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PubMed1997

A method for the isolation of schistosome eggs and miracidia free of contaminating host tissues.

A novel method for the isolation of schistosome eggs and miracidia from livers of mice infected with Schistosoma japonicum or S. mansoni is described. The method employed collagenase B to degrade the interstitial matrix of mouse liver tissue, after which the schistosome eggs were separated from the liver cells by 2 single-step density centrifugations through Percoll. Using this procedure sufficient quantities of miracidia were obtained to generate a cDNA library. Southern blot analysis demonstrated that miracidia isolated by this method were free from contaminating host DNA.

Animals↗

PubMed2000

Methacarn fixation: a novel tool for analysis of gene expressions in paraffin-embedded tissue specimens.

To establish a quantitative method for analysis of gene expressions in small areas of tissue after paraffin embedding, preliminary validation experiments with RT-PCR and Western blotting were performed using methacarn-fixed rodent tissues and a cultured PC12 cell line. A total RNA yield of 52 +/- 15 ng/mm2, sufficient for a quantitative RT-PCR of many genes, could be extracted from a deparaffinized 10-microm-thick rat-liver section by a simple, single-step extraction method. The low concentration of contaminating genomic DNA and the resolution of ribosomal RNAs in RNA gel proved the purity and integrity of the extracted RNA samples, allowing PCR amplification of a long mRNA sequence and mRNA species expressing low copy numbers. PCR amplification of mRNA-derived target gene fragments could be achieved by optimizing the amount of total RNA for reverse transcription and the number of subsequent PCR cycles for each gene. By this validation, organ- and sex-specific mRNA expression could be detected in methacarn-fixed paraffin-embedded tissues without additional DNase treatment of RNA samples. RT-PCR analysis could also be performed with total RNA extracted from deparaffinized tissue dissected with a laser capture microdissection system. In addition, extraction of protein yielded 4.9 +/- 2.1 microg/mm2 from a 10-microm-thick rat-liver section, allowing a quantitative expression analysis of protein by Western blotting. Thus, in addition to its advantages for immunohistochemistry, methacarn-fixed paraffin-embedded tissue has benefits for analysis of both RNAs and proteins in the cells of histologically defined areas.

Acetic Acid↗

PubMed2003

Removal of PCR inhibitors using dielectrophoresis as a selective filter in a microsystem.

Diagnostic PCR has been used to analyse a wide range of biological materials. Conventional PCR consists of several steps such as sample preparation, template purification, and PCR amplification. PCR is often inhibited by contamination of DNA templates. To increase the sensitivity of the PCR, the removal of PCR inhibitors in sample preparation steps is essential and several methods have been published. The methods are either chemical or based on filtering. Conventional ways of filtering include mechanical filters or washing e.g. by centrifugation. Another way of filtering is the use of electric fields. It has been shown that a cell will experience a force when an inhomogeneous electric field is applied. The effect is called dielectrophoresis (DEP). The resulting force depends on the difference between the internal properties of the cell and the surrounding fluid. DEP has been applied to manipulate cells in many microstructures. In this study, we used DEP as a selective filter for holding cells in a microsystem while the PCR inhibitors were flushed out of the system. Haemoglobin and heparin - natural components of blood - were selected as PCR inhibitors, since the inhibitory effects of these components to PCR have been well documented. The usefulness of DEP in a microsystem to withhold baker's yeast (Saccharomyces cerevisiae) cells while the PCR inhibitors haemoglobin and heparin are removed will be presented and factors that influence the effect of DEP in the microsystem will be discussed. This is the first time dielectrophoresis has been used as a selective filter for removing PCR inhibitors in a microsystem.

Animals↗

PubMed1992

Staphylococcus epidermidis bacteremia from transfusion of contaminated platelets: application of bacterial DNA analysis.

Septicemia is a rare complication of platelet transfusion. A case is reported of transfusion-associated septicemia in a 66-year-old man who received a 10-unit pool of platelets. During transfusion, he experienced rigors, wheezing, dyspnea, and fever. A total of four blood cultures drawn 10 and 36 hours after discontinuation of the transfusion grew Staphylococcus epidermidis. Culture of the residual platelet pool yielded S. epidermidis with a colony count of 10(5) organisms per mL. Strain identity of all four blood isolates and the platelet pool isolate was confirmed by gel electrophoresis of EcoRI and HindIII restriction digests of whole-cell DNA. There have been 31 prior reported cases of platelet transfusion-associated septicemia, of which 9 have been caused by coagulase-negative staphylococci. Systemic reactions to platelet transfusions should prompt consideration of transfusion-associated bacteremia as the cause.

Aged↗

PubMed1974

A small number of cistrons for ribosomal RNA in the germinal nucleus of a eukaryote, Tetrahymena pyriformis.

The percentage of DNA complementary to 25S and 17S rRNA has been determined for both the macro- and micronucleus of the ciliated protozoan, Tetrahymena pyriformis. Saturation levels obtained by DNA.RNA hybridization indicate that approximately 200 copies of the gene for rRNA per haploid genome were present in macronuclei. The saturation level obtained with DNA extracted from isolated micronuclei was only 5-10% of the level obtained with DNA from macronuclei. After correction for contamination of micronuclear DNA by DNA from macronuclei, only a few copies (possibly only 1) of the gene for rRNA are estimated to be present in micronuclei. Micronuclei are germinal nuclei. Macronuclei serve as somatic nuclei during vegetative growth but are destroyed every sexual generation and are reformed from products of meiosis, fertilization, and division of the micronuclei. Thus, the hybridization data suggest that the gene for rRNA must be amplified during macronuclear formation with each sexual generation. These observations also demonstrate that the multiple copies of a repeated gene in a somatic nucleus of a eukaryote can be generated from a small number of copies of that gene in a germinal nucleus.

Animals↗

PubMed2006

A new oligonucleotide-based ELISA for the detection of anti-double-stranded DNA antibodies.

The detection and measurement of antibodies to double-stranded (ds) DNA is important in the diagnosis and monitoring of patients with systemic lupus erythematosus (SLE). Several methods are available for their determination but none of them is completely satisfactory. Usually, purified dsDNA from different sources is used as antigen in the solid (enzyme-linked immunosorbent assay, ELISA) or liquid phase (Farr assay). Alternatively, anti-dsDNA antibodies can be demonstrated by immunofluorescence, using the haemoflagellate Crithidia luciliae (CLIFT). We have developed a new oligonucleotide-based anti-dsDNA ELISA in which dsDNA, constituted of a 5'photobiotinylated nucleic acid probe and its highly specific complementary oligonucleotide, is formed onto the solid-phase. To do that, a 40 bp probe is coated on the microplate wells via streptavidin-biotin bond and the in vitro (in solid-phase) developed hybrid between probe and its complementary helix used as capturing antigen. The assay has proved to be specific and the several experiments performed to ascertain the absence of single-stranded DNA (ssDNA) contamination and/or non specific binding to plastic, streptavidin, probe (without complementary chain) have all excluded any significant interference. To evaluate the clinical performance of this new assay, 114 serum samples from 68 SLE patients and 85 samples from 85 disease controls, in addition to 30 blood donors, were studied. The results were compared with commercial ELISAs, Farr assay and indirect immunofluorescence. The sensitivity and specificity were 66.2 and 96.4%, respectively, comparable and even better than those of the commercially available anti-dsDNA kits. Anti-dsDNA antibody levels, measured with the oligonucleotide-ELISA, correlated with SLE clinical activity determined using the European Consensus Lupus Activity Measurement (ECLAM) (r = 0.59, p < 0.0001). In conclusion, this assay has proved to be reproducible, and the results correlate well with other standard anti-dsDNA assays. The features of this new assay make it promising for clinical use.

Antibodies, Antinuclear↗

PubMedDate not supplied

Virulence gene expression during conidial germination in Cochliobolus carbonum.

The fungal pathogen Cochliobolus carbonum race 1 produces a host-selective toxin (HC-toxin) that is responsible for increased virulence on susceptible genotypes of maize. The toxin is synthesized by a peptide synthetase, which is a product of the HTS1 gene. Because the toxin is not stored in dormant conidia, early expression of HTS1 is crucial for extensive colonization of susceptible leaf tissue. To detect the HTS1 transcript and determine the onset of HTS1 gene expression, we analyzed RNA preparations from ungerminated and germinated conidia by reverse transcription-polymerase chain reaction using oligonucleotide primers within the 15.7-kb open reading frame of HTS1. With primer pairs near both the 3'- and the 5'-termini, amplified products of the HTS1 transcript were detected in RNA prepared from dormant conidia. With all primer pairs used, the quantities of transcript increased substantially during germ tube emergence and elongation, indicating that expression of HTS1 is up regulated during spore germination. Digestion with restriction endonucleases confirmed the identity of the amplified products. Amplification of the constitutively expressed beta-tubulin transcript, which is processed to remove introns, as well as the absence of amplification products with primers spanning the HTS1 coding sequence established that cDNA was amplified and not contaminating genomic DNA.

Amino Acid Isomerases↗

PubMed1998

Polymerase chain reaction amplification of bacterial 16S rRNA genes from cold-cup biopsy forceps.

PURPOSE: In looking for a possible infectious cause for interstitial cystitis (IC), we previously determined that bladder tissue specimens from both IC patients and controls were uniformly positive by polymerase chain reaction assay (PCR) for bacterial 16S ribosomal RNA genes from various genera including Escherichia, Propionobacterium, Acinetobacter, and Salmonella. We therefore determined whether the biopsy forceps might be contaminated with bacterial DNA. MATERIALS AND METHODS: A total of 23 samples were obtained following disinfection of 6 cold-cup bladder biopsy forceps (2 to 5 specimens from each forceps over a period of 19 months). DNA was extracted from each sample, and PCR performed using nested primers from a highly conserved region of the bacterial 16S rRNA gene. Amplified DNA was purified and sequenced, and the sequences obtained were compared with bacterial rRNA gene sequences recorded in GenBank. RESULTS: Thirteen of 23 forceps specimens were positive by PCR for bacterial DNA, including at least one rinse from each of the 6 forceps. In comparison, none of 9 negative control specimens (sterile distilled water put into tubes and processed in the same manner as forceps rinses) had detectable bacterial DNA. Sequence data indicated the presence of a predominant organism in 12 of the 13 positive specimens, with >95% homology to DNA from several different genera of bacteria including Escherichia, Propionobacterium, Stenotrophomonas and Pseudomonas. CONCLUSIONS: These data indicate that reusable bladder biopsy forceps are frequently contaminated with bacterial DNA. Tissue specimens procured with such instruments therefore are inappropriate sources to look for the presence of bacterial pathogens by PCR.

Biopsy↗

PubMed2002

16S rDNA sequence analysis of environmental Bdellovibrio-and-like organisms (BALO) reveals extensive diversity.

Bdellovibrio-and-like organisms (BALO) are Gram-negative, predatory bacteria that inhabit terrestrial, freshwater and salt-water environments. Historically, these organisms have been classified together despite documented genetic differences between isolates. The genetic diversity of these microbes was assessed by sequencing the 16S rRNA gene. Primers that selectively amplify predator 16S rDNA, and not contaminating prey DNA, were utilized to study 17 freshwater and terrestrial and nine salt-water BALO isolates. When the 16S rDNA sequences were compared with representatives of other bacterial classes, 25 of the 26 BALO isolates clustered into two groups. One group, supported 100% by bootstrap analysis, included all of the Bdellovibrio bacteriovorus isolates. Each member of this group was isolated from either a freshwater or terrestrial source. The genetic distance between these isolates was less than 12%. The other group, supported 94% by bootstrap analysis, includes Bacteriovorax starrii, Bacteriovorax stolpii and the salt-water isolates. The salt-water isolates form a subgroup (83% by bootstrap) and differ within the subgroup by less than 110%. This observation implies that the salt-water isolates arose from Bacteriovorax progenitors. The difference between isolates in different clades is over 17%, a quantity similar to differences between bacterial species in different classes. However, both the Bdellovibrio and Bacteriovorax clades were closest to other representatives of the delta-Proteobacteria using maximum-likelihood. One freshwater isolate, James Island, was distinct from all other BALO (> 19%), but differed from Pseudomonas putida, a member of the gamma-Proteobacteria, by only 3%. Thus, by 16S rDNA sequence analysis, the BALO appear to have multiple origins, contrary to the unified taxonomic grouping based on morphology and natural history. These observations are consistent with the need to review and revise the taxonomy of these organisms.

Base Sequence↗

PubMed2003

Morphological and phylogenetic characterizations of freshwater Thioploca species from Lake Biwa, Japan, and Lake Constance, Germany.

Filamentous, gliding, sulfide-oxidizing bacteria of the genus Thioploca were found on sediments in profundal areas of Lake Biwa, a Japanese freshwater mesotrophic lake, and were characterized morphologically and phylogenetically. The Lake Biwa Thioploca resembled morphologically Thioploca ingrica, a brackish water species from a Danish fjord. The diameters of individual trichomes were 3 to 5.6 microm; the diameters of complete Thioploca filaments ranged from 18 to 75 micro m. The cell lengths ranged from 1.2 to 3.8 micro m. In transmission electron microscope specimens stained with uranyl acetate, dense intracellular particles were found, which did not show any positive signals for phosphorus and sulfur in an X-ray analysis. The 16S rRNA gene of the Thioploca from Lake Biwa was amplified by using newly designed Thioploca-specific primers (706-Thioploca, Biwa160F, and Biwa829R) in combination with general bacterial primers in order to avoid nonspecific amplification of contaminating bacterial DNA. Denaturing gradient gel electrophoresis (DGGE) analysis of the three overlapping PCR products resulted in single DGGE bands, indicating that a single 16S rRNA gene had been amplified. With the same method, the Thioploca from Lake Constance was examined. The 16S rRNA sequence was verified by performing fluorescence in situ hybridization targeted at specific motifs of the Lake Biwa THIOPLOCA: Positive signals were obtained with the bacterial probe EUB-338, the gamma-proteobacterial probe GAM42a, and probe Biwa829 targeting the Lake Biwa THIOPLOCA: Based on the nearly complete 16S rRNA sequence and on morphological similarities, the Thioploca from Lake Biwa and the Thioploca from Lake Constance are closely related to T. ingrica and to each other.

DNA, Bacterial↗

PubMed1982

Replication of a low-copy-number plasmid by a plasmid DNA-membrane complex extracted from minicells of Escherichia coli.

A DNA-membrane complex was extracted from minicells of an Escherichia coli mutant harboring a "miniplasmid" derivative (11.2 kilobases) of the low-copynumber plasmid RK2 (56 kilobases). The complex contained various species of supercoiled and intermediate forms of plasmid DNA, of which approximately 20% was bound firmly to the membrane after centrifugation in a CsCl density gradient. The plasmid DNA-membrane complex synthesized new plasmid DNA without the addition of exogenous template, enzymes, or other proteins. DNA synthesis appeared to proceed semi-conservatively, was dependent on the four deoxynucleoside triphosphates, partially dependent on ribonucleoside triphosphates, and was sensitive to rifampin, an antibiotic known to inhibit initiation of replication. Novobiocin and nalidixic acid also inhibited synthesis, as did the omission of ATP, N-Ethylmaleimide, an inhibitor of DNA polymerase II and III activity, but not DNA polymerase I activity, also partially inhibited the synthetic reaction, as did chloramphenicol. The plasmid DNA synthetic product was analyzed by alkaline sucrose and dye-CsCl gradient centrifugation, as well as by agarose gel electrophoresis. In each case, the product consisted of parental and intermediate forms of plasmid DNA. Some chromosomal DNA was also synthesized by a contaminating bacterial DNA-membrane complex, but this synthesis was rifampin insensitive and could be separated from plasmid DNA synthesis.

Cell Membrane↗

PubMed1991

The phosphoinositol sphingolipids of Saccharomyces cerevisiae are highly localized in the plasma membrane.

To investigate the vital function(s) of the phosphoinositol-containing sphingolipids of Saccharomyces cerevisiae, we measured their intracellular distribution and found these lipids to be highly localized in the plasma membrane. Sphingolipids were assayed in organelles which had been uniformly labeled with [3H]inositol or 32P and by chemical measurements of alkali-stable lipid P, of long chain bases, and of very long chain fatty acids. We have developed an improved method for the preparation of plasma membranes which is based on the procedure of Duran et al. (Proc. Natl. Acad. Sci. USA 72:3952-3955, 1975). On the basis of marker enzyme and DNA assays carried out with a number of preparations, the plasma membranes contained less than 10% vacuolar membranes (alpha-mannosidase) and nuclei (DNA); the contamination by the endoplasmic reticulum (NADPH-cytochrome c reductase) varied from 0 to 20%. The plasma membrane preparations showed a 13-fold increase in the specific activity of vanadate-sensitive ATPase, compared with that in the homogenate, with a yield ranging from 50 to 80%. A comparison of the distribution of the ATPase with that of sphingolipids assayed by a variety of methods showed that 80 to 100% of the sphingolipids are localized in the plasma membrane; the sphingolipids constitute about 30% of the total phospholipid content of the plasma membrane. Minor amounts of sphingolipids that were found in isolated mitochondria and nuclei can be attributed to the presence of small amounts of plasma membrane in these fractions. These results suggest that one or more essential functions of these lipids is in the plasma membrane. Furthermore, sphingolipids may be useful chemical markers of the plasma membrane of S. cerevisiae.

Adenosine Triphosphatases↗

PubMed1977

Electron microscopy of the segmented RNA genome ofLa Crosse virus: absence of circular molecules.

The three species of single-stranded RNA present in La Crosse virus were examined in the electron microscope. Because large amounts of contaminating cellular DNA are copurified with the virus despite extensive attempts to purify the virus, it was necessary to use procedures that eliminated the bulk of this DNA before the viral RNA was analyzed. When this was done, the modal lengths of La Crosse virus RNA were 0.4, 2.0, and 3.1 mum. These lengths correspond well to their known molecular weights of 0.4 x 106, 1.8 x 106, and 2.9 x 106. Under the denaturing conditions used to permit complete spreading of these single-stranded RNA molecules, no single-stranded circular molecules are observed. Therefore, the circular nucleocapsids present in La Crosse virus and some other bunyaviruses do not appear to be due to convalent linkage of the ends of the RNA genome.

Cell Line↗

PubMed1992

Expression of tumor necrosis factor-alpha in the rat ovary.

Tumor necrosis factor-alpha (TNF-alpha) messenger RNA (mRNA) in rat ovaries was detected by Northern blot analysis and by reverse transcription-polymerase chain reaction (RT-PCR). Northern blot analysis of total cellular RNA (tcRNA) isolated from adult rat ovaries showed a single distinct band at approximately 2 kilobases, while rat white blood cells, used as control, also showed a second lower band at approximately 0.5 kilobases. TNF-alpha expression in ovaries was also detected by RT-PCR, using RNA-specific primers. Southern blot analysis of the RT-PCR products showed a single band of the expected 500 base pairs, from the ovary and white blood cells, using either tcRNA or polyA+ RNA. In order to validate the RT-PCR product, it was digested with restriction enzymes, HhaI, HindIII, and XhoI. The results indicate that the ovarian TNF-alpha mRNA does not contain major alterations with respect to the known structure of rat TNF-alpha mRNA. Ovarian RNA was also subjected to PCR without previous RT in order to amplify, if any, contaminating genomic DNA. A single band of approximately 900 base pairs was observed, which contained introns 1 and 2 (determined by restriction enzyme digestion). In summary, these results indicate that rat ovaries contain TNF-alpha mRNA which makes it a likely source of local TNF-alpha secretion. The possibility exists that ovarian cells and/or macrophages are the source of the ovarian TNF-alpha mRNA.

Animals↗

PubMedDate not supplied

Differential induction of micronuclei in peripheral lymphocytes and exfoliated urothelial cells of workers exposed to 4,4'-methylenebis-(2-chloroaniline) (MOCA) and bitumen fumes.

Cytogenetic end-points used to estimate risk of genotoxic events in workers include the measurement of micronuclei (MN) in exfoliated cells, lymphocytes, and other tissues. Micronuclei are chromatin-containing bodies outside the cell nucleus resulting from contaminant-induced DNA damage. A review of 71 reports of human genotoxic responses to chemical or physical agents published between 1999 and 2001 revealed that 14% of such studies measured genotoxicity endpoints in specific target tissues relevant to the site of disease for the agent examined; 18% used endpoints in surrogate or non-target tissues but considered the relations between endpoints in surrogate and disease target tissues, and 68% measured genotoxicity endpoints in accessible tissues without reference to specific targets for disease. Methylenebis-(2-chloroaniline) (MOCA), used in polyurethane manufacture, is a suspected bladder carcinogen. Bitumen, used in road surfacing, contains skin and lung carcinogens. In this study, we aimed to compare genotoxicity in urothelial cells and in lymphocytes of workers exposed to these materials. Twelve men employed in polyurethane manufacture, twelve bitumen road layers, and eighteen hospital stores personnel (controls) were recruited and all provided blood and urine samples on the same day. Blood cultures were prepared using a cytochalasin B-block method. Exfoliated urothelial cells were collected from urine and stained for light microscopy. The number of MN in urothelial cells was higher in MOCA-exposed (14.27 +/- 0.56 MN/1000, 9.69 +/- 0.32 MN cells/1000) than in bitumen exposed workers (11.99 +/- 0.65 MN/1000, 8.66 +/- 0.46 MN cells/1000) or in control subjects (6.88 +/- 0.18 MN/1000, 5.17 +/- 0.11 MN cells/1000). Conversely, in lymphocytes, MN were higher in bitumen-exposed (16.24 +/- 0.63 MN/1000, 10.65 +/- 0.24 MN cells/1000) than in MOCA-exposed workers (13.25 +/- 0.48 MN/1000, 8.54 +/- 0.14 MN cells/1000) or in control subjects (9.24 +/- 0.29 MN/ 1000, 5.93 +/- 0.13 MN cells/1000). The results of this study suggest that genotoxins can cause different rates of micronuclei formation in different tissues. Thus, the sensitivity and relevance to cancer risk may be greater if the tissues selected for genotoxicity studies reflect the target tissue for the chemicals concerned.

Adult↗

PubMed2002

A simple method for elimination of false positive results in RT-PCR.

Discrimination between the amplification of mRNA and contaminating genomic DNA is a common problem when performing a reverse transcriptase-polymerase chain reaction (RT-PCR). Even after treatment of the samples with DNAse, it is possible that negative controls (samples in which no reverse transcriptase was added) will give positive results. This indicates that there was amplification of DNA, which was not generated during the reverse transcriptase step. The possibility exists that Taq DNA polymerase acts as a reverse transcriptase, generating cDNA from RNA during the PCR step. In order to test this hypothesis, we incubated samples with a DNAse-free RNAse after the cDNA synthesis. Comparison of the results that were obtained from these samples (incubated with or without DNAse-free RNAse) confirms that the reverse transcriptase activity of Taq DNA polymerase I is a possible source of false positive results when performing RT-PCR from intronless genes. Moreover, we describe here a simple and rapid method to overcome the false positive results that originate by this activity of Taq polymerase.

Animals↗

PubMedDate not supplied

[RT-PCR in clinical diagnosis].

Application fields of RT-PCR (reverse transcription-polymerase chain reaction) in clinical diagnosis comprises the assessment of viral load for RNA viruses and the analysis of gene transcription products. RT-PCR is also helpful when large genes have to be sequenced. Developments of quantitative approaches using real-time PCR recently led to a major widening of RT-PCR applications in clinical diagnosis. However, RT reaction is delicate due to its lack of reproducibility and to RNA lability and frequent contamination by DNA. In some cases additional difficulties come from the need to obtain a specific amplification in the presence of homologous sequences which might be present in higher amounts than the sequence of interest. These caveats have to be taken into account, when designing the RT protocol, and when choosing PCR primers and internal and/or external references. This review is aimed at helping the experimental setup of a RT-PCR based assay according to the objectives.

Clinical Medicine↗

PubMed1992

Changing issues of quality control: diploid and non-diploid cell lines.

Early viral vaccines were prepared from primary monkey kidney cell cultures. However, primary cell cultures can be highly variable and also present a risk of contamination by endogenous viruses. The development of human diploid cell lines for vaccine production provide greater assurance of consistency and freedom from contaminating viruses. Continuous cell lines present considerable advantages in the preparation of proteins for therapeutic use. The perceived risks associated with the use of these cell lines include those of retroviral contamination, oncogenic DNA and consistency of final product during the extended life in culture. Advances in molecular biologic and analytical chemistry procedures have enabled extensive characterisation not only of the cells, but also of the product itself. The degree of testing which can now be performed on the product, to ensure its safety and consistency, should lead to a reappraisal of testing regimes applied to the cells themselves.

Animals↗