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PubMed1991

Parameters affecting susceptibility of PCR contamination to UV inactivation.

Contamination of reagents used for PCR is a serious problem. We have recently reported the remarkable effectiveness of UV light in successful decontamination of PCR reagents when the reagents were contaminated with a 6-kb plasmid, followed by amplification of 750-bp segment from the insert. However, further investigation reveals that segment size, sequence and hydration can have a dramatic effect on the efficiency of UV inactivation. Despite some limitations, UV remains a highly effective means of decontamination.

DNA↗

PubMed1990

Oligonucleotide probe for herpes virus: use in paraffin sections.

A method is described for in situ hybridization detection and typing of herpes simplex virus (HSV) using alkaline phosphatase-labeled synthetic oligonucleotide probes in paraffin tissue sections. Sections mounted on slides are prehybridized and denatured before the probe mixture is added. Hybridization proceeds for 1 h at 60 degrees C. Detection of the alkaline phosphatase label is performed using a nitro blue tetrazolium and 5-bromo-4-chloro-3-indolyl phosphate substrate. Specific hybridization with HSV type 1 DNA was found in sections of herpetic esophagitis and encephalitis. There was no discernible background staining. Hybridization with an oligonucleotide probe specific for HSV type 2 was negative. No hybridization occurred to sections of cytomegalovirus- or adenovirus-infected tissue. The development of this technique expands the utility of synthetic oligonucleotide probes to include hybridization reactions in routinely processed and paraffin-embedded tissue. The use of directly labeled oligonucleotide probes for tissue in situ hybridization overcomes problems of probe contamination with vector plasmid DNA, nonspecific avidin binding to tissue, and the danger and inconvenience of working with radioactive materials.

Alkaline Phosphatase↗

PubMed1998

Fundamentals of quality assessment of molecular amplification methods in clinical diagnostics. International Federation of Clinical Chemistry Scientific Division Committee on Molecular Biology Techniques.

The increasing interest in molecular biology diagnostics is a result of the tremendous gain of scientific knowledge in genetics, made possible especially since the introduction of amplification techniques. High expectations have been placed on genetic testing, and the number of laboratories now using the relevant technology is rapidly increasing--resulting in an obvious need for standardization and definition of laboratory organization. This communication is an effort towards that end. We address aspects that should be considered when structuring a new molecular diagnostic laboratory, and we discuss individual preanalytical and analytical procedures, from sampling to evaluation of assay results. In addition, different means of controlling contamination are discussed. Because the methodology is in constant change, no general standards can be defined. Accordingly, this publication is intended to serve as a recommendation for good laboratory practice and internal quality control and as a guide to troubleshooting, primarily in amplification techniques.

Chemistry, Clinical↗

PubMed2006

Hyaluronic acid inhibits the adherence and growth of monolayer keratinocytes but does not affect the growth of keratinocyte epithelium.

Hyaluronic acid (HA) is involved in epidermal biology but evidence for its functional significance is sparse. In this study, low-calcium monolayer and high-calcium epithelium cultures of human keratinocytes were used to study the effect of up to four different HA preparations on keratinocyte growth and on the adherence of proliferating keratinocytes onto the plastic surface coated with different matrix proteins. In suboptimally growing monolayer culture, up to 1,000 microg/ml rooster comb HA and streptococcus equi HA inhibited keratinocyte growth. Instead, all HA preparations tested did not affect the growth and migration of keratinocyte epithelium using optimal or suboptimal growth conditions. In the cell adherence assays, up to 1,000 microg/ml rooster comb HA and streptococcus equi HA inhibited the keratinocyte adherence onto the fibronectin- and collagen-coated substratum. In contrast to other HA preparations, HA from human umbilical cord did not affect the growth of monolayer keratinocytes and it increased markedly the cell adherence onto the collagen-coated substratum. This increase, however, can be attributed to chonroitin sulphate proteoglycan contaminant present in this HA preparation. In conclusion, HA can inhibit the growth and adherence of proliferating monolayer keratinocytes, but it has no apparent effect on the growth and migration of keratinocyte epithelium.

Adjuvants, Immunologic↗

PubMed1994

PCR primers and probes for the 16S rRNA gene of most species of pathogenic bacteria, including bacteria found in cerebrospinal fluid.

A set of broad-range PCR primers for the 16S rRNA gene in bacteria were tested, along with three series of oligonucleotide probes to detect the PCR product. The first series of probes is broad in range and consists of a universal bacterial probe, a gram-positive probe, a Bacteroides-Flavobacterium probe, and two probes for other gram-negative species. The second series was designed to detect PCR products from seven major bacterial species or groups frequently causing meningitis: Neisseria meningitidis, Haemophilus influenzae, Streptococcus pneumoniae, S. agalactiae, Escherichia coli and other enteric bacteria, Listeria monocytogenes, and Staphylococcus aureus. The third series was designed for the detection of DNA from species or genera commonly considered potential contaminants of clinical samples, including cerebrospinal fluid (CSF): Bacillus, Corynebacterium, Propionibacterium, and coagulase-negative Staphylococcus spp. The primers amplified DNA from all 124 different species of bacteria tested. Southern hybridization testing of the broad-range probes with washes containing 3 M tetramethylammonium chloride indicated that this set of probes correctly identified all but two of the 102 bacterial species tested, the exceptions being Deinococcus radiopugnans and Gardnerella vaginalis. The gram-negative and gram-positive probes hybridized to isolates of two newly characterized bacteria, Alloiococcus otitis and Rochalimaea henselii, as predicted by Gram stain characteristics. The CSF pathogen and contaminant probe sequences were compared with available sequence information and with sequencing data for 32 different species. Testing of the CSF pathogen and contaminant probes against DNA from over 60 different strains indicated that, with the exception of the coagulase-negative Staphylococcus probes, these probes provided the correct identification of bacterial species known to be found in CSF.

Bacteremia↗

PubMed1998

Efficient removal of PCR inhibitors using agarose-embedded DNA preparations.

The use of agarose blocks containing embedded DNA improves the PCR amplification from templates naturally contaminated with polysaccharides or humic acids, two powerful PCR inhibitors. Presumably, the difference in size between the DNA macromolecules and these contaminants allows their effective removal from the agarose blocks by diffusion during the washing steps, whereas genomic DNA remains trapped within them. In addition, agarose-embedded DNA can be directly used for PCR since low melting point agarose does not interfere with the reaction. This simple and inexpensive method is also convenient for genomic DNAs extracted by other procedures, and it is potentially useful for samples containing other kinds of soluble inhibitors, overcoming this important problem of current amplification techniques.

DNA↗

PubMed1987

Development of a hepatitis B vaccine from transformed yeast cells.

The production in yeast cells of the recombinant DNA hepatitis B vaccine of SmithKline Biologicals involves an optimized fermentation process followed by cell disruption and extraction, together with other soluble yeast components of the surface antigen of the hepatitis B virus. The subsequent purification process includes precipitation steps, ion exchange and gel permeation chromatography, and caesium chloride ultracentrifugation. The yeast-derived antigen occurs as spherical particles containing the non-glycosylated HBsAg polypeptide, lipid, and Tween 20. The purity of the polypeptide is above 95% and confirmed by the absence of an immune response to yeast-derived contaminants in vaccinees. Yeast DNA levels were less than 10 pg/vaccine dose. Various biochemical analyses showed that the recombinant polypeptide was faithfully expressed and did not undergo unwanted processing or degradation during fermentation or purification. These results indicate that the recombinant HBsAg can be effectively produced in yeast and processed to a high degree of purity to yield HBsAg particles displaying most of the characteristic properties of plasma-derived HBsAg.

Amino Acid Sequence↗

PubMed2004

Isolation of circulating human monocytes with high purity for proteomic analysis.

We describe a simple method for isolation of human blood monocytes with the high purity (95-98%) required for proteomic analysis, which avoids contamination by other blood cells (platelets and lymphocytes) and the most abundant plasma proteins (albumin and immunoglobulins). Blood monocytes were purified by gradient centrifugation followed by positive selection with specific monoclonal antibodies coupled to paramagnetic beads. The elution conditions of the positive selection step were modified to avoid contamination with albumin. This method is compatible with flow cytometry which was used to assess the purity of the cell population. From 28 mL of blood, 10(7) monocytes with > 96% purity are routinely obtained. From the isolated monocytes 200-250 microg of protein could be recovered. The whole method can be performed in three hours. Similar results were obtained using a negative selection step but with lower purity (92%), increased cost and longer time. After solubilization of monocytes, the proteins were analyzed by two-dimensional gel electrophoresis (2-DE) in the 3-10, 4-7, 6-9 and 6-11 pH range. DNA was the main contaminant that interfered with the 2-DE and it was removed by treatment with DNAse. Image analysis of gels allowed the reproducible detection and quantification of 1500 spots in the 4-7 pH range and more than 2000 spots in total by combining (overlapping) 2-D gels in the 4-7, 6-9 and 6-11 pH range. This method is useful for clinical studies of monocytes from a large number of patients due to its rapidity and reproducibility, which permits comparative analysis of normal versus pathological samples and which allows follow up of the expressed proteins of monocytes from each patient.

Blood Proteins↗

PubMed2003

Chimeric and pseudotyped parvoviruses minimize the contamination of recombinant stocks with replication-competent viruses and identify a DNA sequence that restricts parvovirus H-1 in mouse cells.

Recent studies demonstrated the ability of the recombinant autonomous parvoviruses MVMp (fibrotropic variant of the minute virus of mice) and H-1 to transduce therapeutic genes in tumor cells. However, recombinant vector stocks are contaminated by replication-competent viruses (RCVs) generated during the production procedure. To reduce the levels of RCVs, chimeric recombinant vector genomes were designed by replacing the right-hand region of H-1 virus DNA with that of the closely related MVMp virus DNA and conversely. Recombinant H-1 and MVMp virus pseudotypes were also produced with this aim. In both cases, the levels of RCVs contaminating the virus stocks were considerably reduced (virus was not detected in pseudotyped virus stocks, even after two amplification steps), while the yields of vector viruses produced were not affected. H-1 virus could be distinguished from MVMp virus by its restriction in mouse cells at an early stage of infection prior to detectable viral DNA replication and gene expression. The analysis of the composite viruses showed that this restriction could be assigned to a specific genomic determinant(s). Unlike MVMp virus, H-1 virus capsids were found to be a major determinant of the greater permissiveness of various human cell lines for this virus.

Animals↗

PubMed1995

Increased DNA-protein crosslinks in lymphocytes of residents living in chromium-contaminated areas.

It has been known for a number of years that chromium-containing mine slags were used as landfill in residential areas of Hudson County, New Jersey. Since one of the major lesions induced in intact cells by chromate is the DNA-Protein crosslink, we have used this lesion as a biomarker of biological effect of chromium (Cr) exposure. We have previously developed a sensitive and easy-to-perform assay to detect DNA-Protein crosslinks, based on the selective K SDS precipitation of DNA associated with protein. We examined the levels of DNA-Protein crosslinks in peripheral blood mononuclear cells of 33 individuals determined to be at risk for chromium exposure by virtue of their residence in Hudson County and their urinary Cr levels. These data were compared to the levels of DNA-Protein crosslinks among 49 controls who resided in noncontaminated areas. A complete clinical examination and urine analysis did not show any Cr-related abnormalities among the exposed population. The mean DNA-Protein crosslink level in the lymphocytes of the exposed group was 1.3 +/- 0.5% (SD), whereas the unexposed group had 0.8 +/- 0.4% (p < 0.001), after adjustment for age, gender, race, smoking, and weight. Further studies in this population are needed to confirm the possible association between the high levels of DNA-Protein crosslink and Cr exposure.

Adult↗

PubMed2002

A DNA-based method to assay total and infectious particle contents and helper virus contamination in high-capacity adenoviral vector preparations.

High-capacity adenoviral (HC-Ad) vectors are devoid of all viral genes. Therefore, these vectors feature reduced toxicity, immunogenicity, and increased capacity for foreign DNA. HC-Ad vectors are produced in E1-transformed cell lines in the presence of an E1-deleted helper virus that provides in trans all viral functions necessary for vector production. By cre/loxP- or FLPe/Frt-mediated recombination the packaging signal of the helper virus is excised during vector production resulting in nonpackagable helper virus genomes. Although recombinase-mediated excision of the packaging signal from the helper virus genome is highly efficient, a small number of helper virus genomes with retained packaging signals are still packaged into capsids. For clinical trials, HC-Ad vector preparations have to be characterized accurately with respect to the number of (1) total HC-Ad vector particles, (2) infectious HC-Ad vector particles, and (3) the number of contaminating helper virus particles. We describe a fast and versatile DNA-based biologic assay for determination of these three parameters by standard laboratory methods. This assay is a useful tool for determining bioactivity data of adenoviral vector preparations and, importantly, allows their comparison among different studies.

Adenoviridae↗

PubMed1986

An improved filamentous helper phage for generating single-stranded plasmid DNA.

Gene cloning in plasmid vectors that contain a filamentous phage intergenic region presents several advantages. However, technical difficulties have been a problem, primarily low yields of packaged single stranded (ss) plasmid DNA from the rapid, small scale procedures usually employed, and ambiguities in sequencing reactions attributed to the contamination by helper phage ss DNA. We report here the construction and some properties of a new f1 helper phage. Using this phage, R408, plasmid ss DNA is packaged and exported preferentially over phage ss DNA, and the absolute yield of plasmid ss DNA is usually increased.

Base Sequence↗

PubMed1990

Comparison of epidemic and endemic group G streptococci by restriction enzyme analysis.

Restriction enzyme profiles of group G beta-hemolytic streptococci associated with a point source outbreak and an outbreak of sporadic pharyngitis in two different communities were compared. To asses the epidemiologic utility of this approach for studying group G streptococci, DNA fingerprints of strains responsible for a point source outbreak of pharyngitis associated with the consumption of contaminated food were compared with DNA fingerprints of pharyngeal isolates from children with pharyngitis seen at a pediatric practice during a 6-month period. In each epidemiologic situation, a single strain characterized by a unique restriction enzyme pattern predominated. The results are compatible with the conclusion that human infections could be limited to a few strains of group G streptococci which have the capacity to spread through a given population. The restriction enzyme profiles proved to be a highly specific and precise means of evaluating strain relatedness and of providing further understanding of the epidemiology of group G streptococcal infections.

Connecticut↗

PubMed2002

Rapid identification of pathogenic fungi directly from cultures by using multiplex PCR.

A multiplex PCR method was developed to identify simultaneously multiple fungal pathogens in a single reaction. Five sets of species-specific primers were designed from the internal transcribed spacer (ITS) regions, ITS1 and ITS2, of the rRNA gene to identify Candida albicans, Candida glabrata, Candida parapsilosis, Candida tropicalis, and Aspergillus fumigatus. Another set of previously published ITS primers, CN4 and CN5, were used to identify Cryptococcus neoformans. Three sets of primers were used in one multiplex PCR to identify three different species. Six different species of pathogenic fungi can be identified with two multiplex PCRs. Furthermore, instead of using templates of purified genomic DNA, we performed the PCR directly from yeast colonies or cultures, which simplified the procedure and precluded contamination during the extraction of DNA. A total of 242 fungal isolates were tested, representing 13 species of yeasts, four species of Aspergillus, and three zygomycetes. The multiplex PCR was tested on isolated DNA or fungal colonies, and both provided 100% sensitivity and specificity. However, DNA from only about half the molds could be amplified directly from mycelial fragments, while DNA from every yeast colony was amplified. This multiplex PCR method provides a rapid, simple, and reliable alternative to conventional methods to identify common clinical fungal isolates.

Culture Media↗

PubMed1998

DNA damage in mussels at sites in San Diego Bay.

Identification and assessment of introduced and other toxicants is crucial to any comprehensive study of contaminants within the marine environment. The relationship between DNA single-strand breaks and the exposure of marine organisms to environmental contaminants was examined at sites in San Diego Bay, CA. A comprehensive assessment of the extent and consequences of marine environmental contamination in the area of Naval Station San Diego was conducted in the summer of 1995. The study addressed contamination sources, distributions, concentrations, transport, sediment-water exchange, biological effects, and degradation. The biological effects portion of the study (this paper) included contaminant bioaccumulation, organismal growth, and the determination of DNA single-strand breaks using the Comet assay. DNA damage was determined in hemocytes collected from deployed and resident mussels, Mytilus edulis, at six stations in and around the Naval Station San Diego. Deployed mussels were exposed on station for approximately 30 days in plastic mesh bags, placed 1 m above the bottom. Hemocyte samples were collected on days 0, 12, and 32. It was found that stations exhibiting the extremes of contaminant exposure, both highest and lowest concentrations, were easily identified using growth and DNA damage measurements. Sediment chemistry and bioaccumulation data indicated, Hg, Cu, and Zn, to be the most notable contaminants. The Comet assay, and in particular germ cell DNA damage determinations, were found to respond rapidly to station contaminants. Results from this study and an earlier 1993 study suggest that the non-sediment associated effects observed at one station may have been the result of the photoactivation of accumulated PAHs.

Animals↗

PubMed2006

DNA damage and repair process in earthworm after in-vivo and in vitro exposure to soils irrigated by wastewaters.

In this study, DNA damage to earthworms (Eisenia fetida) after in vivo exposure to contaminated soils was measured by detecting DNA strand breakages (DSBs) and causality was analyzed through fractionation based bioassays. A non-linear dose-response relationship existed between DNA damage and total soil PAHs levels. DNA damage, measured with the comet assay, and its repair process, were observed. To identify the chemical causality, an in vitro comet assay using coelomocytes was subsequently performed on the fractionated organic extracts from soils. The results showed that the PAHs in the soils were responsible for the exerting genotoxic effects on earthworms. When normalized to benzo(a)pyrene toxic equivalent (TEQ(BaP)), the saturation dose in the dose-response curve was about 10ng TEQ(BaP) g(-1) soil (dw).

Animals↗

PubMed1975

Isolation of DNA from yeast by chromatography on hydroxyapatite.

A simple procedure is described for isolation of purified non degraded total DNA from yeast cells. The procedure involves conversion of the cells into spheroplasts by enzymatic treatment, lysis of the spheroplasts in 8 M urea - 0.24 M sodium phosphate buffer - 0.01 M EDTA (ethylendiamintetraacetic acid, sodium salt) - 1% SDS (sodium dodecyl sulphate), deproteinization of the lysate with chloroform-phenol and separation of the DNA from proteins, RNA and other contaminants by hydroxyapatite chromatography. The yield is about 90% of the DNA in the starting material (spheroplasts).

Chromatography↗

PubMed2005

13C-carrier DNA shortens the incubation time needed to detect benzoate-utilizing denitrifying bacteria by stable-isotope probing.

The active bacterial community able to utilize benzoate under denitrifying conditions was elucidated in two coastal sediments using stable-isotope probing (SIP) and nosZ gene amplification. The SIP method employed samples from Norfolk Harbor, Virginia, and a Long-Term Ecosystem Observatory (no. 15) off the coast of Tuckerton, New Jersey. The SIP method was modified by use of archaeal carrier DNA in the density gradient separation. The carrier DNA significantly reduced the incubation time necessary to detect the (13)C-labeled bacterial DNA from weeks to hours in the coastal enrichments. No denitrifier DNA was found to contaminate the archaeal (13)C-carrier when [(12)C]benzoate was used as a substrate in the sediment enrichments. Shifts in the activity of the benzoate-utilizing denitrifying population could be detected throughout a 21-day incubation. These results suggest that temporal analysis using SIP can be used to illustrate the initial biodegrader(s) in a bacterial population and to document the cross-feeding microbial community.

Bacteria↗