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PubMed2001

Comparison of the DNA extraction methods for polymerase chain reaction amplification from formalin-fixed and paraffin-embedded tissues.

To obtain an adequate quality and quantity of DNA from formalin-fixed and paraffin-embedded tissue, six different DNA extraction methods were compared. Four methods used deparaffinization by xylene followed by proteinase K digestion and phenol-chloroform extraction. The temperature of the different steps was changed to obtain higher yields and improved quality of extracted DNA. The remaining two methods used microwave heating for deparaffinization. The best DNA extraction method consisted of deparaffinization by microwave irradiation, protein digestion with proteinase K at 48 degrees C overnight, and no further purification steps. By this method, the highest DNA yield was obtained and the amplification of a 989-base pair beta-globin gene fragment was achieved. Furthermore, DNA extracted by means of this procedure from five gastric carcinomas was successfully used for single strand conformation polymorphism and direct sequencing assays of the beta-catenin gene. Because the microwave-based DNA extraction method presented here is simple, has a lower contamination risk, and results in a higher yield of DNA compared with the ordinary organic chemical reagent-based extraction method, it is considered applicable to various clinical and basic fields.

DNA Primers↗
PubMed2002

Identification of Fusarium graminearum in cereal samples by DNA Detection Test Strips.

AIMS: Development of a fast, sensitive and easy to handle method for the detection of Fusarium graminearum contamination in cereal samples by PCR. METHODS AND RESULTS: DNA Detection Test Strips were used for PCR-product detection and the method was compared to agarose gel electrophoresis. A minimum of 0.26 ng of purified target DNA was detectable with the Test Strip Detection limit in less contaminated samples was slightly lower when gel electrophoresis was used for amplicon detection. In highly contaminated samples, detection limits of both methods were similar. CONCLUSIONS: Detection of PCR products was performed in 20 min without the need of special technical equipment or hazardous fluorescent DNA dyes. SIGNIFICANCE AND IMPACT OF THE STUDY: The new method described is useful for the screening of cereals in industrial quality control.

DNA, Fungal↗
PubMed1996

Use of the polymerase chain reaction for the detection of reticuloendotheliosis virus in Marek's disease vaccines and chicken tissues.

Reticuloendotheliosis virus (REV) proviral DNA appears to be a frequent contaminant in Marek's disease (MD) vaccines. A polymerase chain reaction (PCR) was established and evaluated for its ability to detect REV proviral DNA in infected cell cultures and chicken tissues. Deoxynucleotide primers were selected from the highly conserved gag region of the REV genome. The amplification products were identified by electrophoresis, nested PCR and by hybridization with a digoxigenine-labelled oligonucleotide. The PCR results correlated well with the diagnosis obtained by conventional procedures, i.e. virus isolation or indirect immuno-fluorescence test (IIFT).

Animals↗
PubMed1989

32P-postlabeling analysis of DNA adducts in liver of wild English sole (Parophrys vetulus) and winter flounder (Pseudopleuronectes americanus).

The 1-butanol adduct enhancement version of the 32P-postlabeling assay was used to measure the levels of hepatic DNA adducts in the marine flatfish, English sole (Parophrys vetulus), sampled from the Duwamish Waterway and Eagle Harbor, Puget Sound, WA, where they are exposed to high concentrations of sediment-associated chemical contaminants and exhibit an elevated prevalence of hepatic neoplasms. Hepatic DNA was also analyzed from English sole from a reference area (Useless Bay, WA) and from reference English sole treated with organic-solvent extracts of sediments from the two contaminated sites. Autoradiograms of thin-layer chromatograms of 32P-labeled hepatic DNA digests from English sole from the contaminated sites exhibited up to three diagonal radioactive zones, which were not present in autoradiograms of thin-layer chromatogram maps of 32P-labeled DNA digests from English sole from the reference site. These diagonal radioactive zones contained several distinct spots as well as what appeared to be multiple overlapping adduct spots. The levels (nmol of adducts/mol of nucleotides) of total DNA adducts for English sole from Duwamish Waterway and Eagle Harbor were 26 +/- 28 (DS) and 17 +/- 9.6, respectively. All autoradiograms of DNA from fish from the contaminated sites exhibited a diagonal radioactive zone where DNA adducts of chrysene, benzo(a)pyrene, and dibenz(a,h)anthracene, formed in vitro using English sole hepatic microsomes, were shown to chromatograph. English sole treated with extracts of the contaminated sediments had adduct profiles generally similar to those for English sole from the respective contaminated sites. The chromatographic characteristics of the adducts and the similarities in adduct profiles between field-sampled English sole and those treated with contaminated sediment extracts suggested that hydrophobic aromatic compounds of anthropogenic origin were adducted to hepatic DNA of sole from contaminated sites, but not in sole from the reference site. Moreover, an initial study with winter flounder (Pseudopleuronectes americanus) from Boston Harbor, MA, an area where high concentrations of sediment-associated chemicals are present, revealed a pattern of hepatic DNA-adducts (9.0 +/- 7.8 nmol of adducts/mol of nucleotides) similar to that observed for English sole from Eagle Harbor.

Animals↗
PubMed1983

De novo synthesis of DNA in human platelets.

Platelets, incubated with radiolabeled thymidine and purified free of contaminating nucleated cells, were analyzed for their ability to synthesize DNA. The only DNA species isolated from these purified platelets was mitochondrial DNA. The CsCl gradient-purified platelet DNA was treated with the restriction endonucleases EcoRI, HindIII and HpaI yielding the expected pattern for human mitochondrial DNA. Nitrocellulose blots of the electrophoresed, restriction endonuclease-treated DNA were fluorographed. All of the DNA fragments generated by the restriction enzymes were labeled, indicating de novo synthesis. This was further substantiated by inhibition of DNA synthesis by ethidium bromide and 2',3'-dideoxythymidine. Platelet DNA appeared to become greatly fragmented after 4 to 7 days storage while all of the thymidine incorporated was observed in intact mitochondrial DNA. These results indicate a continuous degradation of platelet mitochondrial DNA with no apparent repair mechanism. The ability of platelets to synthesize DNA may be associated with the protein synthetic capacity of platelets previously described.

Blood Platelets↗
PubMed1995

DNA statistics in the Simpson matter.

On 3 October 1995, O.J. Simpson was acquitted of two murders in spite of very strong DNA evidence linking his blood to the crime. Although numerical statements describing the strength of this evidence were made, the DNA profiles included so many loci that the need for presenting numbers in this case, and in others using similarly high numbers of loci, is probably unnecessary. If numbers are to be presented, however, they should be given in the form of likelihood ratios. One thing the verdict in the Simpson case makes clear is that it is essential that the integrity of DNA evidence (with regard to collection, potential contamination or tampering) be beyond doubt.

California↗
PubMed2002

Isolation and characterization of T4 bacteriophage gp17 terminase, a large subunit multimer with enhanced ATPase activity.

Phage T4 terminase is a two-subunit enzyme that binds to the prohead portal protein and cuts and packages a headful of concatameric DNA. To characterize the T4 terminase large subunit, gp17 (70 kDa), gene 17 was cloned and expressed as a chitin-binding fusion protein. Following cleavage and release of gp17 from chitin, two additional column steps completed purification. The purification yielded (i) homogeneous soluble gp17 highly active in in vitro DNA packaging ( approximately 10% efficiency, >10(8) phage/ml of extract); (ii) gp17 lacking endonuclease and contaminating protease activities; and (iii) a DNA-independent ATPase activity stimulated >100-fold by the terminase small subunit, gp16 (18 kDa), and modestly by portal gp20 and single-stranded binding protein gp32 multimers. Analyses revealed a preparation of highly active and slightly active gp17 forms, and the latter could be removed by immunoprecipitation using antiserum raised against a denatured form of the gp17 protein, leaving a terminase with the increased specific activity (approximately 400 ATPs/gp17 monomer/min) required for DNA packaging. Analysis of gp17 complexes separated from gp16 on glycerol gradients showed that a prolonged enhanced ATPase activity persisted after exposure to gp16, suggesting that constant interaction of the two proteins may not be required during packaging.

Adenosine Triphosphatases↗
PubMed1976

Distinguishing cytomegalovirus, mycoplasma, and cellular DNA polymerases.

Cytomegalovirus-induced DNA polymerase can be distinguished from infected-cell enzymes by activity in 100 mM (NH4)2SO4. Virus polymerase is stimulated to 145% of control, whereas mock-infected cell polymerase is inhibited to 12% of control without added salt. Mycoplasmas induce a DNA polymerase in cell extracts that is stimulated to 130 to 180% by 25 mM (NH4)2SO4. Mycoplasma DNA polymerase may be mistaken for a virus-induced polymerase when virus stocks are contaminated. Identification of virus, cellular, and mycoplasma DNA polymerases in total cell extracts is described using sedimentation rate and effect of inhibitors on DNA polymerase activities.

Acetates↗
PubMed1985

In vivo and in vitro covalent binding of chlorobenzene to nucleic acids.

At 22 hr after ip injection into male Wistar rats and BALB/c mice, chlorobenzene was covalently bound to DNA, RNA and proteins of the liver, kidney and lung, as has been found with various weak carcinogens. A microsome-mediated interaction with DNA occurred in vitro. The interaction was enhanced by pretreatment in vivo with phenobarbitone but was suppressed by addition of 2-diethylaminoethyl-2,2-diphenylvalerate HC1 in vitro. These results indicate the involvement of cytochrome P-450. Liver microsomes were efficient bioactivators, whereas cytosol was ineffective. The extent of in vitro interaction of chlorobenzene with synthetic polyribonucleotides was of the same order as that with DNA. Finally, ultraviolet irradiation (lambda = 254 nm or lambda max = 365 nm) activated this environmental contaminant to forms capable of interacting with DNA. The results represent evidence for genotoxicity of chlorobenzene.

Animals↗
PubMed1987

Triiodothyronine binding in adult rat brain: compartmentation of receptor populations in purified neuronal and glial nuclei.

In order to investigate the localization of nuclear T3 receptors in adult rat brain, we have developed a technique for separating neuronal and glial nuclei, and compared nuclear T3 binding in both fractions. Glial and neuronal nuclear populations were prepared by homogenization of the whole brain except the cerebellum, followed by discontinuous density gradient centrifugation in 2.4 and 2.2 M sucrose. For purposes of comparison, liver nuclei were prepared by centrifugation in 2.4 M sucrose. Microscopic examination of the nuclei confirmed the purity of the two nuclear fractions to be above 90% with minimal extranuclear contamination. T3 binding studies were performed on the washed nuclear fractions using saturation analysis techniques. Maximum binding (Bmax) and dissociation constant (Kd) were obtained by nonlinear least-squares regression analysis. After 30 min incubation at 37 C, Bmax in neuronal nuclei was 1203 +/- 118 fmol/mg DNA (mean +/- SE) (n = 6), in comparison with 196 +/- 14 fmol/mg DNA in glial nuclei (n = 7). The corrected value for Bmax in glial nuclei, assuming 8% neuronal nuclear contamination, was 100 fmol/mg DNA. Bmax in liver nuclei was contamination, was 100 fmol/mg DNA. Bmax in liver nuclei was 299 +/- 38 fmol/mg DNA (n = 6). The Kd values were 0.38 +/- 0.04 nM, 0.34 +/- 0.05 nM, and 0.33 +/- 0.04 nM in neuronal, glial, and liver nuclei, respectively. The specificity of T3 binding to the nuclear receptor in both neuronal and glial nuclei was studied in competition studies, and revealed closely similar relative binding affinities (T3 greater than T4 greater than rT3) in both. We conclude that the higher T3 binding capacity of neuronal nuclei may be related to their higher protein synthetic ability, suggesting that T3 may be of importance in a rapid structural turnover in these cells. The effect of T3 on myelination in glial cells may be mediated through the nucleus.

Animals↗
PubMed2003

A comparison of DNA profiling techniques for monitoring nutrient impact on microbial community composition during bioremediation of petroleum-contaminated soils.

Amplicon length heterogeneity PCR (LH-PCR) and terminal restriction fragment length polymorphisms (TRFLP) were used to monitor the impact that nutrient amendments had on microbial community dynamics and structural diversity during bioremediation of petroleum-contaminated soils. Slurried soils contaminated with petroleum hydrocarbons were treated in airlift bench-scale bioreactors and were either amended with optimal inorganic nutrients or left unamended. Direct DNA extraction and PCR amplification of whole eubacterial community DNA were performed with universal primers that bracketed the first two or three hypervariable regions of the 16S rDNA gene sequences. The LH-PCR method profiled a more diverse microbial community than did the TRFLP method. The LH-PCR method also tracked differences between the communities due to nutrient amendments. An in silico database search for bacterial genera with amplicon lengths represented in the community fingerprints was performed. It was possible to qualitatively identify different groups in the microbial community based on the amplicon length variations. A similar "virtual" search was performed for the TRFLP fragments using the web-based TAP-TRFLP program. Cloning and sequencing of the PCR products confirmed the in silico database matches. The application of the LH-PCR method as a monitoring tool for bioremediation could greatly enhance and extend the current understanding of the microbial community dynamics during the biodegradation of environmental contaminants.

Bacteria↗
PubMed2005

Evaluation of genotoxicity of combined soil pollution by cadmium and imidacloprid.

Cadmium (Cd) is one of the important pollutants of soil and the genotoxicity of Cd-contaminated soil was studied in combination with imidacloprid. The single cell gel electrophoresis or comet assay was used to quantify DNA strand breaks as a measure of DNA damage induced by Cd and imidacloprid contamination in soil. The soil was artificially contaminated by Cd (0.0, 0.2, 0.5, 1.0, 2.0 mg x kg(-1) dry soil) or Cd (0.0, 0.2, 0.5, 1.0, 2.0 mg x kg(-1) dry soil) and imidacloprid (0.5 mg x kg(-1) dry soil). Roots of Vicia faba were exposed to the contaminated soil for 2 h at 25 degrees C and were used in the comet assay. DNA damage was measured as the values of percentage of nuclei with tails, tail length, tail DNA, tail moment (TM), and Olive tail moment (OTM). DNA damages of root tips of Vicia faba increased after Cd treatment and there were dose-related increases in DNA damage measured as these parameters. However, the addition of imidacloprid further increased the DNA damage. These data confirmed the genotoxic effect of Cd to plants, and that the combined pollution with imidacloprid can enhance the genotoxicity of Cd.

Cadmium↗
PubMed2004

Potential of using real-time PCR-based detection of spoilage yeast in fruit juice--a preliminary study.

A real-time PCR system was used to differentiate between the common spoilage yeasts, Zygosaccharomyces bailii, Zygosaccharomyces rouxii, Candida krusei, Rhodotorula glutinis and Saccharomyces cerevisiae, based on melting peak Tm analysis of the 5.8S rDNA subunit and the adjacent ITS2 region of these yeasts. By using the real-time PCR system and by targeting the citrate synthase (cs 1) gene of C. krusei, it was possible to develop a sensitive detection system to both identify and quantitate the level of C. krusei growth in an artificially contaminated apple juice sample.

Beverages↗
PubMed2004

Molecular characterization of contaminant-indicative RAPD markers.

This paper describes genetic markers which can be used to study selection and genetic adaptation of organisms to radionuclide and other types of contaminant stress. Previous research using the randomly amplified polymorphic DNA (RAPD) technique has identified several markers which revealed genetic differences between contaminated and reference western mosquitofish (Gambusia affinis) populations. Experimental evidence suggested that these markers may be associated with loci involved in determining relative fitness in radionuclide-contaminated environments ("contaminant-indicative markers"). In the present study, Southern blot analyses show these markers to be highly conserved in DNA sequence and molecular length in sea urchins, mosquitofish, herring gulls and humans. Such conservation is thought to be rare among RAPD bands. Results of DNA sequencing efforts did not provide definitive evidence as to the identity of these loci, but indicated that short segments (<40 bp) of known DNA sequences were homologous to various regions of the RAPD sequences. Furthermore, the regions of homology seemed to be non-randomly distributed along the length of the RAPD markers. Although the identity of these bands is still unknown, the high degree of conservatism suggests that these loci might play an important role in molecular processes.

Animals↗