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Structural features of Borrelia burgdorferi--the Lyme disease spirochete: silver staining for nucleic acids.

Borrelia burgdorferi--the Lyme disease spirochete--was grown in modified Kelly medium and characterized by transmission and by scanning electron microscopy. Using silver staining procedures which preferentially bind to nuclear components of eukaryotic cells, signal could be detected by backscattered electron imaging throughout the length of the prokaryotic spirochete. Interestingly, however, the highest levels of backscattered signal were observed in naturally elaborated membrane blebs that were visible attached to cell surfaces and free in the medium. These membrane vesicles could be enriched by filtration through nitrocellulose or Anopore membranes and by differential centrifugation. The possibility of contaminating cellular DNA coating the membrane vesicles was ruled out by exhaustive digestion with pancreatic DNAse I. Intact DNA was demonstrated both by lysing blebs directly on the surface of microscope grids and by extracting molecules from purified bleb preparation with detergents and solvents. Both linear and circular DNA molecules could be identified in purified membrane blebs. A simple, one-step, alternative silver staining procedure is described which appears to effectively label the protein-nucleic acid complexes contained in the membrane vesicles of the human pathogen B. burgdorferi, and may provide an important method to track and to define the biological function of these structures.

Borrelia burgdorferi↗

Immunofluorescent technique for the detection of antibodies to n-DNA: comparison with radioimmunoassay.

One hundred and six sera from patients with systemic lupus erythematosus (SLE), 20 from patients without SLE but with a positive FANA, and 50 controls were tested for the presence of antibodies to n-DNA, using an immunofluorescent technique with the kinetoplast of Crithidia luciliae as a substrate. A high degree of correlation existed between the results obtained with this technique and a Millipore radioimmunoassay method using a well characterized tritiated native human DNA. The result with the immunofluorescent method could be expressed semiquantitatively as a titer, if serial serum dilutions were used. Results in patients with SLE correlated well with disease activity. We conclude that the immunofluorescent technique can provide a useful alternative to a radioimmunoassay for the detection of antibodies to n-DNA. In addition, as this substrate is known to contain pure n-DNA, problems do not arise with contamination with singlestranded DNA as sometimes occurs with other test antigens. This avoids the detection of antibodies reacting only with single-stranded areas and consequently increased the specificity of the reaction.

Antibodies, Antinuclear↗

Studies on human tonsillar lymphocyte membrane. III. Isolation and characterization of plasma membrane fractions after hypotonic lysis.

Hypotonic lysis was applied for the preparation of lymphocyte plasma membranes. By this method it was possible to separate membrane fractions with a high sialic acid to protein and cholesterol to phospholipid ratio. The plasma membrane fractions had a lower content of endoplasmatic reticulum than the preparations described earlier but were slightly contaminated with DNA. The isolation method proved to useful for the preparation of surface membranes from human lymphocytes

Cell Fractionation↗

Simple method for extracting RNA from cultured cells and tissue with guanidine salts.

We have developed a simple protocol for isolating RNA from both cell culture and tissue from human and animal sources, using guanidine thiocyanate and guanidine hydrochloride, but no organic solvents. The protocol reproducibly yielded 15 to 25 micrograms of high-quality RNA per 10(6) cells of human and animal origin and 1 to 1.1 mg of RNA per gram of human placental tissue. The RNA so obtained was ribonuclease-free and not contaminated by DNA. It was suitable for reverse transcription-polymerase chain reaction, Northern blot analysis, and in vitro expression of proteins. Thus, the molecular assessment of both research and clinical samples can be readily and reliably initiated by the application of this protocol.

Animals↗

Increased expression of histamine H1 receptor mRNA in allergic rhinitis.

BACKGROUND: Histamine plays an important role in producing nasal symptoms via histamine H1 receptor (H1R) in allergic rhinitis. It is reported that the minimum histamine concentration that induces sneezing is lower in allergic patients than in normal control subjects. Previous studies by binding assay on H1R gave divided results on whether the number of H1Rs is increased in allergic rhinitis or not. OBJECTIVE: The objective of this study was to examine if H1R mRNA expression is increased in patients with allergic rhinitis compared with normal healthy volunteers. METHODS: We extracted RNA from scrapings of inferior turbinate mucosa of 10 patients suffering from allergic rhinitis and 10 control subjects. As the H1R gene lacks introns, we treated RNA pellets by DNase to distinguish RNA from contaminating genomic DNA. Since amplification of H1R and beta-actin mRNA remained in an exponential phase at 35 cycles, H1R and beta-actin mRNAs were amplified for 35 cycles by reverse transcription-polymerase chain reaction (RT-PCR). The PCR products were hybridized with internal probes and band intensities were quantitated by a densitometer. RESULTS: The mean +/- SD of H1R/beta-actin ratio was 0.88 +/- 0.62 for the patients with allergic rhinitis and 0.29 +/- 0.17 for the normal subjects; the difference was statistically significant (P < 0.01). CONCLUSIONS: These data suggest that expression of H1R mRNA is increased in the nasal mucosa of the patients with allergic rhinitis.

Actins↗

Analysis of differential gene expression in human colorectal tumor tissues by RNA arbitrarily primed-PCR: a technical assessment.

RNA arbitrarily primed (RAP)-PCR is a powerful tool for studying differential gene expression in cancer cells. Systematic analysis of human tumor samples may provide a list of markers with potential application to the diagnosis, prognostic assessment, and treatment of the disease. Nevertheless, because of characteristics inherent to the samples and technique, artifactual results are likely. We have assessed the effects of several factors on RAP-PCR performance to determine the sensitivity and reproducibility of the technique, as well as the accuracy of its results, under different conditions in human cell lines and in a series of 129 paired human normal colonic mucosa-colorectal carcinoma samples. Our results show that RAP-PCR provides reliable fingerprints in a relatively wide spectrum of circumstances, including variations in RNA concentration and contamination by DNA. Densitometric analysis indicated that relative band-intensity variations more than 20% were reproducible in 95% of the cases. Serial analysis of paired normal-tumor cases yielded a number of bands that were recurrently either underexpressed or overexpressed in tumor relative to normal mucosa. These differentially expressed bands are prime targets of research because they represent candidate tumor-specific up- or down-regulated genes with a relevant role in carcinogenesis.

Colorectal Neoplasms↗

[Determination of circulating immune complexes: comparison between agglutination inhibition and C1Q precipitation in polyethylene-glycol-EDTA (author's transl)].

Three different methods for the determination of circulating immune complexes were compared : precipitation of radioiodinated C1q in polyethyleneglycol-EDTA, inhibition of IgG-coated latex particles agglutination by C1q or polyclonal rheumatoid factor. Normal values and their upper limits as well as the reproducibility of each technique are presented. The possible effect of several factors was investigated : age, sex, anticoagulants, freezing and thawing, contamination by DNA or endotoxin. Comparison of the results obtained with normal or pathological sera revealed a positive correlation between the three techniques. However, the discrepancies noted with some sera make the use of at least two different methods highly recommendable for the study of circulating immune complexes in disease.

Adolescent↗

Maternal contamination of amniotic fluid demonstrated by DNA analysis.

DNA from 16 sets of samples comprising DNA from uncultured amniotic fluid cells, cultured amniotic fluid cells, fetal tissue, and maternal blood was analysed by the polymerase chain reaction (PCR) with AC-repeat primers. The analysis was performed to investigate the presence of contaminating maternal cells in amniotic fluid which would affect the reliability of DNA studies for prenatal diagnosis. In three sets, maternal contamination of uncultured amniotic fluid cells was detected. In one of the three sets, maternal contamination was present in both uncultured and cultured amniotic fluid cells. The use of amniotic fluid cells as a source of DNA for prenatal diagnosis should be limited to cases where the purity of the DNA can be demonstrated prior to the diagnostic test being performed. This limitation in the use of amniotic fluid DNA also extends to other forms of diagnosis relying on the purity of amniotic fluid samples, particularly the new in situ hybridization methods currently being developed.

Amniotic Fluid↗

Environmental whole-genome amplification to access microbial populations in contaminated sediments.

Low-biomass samples from nitrate and heavy metal contaminated soils yield DNA amounts that have limited use for direct, native analysis and screening. Multiple displacement amplification (MDA) using phi29 DNA polymerase was used to amplify whole genomes from environmental, contaminated, subsurface sediments. By first amplifying the genomic DNA (gDNA), biodiversity analysis and gDNA library construction of microbes found in contaminated soils were made possible. The MDA method was validated by analyzing amplified genome coverage from approximately five Escherichia coli cells, resulting in 99.2% genome coverage. The method was further validated by confirming overall representative species coverage and also an amplification bias when amplifying from a mix of eight known bacterial strains. We extracted DNA from samples with extremely low cell densities from a U.S. Department of Energy contaminated site. After amplification, small-subunit rRNA analysis revealed relatively even distribution of species across several major phyla. Clone libraries were constructed from the amplified gDNA, and a small subset of clones was used for shotgun sequencing. BLAST analysis of the library clone sequences showed that 64.9% of the sequences had significant similarities to known proteins, and "clusters of orthologous groups" (COG) analysis revealed that more than half of the sequences from each library contained sequence similarity to known proteins. The libraries can be readily screened for native genes or any target of interest. Whole-genome amplification of metagenomic DNA from very minute microbial sources, while introducing an amplification bias, will allow access to genomic information that was not previously accessible. The reported SSU rRNA sequences and library clone end sequences are listed with their respective GenBank accession numbers, DQ 404590 to DQ 404652, DQ 404654 to DQ 404938, and DX 385314 to DX 389173.

Bacillus Phages↗

nahR, encoding a LysR-type transcriptional regulator, is highly conserved among naphthalene-degrading bacteria isolated from a coal tar waste-contaminated site and in extracted community DNA.

In Pseudomonas putida strain G7, a LysR-type positive transcriptional activator protein encoded by nahR is necessary for activation of two operons involved in naphthalene catabolism [Schell, M. A. & Poser, E. F. (1989). J Bacteriol 171, 837-846]. The role of an nahR homologue, NCIB-nahR, in another naphthalene-metabolizing bacterium, P. putida NCIB 9816-4 was verified. Targeted disruption of NCIB-nahR by homologous recombination resulted in a growth defect in the presence of naphthalene or salicylate as sole carbon and energy source. The nahR homologues and intergenic regions between nahR-like and nahG-like genes from P. putida NCIB 9816-4 and seven bacteria native to a naphthalene-rich coal tar contaminated site were amplified by PCR using degenerate primers. The amplified nahR homologues and the intergenic regions were cloned and sequenced. Alignment of the deduced amino acid sequences from NahR homologues revealed that NahR-like proteins showed only minor variations in all investigated naphthalene-degrading isolates. The intergenic regions, together with known NahR-binding sites showed the consensus NahR-protein-binding sites (5'-ATTCACGCTN(2)TGAT-3'). Surprisingly, amplified intergenic regions from naphthalene-degrading micro-organisms native to this study site were 100% identical to that of the pDTG1 plasmid (an archetypal naphthalene-catabolic plasmid from Pseudomonas putida NCIB 9816-4), but the nahR coding regions were not. DNA representing the uncultured microbial community was extracted from six sediment samples with varying coal tar exposure histories. PCR amplification of nahR from sediment DNA was observed in contaminated samples, but in uncontaminated samples only following laboratory incubation with naphthalene. The sediment-derived PCR products were sequenced and also found to be almost identical to known nahR genes. Thus, the structure and function of nahR-nahG regulatory genes appear to be highly conserved.

Amino Acid Sequence↗

2,3,7,8-Tetrachlorodibenzo-p-dioxin-inducible, Ah receptor-mediated bending of enhancer DNA.

The environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin produces its biological effects by binding to an intracellular protein, the Ah receptor. The liganded receptor activates transcription by binding to a specific recognition motif within a dioxin-responsive enhancer upstream of the target CYP1A1 gene. Here, we have used gel retardation to analyze the interaction between the liganded Ah receptor and five circularly permuted DNA fragments that contain a receptor recognition motif. Our findings indicate that the binding of the liganded receptor to its recognition motif bends the DNA at (or near) the site of the protein-DNA interaction. This observation implies that Ah receptor-induced DNA distortion may contribute to the activation of CYP1A1 transcription by 2,3,7,8-tetrachlorodibenzo-p-dioxin.

Affinity Labels↗

Retrospective detection of laboratory cross-contamination of Mycobacterium tuberculosis cultures with use of DNA fingerprint analysis.

In 1992-1993, we investigated possible cross-contamination of Mycobacterium tuberculosis cultures as part of a study of tuberculosis in Arkansas by using DNA fingerprint analysis. Of patients whose isolates were matched, those for whom smears were negative and only one culture was positive were identified from laboratory records. Clinical, laboratory, DNA fingerprint, and epidemiological data were reviewed. Of 259 patients, nine (3.5%) were judged to be due to cross-contamination. None of these patients had a clinical course consistent with tuberculosis. All nine specimens were processed with another isolate with a matching DNA fingerprint, and epidemiological connections were not identified among any of the patients. To avoid erroneous diagnoses and unnecessary therapy and public health investigations, specimens from patients with tuberculosis whose smears are negative and only one culture is positive should be investigated for cross-contamination. An inconsistent clinical course and a DNA fingerprint that matches those of other culture-positive specimens processed concurrently, coupled with the lack of an epidemiological connection, suggest cross-contamination.

Adult↗

Development of a quantitative real-time PCR assay for the detection of Aspergillus carbonarius in grapes.

Aspergillus carbonarius is the main species responsible for the production of ochratoxin A (OTA) in wine grapes. To monitor and quantify A. carbonarious in grapes, a quantitative real-time PCR assay was developed as a possible tool for predicting the potential ochratoxigenic risk. DNA extraction from grape berries was performed by using conventional extraction and clean up through EZNA Hi-bond spin columns. A TaqMan probe was used to quantify A. carbonarius genomic DNA in grape berries samples. An exogenous internal positive control was used to overcome DNA recovery losses due to matrix inhibition. The quantification of fungal genomic DNA in naturally contaminated grape was performed using the TaqMan signal versus spectrophotometrically measured DNA quantities (Log10) calibration curve with a linearity range from 50 to 5 x 10(-4) ng of DNA. A positive correlation (R2=0.92) was found between A. carbonarious DNA content and OTA concentration in naturally contaminated grape samples. This is the first application of TaqMan real-time PCR for identifying and quantifying A. carbonarius genomic DNA occurring in grapes. The rapid DNA extraction method for grapes, together with the commercial availability of reagents and instrumentation, allows to perform a remarkable number of reproducible assays (96-well format) in less than 4 h.

Aspergillus↗

Genetic effects of mercury contamination on aquatic snail populations: allozyme genotypes and DNA strand breakage.

Allozyme data and DNA strand break frequencies were compared among populations of Pleurocera canaliculatum from five sites with varying mercury contamination on the North Fork Holston River (NFHR) in southwestern Virginia, USA. Allozyme genotype frequencies for four loci were significantly different between populations from the three most highly contaminated sites and those from two lesser contaminated sites. In addition, heterozygosity at three of these loci was significantly lower in the populations from the most highly contaminated sites. The DNA strand break frequency was significantly correlated to whole-body total mercury concentration in snails from three sites. These data add to the evidence supporting the use of DNA strand breakage as an indicator of chemical contamination and the use of allozyme analysis as a marker of contamination and possible selection for pollution resistance. However, the relationship between contaminant-induced changes in the genetic variation of enzymes of central metabolism and the functionalities upon which selection for resistance may act remain unclear, and mechanisms other than selection for resistance must be considered. Use of enzymes from other biochemical pathways may be appropriate for other species or for those under other chemical pollution pressures.

Adaptation, Physiological↗

Protocols for ancient DNA typing.

Molecular analysis of fossil and archaeological remains has been established as a powerful tool in providing new insight in phylogenetic investigations. The overlapping set of molecular modifications and degradation that forensic samples share with archaeological specimen suggests the application of similar technical approaches to the respective biological material. Polymerase chain reaction is the molecular technique of choice for the retrieval of specimen deoxyribonucleic acid (DNA) molecules. Because of intrinsic sensitivity, potential contaminations from exogenous DNA sources must be monitored through the entire process by the introduction of multiple blank controls. Cloning and sequencing of polymerase chain reaction products often is the only way to discriminate between contaminations and endogenous sequences as well as to identify variable positions from nucleotide modifications/DNA polymerase errors. Phylogenetic analysis and investigations of the pattern of substitutions are an additional and necessary step to validate the retrieved sequence. Comparison with available related samples (modern or extinct) is critical to correctly validate the results and to avoid artifactual data.

Archaeology↗

Use of a polymorphic dinucleotide repeat sequence to detect non-blastomeric contamination of the polymerase chain reaction in biopsy samples for preimplantation diagnosis.

Using the polymerase chain reaction (PCR), amplification of two different target DNA sequences has been achieved with high frequency using single human blastomeres as template for the duplex reaction. One sequence is located within the beta-globin gene and contains the sickle cell locus, the other is a polymorphic dinucleotide repeat, which, as well as acting as a positive control for amplification, was used to check the origin of the amplified DNA. A comparison of the sequences amplified from the blastomere with sequences amplified from parental samples confirmed that amplification of blastomeric sequences, but not extraneous contaminating DNA, had taken place in most cases. The efficacy of this system for detecting extraneous DNA was checked by deliberately contaminating single blastomeres with foreign cells. The presence of contamination was detected by the amplification of sequences not present in blastomeric DNA and which therefore must have been amplified from extraneous contaminating DNA.

Adenine↗

Effect of treated-sewage contamination upon bacterial energy charge, adenine nucleotides, and DNA content in a sandy aquifer on Cape Cod.

Changes in adenylate energy charge (ECA) and in total adenine nucleotides (A(T) and DNA content (both normalized to the abundance of free-living, groundwater bacteria) in response to carbon loading were determined for a laboratory-grown culture and for a contaminated aquifer. The latter study involved a 3-km-long transect through a contaminant plume resulting from continued on-land discharge of secondary sewage to a shallow, sandy aquifer on Cape Cod, Mass. With the exception of the most contaminated groundwater immediately downgradient from the contaminant source, DNA and adenylate levels correlated strongly with bacterial abundance and decreased exponentially with increasing distance downgradient. ECAS (0.53 to 0.60) and the ratios of ATP to DNA (0.001 to 0.003) were consistently low, suggesting that the unattached bacteria in this groundwater study are metabolically stressed, despite any eutrophication that might have occurred. Elevated ECAS (up to 0.74) were observed in glucose-amended groundwater, confirming that the metabolic state of this microbial community could be altered. In general, per-bacterium DNA and ATP contents were approximately twofold higher in the plume than in surrounding groundwater, although ECA and per-bacterium levels of A(T) differed little in the plume and the surrounding uncontaminated groundwater. However, per-bacterium levels of DNA and A(T) varied six- and threefold, respectively, during a 6-h period of decreasing growth rate for an unidentified pseudomonad isolated from contaminated groundwater and grown in batch culture.(ABSTRACT TRUNCATED AT 250 WORDS)

Adenine Nucleotides↗