Diagnosis of mutations by the PCR double RFLP method (PCR-dRFLP).
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Base Sequence↗
Biomedical subjects
O Grau
Publications and source records attributed to O Grau.
Development of PCR-based assays for the detection of two human mollicute species, Mycoplasma penetrans and M. hominis.
Recently, a 16S rDNA-based polymerase chain reaction (PCR) assay was developed for the selective and sensitive detection of Mycoplasma pirum. In this study, the same procedure was used in order to selectively detect by PCR two human mycoplasmas, M. hominis and M. penetrans, with a high level of sensitivity even in a context of human DNA. For each assay, the specificity was verified by testing DNA from other mollicute species (including those closely related to the corresponding mycoplasma), from bacteria phylogenetically close to mollicutes, from Escherichia coli and from human peripheral blood mononuclear cells (PBMCs). Each assay proved to be highly sensitive since it reliably detected 10 DNA molecules, even in a context of human DNA. The results of this study demonstrate the suitability of our procedure using primers which were designed for the PCR detection of human mollicutes with a high specificity and a low and reproducible threshold of sensitivity.
Base Sequence↗
Inhibition of HIV type 1 reverse transcriptase assay by nucleases produced by contaminating mycoplasmas.
Mycoplasmal contamination of HIV-1-infected cells has been found to induce reduction of reverse transcriptase (RT) activity; however, the exact mechanism of this phenomenon was not clearly elucidated. Our results indicate that the apparent reduction in RT activity is due to a calcium-dependent nuclease(s) that is (are) produced by contaminating mycoplasmas. The interference with the RT assay was found to be due to the degradation of products of the RT activity. Addition of EGTA at a 1 mM concentration was sufficient to remove the inhibitory effect. The particular HIV-1-producing cell line that was under study was found to be contaminated with Mycoplasma fermentans and Mycoplasma pirum and the latter was isolated in pure culture. Nuclease activity was also observed with pure cultures of mycoplasmas from different species. The activity was found to be of the endonuclease type because it was active with both supercoiled and linear DNAs.
Cell Line↗
The closely related citrus ringspot and citrus psorosis viruses have particles of novel filamentous morphology.
Some properties of the particles of citrus ringspot virus (CtRSV) and the related citrus psorosis-associated virus (CPsAV) are described. The particles of CtRSV have been reported to be sinuous linear structures about 10 nm in diameter and of two lengths (300 to 500 nm and 1500 to 2500 nm) representing 'top' and 'bottom' sedimentation components. We show that these particles are collapsed double-stranded forms of nucleocapsid-like, highly flexuous open circles formed of filaments 3 to 4 nm in diameter. Top-component filaments had contour lengths of 600 to 1000 nm, i.e. twice that reported for the corresponding collapsed form. Bottom-component filaments had contour lengths about four times longer than those of top-component filaments. The structures suggest that CtRSV represents a new genus (possibly family) related to the tenuiviruses. However, we failed to demonstrate any serological relationship between CtRSV and several tenuiviruses; moreover, the capsid protein sizes and host ranges are quite different. We offer the name Ophiovirus for the proposed new genus.
Antibodies, Viral↗
Development of a selective and sensitive polymerase chain reaction assay for the detection of Mycoplasma pirum.
A new assay using the polymerase chain reaction to amplify a 173-nucleotide DNA fragment within the 16S ribosomal RNA gene of Mycoplasma pirum has been developed. The assay selectively amplified DNA from all strains of M. pirum tested with a high level of sensitivity, even in a context of human DNA. DNA from other mollicute species, including those closely related to M. pirum, from bacteria phylogenetically close to mollicutes (Clostridium innocuum, C. ramosum and Bacillus subtilis), from Escherichia coli and from human peripheral blood mononuclear cells, did not produce the amplified DNA product specific for M. pirum.
Base Sequence↗
Detection of mollicute contamination in cell cultures by 16S rDNA amplification.
A polymerase chain reaction (PCR) system was developed for the detection of mollicutes as contaminants of cell cultures. By using three oligonucleotides chosen in the 16S rDNA sequences, two sets of primers able to promote amplification of all Mycoplasma and Ureaplasma (molli1-molli2a) or all Acholeplasma (molli1-molli2b) species examined were determined. This PCR system, first applied to experimentally infected Vero cell lines, was then evaluated for the detection of mollicutes in 86 cell culture samples, comparatively to DNA staining, culture and ELISA. The results obtained by the four techniques were in agreement in 82 cases (36 positive, 46 negative). PCR allowed detection of contamination in one and two cases negative by ELISA and culture, respectively, and confirmed questionable results obtained by DNA staining. As described, PCR seems to be a very convenient tool for routine detection of cell culture contaminants.
Acholeplasma↗
A simple nucleic acid amplification assay for the rapid detection of Junín virus in whole blood samples.
Argentine hemorrhagic fever (AHF) is an endemoepidemic disease with cardiovascular, renal and neurologic alterations acquired in the richest farming land in Argentina. It is caused by Junín virus, one of the few human pathogenic arenaviruses. The S RNA of Junín virus has been molecularly cloned and its nucleotide sequence determined in our laboratory. This information was used to develop a rapid nucleic acid-based diagnostic test commensurate with the low viraemia detected in AHF patients. Junín virus-specific cDNA probes labeled using various methods proved insensitive in dot-hybridizations. Therefore, a RT polymerase chain reaction (PCR) was developed using a pair of oligonucleotide primers to reverse-transcribe and amplify the viral S RNA. The amplification of the target sequences was measured by ethidium bromide staining of the DNA fragments after agarose gel electrophoresis. This type of assay allowed the specific detection of Junín virus RNA sequences present in a single infected BHK21 cell over a background of 10(4) uninfected cells. Control reactions were performed on RNA samples extracted from uninfected cells or cells infected with a high multiplicity of LCMV, another arenavirus present in the AHF endemic area. The PCR was first adapted to detect viral RNA in peripheral blood mononuclear cells, described to harbor most of the virus. A simplification of this assay allows the detection of Junín virus in RNA extracted from 100 microliters of whole blood using guanidium thiocyanate disruption and acid phenol extraction. Under the conditions described in this paper, it is possible to detect up to 0.01 pfu of Junín virus in a blood sample. An early and rapid laboratory diagnostic test for AHF is important since the only effective therapy that reduces the mortality rate from 30% to less than 1% consists of early treatment with immune plasma.
Animals↗
Isolation of RNA from whole blood for reliable use in RT-PCR amplification.
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Humans↗
Phylogenetic relationships of three porcine mycoplasmas, Mycoplasma hyopneumoniae, Mycoplasma flocculare, and Mycoplasma hyorhinis, and complete 16S rRNA sequence of M. flocculare.
The nucleotide sequence of the 16S rRNA gene of Mycoplasma flocculare was determined and was compared with the sequence of a related porcine mycoplasma, Mycoplasma hyopneumoniae. While the overall level of DNA-DNA homology was approximately 11%, sequence alignment of the two 16S rRNA genes yielded a homology value of more than 95%, emphasizing the highly conserved nature of the 16S rRNA gene. Multiple sequence alignments with other mollicutes indicated that M. flocculare, M. hyopneumoniae, and Mycoplasma hyorhinis form a subcluster within the fermentans phylogroup, and this subcluster is distinct from the Mycoplasma pneumoniae phylogroup. Thus, the three mycoplasmas isolated from porcine respiratory systems exhibit phylogenetic similarities.
Animals↗
Identification of a plant-derived mollicute as a strain of an avian pathogen, Mycoplasma iowae, and its implications for mollicute taxonomy.
Strain PPAV, a filamentous but nonhelical mollicute, was isolated from aborted apple seeds in France in late 1979. This organism grew well in SP-4 broth, fermented glucose, and required sterol for growth, and most of its properties suggested that it belonged to the genus Mycoplasma. However, it was serologically distinct; in addition, unlike other Mycoplasma species, genome measurements consistently yielded values of about 1,000 MDa (ca. 1,500 kbp), and the organism had a growth temperature optimum of 43 degrees C. A comparison of strain PPAV 16S rRNA sequences with those of other mollicutes revealed a high degree of sequence similarity to a strain of Mycoplasma iowae, which is commonly encountered in poultry. This relationship was confirmed by performing a restriction endonuclease pattern analysis and DNA-DNA hybridization tests. The genome size of type strain 695 of M. iowae was determined to be about 1,000 MDa (1,500 kbp) by renaturation kinetics, a value which is much higher than any other value known in the genus. Additional measurements by pulsed-field gel electrophoresis yielded values of 1,300 kbp for both strain PPAV and M. iowae. Subsequent phenotypic comparisons supported this relationship. Serologic tests with strain PPAV and other strains of M. iowae confirmed the findings of other investigators that this species is serologically heterogeneous. The high optimum temperature for growth of strain PPAV was also shared by a number of M. iowae isolates. Genome size is an inappropriate character for taxonomic assignment to the family Mycoplasmataceae because strain PPAV and other established species in this family are now known to have genomes ranging in size from 1,000 to 1,400 kbp.
Animals↗
Molecular organization of Junin virus S RNA: complete nucleotide sequence, relationship with other members of the Arenaviridae and unusual secondary structures.
In this study, overlapping cDNA clones covering the entire S RNA molecule of Junin virus, an arenavirus that causes Argentine haemorrhagic fever, were generated. The complete sequence of this 3400 nucleotide RNA was determined using the dideoxynucleotide chain termination method. The nucleocapsid protein (N) and the glycoprotein precursor (GPC) genes were identified as two non-overlapping open reading frames of opposite polarity, encoding primary translation products of 564 and 481 amino acids, respectively. Intracellular processing of the latter yields the glycoproteins found in the viral envelope. Comparison of the Junin virus N protein with the homologous proteins of other arenaviruses indicated that amino acid sequences are conserved, the identity ranging from 46 to 76%. The N-terminal half of GPC exhibits an even higher degree of conservation (54 to 82%), whereas the C-terminal half is less conserved (21 to 50%). In all comparisons the highest level of amino acid sequence identity was seen when Junin virus and Tacaribe virus sequences were aligned. The nucleotide sequence at the 5' end of Junin virus S RNA is not identical to that determined of the other sequenced arenaviruses. However, it is complementary to the 3'-terminal sequences and may form a very stable panhandle structure (delta G-242.7 kJ/mol) involving the complete non-coding regions upstream from both the N and GPC genes. In addition, a distinct secondary structure was identified in the intergenic region, downstream from the coding sequences; Junin virus S RNA shows a potential secondary structure consisting of two hairpin loops (delta G -163.2 and -239.3 kJ/mol) instead of the single hairpin loop that is usually found in other arenaviruses. The analysis of the arenavirus S RNA nucleotide sequences and their encoded products is discussed in relation to structure and function.
Amino Acid Sequence↗
Patterns of transient expression of the arenavirus nucleocapsid protein gene in transfected cells.
The cloned genes for the nucleocapsid proteins N of Junín and LCM (lymphocytic choriomeningitis) arenaviruses were inserted into the SV40-derived expression vector designated pKG4. When BHK-21 (baby hamster kidney fibroblasts) and CV-1 (African green monkey kidney fibroblasts) cell lines were transfected using these constructions, the transient expression yielded a polypeptide that could not be distinguished either by size nor by immunoreactivity from the N protein synthesized during the viral infection. The immunofluorescence analysis showed a pattern of intracellular localization similar to that observed in virus infected cells, i.e. varying from a diffuse cytoplasmic staining to granules, either distributed throughout the cytoplasm or concentrated in the perinuclear region. The association of the N protein with basophilic granules is similar to that observed in the cytopathic effect caused by arenaviruses, and could be related to the physicochemical properties of this polypeptide containing numerous basic amino acid sequences, that would allow for the interaction with cellular RNAs.
Animals↗
Bacteriophage T4 gene 27.
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Amino Acid Sequence↗
Nucleocapsid protein gene of Junin arenavirus (cDNA sequence).
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Amino Acid Sequence↗
Symmetric transcription of bacteriophage T4 base plate genes.
Dot-blot and Northern-blot experiments, using strand-specific RNA probes, show that part of the bacteriophage T4 DNA that codes for six of the base plate structural genes (gp 51, 27, 28, 29, 48 and 54), is transcribed in vivo from both DNA strands. The r DNA strand transcripts contain sequences which are translated into structural proteins. Antisense l strand RNA is about 100 fold less abundant than RNA molecules transcribed from the r DNA strand.
Blotting, Northern↗
Effect of actinomycin D on arenavirus growth and estimation of the generation time for a virus particle.
In an attempt to define the involvement of host transcription in arenavirus growth, a study was made of the effect of actinomycin D (AMD) on the yields of infectious Pichinde, Tacaribe and Junin viruses. The drug was added either immediately after virus adsorption or later after infection, at the stationary phase of virus growth. The time of exposure of the infected cells to the inhibitor was so chosen that the generation and release of virus into the medium took place in the presence of AMD. A double label technique was used to estimate the generation time of an arenavirus particle. This was found to be 6 h or less for all of the arenaviruses examined. The results indicated that treatment of the host cells with AMD, either immediately after virus adsorption or later after infection, does not affect the yield of infectious Pichinde, Tacaribe or Junin viruses, thus implying that continuous host transcription is not required for the replication cycle of these arenaviruses.
Arenaviridae↗
Bacteriophage SPO1 DNA polymerase and the activity of viral gene 31.
Bacteriophage SPO1 DNA-negative (D0) mutants were tested for the induction of viral DNA polymerase during Bacillus subtilis infection. Extracts from SPO1-infected bacteria exhibited enzymatic activity when representative mutants of seven out of the nine known D0 genes were employed. This activity was undetectable in cells infected with mutants in genes 28 and 31. The product of gene 28 (gp28) is known to be responsible for turning on SPO1 middle gene expression. Results show that nonsense mutation in gene 31 leads to the absence of a single polypeptide of 100-105 kDa and that phage DNA synthesis "in vivo" directly depends on gp31 activity. Based on these data it is proposed that SPO1 gene 31 codes for the viral DNA polymerase.
Bacillus subtilis↗
Simultaneous measurement of toxicity and mutagenic activity.
The assay of mutagenic activity of toxic drugs is difficult to perform and analyze, because one needs to know the kinetics of both effects in order to draw reliable conclusions. This is the case with niflumic acid (NA), which reduced the viability of S. typhimurium TA1535 100 times in the Ames test, but the background microcolonies show no difference from controls and the number of revertants was not altered by the drug. A test which measures the kinetics of growth of viable bacteria and mutants in liquid medium has been developed and applied to NA. No mutagenic activity was detected and elimination of the toxicity from the medium is suggested.
Cell Division↗