing of the ends of one of the three clones showed a (CAAA) _n repeat, which revealed a two-allele polymorphism.     

Genetic characterization of an α-specific gene responsible for sexual agglutinability in Saccharomyces cerevisiae: mapping and gene dose effect

Summary A recessive ag1 mutation leads to specific defect in sexual agglutinability specifically in cells of the yeast Saccharomyces cerevisiae. The cryptopleurine resistance gene cry^R 1, closely linked to the mating type locus, was used to select / strains which emerged from / strains by mitotic nonreciprocal recombination, to genetically analyse ag1, since ag1 is expressed only in mating type. The ag1 gene was found to be linked to the centromere tightly, to met3 at 4.4 cM, and to ilv3 at 12 cM on chromosome X. Sexual agglutinability of cells was shown to be dependent on the dose of the AG1 gene, using / isogenic strains carrying AG1/AG1, AG1/ag1 or ag1/ag1. The sst2-1 mutation did not suppress the ag1 mutation. Based on these results, function of the AG1 gene is discussed.Abbreviations cM centimorgan - FDS first division segregation - NPD nonparental ditype - PD parental ditype - SDS second division segregation - TT tetratype     

Inverted repetitive sequences in human papilloma virus 1 (HPV-1) DNA.

Two pairs of inverted repetitive (palindromic) sequences (IR 1a/b and IR 2a/b) were detected electron microscopically within the DNA of human papilloma virus 1 (HPV-1) after cleavage by BamHI or EcoRI endonucleases followed by denaturation and a short period of reassociation. The localization of these sequences within the genome was determined. After separation and isolation of the single HPV-1 DNA strands, IR 1a/b and IR 2a/b were identified by polyacrylamide-gel electrophoresis after prior digestion of the nonhomologous regions with S1 nuclease. The molecular weights of the palindromic sequences were determined to be 0.11 × 10⁶ and 0.10 × 10⁶.     

Distribution and expression of the astA gene (EAST1 toxin) in Escherichia coli and Salmonella

The distribution and expression of the astA gene (EAST1 toxin) among 358 strains of Enterobacteriaceae were studied. The gene was found in 32.6% and 11.9% of Escherichia coli and Salmonella strains, respectively. The majority of E. coli EAST1-positive strains were found among EHEC (88.0%), EAggEC (86.6%), and A-EPEC (58.3%). The gene was present in 16.6% of E. coli strains without known virulence genes. There was no significant variation among the different serotypes of E. coli tested regarding the presence of the gene. For EPEC, 13.7% of the tested strains were astA-positive. Among atypical EPEC (eae+, bfp-, EAF-) and (eae+, bfp+, EAF-) 46.2 and 72.7%, respectively, were positive. The majority of the A-EPEC (87%) and EaggEC (83%) strains expressed the EAST-1 toxin as judged from Ussing chamber experiments. Of 32 EIEC strains studied, 2 possessed and expressed the gene as determined in Ussing chamber experiments. Among the Salmonella strains studied, five strains isolated from food were positive for astA and one strain of S. agona showed biological activity in Ussing chamber experiments.     

Immunization of RANTES expression plasmid with a DNA vaccine enhances HIV-1-specific immunity.

Cytokines play important roles in regulating immune response. This study evaluated the adjuvant effect of an expression plasmid encoding RANTES (regulated on activation normal T-cell expressed and secreted) chemokine on the immunity induced by a DNA vaccine. This vaccine consists of expression plasmids encoding the env and rev genes of human immunodeficiency virus type 1 (HIV-1). DNA vaccination with RANTES plasmid induced significantly higher titers of serum HIV-1-specific IgG and IgG2a antibodies than DNA vaccination alone on both intramuscular and intranasal immunization. This combination also increased HIV-1-specific cytotoxic T lymphocyte activity and delayed-type hypersensitivity. Intranasal immunization induced a higher titer of fecal secretory IgA antibody than intramuscular immunization. These results demonstrate that coadministration of RANTES plasmid dominantly induced HIV-1-specific cell-mediated immunity.     

Identification of Lens culinaris ssp. culinaris chromosomes by physical mapping of repetitive DNA sequences

We describe the characterisation and the chromosomal localisation of two repeated DNA sequences, named pLc30 (466 bp long, 64% AT residues) and pLc7 (408 bp long, 61% AT residues), isolated from lentil (Lens culinaris ssp. culinaris) genomic DNA. The pLc30 family is characterised by four internal repeats organised in a head-to-tail orientation, whereas the pLc7 contains many short direct subrepeats. The two families do not share significant sequence similarity. The distribution of these repetitive sequences in different Lens species and in other legumes was investigated. pLc30 is present in all Lens species investigated but absent from other genera examined. In contrast, pLc7 is present also in the genome of other legumes. As determined by FISH, the pLc30 sequence hybridises on six out of seven lentil chromosome pairs, while pLc7 hybridises on one only. The distribution of the nine different hybridisation sites of pLc30 allows the discrimination of all seven chromosome pairs and the construction of a karyotype of L. culinaris ssp. culinaris. Additionally, the combination of simultaneous and successive FISH with pLc7, 5S rRNA, 18S-5.8S-25S rRNA genes, and a telomeric sequence allowed the assembly of a physical map based on lentil karyotype.     

Distribution of feline leukemia virus DNA sequences in tissues of normal and leukemic domestic cats.

Seroepidemiological studies indicate that leukemia and lymphoma in cats are horizontally transmitted and that feline leukemia virus (FeLV) is the agent responsible for the disease. Yet, in a significant proportion of leukemic cats, FeLV has not been identified, despite the presence of the feline oncornavirus-associated cell membrane antigen (FOCMA) and in some instances, epidemiological evidence indicating exposure to FeLV. Prompted by these so called virus negative cases of cat leukemia, we surveyed a total of 176 tissues from 50 cats for the presence of FeLV proviral DNA sequences. The animals studied included viremic and nonviremic cats that were either healthy or leukemic. We found: (1) DNA from virus-positive tissues from both healthy and leukemic cats hybridized 60–100% of ¹²⁵I-FeLV (strain Rickard) RNA. (These values are normalized to hybrid yield obtained with DNA of cat cells infected with FeLV in culture, which is 55%.) (2) A few virus-negative tissues also hybridized 60–100% of FeLV RNA. These tissues were derived from lymphoma-bearing cats as well as healthy cats. (3) The majority of virus-negative tissues hybridized 30–60% of FeLV RNA, and in this group, tissues from leukemic cats did not show significantly higher hybridization. (4) The results did not define a particular tissue target site since comparable hybridization results were obtained with many different tissues. (5) A few virus-negative tissues from healthy cats hybridized only 15–30% FeLV RNA. This is considerably lower than the level found with the majority of virus-negative tissues (normal or leukemic) and may reflect the true level of endogenous FeLV related sequences in cats. If so, the higher hybridization levels (30–60% of FeLV RNA) observed with most virus-negative tissues indicates more widespread infection in cats than previously believed, and suggests integration of only partial provirus and/or infection of only a fraction of the cells in the tissue. If exogenous FeLV is involved in the leukemogenesis of “virus-negative” cats, the apparent lack of detectable proviral sequences in tissues of many of these cats over and above those of healthy cats could be interpreted in different ways, e.g., partial loss of provirus, integration of a small fragment, or presence of proviral sequences in a limited population of cells. These “virus-negative” cats may serve as a model (S. M. Cotter and M. Essex, 1977, Amer. J. Pathol.87, 265–268) for other animals, including man, where leukemia may sometimes be associated with certain type-C related subviral markers, but detection of provirus is unusual.     

DNA methylation regulates long-range gene silencing of an X-linked homeobox gene cluster in a lineage-specific manner

DNA methylation is a major epigenetic mechanism that has been suggested to control developmental gene regulation during embryogenesis, but its regulatory mechanisms remain unclear. In this report, we show that CpG islands associated with the X-linked homeobox gene cluster Rhox, which is highly expressed in the extraembryonic trophectoderm, are differentially methylated in a stage- and lineage-specific manner during the post-implantation development of mice. Inactivation of both Dnmt3a and Dnmt3b, DNA methyltransferases essential for the initiation of de novo DNA methylation, abolished the establishment of DNA methylation and the silencing of Rhox cluster genes in the embryo proper. The Dnmt3-dependent CpG-island methylation at the Rhox locus extended for a large genomic region ( approximately 1 Mb) containing the Rhox cluster and surrounding genes. Complementation experiments using embryonic stem (ES) cells deficient in the DNA methyltransferases suggested that the CpG-island methylation by Dnmt3a and Dnmt3b was restricted within this large genomic region, and did not affect the neighboring genes outside it, implicating the existence of region-specific boundaries. Our results suggest that DNA methylation plays important roles in both long-range gene silencing and lineage-specific silencing in embryogenesis.     

Microplate-based DNA hybridization assays for detection of human retroviral gene sequences.

Nonisotopic, microwell-based DNA hybridization assays for the specific detection of human immunodeficiency virus type 1 (HIV-1) gag, human T-cell lymphotropic virus type I (HTLV-I) pol, and HTLV-II pol DNA sequences were evaluated. The performances of these detection kits (Gene Detective enzyme oligonucleotide assays; Cellular Products, Inc., Buffalo, N.Y.) were assessed by using clinical samples whose infection status were established by amplification by PCR and then liquid hybridization detection by using virus-specific probes. Peripheral blood mononuclear cell lysates from 59 HIV-1-, 35 HTLV-I-, and 19 HTLV-II-infected individuals and from 15 healthy blood donors were used as substrates for PCR amplification. The results of the study demonstrated a clinical sensitivity of 100%. In addition, the enzyme oligonucleotide assays were able to detect 1 to 10 proviral copies subsequent to PCR amplification, indicating an analytical sensitivity comparable to that of liquid hybridization.