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At least 631 records · Page 35Linked to original sources

PubMed1996

Detection of Kaposi's sarcoma-associated herpesvirus-like DNA sequence in angiosarcoma.

The partial DNA sequence of a putative new herpesvirus has recently been isolated from almost all cases of Kaposi's sarcoma (KS), from a small subset of AIDS-related lymphomas, and from a high proportion of multicentric Castleman's disease. The presence of this KS-associated herpesvirus, which is also known as human herpes virus 8 (KSHV/ HHV8), has not been reported in vascular tumors other than KS. We therefore examined a series of vascular neoplasms of both endothelial and pericyte derivation using polymerase chain reaction to detect a 233-hp segment of the viral DNA. KSHV/HHV8 sequences were found in 7 of 24 (29%) angiosarcomas and 1 of 20 (5%) hemangiomas but not in any hemangiopericytomas (0 of 6). The presence of the virus in angiosarcoma was confirmed by direct sequencing of the polymerase chain reaction product and Southern blotting in one case each. Only one of the affected patients was known to be immunocompromised. By detecting its presence in a significant proportion of angiosarcomas, this study extends the number of tumors associated with KSHV/HHV8, further tightens its association with malignancy, and suggests a tropism of the virus for endothelial cells. The presence of KSHV/HHV8 in angiosarcomas in addition to classical KS also indicates that immunosuppression is not a requisite for viral infection.

Adolescent↗

PubMed1990

A DNA-binding protein containing two widely separated zinc finger motifs that recognize the same DNA sequence.

We have isolated a full-length cDNA clone encoding a protein (PRDII-BF1) that binds specifically to a positive regulatory domain (PRDII) of the human IFN-beta gene promoter, and to a similar sequence present in a number of other promoters and enhancers. The sequence of this protein reveals two novel structural features. First, it is the largest sequence-specific DNA-binding protein reported to date (298 kD). Second, it contains two widely separated sets of C2-H2-type zinc fingers. Remarkably, each set of zinc fingers binds to the same DNA sequence motif with similar affinities and methylation interference patterns. Thus, this protein may act by binding simultaneously to reiterated copies of the same recognition sequence. Although the function of PRDII-BF1 is not known, the level of its mRNA is inducible by serum and virus, albeit with different kinetics.

Amino Acid Sequence↗

PubMed1998

SV40-like DNA sequences in pleural mesothelioma, bronchopulmonary carcinoma, and non-malignant pulmonary diseases.

Pleural and pulmonary malignancies are usually associated with well-known carcinogen exposure. Recently, the presence of simian virus 40 (SV40)-like DNA sequences has been detected in brain and bone-related human cancers and in pleural mesothelioma. In order to determine whether SV40-like DNA sequences are also present in bronchopulmonary carcinoma and non-malignant lung samples, 125 frozen pleural and pulmonary samples (including 21 mesotheliomas, 63 bronchopulmonary carcinomas, 8 other tumours, and 33 non-malignant samples) and 38 additional samples distant from tumours were studied for the occurrence of SV40-like DNA sequences by polymerase chain reaction (PCR) amplification followed by hybridization with specific probes. Sequences related to SV40 large T antigen (Tag) were present in 28.6 per cent of bronchopulmonary carcinomas, 47.6 per cent of mesotheliomas, and 16.0 per cent of cases with non-neoplastic pleural and pulmonary disease. No statistically significant difference in the occurrence of these DNA sequences was found between malignant mesothelioma and bronchopulmonary carcinoma, but a significantly higher number of mesothelioma cases exhibited SV40-like DNA sequences in comparison with cases of non-malignant pleural or pulmonary disease (P < 0.04). Among cases positive for SV40-like DNA sequences, a history of asbestos exposure was found in 3 out of 12 bronchopulmonary carcinomas and 8 out of 10 mesotheliomas. Immunohistochemistry using monoclonal antibodies directed against Tag did not demonstrate nuclear staining. The DNA sequences were not related to BK virus sequences, but three samples were positive with probes hybridizing with JC virus DNA sequences. In conclusion, this study demonstrates the presence of SV40-like DNA sequences in pulmonary neoplasms and in non-malignant lung tissues. It appears that the presence of SV40-like DNA is not unique to cancer.

Adult↗

PubMed1988

Correlation of histologic types of carcinoma of the uterine cervix and human papillomavirus and herpes simplex virus type 2 DNA sequences in the uterine cervical biopsies.

Forty patients with invasive cancer of cervix from New Delhi were examined for the presence of human papillomavirus (HPV) and herpes simplex virus (HSV) type 2 DNA sequences in a Southern hybridization assay. Data were analysed according to the histologic type of cancer. HPV DNA sequences were detected in 82.5% biopsies and HSV-2 DNA sequences were found in 10% biopsies. HPV-16 DNA sequences were found either alone or together with HPV-18 and/or HSV-2 Bgl II N fragment in 55% biopsies from keratinizing squamous cell carcinoma, whereas HPV-18 sequences were found in 35% biopsies. Similarly, 50% biopsies from patients with non keratinizing squamous cell carcinoma contained HPV-16 DNA and 38.9% biopsies had HPV-18 DNA. HSV-2 Bgl II N DNA sequences were present in 10% biopsies which were also positive for HPV-16 and/or HPV-18 DNA sequences. Two biopsies from adenocarcinoma of uterine cervix contained HPV-18 and HPV-16 DNA sequences. Therefore, no significant correlation seems to exist between HPV-types and histologic types or grades of differentiation of tumor.

Adenocarcinoma↗

PubMed1988

Mitochondrial telomeres: surprising diversity of repeated telomeric DNA sequences among six species of Tetrahymena.

The DNA sequences at the ends of the linear mtDNA of 6 species of Tetrahymena encompassing 13 strains were determined. All the strains have variable numbers of a tandemly repeated DNA sequence, 31 bp to 53 bp in size, at their mtDNA termini. Based upon the size and nucleotide sequence of the terminal repeats, the telomeres can be separated into four classes. T. pigmentosa, hyperangularis, and hegewischi have different telomeric repeats on the two ends of their mtDNAs. The only conserved feature of the mtDNA termini is the presence of tandem repeats. The function of the repeats might be to promote unequal crossing over during recombination, thereby overcoming the problem of telomere replication for these linear DNAs.

Animals↗

PubMed1986

Transforming activity of human papillomavirus type 16 DNA sequence in a cervical cancer.

A genomic DNA sample from cervical cancer tissue, containing human papillomavirus (HPV) type 16, was found to induce malignant transformation of NIH 3T3 cells when it was tested by transfection assays using the calcium phosphate coprecipitation technique. The primary and secondary transformants contained the HPV type 16 DNA sequences and human specific Alu family sequences. To the best of our knowledge, it has not been reported previously that HPV type 16 DNA sequences in total genomic DNA from a cervical cancer have transforming activity.

Adenocarcinoma↗

PubMed1983

DNA sequence divergence in the Drosophila virilis group.

DNA sequence divergence was analyzed in some sibling species of the Drosophila virilis group. Clones comprising about 0.1% of the genome DNA were selected at random from a D. virilis library for a comparative study on DNA from D. lummei, D. novamexicana, D. borealis, and D. lacicola. Blot hybridization experiments indicated that about 70% of DNA from D. lummei and D. novamexicana and less than 50% of DNA from D. borealis and D. lacicola share sequences that are homologous to DNA in D. virilis. This finding is in excellent agreement with the genealogical tree based on cytological studies (Throckmorton 1982). - Four plasmids with inserts which are present in one or a few copies per genome were hybridized in situ to polytene chromosomes. These experiments demonstrate that (1) homologous "unique" DNA sequences are localized exclusively in homologous bands and (2) homologous bands that appear to be identical in different species may contain different DNA sequences.

Animals↗

PubMed1994

A stochastic model for the evolution of autocorrelated DNA sequences.

Currently used stochastic models of DNA sequence evolution assume independent and identically distributed nucleotide sites. They are too simple to account for dependence structures obviously present in molecular data. Up to now more realistic stochastic models for nucleotide substitutions have been considered intractable. In this paper a procedure that accounts for non-overlapping correlations among pairs of sites of a DNA sequence is developed. We show that currently used models that ignore correlated sites underestimate distances inferred from observed sequence dissimilarities. For the analyzed mitochondrial sequence data this underestimation is not drastic in contrast to paired regions (stems) of bacterial 23S rRNA sequences.

Animals↗

PubMed1997

Robustness of the estimator of the index of dispersion for DNA sequences.

If substitutions in DNA sequences follow a Poisson process, the ratio of the variance in the number of substitutions to the mean number of substitutions (the index of dispersion) should equal 1. In this paper, the robustness of the commonly applied estimator of the index of dispersion in replacement sites and silent sites to various assumptions regarding DNA evolution is explored using simulation methods. The estimate of the index of dispersion may be strongly biased if the assumptions of the model of substitution are violated. However, the results of this study support the conclusions of studies by Gillespie and Ohta that the process of substitution in replacement sites is overdispersed. This result contradicts those of a recent study and shows that the high index of dispersion for replacement sites is not an artifact caused by the method of estimation.

Computer Simulation↗

PubMed1990

Assignment of 35 single-copy and 17 repetitive sequence DNA probes to human chromosome 3: high-resolution physical mapping of 7 DNA probes by in situ hybridization.

Thirty-five single-copy and 17 repetitive sequence DNA probes specific for human chromosome 3 were isolated from human chromosome 3-derived genomic libraries. Seven DNA clones, including three that are polymorphic for BglII or MspI, were mapped by in situ hybridization. Four probes were mapped to 3p subregions and 3 were mapped to 3q subregions. Three of the DNA sequences map to regions overlapping a segment of chromosome 3 (3p14-23) frequently deleted in small cell lung cancer cells. By Southern blot analysis on a deletion hybrid panel, we previously mapped 6 of these probes to three distinct chromosome 3 subregions. Our in situ data support these assignments and more precisely determine the localization of each clone to the following regions: D3S34 (3p14-21), D3S35 (3p21), D3S39 (3p21), D3S40 (3p12-13), D3S37 (3q21-23), and D3S36 (3q21). Clone pL84c, a low repeat sequence clone (approximately 30 copies), was mapped to the 3q21-29 subregion. These DNA clones mapped by in situ hybridization can provide useful landmarks for the ordering and localization of other clones.

Chromosome Mapping↗

PubMed1997

Insights into the evolutionary process from patterns of DNA sequence variability.

Studies of DNA sequence diversity, particularly in Drosophila, reveal both the complexity of natural selection and the importance of the interaction of natural selection and variation in rates of recombination within genomes and between species in determining levels of sequence variability in different genes and different species. The impact of both adaptive and deleterious mutations are evident. Extension of these types of studies to other organisms has begun in earnest.

Adaptation, Biological↗

PubMed1989

Transcription from the P1 promoters of Micromonospora echinospora in the absence of native upstream DNA sequences.

We demonstrated previously that the 0.4-kilobase DNA fragment from Micromonospora echinospora contains multiple tandem promoters, P1a, P1b, P1c, and P2, which are also functional when cloned into Streptomyces lividans. We now show by in vitro transcription with Streptomyces RNA polymerase that each of these promoters is an authentic initiation site, rather than a processing site for transcripts which initiate further upstream. The DNA sequence requirements for the closely spaced promoters P1a, P1b, and P1c, which are coordinately induced during stationary phase in M. echinospora, were examined by deletional analysis in S. lividans. The P1a and P1b promoters were functional despite deletion of native sequences 5 and 17 base pairs upstream of each initiation site, respectively. Thus, P1a and P1b had greatly reduced upstream DNA sequence requirements compared with typical procaryotic promoters. In contrast, transcription from promoter P1c was significantly decreased when native sequences 34 base pairs upstream were replaced.

Base Sequence↗

PubMed1985

Human DNA sequences exhibiting gamete-specific hypomethylation.

Three human DNA sequences have been cloned from DNA regions which are strikingly undermethylated in sperm, highly methylated in adult somatic tissues, and methylated to an intermediate extent in tissues of extraembryonic origin. It is proposed that some such DNA sequences may function specifically early in embryogenesis or during gametogenesis. They may be subsequently extensively methylated in the embryonic cell lineage and methylated to a lesser extent in extraembryonic tissues in order to allow embryogenesis to proceed.

Base Sequence↗

PubMed2001

Influence of DNA sequence on the positioning of RecA monomers in RecA-DNA cofilaments.

We show that certain DNA sequences have the ability to influence the positioning of RecA monomers in RecA-DNA complexes. A tendency for RecA monomers to be phased was observed in RecA protein complexes with several oligonucleotides containing a recombinational hotspot sequence, the chi-site from Escherichia coli. This influence was observed in both the 5' to 3' and 3' to 5' directions with respect to chi. A 5'-end phosphate group and probably some other features in DNA also influence the phasing of RecA monomers. We conclude that natural DNAs contain a number of features that influence the positioning of RecA monomers. The ability of specific DNA sequences to influence the positioning of RecA monomers demonstrates some specificity in the binding of individual bases at different sites within a RecA monomer and, most likely, reflects the stereochemical non-equivalence of these sites. The possible biological implications of the phasing of RecA monomers in presynaptic DNA-protein cofilaments are discussed.

Base Sequence↗

PubMed1995

Identification of a novel DNA sequence differentially expressed between normal human CD34+CD38hi and CD34+CD38lo marrow cells.

We have applied the recently developed differential display method to extend the molecular characterization of the less mature CD34+CD38lo bone marrow progenitors in comparison with the CD34+CD38hi cells to better understand their functional differences. Immunomagnetic enrichment of CD34+ cells followed by flow cytometry was used to isolate CD34+CD38lo and CD34+CD38hi cells from human organ donor bone marrow. A limited set of the poly A+ RNA sequences present in these two cell populations was amplified by a combination of reverse transcription with an anchored oligo dT-based primer and polymerase chain reaction with the same oligo dT primer and arbitrary decamers. A radioactive tracer allowed these sequences to be displayed as a series of bands on a denaturing polyacrylamide gel. Eight bands were chosen that appeared in multiple displays to represent gene sequences differentially expressed between CD34+CD38hi and CD34+CD38lo cells. Comparison of the sequences with public DNA sequence databases available identified one sequence as myeloperoxidase. Two other clones matched sequence fragments of unknown function, whereas the remaining five are novel sequences not present in existing databases. The relative level of expression of all of the sequences was tested by an independent reverse transcriptase-polymerase chain reaction with sequence-specific oligonucleotide primers. The lower level of myeloperoxidase mRNA in CD34+CD38lo cells was confirmed, as was the higher expression of the novel sequence 345. Sequence 345 expression is highest in CD34+CD38- cells and decreases with increased CD38 expression. It is expressed in negligible amounts in hematopoietic cell lines and other sources of human tissue, suggesting it may have a functional role in normal hematopoiesis.

ADP-ribosyl Cyclase↗

PubMed1973

Separation of DNA sequences complementary to the RNA of avian myeloblastosis virus from chicken DNA by alkaline cesium chloride density sedimentation.

Density gradient sedimentation in alkaline cesium chloride of DNA from normal chicken embryos or leukemic myeloblasts fragmented to a size of 13S revealed that the DNA sequences complementary to 70S avian myeloblastosis virus RNA sedimented in the high guanine plus cytosine region ahead of the main peak of cellular DNA. When the DNA was fragmented into pieces of 6.6S there was a broader distribution of the DNA sequences complementary to the viral RNA. This technique could be employed as a step towards the isolation of DNA copies of the entire viral RNA genome from the mass of host cellular DNA.

Animals↗

PubMed1991

A multivariate representation and analysis of DNA sequence data.

A new way to represent and analyze DNA sequence data is described. This approach complements methods currently used, in that it allows the systematic part of the variation between different sequences to be modeled. This can prove as informative as absence of variation (homology), which is the most widely used criterion for comparing sequence data. A multivariate sequence-activity model (SAM), for DNA-promoter sequences is presented, by which the relative promoter strength is modeled in terms of the primary DNA-sequence. The model is shown to have a good predictive capability. The coefficients from the model are interpreted, and used to design new structures predicted to be strong promoters in the system investigated. The approach described is also applicable to other kinds of sequence data, e.g. RNAs, proteins or peptides.

Base Sequence↗

PubMed1984

'ZSTATS'--a statistical analysis for potential Z-DNA sequences.

We have developed a FORTRAN programme for scanning DNA sequences for potential Z-DNA forming regions using the One-Sample Runs Test. The programme also detects other non-random arrangements of purines and pyrimidines on the same strand and will detect purine- or pyrimidine-rich strands and G:C- or A:T-rich regions. A series of test statistics are produced as a graphical output and these have been used to search a number of beta- type globin DNA sequences for potential Z-DNA regions whose biological significance is briefly discussed.

Adult↗