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PubMed2003

SV40 Tag DNA sequences, present in a small proportion of human hepatocellular carcinomas, are associated with reduced survival.

AIMS: To study the association between simian virus 40 (SV40) and human hepatocarcinogenesis. METHODS: Polymerase chain reaction (PCR) to detect SV40 large T antigen (Tag) DNA was performed on: 50 human hepatocellular carcinoma (HCCs) diagnosed between 1978 and 1989 (cohort A); 20 cases of alcoholic liver cirrhosis from the same period; and 20 HCCs diagnosed after 1997 (cohort B). PCR to detect SV40 regulatory sequence and SV40 Tag immunohistochemistry were performed on selected cases from cohorts A and B. Amplified products were directly sequenced. Immunohistochemistry for p53 and pRb and clinicopathological analyses were performed on selected cases from cohorts A and B. Complete survival data were collected for cohort A. RESULT: SV40 Tag DNA was found in five cohort A HCCs but not in alcoholic liver cirrhosis cases or cohort B HCCs. Neither SV40 regulatory sequence nor SV40 Tag protein were demonstrated in Tag DNA positive HCCs. No clinicopathological differences existed between Tag DNA positive and negative HCCs, but the presence of Tag DNA was associated with reduced disease specific survival. Relatively fewer Tag DNA positive than negative HCCs expressed p53, but loss of pRb expression was similar in the two groups. Patients with Tag DNA positive HCCs were unlikely to have received SV40 contaminated poliovirus vaccine. CONCLUSIONS: SV40 Tag DNA is present in a small proportion of historical HCCs and may contribute to their pathogenesis and influence their outcome. The source of the virus is uncertain and more recent HCCs show no evidence of SV40.

Aged↗

PubMed1991

New molecular approaches for detecting viral genomes.

The impact of a recently developed procedure, the polymerase chain reaction, is to be seen in all areas of molecular biology including virology and viral diagnostics. The power of the technique lies in its ability to amplify specific nucleic acid sequences from extremely low starting levels to amounts which can be readily detected, making it an obvious and attractive technique for the diagnosis of virus contamination. It has been developed for the detection of the hepatitis C virus genome in blood and blood products and it appears to be a more efficient marker for infectivity than the detection of anti-HCV antibodies. Considerable care must be taken in the use of PCR as a diagnostic technique because its exquisite sensitivity can easily give rise to false positives. Whilst PCR has an obvious role in safety testing of biologicals it will not be used in isolation but will complement other tests for infectivity and virus contamination.

Biological Products↗

PubMed2005

"In-gel patch electrophoresis:" a new method for environmental DNA purification.

Most of the microorganism species are largely untapped and could represent an interesting reservoir of genes useful for biotechnological applications. Unfortunately, a major difficulty associated with the methods used to isolate environmental DNA is related to the contamination of the extracted material with humic substances. These polyphenolic compounds inhibit the DNA processing reactions and severely impede cloning procedures. In this work, we describe a rapid, simple, and efficient method for the purification of genomic DNA from environmental samples: we added a chromatography step directly embedded into an agarose gel electrophoresis. This strategy enabled the DNA extraction from various environmental samples and it appeared that the purity grade was compatible with digestion by restriction enzymes and polymerase chain reaction (PCR) amplifications.

Bryophyta↗

PubMedDate not supplied

Isolation of a sex-linked DNA sequence in cranes.

A female-specific DNA fragment (CSL-W; crane sex-linked DNA on W chromosome) was cloned from female whooping cranes (Grus americana). From the nucleotide sequence of CSL-W, a set of polymerase chain reaction (PCR) primers was identified which amplify a 227-230 bp female-specific fragment from all existing crane species and some other noncrane species. A duplicated versions of the DNA segment, which is found to have a larger size (231-235 bp) than CSL-W in both sexes, was also identified, and was designated CSL-NW (crane sex-linked DNA on non-W chromosome). The nucleotide similarity between the sequences of CSL-W and CSL-NW from whooping cranes was 86.3%. The CSL primers do not amplify any sequence from mammalian DNA, limiting the potential for contamination from human sources. Using the CSL primers in combination with a quick DNA extraction method allows the noninvasive identification of crane gender in less than 10 h. A test of the methodology was carried out on fully developed body feathers from 18 captive cranes and resulted in 100% successful identification.

Animals↗

PubMed1984

Rapid and quantitative recovery of DNA fragments from gels by displacement electrophoresis (isotachophoresis).

The use of displacement electrophoresis (synonymous to isotachophoresis, steady-state stacking, and moving boundary electrophoresis) for recovery of DNA fragments from agarose and polyacrylamide gels is described. Complete recovery of DNA molecules ranging from oligonucleotides to 20 000-basepairs-long fragments was achieved. The DNA is recovered in a small volume (0.1-0.3 ml) and can be used directly in enzyme-mediated cleavage and ligation reactions. The recovered DNA contained no inhibitory contaminants as revealed by ligation or restriction enzyme cleavage.

Base Composition↗

PubMed1993

A simple, sensitive, and rapid method for detecting seed contaminated with highly virulent Leptosphaeria maculans.

A primer-directed DNA amplification polymerase chain reaction assay for detection of seed contaminated with highly virulent Leptosphaeria maculans was developed. The primers were derived from a 5,238-bp repetitive sequence present only in the highly virulent isolates of the fungus. A procedure for isolating DNA from organisms infesting germinating seed was also developed. Seeds were added to liquid fungal minimal medium, and the culture was incubated for 3 days at room temperature with shaking. The organisms were collected from the cultures by centrifugation and lysed with a combination of sodium dodecyl sulfate and proteinase K. The DNA was extracted with organic solvents and with a high-salt-cetyltrimethylammonium bromide solution. It was also precipitated with a low-salt-cetyltrimethylammonium bromide solution. The extensive treatments used for minimizing polysaccharide contamination greatly improved the reliability of the assay. The minimum contamination level (2 of 1,000 seeds) that was tested was successfully detected with this DNA isolation procedure. The reliability of the assay was 96% at the 1 to 2% level of seed contamination. The described method is less laborious and requires only 4 to 5 days for completion in comparison to the 11 to 22 days required for the currently employed methods. In addition, large sample sizes can be easily handled, thus reducing the probability of contaminated seed escaping detection.

Ascomycota↗

PubMed2004

A highly parallel nanoliter dispenser for microarray fabrication.

We report about the correlation between satellite free droplet release and liquid viscosity in a highly parallel, pressure driven nanoliter dispenser. In extensive studies, we found that for liquids of different viscosities the duration of the pressure pulse is the predominant effect compared to pressure amplitude. This result is of essential importance when actuation parameters have to be adopted for different media like oligonucleotide, DNA or protein solutions as it is the case for the non-contact high throughput fabrication of microarrays (Ducree et al., 2000). Experiments with oligonucleotides as well as with different proteins showed ascertained carry-over and cross-contamination free printing of DNA and protein microarrays. With it a prime critical point of microarray production is solved, leading to high quality whilst high throughput microarray fabrication. For oligonucleotides printing, we found CVs to be better than 1% within one single dispensing channel and 1.5% within all 24 channels of a 24 channel printhead for each used printing buffer. By optimizing the protein printing buffer the CVs for protein printing were reduced to about 1% within all 24 channels. As a serious practical application test oligonucleotides microarrays were produced using our nanoliter dispenser system. With it a full DNA hybridization experiment was performed. Clear positive signals one hand and no signals in the negative controls on the other hand showed that our system is suited for microarray production.

Adsorption↗

PubMed2003

PCR of cerebrospinal fluid for diagnosis of bacterial meningitis during meningococcal epidemics; an example from Sudan.

Meningococcal disease is feared due to its rapid progression and high case fatality rate, especially in the African meningitis belt, where epidemics of meningococcal meningitis appear cyclically. Culture, direct microscopy and antigen detection are the basic methods for diagnosis and species identification of bacterial meningitis. These methods are known to have limitations, especially in developing countries. The aim of the present study was to document the application of PCR technology for the diagnosis of bacterial meningitis in cerebrospinal fluid (CSF) samples (n = 52) collected during epidemics in Sudan. In the application of PCR for detection of the causative agent of bacterial meningitis (based on the 16S rRNA gene), bacterial DNA was identified in 49 samples. Common bacterial species causing bacterial meningitis could be detected in 31 of the CSF samples (27 meningococci), while 18 contained DNA, mainly from normally contaminating bacteria. A specific PCR for group A meningococci (based on the sacC gene) was positive in 27 of the CSF samples. The results show that PCR technology is a sharp-edged tool for confirmation of a diagnosis of meningococcal meningitis and for obtaining a direct genogrouping of group A meningococci in CSF. It is important to stress the use of direct and specific PCRs to avoid interference by contaminating bacteria, a great problem in samples from areas in the meningitis belt.

Cerebrospinal Fluid↗

PubMed2002

Detection of Y-specific sequences in 122 patients with Turner syndrome: nested PCR is not a reliable method.

The incidence of Y chromosome sequences in patients with Turner syndrome has been evaluated in several studies, and its frequency varied from 0% to 61%, depending on the molecular methodology used. The aim of our study was to screen for Y chromosome sequences in 122 patients with Turner syndrome without cytogenetic evidence of this chromosome. DNA of 100 normal women was also screened and it was used as a negative control. To identify cryptic Y mosaicism, eight regions of Y chromosome were amplified by PCR. In order to increase the sensitivity of Y sequence detection, a nested PCR of the SRY and TSPY genes was also performed. All patients had several stigmata of Turner syndrome and none of them presented with signs of virilization. The most frequent karyotype was 45,X (54.1%), followed by mosaicism involving structural aberration of the X chromosome. There were 12 patients who carried a marker or ring chromosome. First-round PCR identified Y chromosome sequences in only four patients (3%), and all of them had a chromosome mosaicism with at least one cell lineage with a marker chromosome. After nested PCR, 25% of the patients and 14% of the normal women were positive for the presence of Y sequences. Contamination with extraneous genomic DNA was ruled out by microsatellite studies, but we cannot eliminate the possibility of contamination with PCR products, despite careful handling. We conclude that nested PCR overestimated the frequency of Y sequences in patients with Turner syndrome and should be avoided to prevent false positive results, which lead to unnecessary surgical treatment of these patients.

Chromosome Banding↗

PubMed1991

Characterization of taeniid cestodes by DNA analysis.

High molecular weight DNA samples free of contaminating proteins and RNA obtained from one isolate (of Guangzhou origin) of Cysticercus tenuicollis and five isolates (of Tianjin, Harbin, Lanzhou, Shenyang and Zhengzhou origin) of Cysticercus cellulosae were subjected to thermal denaturation, restriction endonuclease digestion, Southern blotting and hybridization analysis. C. cellulosae DNA showed a melting temperature (Tm) of 82 degrees C corresponding to a 31% GC content whereas C. tenuicollis DNA melted at 85 degrees C suggesting 38.3% GC content. Visual inspection of ethidium bromide-stained gel showed differences not only between the DNAs of the two species of Taeniid cestodes, but also among the five isolates of C. cellulosae. Furthermore, we used two fragments (1.9kb and 5.5kb) of HindIII-derived restriction fragments of C. cellulosae DNA (Harbin origin) and pTS10 as probes to hybridize the DNAs of the Taeniid cestodes from six origins to detect inter- and intra-species genetic variation, the restriction fragment length polymorphisms (RFLPs) were identified.

Animals↗

PubMedDate not supplied

Highly sensitive chemiluminescent method for the detection of cell contamination.

Minisatellite analysis is commonly used in forensic disputes but can also be applied to the investigation of cell contamination. Such a problem arises, for example, when transplantation is performed. The presence of contamination has been investigated by other authors using radioactive methods. In the present study we describe a method that allows the detection of contamination with high sensitivity without using radioactive substances. Our technique is based on the use of polymerase chain reaction (PCR) amplification of minisatellite sequences (VNTR), followed by chemiluminescent detection. In particular, biotin-labelled dCTP is included in the PCR mixture and detection of PCR products is obtained following the CSPD chemiluminescent protocol (Southern-Light Nucleic Acid Detection Systems). We applied this method to artificial mixes of DNA of two individuals with alleles of different sizes. We performed progressive dilutions of an individual DNA into the other's DNA and revealed a contamination of 1 in 2500 cells. We also tested our technique searching for maternal contamination in cord blood samples in 60 cases and revealed a 18.3% contamination. The technique that we set up proves to be a very sensitive one which could be applied not only to the detection of maternal cells in cord blood but also in studying any other kind of contamination.

DNA↗

PubMed1991

Distribution of DNA Sequences Encoding Narrow- and Broad-Spectrum Mercury Resistance.

The distribution of DNA sequences homologous with three mer genes was determined in unselected and mercury-resistant water and sediment isolates. The maximum proportions of unselected bacterial isolates containing DNA hybridizing with the 358merA, 358merB, and 501merR probes, derived from gram-negative organisms, were 93.8, 21, and 100%, respectively. Up to 53.3% of mercury chloride-resistant isolates and 54% of methylmercury hydroxide-resistant isolates did not contain DNA homologous with 358merA or 358merB, respectively. Hybridizations performed at high and low stringencies demonstrated that divergence of the merA gene accounted for many of the mercury-resistant but probe-negative isolates. Sixteen mercury-resistant Bacillus spp. isolated from the least contaminated site all contained DNA homologous with 258merA, originally from a gram-positive organism, but only four hybridized weakly with 358merA. The results demonstrate the wide distribution of mercury resistance genes but, because of the diversity of genetic determinants, highlight the importance of using multiple detection techniques and gene probes derived from a variety of origins for such studies.

Journal Article↗

PubMed2006

Very early prenatal diagnosis of genetic diseases based on coelomic fluid analysis: a feasibility study.

BACKGROUND: Coelocentesis may represent the ideal technique for very early prenatal diagnosis. Although cell density in coelomic fluid (CF) is very low, the results of analyses on the cellular compartment have been proposed for prenatal diagnosis. METHODS AND RESULTS: We aimed to evaluate the amount of total DNA (i.e. cellular and cell-free) in 14 samples (0.4-0.8 ml) of CF, taken from women at 8- to 9-week gestation, who are about to undergo termination of pregnancy, and to assess the feasibility of multiple single-gene analyses using multiplex real-time PCR. We found that the amount of total DNA in the CF was very low and varied widely. Genetic testing using multiplex real-time PCR was successfully achieved in 10 of 14 samples (71%). However, when considering samples that could provide a reliable prenatal diagnosis (i.e. successful PCR analysis and no marked maternal contamination), reliable CF-DNA-based prenatal diagnoses were obtained in only 8 of the 14 (58%) samples. CONCLUSION: The development of highly reliable procedures adapted to pauci-cellular CF is crucially needed before coelocentesis could be proposed for early prenatal diagnosis of genetic diseases before 10 weeks.

Body Fluids↗

PubMed1992

Rapid, non-separation electrochemiluminescent DNA hybridization assays for PCR products, using 3'-labelled oligonucleotide probes.

Described are rapid assays for the analysis of PCR products in a one step, non-separation assay based on the use of electrochemiluminescence generated from a tris-bipyridine ruthenium (II) label. The assay uses PCR incorporation of a biotinylated oligonucleotide as a primer, with the inclusion of a labelled oligonucleotide. Oligonucleotides were labelled with an N-hydroxy succinimide ester of tris-bipyridine ruthenium (II) dihexafluorophosphate (Origen-label) by modifying the 3' and 3' 5' ends of the oligonucleotide probes. The assay makes use of the inherent thermal stability and absence of polymerase activity on such probes to allow the PCR and probe hybridization to be completed automatically on the thermocycler. The assay is concluded by the addition of PCR samples to streptavidin beads on an electrochemiluminescence analyser for binding and analysis. Target genes evaluated were the HIV-1 gag gene, and cystic fibrosis delta F-508 deletion mutation. The results obtained from these assays demonstrated the detection of 10 copies of the HIV-1 gag gene, and cystic fibrosis delta F-508 mutation in 1 ng of human DNA within 15 min. This assay format allows a rapid and simple determination of specific amplified DNA sequences, reducing the contamination risks due to washes and multiple pipetting.

2,2'-Dipyridyl↗

PubMed2001

Low prevalence of TT virus in the cerebrospinal fluid of viremic patients with central nervous system disorders.

TT virus (TTV) is a widespread infectious agent of humans identified in 1998. In infected individuals, TTV induces persistent viremia but its life cycle and pathogenic potential are still poorly understood. In the present study, the presence of TTV DNA in 32 consecutive paired serum and cerebrospinal fluid (CSF) samples from patients with neurological (mainly multiple sclerosis) disorders was investigated by means of a sensitive quantitative real-time PCR assay. Of the 24 patients who were found to carry TTV DNA in serum, 3 also had detectable TTV DNA in their CSF. Two TTV positive CSF samples had markers indicative of blood contamination or a disrupted blood-brain barrier and contained considerably lower TTV loads as compared with the corresponding serum samples, thus suggesting that the virus they contained was of plasma origin. These findings indicated that in general TTV does not permeate effectively an intact blood-brain barrier. Furthermore, the CNS does not represent a common site of TTV replication and persistence. However, at least one exception was observed: the third TTV positive CSF sample (obtained from a patient with subacute dementia of unknown origin) showed no markers suggestive of disrupted blood-brain barrier or blood contamination and had a TTV DNA concentration similar to that found in the patient's serum. In addition, the TTV isolates detected in the two body fluids were distinct genetically. The detection of TTV DNA in CSF is of considerable interest but the clinical significance remains unknown.

Adult↗

PubMed2003

DNA damage in blood cells from children exposed to arsenic and lead in a mining area.

In this work, we studied the frequency of DNA damage in children living in Villa de la Paz, Mexico, a mining site contaminated with arsenic and lead. DNA damage in blood cells was assessed using the Comet assay, and the results were compared to those found in children living in a less exposed town (Matehuala). In Villa de la Paz, high concentrations of arsenic and lead in surface soil and household dust were found. All of the soil samples had concentrations above 100 mg/kg of arsenic, and 58% of the samples were higher than 400 mg/kg of lead (these concentrations are used as intervention guidelines by the United States Environmental Protection Agency). In agreement with the environmental results, urinary arsenic in children living in Villa de la Paz (geometric mean 136 microg/g creatinine) was significantly higher than that found in children living in Matehuala (34 microg/g creatinine). Blood lead levels were also significantly higher in children from Villa de la Paz (11.6 microg/dL) than in children from Matehuala (8.3 microg/dL). The results of the Comet assay showed that the tail length and the tail moment in children living in Villa de la Paz were higher than those observed for children in Matehuala (P<0.05). Taking all the data into account, our study has shown increased DNA damage in children exposed to arsenic and lead in the mining site of Villa de la Paz.

Arsenic↗

PubMed1997

A non-isotopic probe-hybridization assay for residual DNA in biopharmaceuticals.

Although most biopharmaceuticals are highly purified, there is a theoretical concern that such recombinant products could be contaminated with oncogenic or bacterial DNA. A crucial part of the control of such biologicals is to ensure they do not contain more residual DNA than a safety limit suggested by the regulatory agency. Currently, the FDA has suggested a 100 pg per dose limit for residual DNA. DNA probes labeled with a radioisotope such as 32P have been commonly used in hybridization tests. Because of the radiation safety concern, we chose to develop a procedure for assessing DNA levels by either a dot or slot blot hybridization technique using a nonisotopic DNA probe and immuno-enzymatic detection. A minimum detectable limit (MDL) of < 10 pg DNA mg(-1) protein can be achieved. Method validation data demonstrated that the precision, reproducibility, and robustness of this approach are appropriate for quality control.

Biopharmaceutics↗

PubMed1982

Distribution of replicating simian virus 40 DNA in intact cells and its maturation in isolated nuclei.

The maturation of replicating simian virus 40 (SV40) chromosomes into superhelical viral DNA monomers [SV40(I) DNA] was analyzed in both intact cells and isolated nuclei to investigate further the role of soluble cytosol factors in subcellular systems. Replicating intermediates [SV40(RI) DNA] were purified to avoid contamination by molecules broken at their replication forks, and the distribution of SV40(RI) DNA as a function of its extent of replication was analyzed by gel electrophoresis and electron microscopy. With virus-infected CV-1 cells, SV40(RI) DNA accumulated only when replication was 85 to 95% completed. These molecules [SV40(RI(*)) DNA] were two to three times more prevalent than an equivalent sample of early replicating DNA, consistent with a rate-limiting step in the separation of sibling chromosomes. Nuclei isolated from infected cells permitted normal maturation of SV40(RI) DNA into SV40(I) DNA when the preparation was supplemented with cytosol. However, in the absence of cytosol, the extent of DNA synthesis was diminished three- to fivefold (regardless of the addition of ribonucleotide triphosphates), with little change in the rate of synthesis during the first minute; also, the joining of Okazaki fragments to long nascent DNA was inhibited, and SV40(I) DNA was not formed. The fraction of short-nascent DNA chains that may have resulted from dUTP incorporation was insignificant in nuclei with or without cytosol. Pulse-chase experiments revealed that joining, but not initiation, of Okazaki fragments required cytosol. Cessation of DNA synthesis in nuclei without cytosol could be explained by an increased probability for cleavage of replication forks. These broken molecules masqueraded during gel electrophoresis of replicating DNA as a peak of 80% completed SV40(RI) DNA. Failure to convert SV40(RI(*)) DNA into SV40(I) DNA under these conditions could be explained by the requirement for cytosol to complete the gap-filling step in Okazaki fragment metabolism: circular monomers with their nascent DNA strands interrupted in the termination region [SV40(II(*)) DNA] accumulated with unjoined Okazaki fragments. Thus, separation of sibling chromosomes still occurred, but gaps remained in the terminal portions of their daughter DNA strands. These and other data support a central role for SV40(RI(*)) and SV40(II(*)) DNAs in the completion of viral DNA replication.

Animals↗