Inexpensive micro-electroelution apparatus for extracting DNA from acrylamide and agarose gels.
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Acrylamide↗
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[Subtractive hybridization--a technique for extracting DNA sequences, discriminating between two closely-related genomes].
This review deals with an analysis of the current status of genomic DNA subtraction. The theoretical calculations of kinetics of different ways of hybridization are implemented. The main conclusion is that the most preferable strategy for such a subtraction is hybridization of single stranded tracer with single-stranded driver DNA.
DNA↗
A simplified method of extracting DNA from gradient-purified bacteriophage lambda.
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Animals↗
Human immunodeficiency virus-1 infection in spouses of seropositive individuals.
BACKGROUND: Unprotected sex can lead to transmission of the human immunodeficiency virus-1 (HIV-1) to the spouse of an infected individual. We studied the incidence of HIV-1 infection in the spouses of cases diagnosed to have HIV-1 infection by serology and the polymerase chain reaction (PCR). METHODS: Blood samples collected from 9 index cases and their respective spouses were tested for HIV-1 infection by ELISA, Western blot (WB) and PCR as well as from 10 healthy individuals with no high-risk behaviour. DNA extracted from both plasma and peripheral blood mononuclear cells was amplified by PCR, using multiple primer pairs for distinct regions of the HIV-1 genome. Specificity of the PCR product was demonstrated by hybridization to an oligonucleotide probe. RESULTS: All the index cases which were seropositive by ELISA and WB were also positive by PCR of plasma extracted DNA. Eight of the spouses were seronegative. Of these seven were positive by PCR--one spouse was negative by ELISA but showed a p55 band on WB and was positive by PCR. One spouse was negative by serology and PCR. The spouse belonging to the lone concordant couple was positive by serology and PCR. Except for one index case, PCR signals were obtainable only from DNA extracted from plasma but not from the DNA extracted from peripheral blood mononuclear cells. The control samples were negative by serology and PCR. CONCLUSION: It is possible to detect HIV-1 infection by PCR using DNA extracted from plasma even when the individuals are negative by ELISA and WB. It can help in the early counselling of HIV infected persons and their spouses.
AIDS Serodiagnosis↗
Evaluation of methods for isolation of DNA from slowly and rapidly growing mycobacteria.
Mycobacteria generally have thick cell walls and contain large amounts of lipid, making them resistant to DNA extraction. Five methods, namely, extensive enzymic digestion method (M1), 2-min mechanical glass-bead disruption method (M2), thermal shock method (M3), modified conventional enzymic digestion method (M4), and manual disruption with modified conventional enzymic digestion method (M5), were used to compare their effectiveness and simplicity in extracting DNA from slowly growing mycobacteria (Mycobacterium leprae, M. lepraemurium and M. bovis BCG), and a rapidly growing mycobacterium (M. phlei). The highest DNA yield was obtained by M2 from M. lepraemurium which produced 2.82 micrograms DNA/mg wet weight of cells, representing a theoretical yield of 78%. M3 gave the lowest DNA yield; 0.01 microgram DNA/mg wet weight of cells of M. lepraemurium was obtained. M4, in which proteinase K was used, is more effective than M1, in which subtilisin and pronase were used. M5 yielded a higher amount of DNA, but it required more manipulations to extract DNA as compared to M4. Extraction of DNA of M. leprae from nude mice is more difficult than that of M. leprae from armadillos by all of the methods used. These results suggest that the biosynthetic capabilities of these two forms of M. leprae may vary, depending on their cultural conditions and/or strain differences. Our results have shown that both M2 and M4 are the simplest, most effective and time-saving methods which are suitable for every routine laboratory to extract DNA from slowly and rapidly growing mycobacteria.
Animals↗
Extraction of DNA from paraffin blocks for Southern blot analysis.
Tissues stored as paraffin blocks are a potential source of DNA for retrospective clinicogenetic analysis. To assess the feasibility of Southern blot analysis, DNA extracted from paraffin blocks was compared with DNA obtained from fresh-frozen controls of the same tissues. Sections 50-100 microns thick cut from paraffin blocks of 11 normal tissues, 18 lymphoid lesions, and 9 gastric carcinoma samples were deparaffinized and incubated at 45 degrees C for 48 to 72 h in a sodium dodecyl sulfate (SDS)/proteinase K solution. Following organic extraction, alcohol precipitation, restriction endonuclease digestion, and gel electrophoresis, DNA was transferred to nylon membranes. 32P-labelled DNA probes for the immunoglobulin heavy-chain locus and T-cell receptor beta-chain gene were hybridized to the normal tissue and lymphoid samples; the gastric cancers were probed for the HER-2/neu protooncogene. Intact DNA was obtained from the majority of formalin-fixed samples, yielding results qualitatively similar to those from fresh tissues. Degradation is the most significant problem in analyzing DNA extracted from paraffin blocks and compromises accurate quantitation. DNA analysis using paraffin-embedded tissue has potential clinical and research applications and may be a particularly useful way to study gene abnormalities in unusual tumors infrequently available as fresh specimens.
Autoradiography↗
Amplification of mitochondrial DNA from archival temporal bone specimens.
Archival temporal bone collections are an invaluable resource for studying the molecular genetics of many types of otopathology. The irreplaceable nature of temporal bone sections makes efficiency of DNA extraction of paramount importance. Several protocols are available for extracting DNA from fresh and preserved tissue. To establish the best protocol for reliably extracting DNA from celloidin-embedded temporal bone sections, a variety of DNA extraction techniques were tested. Using the optimum protocol, mitochondrial DNA fragments ranging in size from less than 100 base pairs to more than 400 base pairs were amplified, and the authenticity of polymerase chain reaction (PCR) products was confirmed through comparative sequence analysis.
Acetates↗
Rapid and reliable extraction of genomic DNA from various wild-type and transgenic plants.
BACKGROUND: DNA extraction methods for PCR-quality DNA from calluses and plants are not time efficient, since they require that the tissues be ground in liquid nitrogen, followed by precipitation of the DNA pellet in ethanol, washing and drying the pellet, etc. The need for a rapid and simple procedure is urgent, especially when hundreds of samples need to be analyzed. Here, we describe a simple and efficient method of isolating high-quality genomic DNA for PCR amplification and enzyme digestion from calluses, various wild-type and transgenic plants. RESULTS: We developed new rapid and reliable genomic DNA extraction method. With our developed method, plant genomic DNA extraction could be performed within 30 min. The method was as follows. Plant tissue was homogenized with salt DNA extraction buffer using hand-operated homogenizer and extracted by phenol:chloroform:isoamyl alcohol (25:24:1). After centrifugation, the supernatant was directly used for DNA template for PCR, resulting in successful amplification for RAPD from various sources of plants and specific foreign genes from transgenic plants. After precipitating the supernatant, the DNA was completely digested by restriction enzymes. CONCLUSION: This DNA extraction procedure promises simplicity, speed, and efficiency, both in terms of time and the amount of plant sample required. In addition, this method does not require expensive facilities for plant genomic DNA extraction.
Blotting, Southern↗
Evaluation of methods for extracting Xylella fastidiosa DNA from the glassy-winged sharpshooter.
The recent spread of the plant pathogenic bacterium Xylclla fastidiosa Wells et al. by an invasive vector species, Homalodisca coagulata Say, in southern California has resulted in new epidemics of Pierce's disease of grapevine. Our goal is to develop an efficient method to detect low titers of X. fastidiosa in H. coagulata that is amenable to large sample sizes for epidemiological studies. Detection of the plant pathogenic bacterium X. fastidiosa in its insect vector is complicated by low titers of bacteria, difficulty in releasing it from the insect mouthparts and foregut, and the presence of substances in the insect that inhibit polymerase chain reaction (PCr). To select the optimal protocol for DNA extraction to be used with PCR, we compared three standard methods and 11 commercially available kits for relative efficiency of X. fastidiosa DNA extraction in the presence of insect tissue. All of the protocols tested were proficient at extracting DNA from pure bacterial culture (1 x 10(5) cells), and all but one protocol successfully extracted sufficient bacterial DNA in the presence of insect tissue. Three DNA extraction techniques, immunomagnetic separation, the DNeasy Tissue kit (Qiagen, Hercules, CA), and Genomic DNA Purification kit (Fermentus, Hanover, MD), were compared more closely using a dilution series of X. fastidiosa (5000-0 cells) with and without insect tissue present. The DNeasy Tissue kit was the best kit tested, allowing detection of 5 x 10(3) X. fastidiosa cells with an insect head background.
Animals↗
Development of a quality, high throughput DNA analysis procedure for skeletal samples to assist with the identification of victims from the World Trade Center attacks.
The attacks on the World Trade Center (WTC) Towers on September 11, 2001, represented the single largest terrorist-related mass fatality incident in the history of the United States. More than 2,700 individuals of varied racial and ethnic background lost their lives that day. Through the efforts of thousands of citizens, including recovery workers, medical examiners, and forensic scientists, the identification of approximately 1,500 victims had been accomplished through June 2003 (the majority of these identifications were made within the first 8-12 months). The principal role of The Bode Technology Group (Bode) in this process was to develop a quality, high throughput DNA extraction and short tandem repeat (STR) analysis procedure for skeletal elements, and to provide STR profiles to the Office of the Chief Medical Examiner (OCME) in New York City to be used for identification of the victims. A high throughput process was developed to include electronic accessioning of samples, so that the numbering system of the OCME was maintained; rapid preparation and sampling of skeletal fragments to allow for the processing of more than 250 fragments per day; use of a 96-well format for sample extraction, DNA quantification, and STR analysis; and use of the Applied Biosystems 3100 and 3700 instrumentation to develop STR profiles. Given the highly degraded nature of the skeletal remains received by Bode, an advanced DNA extraction procedure was developed to increase the quantity of DNA recovery and reduce the co-purification of polymerase chain reaction (PCR) amplification inhibitors. In addition, two new STR multiplexes were developed specifically for this project, which reduced the amplicon size of the STR loci, and therefore, enhanced the ability to obtain results from the most challenged of samples. In all, the procedures developed allowed for the analysis of more than 1,000 skeletal samples each week. Approximately 13,000 skeletal fragments were analyzed at least once, for a total of more than 18,000 analyses, and greater than 8,000 of the skeletal samples produced STR results (65%). The percentage of successful results was low in relation to previous mass fatality incidents involving airline disasters. However, when this same process was applied to the analysis of skeletal remains from the American Airlines Flight 587 disaster that occurred on November 12, 2001, the success rate was in line with expected results (ie, greater than 92% of the skeletal remains produced results). This illustrated the quality aspects of the procedure and the degree of degradation that had occurred for the remains of the WTC victims. For future mass fatality incidents, the quality, high throughput procedures developed by Bode will allow for more rapid DNA analysis of victim remains, more rapid identification of victims, and thus more rapid return of remains to family members.
Bone and Bones↗
A novel approach in personal identification from tissue samples undergone different processes through STR typing.
Short tandem repeats (STRs) or microsatellites have been recognized worldwide as a powerful tool for human identification. They have become widely used in human identification especially in criminal cases and mass disasters. Police departments are often interested in cases where tissues are already decomposed and only do bones remain to let them perform laboratory analyses. Bone is the most resistant tissue in animal body to time depending degradation and putrefaction, but it is often hard to extract DNA from it because of its highly mineralized structure, which makes DNA extraction and/or amplification hard to carry out. We have performed human nuclear DNA extraction and STR typing in three different cases, on bones and bone fragments from long time dead persons found buried, in the sea, almost completely burnt and whose tissues were already decomposed. We report these caseworks as we would like to show how forensic scientists are improving their skill in identifying people whose corps have undergone several kinds of processes, even independently on the time passed and the level of putrefaction of their tissues.
Bone and Bones↗
Development and evaluation of a real-time fluorescent polymerase chain reaction assay for the detection of bovine contaminates in cattle feed.
A real-time fluorescent polymerase chain reaction assay for detecting prohibited ruminant materials such as bovine meat and bone meal (BMBM) in cattle feed using primers and FRET probes targeting the ruminant specific mitochondrial cytochrome b gene was developed and evaluated on two different types of cattle feed. Common problems involved with PCR based testing of cattle feed include the presence of high levels of PCR inhibitors and the need for certain pre-sample processing techniques in order to perform DNA extractions. We have developed a pre-sample processing technique for extracting DNA from cattle feed which does not require the feed sample to be ground to a fine powder and utilizes materials that are disposed of between samples, thus, reducing the potential of cross contamination. The DNA extraction method utilizes Whatman FTA card technology, is adaptable to high sample throughput analysis and allows for room temperature storage with established archiving of samples of up to 14 years. The Whatman FTA cards are subsequently treated with RNAse and undergo a Chelex-100 extraction (BioRad, Hercules, CA), thus removing potential PCR inhibitors and eluting the DNA from the FTA card for downstream PCR analysis. The detection limit was evaluated over a period of 30 trials on calf starter mix and heifer starter ration feed samples spiked with known concentrations of BMBM. The PCR detection assay detected 0.05% wt/wt BMBM contamination with 100% sensitivity, 100% specificity, and 100% confidence. Concentrations of 0.005% and 0.001% wt/wt BMBM contamination were also detected in both feed types but with varying levels of confidence.
Animal Feed↗
Extraction of DNA from paraffin-embedded tissue for analysis by polymerase chain reaction: new tricks from an old friend.
For decades virtually all human tissues have been fixed in formalin and embedded in paraffin. The DNA present in fixed tissues is degraded in size but can be analyzed by the polymerase chain reaction (PCR) for specific genetic alterations. The original purpose of fixation, to optimally preserve complex histological and spatial features, is lost with bulk DNA extraction. Because the PCR allows the analysis of even a single molecule of DNA, it is possible to genetically analyze small groups of cells on a microscope slide with techniques such as selective ultraviolet radiation fractionation (SURF). The direct correlation of histological phenotype with genotype provides information that is difficult to obtain by other methods and allows a more precise translation between molecular studies and the current vast histological database.
Chemical Fractionation↗
Method for improved extraction of DNA from Nocardia asteroides.
In a variation of standard DNA extraction methods, Nocardia asteroides was repeatedly exposed to sodium dodecyl sulfate at 60 degrees C for 30 min; each extraction was followed by centrifugation, removal of the nucleic acid-rich supernatant, and suspension of the cell pellet in fresh sodium dodecyl sulfate. The pooled supernatants contained a substantially higher amount of DNA than the first supernatant alone. The possible implications of this procedure on the development of DNA probes are discussed.
DNA Probes↗
Polymerase chain reaction-gene probe detection system specific for pathogenic strains of Yersinia enterocolitica.
The polymerase chain reaction technique was used to develop a rapid diagnostic assay for detection of pathogenic Yersinia enterocolitica strains. The assay targeted a stretch of 163 bp of the yst gene and could be applied to both pure cultures and crude DNA extracted from feces. The defined primer pair amplified the targeted sequence from only pathogenic strains and fecal samples seeded with the serotype O:3 strain of Y. enterocolitica, whereas neither nonpathogenic strains nor normal stools yielded any amplified fragments. Of the other Yersinia species and non-Yersinia species tested, only two strains of Y. kristensenii yielded the same amplified product. A 20-mer oligonucleotide probe specifically hybridized within the amplified yst fragment of Y. enterocolitica but did not hybridize with the amplified yst fragment of Y. kristensenii by Southern and dot blot hybridizations. This confirms the reliability of this diagnostic assay in both clinical and epidemiological studies. The availability of the extracted DNA for the polymerase chain reaction was checked by simultaneous amplification of a part of the 16S rDNA and the yst gene. The entire diagnostic assay, including a simplified technique for DNA extraction, the amplification process, and gel electrophoresis, could be completed within 1 working day, which is better than the time required for the time-consuming traditional techniques used in clinical laboratories.
Base Sequence↗
Rapid, direct extraction of DNA from soils for PCR analysis using polyvinylpolypyrrolidone spin columns.
Polyvinylpolypyrrolidone spin columns were used to rapidly purify crude soil DNA extracts from humic materials for polymerase chain reaction (PCR) analysis. The PCR detection limit for the tfdC gene, encoding chlorocatechol dioxygenase from the 2,4-dichlorophenoxyacetic acid degradation pathway, was 10(1)-10(2) cells/g soil in inoculated soils. The procedure could be applied to the amplification of biodegradative genes from indigenous microbial populations from a wide variety of soil types, and the entire analysis could be performed within 8 h.
2,4-Dichlorophenoxyacetic Acid↗
Direct identification of Mycobacterium tuberculosis from sputum on Ziehl-Neelsen acid fast stained slides by use of silica-based filter combined with polymerase chain reaction assay.
This paper describes a method for isolation of deoxyribonucleic acid (DNA) from Ziehl-Neelsen stained sputum smears on glass slides; and isolated DNA was used for the IS6110 polymerase chain reaction (PCR)-based identification of M. tuberculosis. A total of 221 samples from newly diagnosed suspected tuberculosis cases were first examined by microscopic examination. For DNA extraction by silica-based filter, a home-made modified spin column gave the efficacy as did the nucleospin tissue reagent kit and therefore was selected for PCR template preparation. The extracted DNA was amplified by the IS6110 PCR using a primer pair that amplifies a 377-bp target, and the product was analyzed by agarose gel electrophoresis with confirmation by Southern blot hybridization. In comparison with culture, PCR with template prepared by the silica based filter showed overall sensitivity and specificity of 91.7 and 100 per cent, respectively. This study used the over one year and less than one year slides samples to study the effect of storage time. In the more than one year storage group, PCR assay gave a sensitivity and specificity of 83.3 and 100 per cent, respectively. In conclusion, the applicability of the PCR directly to DNA extracted from Ziehl-Neelsen stained smears could become a valuable alternative approach for rapid identification of M. tuberculosis, and could be used to evaluate quality of the control of local laboratories in tuberculosis (TB) screening and solve the problem of specimen transportation. In addition, the method could be used in retrospective studies involving a wide range of PCR-based analyses, such as detection of rifampicin resistant gene in multidrug-resistant tuberculosis (MDR-TB) study.
Bacteriological Techniques↗
Coinfection of the central nervous system by cytomegalovirus and herpes simplex virus type 1 or 2 in AIDS patients: autopsy study on 82 cases by immunohistochemistry and polymerase chain reaction.
We evaluated the frequency and histopathological features of concomitant infections of the central nervous system (CNS) with cytomegalovirus (CMV) and herpes simplex viruses type 1 or 2 (HSV1/2) in a large series of patients who had died from AIDS. Eighty-two autopsy cases with a histological diagnosis of CMV necrotizing encephalitis were examined retrospectively. CMV and HSV1/2 were detected by immunohistochemistry (IHC) with poly- and monoclonal antibodies and by nested polymerase chain reaction (PCR) for HSV 1 and 2 on DNA extracted from paraffin blocks. PCR for a beta-globin genomic sequence was performed in all IHC-positive cases to verify the integrity of extracted DNA. Concomitant CMV/HSV infections were demonstrated by IHC in 13 cases (16%); using monoclonal antibodies, HSV1 was found in 9 cases and HSV2 in 4 cases. In half of the cases, HSV1- or HSV2-positive cells represented more than 25% of immunopositive CMV cells. In all 13 cases, double immunochemical staining showed cells containing both CMV and HSV antigens. PCR for HSV1 and 2 was positive in only 7 of 13 cases (5 HSV1 and 2 HSV2). In the remaining 6 negative cases PCR for beta-globin was also repeatedly negative. HSV1 or 2 infection can be demonstrated by IHC in a significant proportion of AIDS cases with necrotizing CMV encephalitis. Nested PCR for HSV1 and 2 on DNA extracted from formalin-fixed and paraffin-embedded autopsy tissues was positive in only slighty above 50% of IHC-positive cases.
AIDS-Related Opportunistic Infections↗