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At least 685 records · Page 38Linked to original sources
PubMed2005

Sensitive and rapid detection of herpes simplex virus and varicella-zoster virus DNA by loop-mediated isothermal amplification.

Loop-mediated isothermal amplification (LAMP) is a novel nucleic acid amplification method in which reagents react rapidly and efficiently, with a high specificity, under isothermal conditions. We used a LAMP assay for the detection of herpes simplex virus type 1 (HSV-1), herpes simplex virus type 2 (HSV-2), and varicella-zoster virus (VZV). The virus specificities of primers were confirmed by using 50 HSV-1, 50 HSV-2, and 8 VZV strains. The assay was performed for 45 min at 65 degrees C. The LAMP assay had a 10-fold higher sensitivity than a PCR assay. An analysis of nucleotide sequence variations in the target and primer regions used for the LAMP assay indicated that 3 of 50 HSV-1 strains had single nucleotide polymorphisms. No HSV-2 or VZV strains had nucleotide polymorphisms. Regardless of the sequence variation, there were no differences in sensitivity with the HSV-1-specific LAMP assay. To evaluate the application of the LAMP assay for clinical diagnosis, we tested clinical samples from 40 genital herpes patients and 20 ocular herpes patients. With the LAMP assay, 41 samples with DNA extraction and 26 direct samples without DNA extraction were identified as positive for HSV-1 or HSV-2, although 37 samples with DNA extraction and just one without DNA extraction were positive by a PCR assay. Thus, the LAMP assay was less influenced than the PCR assay by the presence of inhibitory substances in clinical samples. These observations indicate that the LAMP assay is very useful for the diagnosis of HSV-1, HSV-2, and VZV infections.

Animals↗
PubMed2004

Does extraction of DNA and RNA by magnetic fishing work for diverse plant species?

An automated nucleic acid extraction procedure with magnetic particles originally designed for isolation of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) from animal tissues was tested for plant material. We isolated genomic DNA and total RNA from taxonomically diverse plant species representing conifers (Scots pine), broad-leaved trees (silver birch and hybrid aspen), dwarf shrubs (bilberry), and both monocotyledonous (regal lily) and dicotyledonous (Saint John's wort, round-leaved sundew, and tobacco) herbaceous plants. Buffers developed for DNA extraction were successfully used in addition to manufacturer's extraction kits. The quality of RNA was appropriate for many applications, but the quality of DNA was not always sufficient for polymerase chain reaction (PCR) amplification. However, we could strikingly improve the quality by eliminating the adherent compounds during the extraction or later in the PCR phase. Our results show that the use of the procedure could be extended to diverse plant species. This procedure is especially suitable for small sample sizes and for simultaneous processing of many samples enabling large-scale plant applications in population genetics, or in the screening of putative transgenic plants.

Chemical Fractionation↗
PubMed2006

Extremely rapid extraction of DNA from bacteria and yeasts.

A very simple and rapid method for extracting genomic DNA from Gram-negative bacteria, Gram-positive bacteria and yeasts is presented. In this method, bacteria or yeasts are lysed directly by phenol and the supernatant is extracted with chloroform to remove traces of phenol. The supernatant contains DNA that is suitable for molecular analyses, such as PCR, restriction enzyme digestion and genomic library construction. This method is reproducible and simple for the routine DNA extraction from bacteria and yeasts.

Chloroform↗
PubMed1994

Induction and repair of DNA base damage studied in X-irradiated CHO cells using the M. luteus extract.

DNA base damage was measured in Chinese hamster ovary cells X-irradiated under aerobic conditions using an extract of the bacterium Micrococcus luteus. The glycosylases and endonucleases present in this extract recognize damaged bases and convert them into strand breaks (termed endonuclease-sensitive sites, enss). Strand breaks were detected by the alkaline unwinding technique. The induction of enss was measured for X-ray doses ranging up to 45 Gy. The relative frequency of all enss related to all radiation induced strand breaks was 1.7 +/- 0.4. Repair of enss was studied for a radiation dose of 45 Gy. The number of enss was found to decrease exponentially with time after irradiation with a half-time of tau enss = 37 +/- 8 min. The repair kinetics that were also measured for all X-ray-induced DNA strand breaks were found to consist of three phases: fast, intermediate and slow. The intermediate phase was fitted under the assumption that this phase results from the formation and repair of secondary single-strand breaks generated by enzymatic incision at the sites of base damage repair. The relative frequency of base damage derived from this fit was 1.8 +/- 0.5 and the half-time of base damage repair was tau in = 32 +/- 6 min. The agreement of this half-time with the half-time obtained when base damage was measured directly using the M. luteus assay gives support to the interpretation that the intermediate phase of the total repair curve represents the kinetics of secondary strand breaks resulting from base damage by enzymatic incision.

Animals↗
PubMed2001

DNA fragmentation, an indicator of apoptosis, in cultured black tiger shrimp Penaeus monodon infected with white spot syndrome virus (WSSV).

Fifty black tiger shrimp Penaeus monodon from commercial cultivation ponds in Malaysia were examined by Tdt-mediated dUTP nick-end labeling (TUNEL) fluorescence assay and agarose gel electrophoresis of DNA extracts for evidence of DNA fragmentation as an indicator of apoptosis. From these specimens, 30 were grossly normal and 20 showed gross signs of white spot syndrome virus (WSSV) infection. Of the 30 grossly normal shrimp, 5 specimens were found to be positive for WSSV infection by normal histology and by nested polymerase chain reaction (PCR) analysis. All of the specimens showing gross signs of WSSV infection were positive for WSSV by normal histology, while 5 were positive by nested PCR only (indicating light infections) and 15 were positive by 1-step PCR (indicating heavy infections). Typical histological signs of WSSV infection included nuclear hypertrophy, chromatin condensation and margination. None of the 25 grossly normal shrimp negative for WSSV by 1-step PCR showed any signs of DNA fragmentation by TUNEL assay or agarose gel electrophoresis of DNA extracts. The 10 specimens that gave PCR-positive results for WSSV by nested PCR only (i.e., 5 grossly normal shrimp and 5 grossly positive for WSSV) gave mean counts of 16 +/- 8% TUNEL-positive cells, while the 25 specimens PCR positive by 1-step PCR gave mean counts of 40 +/- 7% TUNEL-positive cells. Thus, the number of TUNEL positive cells present in tissues increased with increasing severity of infection, as determined by gross signs of white spots on the cuticle, the number of intranuclear inclusions in histological sections, and results from single and nested PCR assays. DNA extracts of PCR-positive specimens tested by agarose gel electrophoresis showed indications of DNA fragmentation either as smears or as 200 bp ladders. Given that DNA fragmentation is generally considered to be a hallmark of apoptosis, the results suggested that apoptosis might be implicated in shrimp death caused by WSSV.

Animals↗
PubMed2002

Evaluation of extraction and purification methods for obtaining PCR-amplifiable DNA from compost for microbial community analysis.

Analysis of microbial community structure in complex environmental samples using nucleic acid techniques requires efficient unbiased DNA extraction procedures; however, humic acids and other contaminants complicate the isolation of PCR-amplifiable DNA from compost and other organic-rich samples. In this study, combinations of DNA extraction and purification methods were compared based on DNA yield, humic acid contamination, PCR amplifiability, and microbial community structure assessed by terminal restriction fragment length polymorphisms (TRFLP) of amplified 16S rRNA genes. DNA yield and humic acid contamination, determined by A230, varied significantly between extraction methods. Humic acid contamination of DNA obtained from compost decreased with increasing salt concentration in the lysis buffer. DNA purified by gel permeation chromatography (Sepharose 4B columns) gave satisfactory PCR amplification with universal eubacterial 16S rRNA gene primers only when A260/A280 ratios exceeded 1.5. DNA purified with affinity chromatography (hydroxyapatite columns), and showing A260/A280 ratios as high as 1.8, did not show consistently satisfactory PCR amplification using the same 16S rRNA primers. Almost all DNA samples purified by agarose gel electrophoresis showed satisfactory PCR amplification. Principal components analysis (PCA) of TRFLP patterns differentiated compost types based on the presence/absence of peaks and on the height of the peaks, but differences in TRFLP patterns were not appreciable between extraction methods that yielded relatively pure DNA. High levels of humic acid contamination in extracted DNA resulted in TRFLP patterns that were not consistent and introduced a bias towards lower estimates of diversity.

Bacteria↗
PubMed1997

Rapid method for detecting Desulfitobacterium frappieri strain PCP-1 in soil by the polymerase chain reaction.

A rapid method was developed for detecting in soil Desulfitobacterium frappieri strain PCP-1, an anaerobic gram-positive bacterium, isolated from a methanogenic consortium degrading pentachlorophenol. The method involved the establishment of a protocol for extracting total DNA from soil with the least contamination, and the use of the polymerase chain reaction (PCR) to detect strain PCP-1 with primers targeted with PCP-1 16S rRNA. To optimize the DNA extraction conditions, a glass mill homogenizer and a low-salt buffer containing polyvinylpolypyrrolidone were used on a black soil rich in organic matter. Recovered DNA was further purified with phenol/chloroform extractions, ammonium acetate precipitation and a G200 Sephadex gel-filtration column. DNA was extracted from soil supplemented with different concentrations of PCP-1 cells. Detection of PCP-1 was by PCR. The limit of detection was 800 added PCP-1 cells/g dry soil. This level of detection was achieved when the T4 gene-32 protein and 1 microgram soil DNA were added to the PCR mixture followed by a nested PCR. This method is quick, sensitive, and can process several samples at the same time.

Bacteria, Anaerobic↗
PubMed2006

A useful protocol for analyses of mutations of the epidermal growth factor receptor gene.

Recent studies have reported that mutations of the epidermal growth factor receptor (EGFR) gene are associated with the responsiveness of tyrosine kinase inhibitors (TKIs), which are molecular targets for non-small cell lung cancer (NSCLC). To provide genetic analyses for NSCLC patients, a simple and reliable method using paraffin-embedded materials is needed. The DEXPAT DNA extraction kit was used for DNA extraction from paraffin-embedded materials. DNA was amplified using the nested PCR technique, then analyzed by direct sequencing for EGFR mutations (exons 18 to 21). The phenol/chloroform extraction for DNA was also performed for comparison. When the DEXPAT kit was used, distinct bands were observed in all products after nested PCR assays of paraffin-embedded materials. Distinct sequencing signals were obtained. Results from the sequencing analysis of paraffin-embedded materials and frozen materials were completely concordant. The current study suggests that DNA extraction with the DEXPAT kit followed by nested PCR is a simple and reliable technique for analyzing the EGFR gene status with paraffin-embedded samples.

Base Sequence↗
PubMed1997

Summary of validation studies from twenty-six forensic laboratories in the United States and Canada on the use of the AmpliType PM PCR amplification and typing kit.

A cooperative study was undertaken to collect and summarize the results of validation studies from forensic laboratories in the United States and Canada on the use of the AmpliType PM PCR amplification and typing kit for genetic typing of forensic biological evidence. This report compiles data from 26 laboratories on: 1) reproducibility studies on DNA extracted from various samples, 2) genetic typing of DNA extracted from a variety of biological samples on various substrates, 3) the effects of exogenous chemicals, materials, and environmental factors on test results, 4) sensitivity studies to determine the least detectable amount of extracted genomic DNA that can be reliably typed, 5) analysis of mixtures containing two sources of genomic DNA, 6) cross-hybridization with DNA extracted from various nonhuman species, and 7) evaluation of assay performance on parallel studies with other genetic typing systems on proficiency test panels, mock cases, and adjudicated/nonprobative casework. Equivalent results were obtained by each laboratory that supplied data, demonstrating the reliability and consistency of the test. Overall, it can be concluded from this study that the AmpliType PM PCR amplification and typing kit meets the guidelines of the Technical Working Group on DNA Analysis Methods (TWGDAM) and there is general scientific acceptability of this kit for forensic DNA testing.

Canada↗
PubMed2003

Direct extraction of DNA from soils for studies in microbial ecology.

Molecular analyses for the study of soil microbial communities often depend on the extraction of DNA directly from soils. These extractions are by no means trivial, being complicated by humic substances that are inhibitory to PCR and restriction enzymes or being too highly colored for blot hybridization protocols. Many different published protocols exist, but none have been found to be suitable enough to be generally accepted as a standard. Most direct extraction protocols start with relatively harsh cell breakage steps such as bead-beating and freeze-thaw cycles, followed by the addition of detergents and high salt buffers and/or enzymic digestion with lysozyme and proteases. After typical organic extraction and alcohol precipitation, further purification is usually needed to remove inhibitory substances from the extract. The purification steps include size-exclusion chromatography, ion-exchange chromatography, silica gel spin columns, and cesium chloride gradients, among others. A direct DNA extraction protocol is described that has been shown to be effective in a wide variety of soil types. This protocol is experimentally compared to several published protocols.

DNA↗
PubMed1990

Extraction of DNA from exfoliative cytology specimens and its suitability for analysis by the polymerase chain reaction.

The extraction of DNA from archival exfoliative cytology samples would allow the molecular biological analysis of this readily available material using the polymerase chain reaction (PCR). We have quantitatively and qualitatively studied the extraction of DNA from a variety of cytological preparations. For both fresh and archival cervical smears, overnight incubation with proteinase K produces high yields of high molecular weight DNA, but simply boiling the samples produces DNA suitable for PCR amplification of a single copy gene. Increasing the proteinase K incubation to several days allows the extraction of DNA from fixed and stained archival cytology slides from a variety of sites. The extracted DNA was again suitable for PCR analysis. Fresh and archival cytological material can be utilized for molecular biological study of disease processes using PCR. Archival cytological material is probably the best source of DNA and RNA after stored frozen tissue.

DNA↗
PubMed2002

Performance characteristics of an automated PCR assay for the quantification of cytomegalovirus DNA in plasma.

The COBAS Amplicor CMV Monitor test (Roche Diagnostics), an automated polymerase chain reaction (PCR) assay for the quantification of cytomegalovirus (CMV) DNA in plasma samples, was evaluated in a routine diagnostic laboratory. Using cell culture-derived CMV and CMV-negative human plasma, the linear detection range of the assay as well as its intra-and inter-assay variabilities were assessed. The study design allowed distinguishing variations in results related to amplification and detection from those caused by differences in the efficiency of DNA extraction. The assay was able to identify the majority of samples correctly as positive with CMV DNA concentrations above the limit of detection. However, the reported values were often twofold or more different from the (theoretical) input, which could be explained partly by inefficient DNA extraction. The following values were computed for the coefficients of determination R(2): inter-assay variability excluding DNA extraction, R(2)=0.982; including DNA extraction, R(2)=0.977; intra-assay variability excluding DNA extraction, R(2)=0.992; including DNA extraction, R(2)=0.992. On balance, the test has acceptable within-run and between-run reproducibility. It therefore allows the comparison of results obtained at different time-points as well as in different laboratories, e.g. in multi-centre studies.

Automation↗
PubMed2000

Evaluation of an alkaline lysis method for the extraction of DNA from whole blood and forensic stains for STR analysis.

A modified alkaline lysis protocol for extracting DNA from forensically relevant specimens is evaluated and compared with the chelex 100 method. For whole blood, bloodstains and sperm stains, both methods yielded comparable results after amplification for a pentameric STR locus (HumCD4). The main advantages of the new method are: only approximately ten minutes and two pipetting steps are necessary and the expenses for the extraction are extremely low as only NaOH, TrisHCl buffer and a single microcentrifuge tube are required. Alkaline lysis also proved to yield DNA suitable for typing longer STRs by using dye-labeled primers and capillary electrophoresis. These advantages should render this protocol especially interesting for high-throughput laboratories in combination with multiplex PCR and fluorescent dye technology, although the storability of the extracts proved to be problematic.

Blood Chemical Analysis↗
PubMed1999

Combination of biomolecular and stable isotope techniques to determine the origin of organic matter used by bacterial communities: application to sediment.

Natural isotopic composition is a good tool to trace organic matter in ecosystems. Recent studies used a combination of molecular and stable isotope techniques to determine the origin of the organic carbon used by bacteria in the water column. In our study, we show that this procedure can be used for analysis of sediment bacterial communities with few modifications. In the water column, bacterial recovery is done before DNA extraction. In the sediment, we tested qualitatively and quantitatively a direct and indirect extraction of DNA. The direct extraction was the most efficient. It recovered between 3.1 and 15.8 microg DNA g(-1) dry sediment and the contamination of field samples by eucaryotic DNA was less than 13%. In this preliminary study of the salt marsh ecosystem, the delta(13)C values of DNA (-26 to - 24%) recovered from the sediment were close to the delta(13)C values of halophytic plants (-26.4 and - 25.3%) showing a relationship between plants and microorganisms. Thus, this procedure can be used to trace the flow of carbon through the sediment microbial biomass and to understand the variation of bacterial activity according to the inputs of allocthonous and autochtonous organic matter.

Bacteria↗
PubMed2000

Deoxyribonucleic acid preparation in polymerase chain reaction genotyping of transgenic mice.

BACKGROUND AND PURPOSE: In an attempt to find a rapid and reproducible method for routine polymerase chain reaction genotyping of transgenic mice, two novel approaches were developed. METHODS: One approach allowed reproducible amplification from crude lysates of tail snips, using a thermally activated polymerase. In a second approach, for situations in which non-invasive techniques are necessary, oral swab specimens were amplified after DNA extraction by use of an isolation kit. Samples from 10 transgenic factor VIII knockout mice were genotyped after processing by use of these and other methods. RESULTS: False-negative results were not obtained by use of the two novel approaches. Despite their relative simplicity, both approaches yielded results comparable to those obtained by use of procedures known to be reliable, such as organic extraction and a DNA extraction kit. CONCLUSION: Both approaches are useful for PCR-amplification of DNA from mammalian sources.

Animals↗
PubMed2005

Comparison of several methods for the extraction of DNA from potatoes and potato-derived products.

Eight methods were compared for the extraction of DNA from raw potato tubers, and nine methods were evaluated for the extraction of DNA from dehydrated potato slices, potato flakes, potato flour, potato starch, and two ready-to-eat potato snack foods. Extracts were assessed for yield using a fluorescence-based DNA quantification assay. Real-time amplification of an endogenous gene, sucrose synthase (sus), was used to assess extract and template quality. A CTAB-based method extracted the highest DNA yields from the tuber material. An in-house method, which utilized the Kingfisher magnetic particle processor, yielded the highest template quality from the tubers. For most of the tuber samples, the Kingfisher and CTAB methods recovered the highest levels of amplifiable sus. DNA yields for potato-derived foods generally decreased with the extent that the product had been processed. The methods that utilized the magnetic particle processor delivered the highest template quality from one of the snack products that was particularly high in fat. For most of the remaining processed products, the levels of amplifiable target DNA recovered were roughly correlated with total DNA recovery, indicating that overall yield had greater influence over sus amplification than template quality. The Wizard method was generally the best method for the extraction of DNA from most of the potato-derived foods.

Cetrimonium↗
PubMed2003

Quantitative polymerase chain reaction-based assay for estimating DNA yield extracted from domestic cat specimens.

A quantitative polymerase chain reaction (PCR) assay has been developed for the quantification of genomic DNA extracted from domestic cat samples. The assay, which targets highly repetitive genomic short interspersed nuclear elements (SINE), can be performed rapidly and is highly sensitive, detecting as little as 10 fg of feline genomic DNA. The assay was linear over a 10(6) dilution range. We have recently developed a short tandem repeat (STR) multiplex panel for forensic analysis of feline specimens. The SINE assay is an integral part of the forensic typing system. The sensitivity of the assay will enable forensic examiners to determine the likelihood of success of genotyping sample extracts with the STR panel without sacrificing valuable DNA necessary to perform genotyping of samples.

Animals↗
PubMed2004

[A simple, low-cost and non-invasive method for screening Y microdeletions in infertile men].

OBJECTIVES: Recent investigations showed a high prevalence of Y chromosome microdeletions in men with severely impaired spermatogenesis. Screening for these men is recommended prior to assisted reproduction techniques. The aim of this study was to set up a simple method to detect Y deletion in infertile men. First, we tested the feasibility of cytobrush to collect oral cells as source of DNA. Second, we compared a classic PCR corresponding to European recommendations to the Promega kit. PATIENTS AND METHODS: Seventeen infertile male patients with previously characterized deletions were included in the present study, after fully informed written consent. Both oral cells and blood were used for DNA extraction. A specific DNA extraction protocol was carried out on the buccal cells. The DNAs were tested for Y deletion screening by two different methods. RESULTS: We retrieved between 4 and 10 microg of DNA per brush from buccal cells, allowing several multiplex PCR. The Promega kit detected all the deletions but one: an AZFa deletion was not detected by the two markers of the kit covering this region. In addition, sY130, sY133 and SY153, included in the kit, are not reliable. DISCUSSION AND CONCLUSIONS: Buccal cells represent a convenient substitute for blood in testing for Y microdeletions. Both false negative and false positive results were obtained with Promega Kit. On the opposite, PCR according to the European recommendations allow the accurate detection of Y microdeletion in our 17 cases, at a lower cost.

Chromosomes, Human, Y↗