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At least 217 records · Page 12Linked to original sources
PubMed1991

Characterization of clinically significant isolates of Staphylococcus epidermidis from patients with cerebrospinal fluid shunt infections.

Biotyping, slime production, antibiograms, extrachromosomal DNA banding and total DNA restriction analysis were used to characterize Staphylococcus epidermidis strains causing cerebrospinal fluid shunt infections in 11 patients. Infections considered to be community acquired and those acquired in the first 2 weeks of hospital admission were due to oxacillin-susceptible isolates. Multiply resistant strains were isolated from patients who were in hospital for more than 1 month before tube implantation. Slime was detected in staphylococci for 54% of cases, but its expression varied. Strains from different patients could be differentiated from one another by the extrachromosomal DNA bandings and total DNA restriction patterns, but isolates from the same patient were usually similar. During the period of external drainage, epidemiological markers were useful in differentiating persistence of infection from contamination or re-infection by a new strain.

Adult↗
PubMedDate not supplied

[Usefulness of 5 microbiological markers for the differentiation of strains of Klebsiella ozaenae causing an outbreak of nosocomial infection].

Five different microbiological markers (biotyping, antimicrobial susceptibility, heavy-metal susceptibility, klebocin susceptibility and number of extrachromosomal DNA fragments) were utilized in order to distinguish between Klebsiella ozaenae strains arising from a nosocomial infection outbreak and strains of some species isolated from hospital environment. Antimicrobial susceptibility pattern to 13 different antibiotics was the most reliable maker, because 85% of the outbreak strains shown resistance to 8-10 antibiotics and only two strains of hospital environment had similar pattern. Sensitivity for this marker was 85.0% specificity 93.5% and positive predictive value of 89.5%. Other markers were less efficient with a positive predictive value of 79.2%, for biotyping, 70.4% for klebocin susceptibility, 69.2% for number of extrachromosomal DNA fragments and 60.6% for heavy-metals susceptibility. We discuss the applicability of each one of these markers in different circumstances.

Bacteriocins↗
PubMed1995

The short DNA sequences in the cytoplasm of Ehrlich ascites tumor cells are tightly associated with proteins.

Mouse Ehrlich tumor cells harbor extrachromosomal DNA elements in a non-mitochondrial fraction of the cytoplasm (Abken et al., Proc. Natl. Acad. Sci USA 90: 6518-6522, 1993). The cytoplasmic DNA sequences constitute a distinct group of extrachromosomal genetic elements with common properties: (i) the DNA molecules are 50-500 bp in length and of linear configuration, (ii) most of the DNA sequences exhibit the potential to modulate the activity of a transcriptional promoter, and (iii) the DNA elements are preferentially found in tumor cells, not in cells with normal phenotype. Unexpectedly, the extrachromosomal DNA sequences are found to be tightly associated with at least three proteins (52 kD, 62 kD, 64 kD) forming DNA-protein (DNP) complexes. The DNA-protein interaction is stable during extraction with phenol and chloroform and during incubation with proteinase K and pronase P, in the presence of detergents (SDS, NP40), guanidine-HCl, high salt concentrations, and alkali. Hydrolysis of the DNA by DNAse I makes the proteins of the DNP complex accessible to proteolytic degradation. Western blot analyses imply that the proteins associated with the cytoplasmic DNA sequences are antigenically related to nucleomatrix proteins that are covalently bound to certain regions of chromosomal DNA. Covalent bonds between the cytoplasmic DNA and the polypeptides would explain the unexpected high stability of the cytoplasmic DNA-protein complexes in tumor cells.

Animals↗
PubMed1994

The E6/E7 promoter of extrachromosomal HPV16 DNA in cervical cancers escapes from cellular repression by mutation of target sequences for YY1.

Human papillomavirus type 16 (HPV16) induces squamous intraepithelial lesions of the cervical mucosa which may develop into invasive cancer. The expression of viral oncogenes in advanced neoplasias appears increased relative to the proliferating cell layers of low grade lesions raising questions about molecular mechanisms of deregulation of transcription. In a lymph node metastasis of a cervical cancer, we observed full-length HPV16 plasmids and molecules with a small deletion, which was mapped to the long control region (LCR). Both wild type and shortened LCR were amplified by PCR, cloned into the promoter test plasmid pBLCAT6 and sequenced to identify a 107 bp deletion from position 7794 to 7901 in the short LCR. CAT expression in cervical cancer-derived HT3, SiHa and CaSki cells appeared 5- to 6-fold increased under the control of the short LCR. This could be traced back to elevated levels of mRNA initiated at the viral oncogene promoter. A slight further increase in CAT expression was noted in the presence of the HPV16 E2 protein which is probably due to the deletion of one E2 binding site and consequent relief from E2 repression. Computer-assisted sequence analysis and band-shift experiments with purified YY1 protein and wild type or mutated oligonucleotides identified four binding sites for this cellular transcriptional repressor within the promoter-proximal segment of the HPV16 LCR, three of which were removed by the deletion. A LCR fragment comprising these YY1 binding sites was cloned in front of the heterologous thymidine kinase gene promoter and suppressed CAT expression 3- to 4-fold.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗
PubMed1993

Occurrence of extrachromosomal deoxyribonucleic acids in spiroplasmas associated with plants, insects, and ticks.

Several spiroplasmas (helical, motile mollicutes) were previously shown to contain extrachromosomal DNA (E-DNA) elements in the form of viruses (double-stranded viruses or the replicative form of single-stranded viruses) or plasmids. These elements are now being investigated as potential vectors for use in spiroplasma transformation systems. Described herein is the first extensive survey of spiroplasma E-DNA in 23 spiroplasma groups (30 strains), a study facilitated by improvements in protocols for E-DNA extraction. E-DNA elements were found in spiroplasmas associated with leafhoppers/plants (spiroplasma subgroups I-1, I-3, and I-8), other insects (subgroups I-2, I-5, I-6, and I-7 and groups IV and XXII), and ticks (subgroup I-4 and groups V and VI). Elements, maintained by passage with their host spiroplasmas, were often lost after extended passage. Whether the current distribution of E-DNA elements is indicative of historical or proximate factors is not known. Many elements (about 75%) from group I spiroplasmas hybridized with Spiroplasma citri viruses SpV1 or SpV3. Of the elements associated with other spiroplasma groups, none hybridized with either virus. These include Spiroplasma apis strains B31 (18 kb) and L89 (18 and 20 kb), S. mirum strains SMCA (20 kb) and Anderson (16 and 20 kb), group VI strain Y32 (7, 9, 10, and 16 kb), and group XXII strain CT-1 (8 kb). Several of these elements will be characterized and examined for their suitability as spiroplasma cloning vectors.

Animals↗
PubMed1994

Extrachromosomal plasmids in the plant pathogenic fungus Rhizoctonia solani.

Extrachromosomal DNA elements were found in field isolates of Rhizoctonia solani belonging to anastomosis groups (AG) 1-5. An isolate of AG-5 (Rh41) contains a 3.6-kbp plasmid (pRS188) which has a similar A+T content to mitochondrial DNA. pRS188 is linear and has knob structures at its ends, as revealed by electron microscopy. Exonuclease digestions show that the linear ends of pRS188 are protected, and remain protected even after proteinase K digestion. pRS188 does not hybridise to nuclear or mitochondrial DNAs of its host isolate (Rh41), to total DNAs of other plasmid-less AG-5 isolates, or to total DNA of plasmid-harbouring isolates belonging to different AGs. Cellular-fractionation experiments suggest that pRS188 is associated with mitochondria, but it remains undecided whether this occurs inside or outside of the organelles. The nucleotide sequence of about 60% of the plasmid has been determined, revealing no open reading frame longer than 91 amino acids, and no known gene or genetic element is detected in the sequence contigs of 300-1572 bp length. Similar studies were performed with the plasmid pRS104 present in an isolate of AG-4 (Rh36), the sequence of which exhibits essentially the same features as pRS188 except that its A+T content resembles that of nuclear DNA. Pathogenicity tests reveal that the isolates Rh41 and R36 are as virulent as the plasmid-less isolates of AG-4 and -5, indicating that the plasmids do not play any role in pathogenicity.

Base Composition↗
PubMed1983

Possible plasmid involvement in turimycin production in Streptomyces hygroscopicus.

Streptomyces hygroscopicus JA 6599 is the producer of the macrolide antibiotic turimycin. Mapping analysis by conventional matings and protoplast fusion techniques were carried out. The sequence of auxotrophic markers determined by using the method of minimizing the frequency of quadruple crossover recombinants, could be shown to be in accordance with the related marker sequence of Streptomyces coelicolor after both conjugation and protoplast fusion. However, the tur locus could localized between chromosomal markers only assuming quadruple crossover. Moreover, after conventional crosses the tur marker has to be localized at quite another site than after protoplast fusion. Regarding also our results on the evidence of extrachromosomal DNA in strains of S. hygroscopicus, the following hypothesis is proposed: the structural genes for turimycin biosynthesis are localized on the bacterial genome, but plasmid-borne genes might be involved in the control of the antibiotic production in a yet unknown way, possibly by inducing chromosomal rearrangements.

DNA, Bacterial↗
PubMed1980

Chromosomal penicillin resistance in Staphylococcus aureus strains of phage group II.

The markers coding for serotype B penicillinase (PcB) in wild type strains of group II of S. aureus behaved as chromosomal characters in 6 out of 7 cases. The restriction deficient mutants also to some strains of group I. No extrachromosomal DNA could be detected in the transductants. The low frequency of transduction of chromosomal markers as well as the high restriction barrier seem to limit the spread of these markers outside group II.

Bacteriophage Typing↗
PubMed1985

Transposon-like sequences in extrachromosomal circular DNA from mouse thymocytes.

Small polydisperse circular (spc) DNA was isolated from mouse thymocytes and cloned into the HindIII site of lambda vector Charon 7. Fifty-six recombinants from this spc DNA library were analyzed. R repeats, which were originally found near immunoglobulin genes, were enriched in spc DNA clones relative to their representation in the chromosome. In one clone, the R sequence was linked to Bam and MIF sequences and the contiguous arrangement was truncated from both ends. In another clone, composite Bam/R and R repeats existed as a pair in inverted repeat orientation. Truncation occurred from the 5' side without affecting the 3' ends. In both clones, short direct repeats flanked the repeated sequences. The possible role of R sequences in transposition and circular formation is discussed.

Animals↗
PubMed1986

DNA amplification and neoplastic transformation mediated by a herpes simplex DNA fragment containing cell-related sequences.

The transforming potential of the herpes simplex virus type 2 (HSV-2) BamHI fragment E (map position 0.533-0.583) encoding the 140-kDa ribonucleotide reductase was assayed by transfection in established Rat-2 cells. Foci of refractile, morphologically distinguishable cells were induced at lower efficiency and after a longer incubation period as compared to the human tumor oncogene EJ-Ha-ras. Focus-derived BamHI fragment E-transformed cell lines formed medium-to-large (0.1-0.25 mm) colonies in soft agar and were tumorigenic in immunocompetent syngeneic rats. Southern blot analysis of normal rat DNA after EcoRI digestion revealed specific DNA segments homologous to HSV-2 BamHI fragment-E DNA. In BamHI fragment E-transformed and tumor-derived lines, about 8- to 30-fold amplification was detected in a subset of the specific HSV-related DNA segments. In addition, extrachromosomal DNA was isolated from transformed cells by plasmid rescue and contained the left-hand 70% of HSV-2 Bam HI fragment E fused to rat DNA. These results indicate the presence in normal cells of nonrepetitive DNA segments, related to the transforming HSV-2 fragment, that can be targeted for genetic alterations associated with neoplastic transformation.

Animals↗
PubMed1986

Multiple mechanisms generate extrachromosomal circular DNA in Chinese hamster ovary cells.

Seven cloned small circular DNA molecules from CHO cells were sequenced and examined for the presence of homologies to each other and to a number of other functional sequences present in transposable elements, retroviruses, mammalian repeat sequences, and introns. The sequences of the CHO cell circular DNA molecules did not reveal common structural features that could explain their presence in the circular DNA population. A gene bank was constructed for CHO chromosomal DNA and sequences homologous to two of the seven small circular DNA molecules were isolated and sequenced. The nucleotide sequences present at the junction of circular and chromosomal DNA suggest that a recombination process involving homologous pairing may have been involved in the generation of one, but not the other, of the two circular DNA molecules.

Animals↗
PubMed1992

Singlet oxygen induced DNA damage and mutagenicity in a single-stranded SV40-based shuttle vector.

The effects of singlet oxygen (1O2), generated by the thermal decomposition of water soluble NDPO2 (endoperoxide of the disodium 3,3'-(1,4-naphthylidene) dipropionate), on a single-stranded shuttle vector were analysed. 1O2 induces a much higher level of breaks in the phosphodiester backbone of single-stranded than double-stranded DNA. This may be due to a higher accessibility of guanine residue, primarily damaged by 1O2. The damaged vector was transfected into monkey COS7 cells where single-stranded DNA was converted to the double-stranded replicative form DNA. After 3 days, extrachromosomal DNA was extracted and the plasmids rescued in E. coli to study mutagenesis. There is a significant increase in mutation frequency of damaged single-stranded DNA in comparison to untreated DNA. It is concluded that 1O2 induces breaks in the backbone of single-stranded DNA and that the 1O2-damaged molecules are mutated after passage through mammalian cells.

Animals↗
PubMed1999

Efficient persistence of extrachromosomal KSHV DNA mediated by latency-associated nuclear antigen.

Primary effusion lymphoma (PEL) cells harbor Kaposi's sarcoma-associated herpesvirus (KSHV) episomes and express a KSHV-encoded latency-associated nuclear antigen (LANA). In PEL cells, LANA and KSHV DNA colocalized in dots in interphase nuclei and along mitotic chromosomes. In the absence of KSHV DNA, LANA was diffusely distributed in the nucleus or on mitotic chromosomes. In lymphoblasts, LANA was necessary and sufficient for the persistence of episomes containing a specific KSHV DNA fragment. Furthermore, LANA colocalized with the artificial KSHV DNA episomes in nuclei and along mitotic chromosomes. These results support a model in which LANA tethers KSHV DNA to chromosomes during mitosis to enable the efficient segregation of KSHV episomes to progeny cells.

Antigens, Viral↗
PubMed1996

Ty3 integrase mutants defective in reverse transcription or 3'-end processing of extrachromosomal Ty3 DNA.

Ty3, a retroviruslike element in Saccharomyces cerevisiae, encodes an integrase (IN) which is essential for position-specific transposition. The Ty3 integrase contains the highly conserved His-Xaa(3-7)-His-Xaa(23-32)-Cys-Xaa(2)-Cys and Asp, Asp-Xaa(35)-Glu [D,D(35)E] motifs found in retroviral integrases. Mutations were introduced into the coding region for the Ty3 integrase to determine the effects in vivo of changes in conserved residues of the putative catalytic triad D,D(35)E and the nonconserved carboxyl-terminal region. Ty3 viruslike particles were found to be associated with significant amounts of linear DNA of the approximate size expected for a full-length reverse transcription product and with plus-strand strong-stop DNA. The full-length, preintegrative DNA has at each 3' end 2 bp that are removed prior to or during integration. Such 3'-end processing has not been observed for other retroviruslike elements. A mutation at either D-225 or E-261 of the Ty3 integrase blocked transposition and prevented processing of the 3' ends of Ty3 DNA in vivo, suggesting that the D,D(35)E region is part of the catalytic domain of Ty3 IN. Carboxyl-terminal deletions of integrase caused a dramatic reduction in the amount of Ty3 DNA in vivo and a decrease in reverse transcriptase activity in vitro but did not affect the apparent size or amount of the 55-kDa reverse transcriptase in viruslike particles. The 115-kDa viruslike particle protein, previously shown to react with antibodies to Ty3 integrase, was shown to be a reverse transcriptase-IN fusion protein. These results are consistent with a role for the integrase domain either in proper folding of reverse transcriptase or as part of a heterodimeric reverse transcriptase molecule.

Amino Acid Sequence↗
PubMed1990

[Antibiotic resistance plasmids in Salmonella strains isolated from various sources].

Resistance of 60 Salmonella strains to aminoglycoside antibiotics was studied. It was found that 51 strains had a multiple resistance to the antibiotics used. By the antibiotic resistance phenotypes, the strains were divided into three major groups. Analysis of the extrachromosomal DNA revealed the presence of plasmids in 48 antibiotic resistant strains and 6 antibiotic sensitive strains. The plasmids transferred by conjugation to the E. coli recipient from 21 antibiotic resistant strains. The 150-kb plasmids transferred in all the strains. The 100-kb plasmids additionally transferred in 5 strains. The high molecular weight plasmids that transferred to the recipient strain by conjugation encoded resistance to all the aminoglycosides used.

Aminoglycosides↗
PubMed1987

[The Mycoplasma genome].

A review is presented of the available data on the nature of chromosomal and extrachromosomal DNA of Mollicutes (mycoplasmas)--the smallest and simplest procaryotic organisms.

Base Sequence↗