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At least 163 records · Page 9Linked to original sources
PubMed2007

Comparative analysis of environmental DNA extraction and purification methods from different humic acid-rich soils.

AIM: To establish a rapid, improved soil environmental DNA extraction and purification protocol. METHODS AND RESULTS: Three different soil DNA isolation and four purification strategies were compared on different soil samples with variable rates of success. Bead beating extraction gave significantly higher DNA yields than microwave-based and liquid nitrogen grinding DNA extraction methods. The inclusion of soil washing prior to cell lysis decreased the amount of purification steps required. Although these soil types differed, polyvinylpolypyrrolidone (PVPP)-sepharose 2B column elution was sufficient for all three samples, yielding DNA pure enough for successful application in molecular studies. One soil sample retained 80% of the initial DNA after successful purification. CONCLUSIONS: Optimization of a purification protocol confirmed that only a combination of previously described methods proved sufficient in yielding pure environmental DNA from humic-rich soils. Total processing time for DNA extraction and subsequent purification from multiple samples was considerably more rapid than the previously described methods. SIGNIFICANCE AND IMPACT OF THE STUDY: This study developed a new optimized soil DNA extraction and purification protocol that is suitable for different environmental sources that are rich in humic acid content.

Bacillus↗
PubMed1999

DNA extraction from activated sludges.

To optimize the cell lysis step for DNA extraction from activated sludge samples, two floc dispersion methods (sonication versus stirring with a cation exchange resin), and three cell lysis treatments (lysozyme + SDS, sonication in a water bath, and thermal shock) were tested. For dispersion, stirring with cation exchange resin was more efficient than sonication. The cell lysis procedures were applied in two sequences, and DNA was quantified after each cell lysis treatment. Lysozyme + SDS was the most effective step in the cell lysis procedures. The cell lysis treatment sequences giving the highest DNA yields were not the same for all the sludges. The differences in sludge microbial compositions and floc structures required specifically adapted cell lysis protocols. The proposed protocols were highly efficient for DNA extraction, yielding about 50 mg DNA g-1 volatile suspended solids, and allowed PCR amplification of 16S rDNA.

Bacteria↗
PubMed1998

Comparison of C18-carboxypropylbetaine and glass bead DNA extraction methods for detection of Mycobacterium bovis in bovine milk samples and analysis of samples by PCR.

The purpose of this prospective study was to compare two different milk preparation methods to assay for the presence of Mycobacterium bovis by PCR. Detection by a C18-carboxypropylbetaine (CB-18)-based sample processing method was compared to extraction of DNA from milk with glass beads. Samples from 17 skin test-positive cattle were analyzed. Following CB-18 processing and glass bead extraction, the sensitivity of IS6110-based PCR was 94.1 and 58.8%, respectively (P < 0.025). Because CB-18 processing will permit the proficient use of PCR for diagnosis and surveillance of bovine tuberculosis, it will contribute to the more efficient detection and control of tuberculosis.

Animals↗
PubMed1997

K-ras mutations are found in DNA extracted from the plasma of patients with colorectal cancer.

BACKGROUND & AIMS: Circulating DNA can be isolated from the plasma of healthy subjects and from patients with cancer. The aim of this study was to detect K-ras mutations in DNA extracted from the plasma of patients with colorectal cancer. METHODS: Tumor and plasma DNA were extracted from 14 patients with colorectal cancer (stages A-D), and K-ras alterations were detected using a polymerase chain reaction assay that uses sequence-specific primers to amplify mutant DNA. These results were confirmed with another polymerase chain reaction assay that creates an enzyme restriction site in the absence of a K-ras mutation followed by direct sequencing and additional cloning techniques. RESULTS: Seven patients (50%) had a codon 12 K-ras mutation within their primary tumor, and identical mutations were found in the plasma DNA of 6 patients (86%). Mutant DNA was not detected in the plasma specimens of 7 patients whose tumors tested negative for K-ras alterations or in healthy control subjects. Similar results were obtained using all three molecular biological techniques. CONCLUSIONS: K-ras abnormalities can be detected in circulating DNA extracted from the plasma specimens of patients with colorectal cancer. If these results are confirmed in larger studies, genetic analysis of plasma DNA may have clinical applications in the future.

Adult↗
PubMed2000

Chloroplast DNA extraction from herbaceous and woody plants for direct restriction fragment length polymorphism analysis.

The technique described here is a fast and simple method of extracting chloroplast DNA (cpDNA). It overcomes the need for differential centrifugation using density gradients. The leaves do not have to be kept in the dark and lyophilized before extraction, but lyophilization is still possible. The chloroplasts are specifically lysed in a cell extract of leaves, using a non-ionic detergent. After isolation by centrifugation, the cpDNA is purified by the combined action of proteolytic enzymes and detergents, followed by the elimination of proteins using a mixture of chloroform and isoamyl alcohol. This method provided good quality restriction profiles for all species analyzed.

DNA Restriction Enzymes↗
PubMed2000

Immunoglobulin heavy-chain gene rearrangement studies by Southern blot using DNA extracted from formalin-fixed, paraffin-embedded tissue.

BACKGROUND: In most clinical molecular diagnostics laboratories, Southern blots for gene rearrangement studies are not routinely performed on formalin-fixed, paraffin-embedded (FFPE) tissue samples. In this study, immunoglobulin heavy-chain gene rearrangements by Southern blot using DNA extracted from FFPE tissue samples were studied. METHODS AND RESULTS: Eleven paired freshly frozen and FFPE tissue samples were evaluated for immunoglobulin gene rearrangements by PCR and Southern blot analyses. An additional 14 selected samples sent to our laboratory to rule out lymphoma, for which only FFPE tissue (no frozen tissue) was available and for which PCR was interpreted as negative, were evaluated by the same techniques. Southern blots generated from DNA extracted from FFPE tissues were qualitatively identical to those generated from DNA extracted from fresh or freshly frozen tissue and correlated well with the final diagnoses. Ten interpretable Southern blots were generated in the 14 cases in which no frozen tissue was available. Four of these ten blots were interpreted as positive for an immunoglobulin gene rearrangement. Although the number of samples analyzed is small, success with Southern blotting correlated with increased sample size and sample width (1.17 vs 0.49 cm(2); P <.024; 0.71 vs 0.43 cm; P <. 049, respectively). CONCLUSION: DNA extracted from FFPE tissue samples using the simple, efficient, and nontoxic techniques described in this report can be used in many cases for Southern blotting for the detection of clonality by gene rearrangement studies.

Blotting, Southern↗
PubMed2005

A simple method of DNA extraction in solving difficult criminal cases.

AIM: We examined combined use in house method and DNA IQ system (Promega) procedure for the extraction DNA from biological trace in order to help the solving some crime cases. METHOD: Simple and efficient method for extraction of the DNA from biological trace samples included the well washed trousers and the knife without any visual biological trails (from some one hard criminal case). In this method there were used: centrifuge, microwave oven, shaker, chelex, proteinase K, DNA IQ System (Promega). RESULTS: The extraction of DNA could be done within 2.5 hours or over the night. The DNA prepared on this way was good quality and could be used for STR analysis. CONCLUSIONS: This combined, simple, and safe method could be used for extraction DNA from samples containing a minute amount of the biological trace.

DNA↗
PubMed2004

Rapid and reliable DNA extraction techniques from trypan-blue-stained mycorrhizal roots: comparison of two methods.

Two improved DNA extraction techniques from trypan-blue-stained root fragments were developed and compared for rapid and reliable analyses. In Method A, 1 cm trypan-blue-stained mycorrhizal root fragments were individually isolated, crushed by bead beating, and purified with Chelex-100 (Bio-Rad). In Method B, DNA extraction was carried out using an UltraClean microbial DNA isolation kit (MoBio Laboratories). DNA was extracted from the mycorrhizal roots of four plant species, quantified by UV absorbance, and PCR-amplified with primers specific to arbuscular mycorrhizal fungi. Although PCR inhibitors might still exist when using Method A, appropriate dilution and employment of nested-PCR overcame this problem. Method B removed PCR inhibitors, but sometimes, depending on the mycorrhizal colonization within the root fragments, it also required nested PCR. In conclusion, both methods enabled us to handle many samples in a short time. Method B provided greater reliability and Method A provided better cost performance. Both techniques can be useful for PCR-based applications to identify species and estimate species composition after measuring mycorrhizal colonization rate with trypan blue staining.

DNA Primers↗
PubMed2000

Preliminary report on a method of human papillomavirus DNA extraction from verruca plantaris for polymerase chain reaction studies.

This preliminary report on the Chelex-based extraction method of HPV DNA from verruca plantaris is the first step in a series of studies on verruca plantaris undertaken, jointly, by the Departments of Podiatric Medicine and Microbiology at Des Moines University-Osteopathic Medical Center, Des Moines, Iowa. Current projects include the development of new primers for PCR studies of HPV, exploration of different viral DNA extraction methods, and surveys concerning treatment, success of therapies, and the epidemiology of verruca plantaris.

DNA, Viral↗
PubMed2003

Evaluation of DNA extraction methods for use in combination with SYBR green I real-time PCR to detect Salmonella enterica serotype enteritidis in poultry.

The objective of this study was to develop a rapid, reproducible, and robust method for detecting Salmonella enterica serotype Enteritidis in poultry samples. First, for the extraction and purification of DNA from the preenrichment culture, four methods (boiling, alkaline lysis, Nucleospin, and Dynabeads DNA Direct System I) were compared. The most effective method was then combined with a real-time PCR method based on the double-stranded DNA binding dye SYBR Green I used with the ABI Prism 7700 system. The specificity of the reaction was determined by the melting temperature (T(m)) of the amplicon obtained. The experiments were conducted both on samples of chicken experimentally contaminated with serotype Enteritidis and on commercially available poultry samples, which were also used for comparisons with the standard cultural method (i.e., ISO 6579/2001). The results of comparisons among the four DNA extraction methods showed significant differences except for the results from the boiling and Nucleospin methods (the two methods that produced the lowest threshold cycles). Boiling was selected as the preferred extraction method because it is the simplest and most rapid. This method was then combined with SYBR Green I real-time PCR, using primers SEFA-1 and SEFA-2. The specificity of the reaction was confirmed by the T(m), which was consistently specific for the amplicon obtained; the mean peak T(m) obtained with curves specific for serotype Enteritidis was 82.56 +/- 0.22 degrees C. The standard curve constructed using the mean threshold cycle and various concentrations of serotype Enteritidis (ranging from 10(3) to 10(8) CFU/ml) showed good linearity (R(2) = 0.9767) and a sensitivity limit of less than 10(3) CFU/ml. The results of this study demonstrate that the SYBR Green I real-time PCR constitutes an effective and easy-to-perform method for detecting serotype Enteritidis in poultry samples.

Animals↗
PubMed1990

[DNA extraction and Southern blot analysis in paraffin embedded material].

DNA was extracted from formaldehyde fixed and paraffin embedded tissue by the use of a modified extraction protocol. In all cases the recovered DNA was more degraded than DNA from fresh or frozen tissue. Fixation times of more than 4 days made it impossible to use the extracted DNA for Southern Blotting; DNA from paraffinized tissues not older than 1 or 2 years could be used for Southern Blotting after digestion with restriction enzymes, but we did not succeed in showing bands with restriction fragments more than 10 kb in length. We conclude that SBA analysis for malignant lymphomas with DNA extracted from routinely paraffin-embedded tissues isn't possible, because the restriction fragments looked for are in many cases longer than 10 kb.

Blotting, Southern↗
PubMed2006

A simple and reliable method for DNA extraction from bivalve mantle.

A simple and reliable method was developed for extracting genomic DNA from preserved mantle tissues of Pacific oyster Crassostrea gigas for reproducible PCR amplification. The method was based on destruction of the tissue using Proteinase K, Chelex 100 resin, detergents, and urea, followed by preferential capturing of genomic DNA with silica particles. Approximately 5 mg of mantle tissue provided a sufficient quality and quantity of DNA for several hundreds of PCR reactions amplifying the hypervariable mitochondrial DNA intergenic spacer, which is a useful genetic marker for population structure analysis of Pacific oyster. The method can be applied for DNA preparation from not only fresh and frozen but also ethanol-preserved mantle tissues, so this rapid and economical method can serve for investigating a large number of bivalve specimens collected in the field and next transported in ethanol at ambient temperature.

Animals↗
PubMed1995

A simple method of DNA extraction from Mycobacterium tuberculosis.

The application of molecular biology methods has contributed significant insight into the epidemiology of infections caused by Mycobacterium tuberculosis. However, most of the techniques remain out of reach of laboratories in the tropics. We describe here a simple method for extraction of DNA from the pathogen, a first step in the application of molecular biology tools.

Bacteriological Techniques↗
PubMed2003

DNA extraction using bacterial magnetic particles modified with hyperbranched polyamidoamine dendrimer.

A cascading hyperbranched polyamidoamine dendrimer was synthesized on the surface of bacterial magnetite from Magnetospirillum magneticum AMB-1 to allow enhanced extraction of DNA from fluid suspensions. Characterization of the synthesis revealed linear doubling of the surface amine charge from generations one through five starting with an amino silane initiator. Furthermore, transmission electron microscopy revealed clear dispersion of the single domain magnetite in aqueous solution. The dendrimer modified magnetic particles have been used to carry out magnetic separation of DNA. Binding and release efficiencies increased with the number of generations and those of bacterial magnetite modified with six generation dendrimer were 7 and 11 times respectively as many as those of bacterial magnetite modified with only amino silane.

Coated Materials, Biocompatible↗
PubMed1998

A rapid method for DNA extraction from fine-needle aspiration biopsies of thyroid tumors, and subsequent RET mutation analysis.

The presence of germline and somatic mutations in the RET proto-oncogene (RET) in patients with hereditary and sporadic medullary thyroid carcinoma (MTC) may have important ramifications for patient management. It has been suggested that the presence of the mutation ATG-->ACG at codon 918 in sporadic MTC is associated with a worse prognosis, and hence the need for more aggressive surgical, or other, treatment. Since fine-needle aspiration biopsy (FNAB) is an important component of the preoperative management of patients with thyroid tumors, we developed a rapid (20-min) method that enables extraction of DNA from FNABs for RET mutation analysis. The method allows preoperative genetic analysis to aid in management of patients with MTC, and may be applied to other tumor types where a preoperative mutation analysis based on polymerase chain reaction amplification is desired.

Biopsy, Needle↗
PubMed1986

Southern blot analysis of DNA extracted from formalin-fixed pathology specimens.

We have developed a method for the extraction of DNA from formalin-fixed, paraffin-embedded pathology specimens. High-molecular-weight DNA was recovered from well-fixed nonautolyzed samples of viable tissue. DNA recovered from samples exposed to picric acid or mercuric chloride containing fixatives was not intact. Increasing the formalin fixation time decreased the amount of intact DNA available. When these limitations were taken into consideration, the procedure allowed for the removal of degraded and chemically modified DNA from the preparation, and the final product was suitable for quantitative and qualitative analysis by Southern or dot blotting techniques. Digestion with methylation-sensitive restriction endonucleases showed that DNA methylation patterns were not altered after formalin fixation.

DNA↗