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PubMed1977

Endonuclease activities in extracts of Micrococcus luteus that act on gemma-irradiated DNA.

Several protein fractions containing endonuclease activity against gemma-irradiated DNA (gamma-endonuclease) were isolated from M. luteus. The crude extract was eluted on a phosphocellulose column and chromatographed on TEAE cellulose and subsequently on hydroxyapatite. Five peaks of gamma-endonuclease were obtained from each preparation. Repeated experiments showed comparable chromatographic behavior of the fractions. There was no detectable activity of U.V.-endonuclease in the fractions with gamma-endonuclease but a small contamination of endonuclease against unirradiated DNA and against DNA with apurinic sites. The gamma-endonuclease is stimulated by, but is not dependent on, magnesium. Several tests for endonuclease activity have been used: the analysis of strand breaks in calf-thymus DNA or in PM2 DNA, and the determination of end-groups formed by endonuclease, either 3'OH end-groups or phosphomonoester end groups. From the results obtained it can be assumed that the strand breaks induced by the gamma-endonuclease carry 3'OH and 5' phosphate end groups.

Cobalt Radioisotopes↗

PubMed1992

The metabolism of 1,6-dinitropyrene in rat hepatocytes.

This paper reports investigations using hepatocytes to study the metabolism and DNA binding of the environmental contaminant, 1,6-dinitropyrene. Since 1,6-dinitropyrene is not believed to be mutagenic per se, metabolites were synthesized and the metabolism of 1,6-dinitropyrene was subsequently studied in rat hepatocytes. The mode of activation of dinitropyrenes is reduction of one of the nitro groups. Nitroreduction has been shown previously to be oxygen sensitive and therefore the effect of oxygen on the metabolic pattern and DNA binding was investigated by comparing results from aerobic and anaerobic conditions. The binding of [14C]1,6-dinitropyrene equivalents to rat hepatocyte DNA was increased by 15% in the presence of oxygen. Although there was little difference in the rate of 1,6-dinitropyrene metabolism, with or without O2, there was a difference in the metabolic pattern. Under anaerobic conditions there was an increase in the level of the terminal reduction product 1-amino-6-nitropyrene.

Animals↗

PubMed2002

Ralstonia pickettii traced in blood culture bottles.

Over a 9-month period, 14 strains of Ralstonia pickettii were isolated from various biological samples inoculated in a blood culture medium. Molecular epidemiological investigation confirmed the relatedness of the strains. The source of the contamination proved to be the blood culture bottle caps.

Bacteriological Techniques↗

PubMed1982

A method for the specific inhibition of poly[d(A-T)] synthesis using the A-T specific quinoxaline antibiotic TANDEM.

A serious problem in the replication of repeating-sequence DNa polymers using Escherichia coli DNA polymerase I arises from the fact that this polymerase has a very strong preference for the replication of poly[d(A-T)]. Thus reactions primed with DNA containing small amounts of contaminating poly[d(A-T)] will eventually result in complete domination of the synthesis by poly[d(A-T)]. This problem can be overcome by the addition to the reaction mixture of the synthetic quinoxaline antibiotic TANDEM which binds specifically to poly[d(A-T)] completely inhibiting its replication. Using thermal denaturation experiments it can be shown that TANDEM does not bind to most other synthetic DNA polymers (e.g., poly(dA) . poly(dT) and poly[d(A-T-C)] . poly[d(G-A-T)] and therefore their replication is not inhibited. The only exception we have encountered is poly[d(T-A-C)] . poly[d(G-T-A)] which does bind TANDEM and therefore the drug cannot be used during the synthesis of this polymer. The fact that poly[d(T-A-C)] . poly[d(G-T-A)] does bind TANDEM while poly[d(A-T-C)] . poly[d(G-A-T)] does not, suggests that the drug recognizes T-A rather than A-T sequences.

Anti-Bacterial Agents↗

PubMed1999

A RAPID algorithm for sequence database comparisons: application to the identification of vector contamination in the EMBL databases.

MOTIVATION: Word-matching algorithms such as BLAST are routinely used for sequence comparison. These algorithms typically use areas of matching words to seed alignments which are then used to assess the degree of sequence similarity. In this paper, we show that by formally separating the word-matching and sequence-alignment process, and using information about word frequencies to generate alignments and similarity scores, we can create a new sequence-comparison algorithm which is both fast and sensitive. The formal split between word searching and alignment allows users to select an appropriate alignment method without affecting the underlying similarity search. The algorithm has been used to develop software for identifying entries in DNA sequence databases which are contaminated with vector sequence. RESULTS: We present three algorithms, RAPID, PHAT and SPLAT, which together allow vector contaminations to be found and assessed extremely rapidly. RAPID is a word search algorithm which uses probabilities to modify the significance attached to different words; PHAT and SPLAT are alignment algorithms. An initial implementation has been shown to be approximately an order of magnitude faster than BLAST. The formal split between word searching and alignment not only offers considerable gains in performance, but also allows alignment generation to be viewed as a user interface problem, allowing the most useful output method to be selected without affecting the underlying similarity search. Receiver Operator Characteristic (ROC) analysis of an artificial test set allows the optimal score threshold for identifying vector contamination to be determined. ROC curves were also used to determine the optimum word size (nine) for finding vector contamination. An analysis of the entire expressed sequence tag (EST) subset of EMBL found a contamination rate of 0.27%. A more detailed analysis of the 50 000 ESTs in est10.dat (an EST subset of EMBL) finds an error rate of 0.86%, principally due to two large-scale projects. AVAILABILITY: A Web page for the software exists at http://bioinf.man.ac.uk/rapid, or it can be downloaded from ftp://ftp.bioinf.man.ac.uk/RAPID CONTACT: crispin@cs.man.ac.uk

Algorithms↗

PubMed2005

Improved method of detection and molecular typing of Borrelia burgdorferi sensu lato in clinical samples by polymerase chain reaction without DNA purification.

A simple assay by polymerase chain reaction was used for the of detection of Borrelia burgdorferi, causative agent of Lyme borreliosis (LB). It involves no DNA purification and is based on the amplification of a specific region of ospA gene of B. burgdorferi, followed by direct detection of the PCR product with SYBR Green I by agarose gel electrophoresis. The method was used to analyze samples from patients with LB diagnosis, with presumable infection with the LB spirochete, those with unclear clinical symptoms and after the course of an antibiotic treatment. Spirochetal DNA was detected by PCR even in contaminated samples in which B. burgdorferi was overgrown by fungi and other bacteria. Spirochetal DNA was detected and borrelia species was identified in cerebrospinal fluid of two patients hospitalized with the diagnosis "fever of unknown origin". Western blot and ELISA were negative in both cases. Total analysis of 94 samples from the hospital in Ceské Budejovice (South Bohemia, Czechia) showed infection with B. burgdorferi sensu stricto in 11% and B. garinii in 15% of cases. The highest prevalence was found for B. afzelii (43%). Co-infection was confirmed in 24 % of the analyzed symplex; 7% of samples that were B. burgdorferi sensu lato positive gave no results in DNA amplification with B. burgdorferi sensu stricto-, B. garinii- and B. afzelii-specific primers. The proposed reliable, rapid, unexpensive and specific technique could form the basis of laboratory tests for routine detection and identification of Lyme-disease spirochete in different samples.

Antibodies, Bacterial↗

PubMed2004

Anoxybacillus contaminans sp. nov. and Bacillus gelatini sp. nov., isolated from contaminated gelatin batches.

Aerobic, endospore-forming bacteria that are attributed to the genus Bacillus or related genera constitute a hazard to the quality of gelatin. During repetitive extragenic palindromic DNA (rep)-PCR screening of gelatin isolates, a group of five isolates (group 1) and a group of 66 isolates (group 2) that did not match any pattern in our database were found. On the basis of 16S rDNA sequence analysis, representative strains of the different rep-PCR fingerprint types of group 1 were shown to be related most closely to Anoxybacillus species, but with sequence similarity of <97 %. Likewise, representative strains of group 2 were shown to be related most closely to Bacillus species, with 16S rDNA sequence similarity of <97 %. DNA-DNA reassociation values of isolates that displayed the most divergent rep-PCR profiles revealed that strains within each group belonged to a single species, according to recommendations for species delineation. A mean fatty acid profile could be calculated for each group. Isolates within a single group had similar patterns of results in API and other phenotypic tests; no correlation of patterns of results with rep-PCR groups was seen. Physiological characterization of group 1 isolates allows their distinction from other Anoxybacillus species. Despite the weak reaction of group 2 isolates in API tests, physiological characterization allows distinction between Bacillus species that react weakly in API tests. Two novel species are therefore proposed, with the names Anoxybacillus contaminans sp. nov. (type strain, LMG 21881(T)=DSM 15866(T)) and Bacillus gelatini sp. nov. (type strain, LMG 21880(T)=DSM 15865(T)).

Bacillaceae↗

PubMed1991

Polymerase chain reaction identification of Vibrio vulnificus in artificially contaminated oysters.

DNAs extracted from Vibrio vulnificus seeded into oyster homogenates were evaluated as templates for the polymerase chain reaction. Several extraction procedures were examined, and it was determined that DNA recovered from cells lysed by guanidine isothiocyanate, extracted with chloroform, and precipitated with ethanol was most suitable for use as a polymerase chain reaction template. The region targeted was a 519-bp portion of the cytotoxin-hemolysin gene of V. vulnificus. This region was amplified only when DNA from this species was present in the homogenate. V. vulnificus seeded into oyster homogenates at an initial level of 10(2) CFU/g of oyster meat was consistently observed after 24 h of incubation in alkaline peptone water.

Animals↗

PubMed1998

A convenient method of DNA extraction from blood anticoagulated with EDTA.

Surplus blood often remains after routine clinical tests using EDTA-anticoagulated samples. To use this blood for DNA analysis, we isolated white cells by adherence to polyethylene terephthalate fibers, which could be stored for several weeks transported by mail after methanol fixation. DNA yield was sufficient and correlated with white cell count. Extracted DNA was free of hemoglobin contamination and durable to polymerase chain reaction and enzyme digestion, which yielded products visualized as well-separated bands on electrophoresis. We found our method to be practical for the routine clinical laboratory.

Adult↗

PubMed1988

Gene probes to detect cross-culture contamination in hormone producing cell lines.

Cross-culture contamination of cell lines propagated in continuous culture is a frequent event and particularly difficult to resolve in cells expressing similar phenotypes. We demonstrate that DNA-DNA hybridization to blotted endonuclease-digested cell DNA effectively detects cross-culture contamination to monitor inter-species as well as intra-species cross contamination. An insulin-producing cell-line, Clone-16, originally cloned from a human fetal endocrine pancreatic cell line did not produce human c-peptide as anticipated. DNA from these cells showed no hybridization to the human ALU sequence probe, BLUR, and lacked restriction fragment length polymorphism typical for the human HLA-DQ beta-chain gene. Although a human insulin gene probe showed a weak, nonhuman hybridization pattern, a cDNA probe for the Syrian hamster insulin gene hybridized strongly consistent with a single copy hamster insulin gene. Karyotyping confirmed the absence of human chromosomes in the Clone-16 cells while sizes, centromere indices, and banding patterns were identical to Syrian hamster fibroblasts. We conclude that the insulin-producing Clone-16 cells are of Syrian hamster origin and demonstrate the effective use of gene probes to control the origin of cell cultures.

Adenoma, Islet Cell↗

PubMed1993

A quality control algorithm for DNA sequencing projects.

Heterologous DNA sequences from rearrangements with the genomes of host cells, genomic fragments from hybrid cells, or impure tissue sources can threaten the purity of libraries that are derived from RNA or DNA. Hybridization methods can only detect contaminants from known or suspected heterologous sources, and whole library screening is technically very difficult. Detection of contaminating heterologous clones by sequence alignment is only possible when related sequences are present in a known database. We have developed a statistical test to identify heterologous sequences that is based on the differences in hexamer composition of DNA from different organisms. This test does not require that sequences similar to potential heterologous contaminants are present in the database, and can in principle detect contamination by previously unknown organisms. We have applied this test to the major public expressed sequence tag (EST) data sets to evaluate its utility as a quality control measure and a peer evaluation tool. There is detectable heterogeneity in most human and C.elegans EST data sets but it is not apparently associated with cross-species contamination. However, there is direct evidence for both yeast and bacterial sequence contamination in some public database sequences annotated as human. Results obtained with the hexamer test have been confirmed with similarity searches using sequences from the relevant data sets.

Algorithms↗

PubMed2004

Immunohistochemical analysis of oxidative DNA damage in arsenic-related human skin samples from arsenic-contaminated area of China.

The appearance of 8-oxo-2'-deoxyguanosine (8-oxodG) was examined immunohistochemically using an 8-oxodG-monoclonal antibody in 28 cases of arsenic-related human skin tumors and in 20 cases of arsenic-unrelated human skin cancer to determine if the induction of oxidative stress participates in skin tumorigenesis caused by arsenics. The rate of 8-oxodG-positive was significantly higher in arsenic-related human skin cancer (28 of 28, 100%) than in arsenic-unrelated human skin cancer (3 of 20, 15%, P<0.01 by Chi2 test). Moreover, in all the arsenic-related skin samples, 8-oxodG was detected not only in tumor tissues but also in keratosis and normal tissues. These results suggest that the induction of oxidative stress may play an important role in arsenic carcinogenesis.

8-Hydroxy-2'-Deoxyguanosine↗

PubMed2003

Quantification of DNA in forensic samples.

Quantification of DNA in a forensic sample is of major importance for proper DNA amplification and STR profiling. Several methods have been developed to quantify DNA, from basic UV spectrometry, through gel-based techniques, to dye staining, blotting techniques, and, very recently, DNA amplification methods (polymerase chain reaction, PCR). Early techniques simply measured total DNA, but newer techniques can specifically measure human DNA while excluding non-human DNA (foodstuff, animal, or bacterial contamination). These newer assays can be faster and less expensive than traditional methods, making them ideal for the busy forensic laboratory. This paper reviews classic and newer quantification techniques and presents methods recently developed by the authors on the basis of PCR of Alu sequences.

Animals↗

PubMed1991

Use of a most probable number method modified with a deoxyribonucleic probe to monitor control by food preservatives of natural Salmonella contamination in animal meat meals.

A most probable number (MPN) technique using a DNA probe was developed for determination of Salmonella in naturally contaminated meat meals. The method eliminated the need for 180 selective plates and 75 selective tubes and saved 27 h when compared with a traditional technique; yet it still yielded identical MPN of Salmonella per 100 g in five naturally contaminated samples. The method was used to monitor the effect of a commercial food preservative (Sal Curb) at 0, .25, .50, 1.0, and 2.0% in meat meals with initial contaminations of 1,100, 93, or 7 MPN organisms/100 g. The preservative greatly reduced MPN in the 1,100 and 93 MPN samples in a time and dose-dependent manner, but in the sample with 7 MPN organisms/100 g of material, it resulted in 0 MPN organisms per 100 g after 24 h at all levels tested.

Animal Feed↗

PubMed2006

AFLP characterization of Southern Europe population of Aspergillus Section Nigri from grapes.

Members of Aspergillus belonging to Section Nigri are distributed worldwide and are mainly responsible for the ochratoxin A accumulation in grapes and wine, particularly in Southern Europe. Limited information is available on the species composition and genetic variability of black Aspergilli strains occurring on grapes. We analyzed 283 representative strains from the main wine producing European countries collected in 2001-2002 (Italy, France, Spain, Portugal, Greece and Israel) using amplified fragment length polymorphisms (AFLP) technique. Four main groups were obtained by AFLP clustering analysis of these strains and three of them showed a well defined homogeneous population/species with intraspecific homology higher than 48%: Aspergillus carbonarius (105 strains), Aspergillus tubingensis (69 strains), and Aspergillus "uniseriate" (56 strains) with a similarity less than 20% to the Aspergillus japonicus type strain. The fourth cluster, that we called "A. niger like" (44 strains), showed low homology with A. niger type strain (35%) and high internal heterogeneity. Finally, nine strains could not be assigned readily to any of the type strain of the A. nigri Section. These findings indicate that the Aspergillus Section Nigri strains occurring on grapes in Southern Europe represent a complex of species, and some of these are peculiar to grapes.

Aspergillus niger↗

PubMed1995

Cytophotometric and flow cytometric DNA content of isolated glands in gastric neoplasia.

The gland isolation method was applied to various gastric lesions to measure DNA content by cytophotometry and flow cytometry for the first time. By incubating and agitating fresh specimens from surgically resected stomachs in calcium-magnesium free Hanks's balanced salt solution (CMFH) containing EDTA, many neoplastic glandular epithelial cells were successfully isolated from the stroma, and their characteristic three dimensional features were seen morphologically. The DNA content of pure nuclear suspensions of isolated glands was obtained by cytophotometry and flow cytometry staining with 4',6-diamino-2-phenylindole dihydrochloride (DAPI) and propidium iodide, respectively. Compared with histological grading, the frequency of the DNA aneuploidy of cancer with moderate or poor differentiation by cytophotometry (75%) was significantly higher than that of well differentiated cancer (25%), but the histological typing of gastric cancer DNA frequency were not correlated. This method allowed us to detect small aneuploid peaks by flow cytometry, which were previously masked by contaminating interstitial cells. The frequency of DNA aneuploidy detected by flow cytometry (87.5%) was higher than detected by cytophotometry (58.3%). The results of these studies shows the feasibility of this technique for analysing the DNA content of various lesions of the stomach.

Adenocarcinoma↗

PubMed2006

[High specific PCR identification of Bungarus multicinctus and its adulterants].

OBJECTIVE: To develop a convenient and effective method for the identification of Bungarus multicinctus. METHOD: Based on the sequence of Cyt b gene fragment of B. multicinctus and its adulterants, a pair of highly specific primer (HJL- and HJH-) were designed for distinguishing B. ulticinctus from other species of snake. To establish specific PCR reaction condition, the primers were employed to amplify the DNA templates extracted from B. multicinctus and 6 other species of snake, under different annealing temperature. Using this method, B. multicinctus was identified from 18 samples bought from many drugstores. RESULT: A 230 bp DNA fragment was amplified from B. multicinctus in PCR with annealed temperature at 67 degrees C, whereas no DNA fragment was amplified from other snake samples under the same reaction condition, B. multicinctus could be clearly distinguished from others by PCR reaction with the highly specific primers. In the present study, 18 sample, bought from different drugstores, were also identified by the highly specific PCR with the primers. The results indicated that 14 samples were B. multicinctus and the other 4 were adulterant, which was consistent with the conclusion of authentication based on morphological. CONCLUSION: The primers designed in the present study were highly specific for B. multicinctus.

Animals↗

PubMed2003

Simian virus 40 and malignant mesothelioma (Review).

Simian virus 40 (SV40) was recognized as a contaminant of early poliovirus vaccines that were provided to millions of individuals in Europe and in the USA between 1955 and 1963. SV40, a DNA virus of the family of papovaviridae, was proven to be oncogenic in rodents and able to transform human and animal cells in vitro. In 1993 SV40 was accidentally discovered to produce mesotheliomas in hamsters when it was injected in visceral cavities. Afterwards, SV40 DNA sequences were detected with significative frequency in human pleural mesotheliomas by using polymerase chain reaction (PCR) and then SV40 DNA oncogenicity was associated with its large T antigen (Tag). This finding was confirmed by many laboratories, while a few research groups failed to replicate these data and argued that the SV40 DNA detection might be a PCR contamination artefact. In this review the dispute is examined in the light of recent experiments performed to identify molecular and cellular aspects of carcinogenicity and/or co-carcinogenicity of SV40 in human mesothelioma.

Animals↗