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At least 289 records · Page 16Linked to original sources
PubMed1998

Pretreatment with restriction enzyme or bovine serum albumin for effective PCR amplification of Epstein-Barr virus DNA in DNA extracted from paraffin-embedded gastric carcinoma tissue.

An association between Epstein-Barr virus (EBV) and gastric carcinoma has been studied through the EBV genome present in the carcinoma cells. Recently, we found that EBV DNA in paraffin-embedded gastric carcinoma tissue was detected effectively by PCR after pretreatment of the extracted DNA with a restriction enzyme, BamHI or EcoRI. Here, we show that the PCR amplification was also enhanced by pretreatment of the DNA with other restriction enzymes or with bovine serum albumin and several other proteins. Treatment with these proteins may remove a PCR inhibitor(s) in the DNA samples extracted from the paraffin blocks.

Animals↗
PubMed1999

Convenient and versatile DNA extraction using agarose plugs for ribotyping of problematic bacterial species.

We describe a convenient, versatile and safe method for preparing bacterial DNA for ribotyping analysis. In this method, extraction of bacterial DNA from Salmnonella typhi and Burkholderia pseudomallei. and subsequent restriction endonuclease digestion, was performed in agarose blocks/plugs thus minimizing shearing and loss of DNA, problems commonly associated with liquid phase phenol extraction. Digested DNA in the plugs was then electrophoresed directly, transferred to nylon membranes and hybridized with labeled rDNA probes in the usual manner to provide reproducible restriction patterns. This method is particularly useful for bacterial species where standard DNA extraction in the liquid phase using phenol has been problematic (e.g. B. pseudomallei) but can be used for any bacterial species. The DNA extracted within the agarose plugs can be stored for long periods and can be used in other, widely-used typing methods such as pulsed-field gel electrophoresis (PFGE) and PCR-based techniques. Embedding live cells directly in agarose plugs also minimizes the risk of exposure to these virulent human pathogens among laboratory workers.

Bacterial Typing Techniques↗
PubMed2006

A rapid and simple method for DNA extraction from yeasts and fungi isolated from Agave fourcroydes.

A simple and easy protocol for extracting high-quality DNA from different yeast and filamentous fungal species is described. This method involves two important steps: first, the disruption of cell walls by mechanical means and freezing; and second, the extraction, isolation, and precipitation of genomic DNA. The absorbance ratios (A(260)/A(280)) obtained ranged from 1.6 to 2.0. The main objective of this procedure is to extract pure DNA from yeast and filamentous fungi, including those with high contents of proteins, polysaccharides, and other complex compounds in their cell walls. The yield and quality of the DNAs obtained were suitable for micro/minisatellite primer-polymerase chain reaction (MSP-PCR) fingerprinting as well as for the sequence of the D1/D2 domain of the 26S rDNA.

Agave↗
PubMed1996

A new, fast, and simple DNA extraction method for HLA and VNTR genotyping by PCR amplification.

In the present study a new DNA extraction method is described. The new protocol, which uses caprylic acid for isolating DNA, is technically simple and very fast, as it enables us to obtain DNA from peripheral blood in only 10 minutes. Moreover, DNA preparations obtained with this procedure can be effectively used for HLA class II and variable number tandem repeat genotyping by polymerase chain reaction, so the new method is well suited for routine clinical use in any type of analysis requiring DNA typing for individual characterization.

Caprylates↗
PubMed2000

[Evaluation of a simple and rapid method of Plasmodium falciparum DNA extraction using thick blood smears from Gabonese patients].

In field-based studies, sometimes it is difficult to collect and store samples. We have evaluated a method of malaria parasite deoxyribonucleic (DNA) extraction from non-stained thick dried blood smears collected from 108 Gabonese patients. This method of DNA isolation was compared to those using phenol/chloroform. Patients parasitemia ranged from 0 to 240,000 parasites/microliter of blood. Both methods of DNA preparation gave similar results. Of the 108 slides, 57% were Plasmodium falciparum positive after PCR analysis of the MSA-2 gene and 34% were positive by microscopical examination. Thirty-six and seventy-two blood smears from patients were also tested after one and four weeks' storage respectively, at room temperature, and the parasite DNA was successfully extracted. We conclude that this simple method of collection and rapid procedure of parasite DNA isolation are adequate and convenient in the field when a large number of samples are required and in the case of repetitive samplings of patients.

Animals↗
PubMed2005

Standardization of parvovirus B19 DNA extraction from serum and quantitative PCR.

Human parvovirus B19 (B19) is a newly emerging virus causing a wide spectrum of clinical conditions. The corner stone of diagnosis of acute B19 infection is demonstration of anti-B19 IgM antibodies and its DNA by PCR. Sera of patients infected with B19 acutely or persistently shows intense viraemia (up to 10(12) virus particles/ ml) but extraction of B19 DNA from serum is a problematic task. There is no single standardized, cost-effective in-house method, which can successfully extract DNA of B19 from serum samples and which has been subsequently tested repeatedly by many investigators over time. We describe here an efficient in-house method of extraction of B19 DNA from serum and quantitate extracted DNA by PCR. Firstly, a quantitative PCR was done using 3 microl of a cloned B19 DNA (33.3 pg/ml) mixed in 47 microl of sterile distilled water which were further diluted from 10(-1) up to 10(-7) to find the lower limit of DNA detection. To mimic human serum samples with known quantity of B19, 3 ml of cloned B19 DNA (33.3 pg/ml) were mixed with 47ml of fetal calf serum (FCS; free of B19) and were similarly log diluted from 10(-1) to 10(-7) in 50 ml volume. In-house method of DNA extraction from serum (FCS+B19 DNA) were then performed followed by quantitative PCR. In both the cases, we were able to detect B19 DNA up to 10(-4) dilution which contained 0.6 fg of B19 DNA corresponding to 12 B19 genome equivalents/PCR reaction or 2.4 x 10(2) genome quivalents/ml of serum. Further, the entire procedure was repeated two more times and identical results were obtained confirming its reproducibility. Using this in-house method we extracted and amplified B19 DNA successfully from sera of clinically suspected cases of B19 infection (data not shown). Compared to other studies, the sensitivity of our in-house method was found to be superior hence recommended for developing countries as commercial kits are too costly.

Animals↗
PubMed2004

[A study on the method of DNA extraction from unbuffered formalin-fixed and paraffin-embedded samples].

BACKGROUND & OBJECTIVE: Unbuffered formalin is widely used to fix resected specimens in China. The DNA in unbuffered formalin-fixed and paraffin-embedded tissues is usually degraded seriously, so the extraction of DNA from these samples is difficult. This study was conducted to seek an optimal method to extract DNA from these samples. METHODS: Fifteen blocks of esophageal carcinoma resected in Fourth Hospital of Hebei Medical University in 2000 were selected. The cells were lyzed by proteinase K digestion or heating under different pH values, then DNA was extracted by phenol:chloroform. After that, four parameters (deparaffined by xylene or histolene; digested for 48 h or 72 h at 37 degrees C or 56 degrees C; extracted by salting-out or phenol:chloroform) were optimized according to the principle of cross design. At last, the quality of obtained DNA was analyzed with electrophoresis and PCR amplification. RESULTS: The quality and quantity of DNA obtained by proteinase K digestion (the average yield is 17.88 microg) were better than that of heating under different pH (7-12)(P< 0.05). The quality and quantity of DNA digested at 56 degrees C were better than that at 37 degrees C, and similarly, digestion for 72 hours was better than that for 48 hours. The methods of deparaffin and extraction had no obvious influence on the quality and quantity of DNA. CONCLUSION: By means of NaCl salting-out after proteinase K digestion, more reliable quality of DNA can be obtained from unbuffered formalin-fixed and paraffin-embedded samples. Furthermore,digestion for three days at 56 degrees C is more likely to obtain DNA with high quality and quantity.

DNA↗
PubMed1999

Use of magnetic beads for tissue DNA extraction and IS6110 Mycobacterium tuberculosis PCR.

Polymerase chain reaction (PCR) techniques are used increasingly for the diagnosis of Mycobacterium tuberculosis infection and can be used on the DNA obtained from both frozen and formalin fixed, paraffin wax embedded tissues. However, the extraction of DNA by means of the conventional phenol/chloroform method is time consuming and requires the use of potentially dangerous chemical reagents. This paper describes a method based upon the use of magnetic beads for the extraction of M tuberculosis DNA from both routinely formalin fixed, paraffin wax embedded tissues and frozen tissues. Magnetic bead extracted DNA from brain, lymph node, and lung tissues collected from patients with human immunodeficiency virus and tuberculosis was compared with that extracted using the phenol/chloroform method. The magnetic bead extraction procedure requires less than two hours, including the time necessary to dewax the tissue sections. In all cases, the DNA extracted with both methods was amplified successfully by PCR for the M tuberculosis IS6110 sequence. Magnetic bead DNA extraction can be used on both frozen and archival tissues: the method is reliable, simple, sensitive, and rapid; in addition, it does not use hazardous procedures or specialised laboratory equipment and can be used for routine DNA isolation from various human tissues.

Brain↗
PubMed1989

Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification.

Several chemical and enzymatic properties were examined in the DNA extracted from dry remains of soft tissues that vary in age from 4 to 13,000 years and represent four species, including two extinct animals (the marsupial wolf and giant ground sloth). The DNA obtained was invariably of a low average molecular size and damaged by oxidative processes, which primarily manifest themselves as modifications of pyrimidines and sugar residues as well as baseless sites and intermolecular cross-links. This renders molecular cloning difficult. However, the polymerase chain reaction can be used to amplify and study short mitochondrial DNA sequences that are of anthropological and evolutionary significance. This opens up the prospect of performing diachronical studies of molecular evolutionary genetics.

Animals↗
PubMed1966

Studies on viral plasmacytosis (Aleutian disease) of mink. VII. Infection of mink with DNA extracted from diseased spleens.

Lesions considered typical of aleutian disease developed in three of four mink inoculated with DNA extracted from spleens of mink with viral plasmacytosis. Control mink inoculated with buffered saline or DNA treated with specific enzyme (DNAase) remained normal. It is inferred that the infective DNA corresponds to viral DNA. This DNA preparation was used in an attempt to infect tissue cultures from mink testis cells but the results were equivocal.

Animals↗
PubMed2005

DNA extraction from human saliva deposited on skin and its use in forensic identification procedures.

Saliva is usually deposited in bite marks found in many homicides, assault and other criminal cases. In the present study, saliva obtained from volunteers was deposited on skin and recovered for DNA extraction and typing in order to evaluate its usefulness for practical case investigation and discuss the contribution of forensic dentistry to saliva DNA typing. Twenty saliva samples were collected from different donors and used as suspects' samples. Five of these samples were randomly selected and deposited (250 microl) on arm skin. Saliva was collected from skin using the double swab technique. DNA from saliva and skin-deposited saliva samples was extracted by the phenol-chloroform method. DNA samples were amplified by PCR for DNA typing using a set of 15 STRs. The recovery of DNA from saliva deposited in the skin was 14 to 10 times lower than DNA quantity from saliva samples. DNA typing was demonstrated in 4 of 5 deposited saliva samples, the likelihood ratios estimated for these samples based on data of the Brazilian population were 1:11, 1:500, 1:159.140 and 1:153.700.123. Our results indicate that standardized procedures used for DNA collection and extraction from skin-deposited saliva can be used as a method to recover salivary DNA in criminal cases. However, it is important to observe that DNA recovery in forensic samples can be difficult. This study suggests that the analysis of saliva deposited on skin be incorporated into a criminal investigation since it may have great discriminatory power.

Adult↗
PubMed1992

A method to extract DNA for molecular studies from cells fixed in Carnoy.

We describe a simple method for isolation of high-molecular-weight DNA from cells fixed in Carnoy's solution for cytogenetic studies. DNA samples were extracted from NIH3T3 cells, and no apparent degradation was noticed. This method should be useful for molecular analysis of cells fixed for cytogenetic studies.

3T3 Cells↗
PubMed2002

Application of a convenient DNA extraction method and multiplex PCR for the direct detection of Staphylococcus aureus and Yersinia enterocolitica in milk samples.

The application of PCR for the direct and sensitive detection of food-borne pathogens is largely affected by the quality of the template DNA prepared from food samples. In the present study, a chemical extraction method of bacterial DNA from spiked milk samples for the direct detection of Staphylococcus aureus and Yersinia enterocolitica was evaluated by PCR. Gene specific primers were designed to target the nuclease (nuc) and the attachment invasion locus (ail) genes of S. aureus and Y. enterocolitica, respectively and used in PCR. A combination of organic solvents, detergents and alkali in the DNA extraction method permitted a detection limit of 10 cfu ml(-1) milk for both the pathogens. When equal numbers of S. aureus and Y. enterocolitica were spiked in milk samples, the individual detection limit was determined to be 10(3) cfu ml(-1) milk. Simultaneous amplification of 482 and 359 bp fragments of the nuc and ail genes was obtained using the primer pairs in a single reaction. Multiplex PCR enabled the detection of 10(4) cfu ml(-1) milk of S. aureus and Y. enterocolitica without any pre-enrichment step. A combination of conventional isolation technique and PCR using DNA extracted by the proposed method was used to test raw milk samples for possible contamination with S. aureus and Y. enterocolitica. The presence of S. aureus in the tested samples was indicated by both the methods while Y. enterocolitica could not be detected in any of the samples. The template DNA extraction method developed in this study is rapid, sensitive and avoids interference from potential PCR inhibitors and demonstrates the potential of detecting multiple pathogens in milk samples without any enrichment.

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↗
PubMed1995

Improved genomic/nuclear DNA extraction for 8-hydroxydeoxyguanosine analysis of small amounts of rat liver tissue.

Using two different commercially available extraction kits, genomic/nuclear DNA could be recovered from rat liver samples as small as 10 mg. Background 8-hydroxydeoxyguanosine levels in such DNA were low and stable at 0.26-0.30 +/- 0.01-0.03/10(5) guanine residues. The minimum tissue wet weight required for the accurate 8-hydroxydeoxyguanosine analysis was 25 mg. The present results indicate that routine and reliable assessment of the involvement of oxidative DNA damage in the development of various diseases, including cancer, is feasible using a variety of tissue sources.

8-Hydroxy-2'-Deoxyguanosine↗
PubMed1995

[A polymorphism study of the DNA extracted from dental tissues].

Often teeth are the only items which can be used for personal identification in forensic medicine. In the present work we describe a method to extract and amplify DNA from dental elements ranging from 2 weeks to 5 year from the avulsion. PCR (polymerase chain reaction) was used to amplify VNTR sequences; the alleles products were electrophoresed, visualized by traditional methods and compared to the amplified products obtained from the matching blood sample. Our results give a new and powerful investigative tool for personal identification in the field of forensic odontostomatology, since such a procedure can be successfully applied both to recent and to ancient teeth.

Apolipoproteins B↗