[Detection of STLV-1 integration in DNA extracted from formalin-fixed and paraffin-embedded material from M. arctoides lymphoma by the polymerase chain reaction].
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Animals↗
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Estimation of the rate of SNP genotyping errors from DNA extracted from different tissues.
High density single nucleotide polymorphism (SNP) genotyping panels provide an alternative to microsatellite markers for genome scans. However, genotype errors have a major impact on power to detect linkage or association and are difficult to detect for SNPs. We estimated error rates with the Affymetrix GeneChip SNP platform in samples from a family with a mixed set of monozygotic (MZ) and dizygotic (DZ) triplets using lymphocyte, buccal DNA and samples from whole genome amplification using the multiple displacement amplification (MDA) technique. The average call rate from 58,960 SNPs for five genomic samples was 99.48%. Comparison of results for the MZ twins showed only three discordant genotypes (concordance rate 99.995%). The mean concordance rate for comparisons of samples from lymphocyte and buccal DNA was 99.97%. Mendelian inconsistencies were identified in 46 SNPs with errors in one or more family members, a rate of 0.022%. Observed genotype concordance rates between parents, between parents and children, and among siblings were consistent with previously reported allele frequencies and Hardy-Weinberg equilibrium. Using the MDA technique, results for two samples had equivalent high accuracy to results with genomic samples. However, the SNP call rate for the remaining seven samples varied from 72.5% to 99.5%, with an average of 86.11%. Quality of the DNA sample following the MDA reaction appears to be the critical factor in SNP call rate for MDA samples. Our results demonstrate highly accurate and reproducible genotyping for the Affymetrix GeneChip Human Mapping Set in lymphocyte and buccal DNA samples.
Adolescent↗
Sample preparation and DNA extraction procedures for polymerase chain reaction identification of Listeria monocytogenes in seafoods.
Five grams of seafood products were inoculated with one to 500 viable or 10(9) heat-killed cells of Listeria monocytogenes. The presence of the pathogen was detected by the polymerase chain reaction (PCR) with primers specific for fragments of the listeriolysin O (hly) gene (two sets) and for the invasion-associated protein (iap) gene (one set). For DNA preparation, boiling, either alone or in combination with lysozyme and proteinase K treatment, was not always sufficient to lyse L. monocytogenes, while treatment with Triton X-100 produced consistently good DNA suitable for amplification. To avoid false-negative and false-positive results, 48 h incubations were necessary and a subculturing step after an initial 24 h incubation greatly improved the results. The primers that amplified regions of the listeriolysin O gene gave clearer and stronger products than primers for the invasion-associated protein gene. Using this method we were able to detect one to five L. monocytogenes cells in 5 g of product in a total of 55 h.
Animals↗
Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts.
Terminal restriction fragment length polymorphism (T-RFLP) analysis is a widely used method for profiling microbial community structure in different habitats by targeting small-subunit (SSU) rRNA and also functional marker genes. It is not known, however, whether relative gene frequencies of individual community members are adequately represented in post-PCR amplicon frequencies as shown by T-RFLP. In this study, precisely defined artificial template mixtures containing genomic DNA of four different methanogens in various ratios were prepared for subsequent T-RFLP analysis. PCR amplicons were generated from defined mixtures targeting not only the SSU rRNA but also the methyl-coenzyme M reductase (mcrA/mrtA) genes of methanogens. Relative amplicon frequencies of microorganisms were quantified by comparing fluorescence intensities of characteristic terminal restriction fragments. SSU ribosomal DNA (rDNA) template ratios in defined template mixtures of the four-membered community were recovered absolutely by PCR-T-RFLP analysis, which demonstrates that the T-RFLP analysis evaluated can give a quantitative view of the template pool. SSU rDNA-targeted T-RFLP analysis of a natural community was found to be highly reproducible, independent of PCR annealing temperature, and unaffected by increasing PCR cycle numbers. Ratios of mcrA-targeted T-RFLP analysis were biased, most likely by PCR selection due to the degeneracy of the primers used. Consequently, for microbial community analyses, each primer system used should be evaluated carefully for possible PCR bias. In fact, such bias can be detected by using T-RFLP analysis as a tool for the precise quantification of the PCR product pool.
Bias↗
Validation of a Rickettsia prowazekii-specific quantitative real-time PCR cassette and DNA extraction protocols using experimentally infected lice.
The presence of R. prowazekii in lice using R. prowazekii-specific qPCR cassettes showed the changes of the rickettsial burden in the lice post-infection.
Animals↗
Detection of Chlamydia trachomatis infection with DNA extracted from formalin-fixed paraffin-embedded tissues.
It is a well-known fact that tubal stenosis and/or peritubal adhesion are often associated with Chlamydia trachomatis infection. Although tubal pregnancy may be attributed to this infection, there are only extremely rare cases in which the presence of C. trachomatis has been confirmed by immumo-histochemical examination on tissues isolated from patients with tubal pregnancy. We thus tried to confirm the presence of C. trachomatis infection by detecting DNA of the organism in tissues surgically isolated from patients with tubal pregnancy. Two detection methods, a ligase chain reaction (LCR) method and an immuno-histochemical staining which detects an antigen of C. trachomatis, were compared using paraffin-embedded tissue samples which were surgically isolated from patients with tubal pregnancy or hydrosalpinx. The LCR method was capable of detecting DNA of C. trachomatis in tissue samples in which the C. trachomatis-specific antigen could not be detected using immuno-histochemical staining. This was due to the fact that immuno-histochemical staining methods are applicable to the analysis of sequences the length of which range from 200 to 400 bp (base pairs), while the LCR method used here allows the analysis of sequences as small as 48 bp. This fact makes the LCR method a very convenient tool, as compared with immuno-histochemical methods, for analysis of the paraffin embedded tissue samples where by effects of formalin--used for fixation for pathologic diagnosis--the risk of fragmenting the DNA samples is relatively high. Presence of C. trachomatis DNA as detected by LCR method in surgically isolated samples from patients with tubal pregnancy supports the involvement of Chlamydia trachomatis infection in the occurrence of tubal pregnancy. Accordingly the LCR method is capable of detecting DNA of C. trachomatis in paraffin-embedded samples of tubal tissue in which presence of C. trachomatis could not be confirmed by an immuno-histochemical staining method.
Adult↗
Quantification of the 35S promoter in DNA extracts from genetically modified organisms using real-time polymerase chain reaction and specificity assessment on various genetically modified organisms, part I: operating procedure.
A highly sensitive quantitative real-time assay targeted on the 35S promoter of a commercial genetically modified organism (GMO) was characterized (sF/sR primers) and developed for an ABI Prism 7700 Sequence Detection System and TaqMan chemistry. The specificity assessment and performance criteria of sF/sR assay were compared to other P35S-targeted published assays. sF/sR primers amplified a 79 base pair DNA sequence located in a part of P35S that is highly conserved among many caulimovirus strains, i.e., this consensus part of CaMV P35S is likely to be present in many GM events. According to the experimental conditions, the absolute limit of detection for Bt176 corn was estimated between 0.2 and 2 copies of equivalent genome (CEG). The limit of quantification was reached below 0.1% Bt176 content. A Cauliflower Mosaic Virus control (CaMV) qualitative assay targeted on the ORF III of the viral genome was also used as a control (primers 3F/3R) to assess the presence of CaMV in plant-derived products. The specificity of this test was assessed on various CaMV strains, including the Figwort Mosaic Virus (FMV) and solanaceous CaMV strains. Considering the performance of sF/sR quantification test, the highly conserved sequence, and the small size of the amplicon, this assay was tested in a collaborative study in order to be proposed as an international standard.
DNA Primers↗
Restriction fragment length polymorphism (RFLP) typing of DNA extracted from nasal secretions.
The restriction fragment length polymorphism (RFLP) analysis of blood, semen, and other body fluids, has become increasingly important in violent criminal cases. The identification of additional tissues suitable for comparison with suspected donors has obvious potential benefit. One type of tissue, that found in nasal secretions, has previously received little attention with regards to genetic analysis. We collected blood and nasal secretion samples from eight individuals, subjected them to traditional RFLP typing methods, and analyzed the results using probes for loci D2S44, D1S7, D10S28, D4S139, and D17S79. All nasal samples provided high DNA yields and hybridization results that matched the corresponding blood standards. Thus, nasal secretions are shown to have potentially significant evidentiary value.
Blood↗
K-ras mutations in DNA extracted from the plasma of patients with pancreatic carcinoma: diagnostic utility and prognostic significance.
PURPOSE: Previous studies have demonstrated the presence of K-ras mutations in the plasma of patients with pancreatic carcinoma. However, the diagnostic utility and the prognostic significance of this finding have never been addressed. PATIENTS AND METHODS: Forty-four consecutive patients with histologically confirmed primary pancreatic ductal adenocarcinoma were included. A control group of 37 patients with chronic pancreatitis, 10 patients with other tumors of the pancreatic area, nine patients with acute pancreatitis, and four healthy volunteers was also included. Plasma DNA was isolated and K-ras codon-12 mutations were analyzed by means of restriction fragment length polymorphism-polymerase chain reaction and single-strand conformation polymorphism techniques. Patients were followed up to establish their clinical outcome. RESULTS: The mutant-type K-ras gene was found in plasma DNA samples of 12 (27%) of 44 patients with pancreatic ductal adenocarcinoma; this finding was related to the tumor stage (P = .05), mainly in the presence of distant metastases (P = .02). In addition, K-ras mutations were detected in the plasma DNA of two (5%) of 37 patients with chronic pancreatitis. In the subset of patients with pancreatic masses, the sensitivity and specificity of plasma K-ras analysis for pancreatic adenocarcinoma were 27% and 100%, respectively. Finally, pancreatic carcinoma patients with the mutant-type K-ras gene in plasma DNA exhibited a shorter survival time than patients with the wild-type gene (P<.005), and plasma K-ras mutations were identified as the only independent prognostic factor (odds ratio, 1.51; 95% confidence interval, 1.02 to 2.23). CONCLUSION: Plasma K-ras analysis is a highly specific, low-sensitivity approach that has diagnostic and prognostic clinical implications in patients with pancreatic carcinoma.
Adenocarcinoma↗
Viral encephalomyelitis of pigeons. VI. Some physico-chemical properties of the virus and extracted viral DNA.
Pigeon herpes encephalomyelitis virus (PHEV) was stable at -70 C for at least 4 months. When stored at -20 C, the virus lost 80% of its infective titers in 4 months. When stored at -10 C, however, the titers decreased rapidly; no detectable virus remained within 12 weeks. PHEV was thermolabile: it was completely inactivated at 56 and 60 C for 10 and 2 min respectively. It was also killed by 1% cresol and 2% sodium hydroxide for two hr and 2% septol for 24 hr. Two-percent phenol or formaline for 2 hr, however, significantly decreased virus infective titers. Phenol-purified DNA extracted from PHEV showed an ultraviolet spectrum of typical nucleic acids that had ratios of absorbancies at 265 nm/280 nm between 2 and 2.3. The extracted viral DNA was infectious in chorioallantoic membrane and chick embryo fibroblast cell cultures, but it was not noninfectious when given to pigeons. DNA infectivity was destroyed by DNAse but not RNAse treatment. Extracted DNA was not neutralized by antiserum against the intact virus, and it lost its infectivity property when heated at 70 C for 10 min.
Animals↗
Evaluation of different methods for the extraction of DNA from fungal conidia by quantitative competitive PCR analysis.
Five different DNA extraction methods were evaluated for their effectiveness in recovering PCR templates from the conidia of a series of fungal species often encountered in indoor air. The test organisms were Aspergillus versicolor, Penicillium chrysogenum, Stachybotrys chartarum, Cladosporium herbarum and Alternaria alternata. The extraction methods differed in their use of different cell lysis procedures. These included grinding in liquid nitrogen, grinding at ambient temperature, sonication, glass bead milling and freeze-thawing. DNA purification and recovery from the lysates were performed using a commercially available system based on the selective binding of nucleic acids to glass milk. A simple quantitative competitive polymerase chain reaction (QC-PCR) assay was developed for use in determining copy numbers of the internal transcribed spacer (ITS) regions of the ribosomal RNA operon (rDNA) in the total DNA extracts. These quantitative analyses demonstrated that the method using glass bead milling was most effective in recovering PCR templates from each of the different types of conidia both in terms of absolute copy numbers recovered and also in terms of lowest extract to extract variability. Calculations of average template copy yield per conidium in this study indicate that the bead milling method is sufficient to support the detection of less than ten conidia of each of the different organisms in a PCR assay.
DNA, Fungal↗
Somatic cell heterogeneity between DNA extracted from lymphocytes and skeletal muscle in congenital myotonic dystrophy.
Myotonic dystrophy (DM) results from the expansion of an unstable CTG trinucleotide repeat in the 3' untranslated region of mRNA encoding a putative serine/threonine protein kinase. The degree of the CTG repeat amplification in genomic DNAs extracted from lymphocytes correlates with disease severity. We have analyzed the amplification of the CTG repeat of DNAs extracted from skeletal muscles and lymphocytes in five congenital DM patients. The amplification from skeletal muscles showed an increase of about 1.5 kb to 3.5 kb larger than that from lymphocytes in all patients. Furthermore, we have investigated the somatic instability of the CTG repeat in various tissues from a severe congenital DM patient.
Adolescent↗
An efficient DNA extraction method for small metazoans.
The isolation of total nucleic acids from small metazoan taxa is difficult and often leads to an unacceptably large percentage of unsuccessful polymerase chain reaction (PCR) amplifications. Our work with the evolutionary genetics of harpacticoid copepods was an incentive to refine techniques such that consistent amplifications from minute marine organisms were feasible. We describe these modifications and demonstrate their utility for the amplification of multiple loci from single harpacticoid copepods.
Animals↗
K-ras codon 12 mutations of the super-minute dysplasia in Barrett's esophagus by DNA extraction using a microdissection method.
The aim of this study was to clarify the histogenesis of Barrett's cancer. First, 28 lesions of the super-minute dysplasia AGT), and 5 among 25 lesions with an average p53-LI of 58%, which were considered to be morphologically low grade dysplasia, showed K-ras mutation (four lesions: GGT-->GAT, 1 lesion: GGT-->AGT). This current study shows that some dysplasia lesions have K-ras mutations in their initial condition, whether these atypical tubule lesions are low grade dysplasia or high grade dysplasia (intramucosal adenocarcinoma), and supports the dysplasia-carcinoma sequence in the histogenesis of Barrett's cancer and synchronously suggests that there is a different route to it.
Barrett Esophagus↗
Sex determination by PCR analysis of DNA extracted from incinerated, deciduous teeth.
Establishing the biological sex of human remains is a very important part of identifying victims of fire when severe soft tissue destruction has occurred. Deciduous (children's) teeth were exposed to a range of incineration temperatures 100-500 degrees C for 15 minutes. Polymerase Chain Reaction (PCR) amplification was used to identify specific human amelogenin regions. There was successful identification of human biological sex, from deciduous teeth exposed to incineration temperatures of 200 degrees C and below, using standard ethidium bromide gel staining. There was greater sensitivity using fragment analysis by laser induced fluorescence which achieved sex identification from some teeth heated to 400 degrees C.
DNA↗
Evaluation of the Roche LightCycler: a simple and rapid method for direct detection of factor V Leiden and prothrombin G20210A genotypes from blood samples without the need for DNA extraction.
The Roche LightCycler is a micro-volume thermocycler that combines extremely rapid polymerase chain reaction with fluorescence resonance energy transfer analysis of amplified products. We have evaluated the use of minimally processed blood samples for detection of two point mutations known to increase the risk of venous thromboembolism. Results from the LightCycler using the supernatant of diluted heated blood were compared with those gained by traditional methods based on polymerase chain reaction and restriction enzyme digestion. For factor V Leiden mutation, there was complete agreement between both methods in detection of wild-type (n = 82), heterozygous (n = 100) and homozygous (n = 18) genotypes. Similarly, the prothrombin G20210A mutation showed complete agreement for wild-type (n = 135), heterozygous (n = 63) and homozygous (n = 2) subjects.
3' Untranslated Regions↗
Studies of mitochondria and mitochondrial DNA extracted from organelles harboring an intramitochondrial virus.
(1) Two viper cells lines were investigated, one which harbors IMV in the mitochondria (VSW cells) and one without detectable IMV (VH3 cells). (2) The size of closed circular mtDNA molecules from both VSW and VH3 cells was found to be significantly greater (5.4 to 5.6 micron) than the contour lengths of typical mammalian cells (4.8 to 5.2 micron). (3) A small percentage of mini-circles ranging in size from 0.1 to 0.6 micron was observed to band with closed circular mtDNA from both cell lines. Minicircles were especially abundant in VH3 cells. (4) MtDNA from VSW cells contained 34.1% dimers plus oligomers (10.2% oligomers), whereas VH3 cells had only 14.8% dimeric and oligomeric forms (5.4% oligomers). (5) Treatment of VSW cells with 1 microng/ml ethidium bromide for 48 hours resulted in an increased incidence of IMV (IMV in 15% of mitochondrial sections) as compared with untreated VSW cells (IMV in 3% of mitochondrial sections).
Cell Line↗
A highly sensitive, nested polymerase chain reaction based method using simple dna extraction to detect malaria sporozoites in mosquitos.
Dried Anopheles farauti mosquitos caught in Solomon Islands in 1990 were examined for malaria sporozoites by ELISA and nested polymerase chain reaction (PCR). Only heads and thoraces were used. Plasmodium genus-specific nested PCR amplifications were carried out on all samples. Of the 402 pools of mosquitos that were processed, 30 were positive for malaria. Nest 1 products of positive samples were subjected to further PCR amplifications with species-specific primers for P. falciparum and P. vivax. Twenty pools were positive for P. vivax by PCR while only 7 were positive by ELISA. For P. falciparum 2 pools were positive by both ELISA and PCR, and one of these was a pool which was positive for P. vivax by PCR and ELISA. Thus the sensitivity of PCR for P. vivax was 100% while the specificity was 96.7%. For P. falciparum the sensitivity and specificity were 100%. The PCR technique is highly sensitive and can be used on dried mosquitos which makes it a valuable tool for determining sporozoite rates of mosquitos, even in remote areas.
Animals↗