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A modified procedure is proposed for chromosomal DNA extraction based on a cell-wall lytic enzyme never applied before in pulsed field gel electrophoresis. Protoplasting efficiency is retained under very challenging conditions for enzyme activity, such as those required for non-Saccharomyces yeasts often characterized by cell walls highly resistant to lysis.
BACKGROUND: Ostrich (Struthio camelus) breeds have been gaining increasing significance around the world. The large-scale sex determination of chicks is an important task in the development of these breeds. To date, two PCR-based methods have been established for ostrich sex typing, neither of them intended for large-scale analyses. Here, we report on a protocol adapted to carry out large-scale gender scoring using DNA obtained from chick feathers. RESULTS: The DNA was extracted using a fast and simple alkaline extraction protocol that provided sufficient template for an early diagnosis. Tests with several primer sets enabled us to determine the best internal control primers associated with the sex-specific primers, avoiding spurious bands. Using DNA extracted from a single bulb and the best set of primers, we applied this protocol to simultaneously sex-type 96 individuals accurately. CONCLUSION: We have established a fast, safe, accurate and inexpensive procedure for large-scale sex typing of ostriches using DNA extracted from feathers. This procedure is useful for the gender identification of chicks in the first days of nestling life.
Real-time PCR methods have recently been developed for the quantification of Helicobacter pylori from infected mouse stomachs. However, the extent to which results is affected by the efficiency of different methods of DNA extraction and the degree of inhibition of the subsequent PCR have largely been ignored. In this study, mouse stomachs were processed using two homogenisation methods: complete disruption using a blender and homogenisation by vortexing with glass beads. Each procedure was followed by DNA purification by three different protocols-two commercially available kits-Qiagen DNA Mini Tissue kit and Qiagen Stool Kit and a phenol-chloroform extraction method. PCR inhibition was assessed by screening for mouse DNA and for H. pylori DNA after spiking stomach extracts with H. pylori 16S rDNA. PCR inhibition was found to be lower in DNA samples prepared by vortexing and processed by column kits. Validation of procedures was performed by quantification of H. pylori DNA and mouse DNA in infected mouse stomachs. Homogenisation with glass beads followed by the Qiagen Tissue kit was found to be the most suitable protocol combining high extraction and detection efficiency of 16S rDNA in the presence of a mouse DNA background.
OBJECTIVES: To detect mutations of the K-ras codon 12 in DNA extracted from the plasma of patients with pancreatic cancer, and to explore the possibility of using this method in early diagnosis of pancreatic cancer. METHODS: Plasma DNA was isolated from the blood of 22 patients with pancreatic cancer and from 20 normal controls. K-ras codon 12 mutations were detected by mutant enriched polymerase chain reaction-restriction fragment length polymorphism technique and subsequent product sequencing. The relation of K-ras mutations in plasma to clinical features in pancreatic cancer patients was analyzed. RESULTS: Seventeen (77.3%) of 22 patients with pancreatic cancer had a codon 12 K-ras mutation in their plasma DNA. In two patients, the PCR products were sequenced and the mutations were confirmed. The occurrence of K-ras mutations in the plasma DNA was not related to tumor location, tumor size, and TNM stage. No K-ras mutation was detected in the plasma specimen of any of the normal controls. CONCLUSIONS: K-ras mutations are frequently found in the plasma DNA of patients with pancreatic cancer. Analysis of K-ras mutation in the plasma DNA may be useful in the early detection of pancreatic cancer.
We have developed a very simple and inexpensive method for high-throughput DNA extraction from animal tissues. The procedure contains three steps (digestion, heating, and centrifugation) and it is compatible with the 96-well plate format commonly used in polymerase chain reaction (PCR) amplifications. The duration for processing a plate is about 1.5 h; therefore, one researcher can isolate DNA from up to 1000 samples during a single workday. A small piece of tissue (ca. 10-20 mg) yields enough template for at least 50-70 PCR amplifications, as demonstrated by using the processed samples as templates successfully for long distance PCR, multiplex PCR, and randomly amplified polymorphic DNA (RAPD) assay. The application of our method is expected to facilitate studies that require high-throughput DNA isolation for PCR amplification, such as genotyping by microsatellites for mapping and genetic diversity studies, as well as mutant screening in zebrafish.
The purpose of this study is to evaluate the applicability of a nonorganic DNA extraction method for use in the analysis of environmentally compromised forensic hair shaft and tooth samples. The condition of the samples included cases of water decomposition, severe incineration, and varying stages of putrefaction. Enzymatic amplification and manual sequencing of the first segment of the mitochondrial hypervariable region were performed successfully on each of the 20 autopsied individuals. The results indicate that the silica-based extraction method produces mtDNA suitable for genetic identification from forensic samples including hair shafts and teeth.
Nuclear and mitochondrial DNA were extracted from gray matter of human cerebral cortex which had either been formalin-fixed and embedded into paraffin or stored in formalin for up to 26 years. Extraction conditions were optimized for proteinase K digestion, i.e., enzyme concentration, digestion temperature and incubation time. Using the polymerase chain reaction (PCR), DNA was successfully amplified from archival material and sequenced employing a direct nonradioactive cycle sequencing protocol. In general, tissue embedded into paraffin following brief fixation in formalin gave good quantitative results, i.e., up to 1 microgram DNA/mg tissue were extracted. This yield was at least one order of magnitude higher than that obtained with tissue stored in formalin. However, paraffin-embedded neuropathological material was found to contain an as-yet-unidentified PCR inhibitor, and a deleterious effect of long-term fixation in unbuffered low-grade formalin was clearly detectable. Importantly, both paraffin-embedded tissue blocks and human brain that had been stored in formalin for many years yielded DNA sufficient for qualitative analysis. The implications of these findings for the use of neuropathological material in molecular genetic studies are discussed.
DNA can be formulated with synthetic polymers such as poly(lactide-co-glycolide) (PLG) to generate microparticles. Researchers have used either UV spectroscopy or fluorometry with PicoGreen((R)) dye to quantify PLG-encapsulated DNA. While the sensitivity of DNA detection and quantification by PicoGreen is higher ( approximately 12 pg/ml) compared to UV ( approximately 0.5 microg/ml), each method as an analytical tool has limitations. The premise of this work addresses the usefulness and limitations of each method to determine encapsulation efficiencies in PLG microspheres post-process, and to quantify release of DNA from microspheres during in vitro release experiments. In addition, assay conditions for accurate and reproducible extraction of DNA from PLG microspheres using a biphasic (aqueous/organic) solvent system are described. It was also determined that residual poly(vinyl alcohol) and DNA isoforms (linear, nicked, supercoiled) affected PicoGreen/DNA fluorescence values.
South american precolumbian male mummies were employed as source material for a comparative investigation of bone and soft tissues by DNA analysis. The suitability of the DNA extracts from both sources was tested and evaluated by their effectiveness as target DNA in PCR amplifications. The results suggest that skeletal material should be given preference over soft tissues for PCR analysis if the material is severely degraded. This seems to be independent of the specific anatomical origin of the samples.
A theory for DNA double-strand break (dsb) analysis by pulsed field electrophoresis is presented, based on the size distribution of DNA fragments, which converts an induction of dsb linear with dose into a nonlinear fraction of extractable DNA, in agreement with experimental observations.
DNA was extracted from human bones remained for 3 to 15 years by using the method developed in our laboratory. A pair of X-Y homologous primer were used to amplify the specific DNA fragments of Amelogenin gene. All the 35 samples yielded correct results. Our method is rapid, sensitive and reliable for the sex determination of skeletal remains.
As a first step in developing a molecular method for the individualization of marijuana samples, we evaluated a plant DNA extraction kit. The QIAGEN plant DNeasy method uses a spin column format for recovery of DNA and is effective for obtaining high molecular weight DNA from leaf, flower (bud), and seed samples of marijuana. The average DNA yield was 125-500 ng per 100 milligrams of fresh plant tissue. The recovered DNA was of polymerase chain reaction (PCR) quality as measured by the ability to generate reproducible amplified fragment length polymorphism (AFLP) profiles. AFLP is a technique used to create a DNA profile for plant varieties and is being applied to marijuana samples by the authors to link growers and distributors of clonal material. The QIAGEN plant DNeasy method was simple, efficient, and reproducible for processing small quantities of marijuana into DNA.
The incorporation and uptake of (3H) thymidine into HeLa cells markedly decreased in the presence of nuclear homogenates and DNA extracts that have been derived from normal diploid cell cultures. On the other hand, uridine uptake and incorporation were stimulated under the same conditions. The inhibition could be reversed immediately upon removal of the exogenous fraction from the culture medium. The inhibitory properties of the extracts are propagated by excreted cellular components as well as after DNAase treatment. The inhibitory factor is thermostable, resistant to pronase treatment, and seems to be related to nucleic acid.
Polymerase chain reaction (PCR) was used after a short pre-enrichment culture to detect Salmonella subspecies in chicken fillets. A direct PCR assay performed with chicken meat inoculated with Salmonella Typhimurium produced no PCR products. Six different DNA extraction protocols were tested to recover efficiently Salmonella DNA after a short incubation period. Three of them gave results that were reliable, rapid and sensitive. Successful protocols used Proteinase K and/or a centrifugation step to concentrate the samples. For reliable detection of Salmonella subspecies, a few thousand bacterial cells per ml must be present. To obtain this number of bacterial cells with an inoculation of about one cell in 25 g of ionized food products, it was necessary to incubate samples for at least 10 h before PCR. A larger inoculum of approximately 10 cells in 25 g of ionized food products, required 8 h in culture broth to give positive results by PCR-based assay.
A novel method of DNA extraction and purification was developed and was used in conjunction with a multiplex real-time PCR assay for the simultaneous detection of Salmonella and Listeria monocytogenes in a raw meat sample. The PCR used primers targeting the invA gene of Salmonella and the hlyA gene of L. monocytogenes, and PCR products were detected with a LightCycler on the basis of fluorescence from SYBR Green and melting temperature. The assay allowed the detection of 3 Listeria cells and 4 Salmonella cells per g of the original sausage within 10 h, including an enrichment period of 6 to 8 h.
No systematic comparison of DNA extraction strategies exists for minute Vertiginidae (shell height < 3 mm), a group posing a dual analytical challenge: extremely low tissue input and co-purified PCR-inhibitory mucus. For legally protected species, an additional requirement to preserve the shell voucher further constrains available protocols. Using Vertigo antivertigo as the model species, we compared six approaches applied to specimens preserved in 96% ethanol (n = 10 per method): two HotSHOT alkaline-lysis protocols (destructive and non-destructive shell-preserving variants), a modified CTAB protocol supplemented with PVP-40 and DTT, and three commercial silica-column kits (GeneJET Genomic, DNeasy Blood & Tissue, QIAamp DNA Micro). DNA yields were quantified by QuantiFluor fluorometry, and PCR performance was subsequently assessed across four loci (COI barcode, COI mini-barcode, ITS1, ITS2). DNeasy Blood & Tissue produced the highest fluorometric concentrations; QIAamp DNA Micro and CTAB + PVP-40 gave intermediate values. The shell-preserving HotSHOT variant yielded lower concentrations but improved A260/230 ratios. BSA and trehalose supplementation increased PCR success in inhibition-prone HotSHOT extracts from 70% to 100%. ITS1 Sanger sequencing of three Vertigo species listed in Annex II of the EU Habitats Directive, all extracted with the shell-preserving protocol, confirmed species-level identification (99.8%-100% BLASTn identity; mean Phred Q > 51). The shell-preserving non-destructive HotSHOT protocol yields sequenceable DNA from protected Vertiginidae while retaining the morphological voucher, making it the preferred option for conservation-genetic monitoring. The practical decision framework documented here-integrating voucher preservation, amplification robustness and per-sample cost-has broad applicability to other minute terrestrial gastropods processed in large-scale biodiversity surveys.
AIM: To establish a simple and reliable polymerase chain reaction (PCR) methodology for random amplification of whole genomic DNA from limited histopathological samples. METHODS: Trace amounts of genomic DNA extracted from fresh tissue and individual lymphoid follicles microdissected from archival paraffin wax tissue sections were amplified using a two-phase PCR protocol with random hexamers as primers (RP-PCR). The randomly amplified DNA samples were used as templates for specific PCR amplifications. To check the fidelity of the RP-PCR, products of the specific PCR amplifications were further analysed by single stranded conformation polymorphism (SSCP) or sequencing. RESULTS: Using a minute fraction of RP-PCR template pool, multiple PCR analyses, including those for beta globin gene, p53 gene (exon 5-6, exon 7, exon 8-9 and exon 7-9), and rearranged immunoglobulin heavy chain gene fragments (VH framework 3 to JH and VH framework 2 to JH) were successfully performed. No artefactual mutations were identified in the products of these specific PCR reactions by SSCP or sequencing when compared with the products from the original DNA. CONCLUSION: This method is simple and reliable, and permits multiple genetic analyses when only a limited amount of tissue is available.
Abstract Genetic analysis using noninvasively collected samples such as faeces continues to pose a formidable challenge because of unpredictable variation in the extent to which usable DNA is obtained. We investigated the influence of multiple variables on the quantity of DNA extracted from faecal samples from wild mountain gorillas and chimpanzees. There was a small negative correlation between temperature at time of collection and the amount of DNA obtained. Storage of samples either in RNAlater solution or dried using silica gel beads produced similar results, but significantly higher amounts of DNA were obtained using a novel protocol that combines a short period of storage in ethanol with subsequent desiccation using silica.