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PubMed2001

TT virus contaminates first-generation recombinant factor VIII concentrates.

Recombinant factor VIII and factor IX concentrates, human-plasma-derived albumin, and samples from previously untreated patients with hemophilia were examined for the presence of TT virus (TTV) by using polymerase chain reaction testing. Blood samples from the patients were obtained prospectively before and every 3 to 6 months after therapy was begun. TTV was detected in 23.5% of the recombinant-product lots and 55.5% of the albumin lots tested. Only first-generation factor VIII recombinant concentrates stabilized with human albumin were positive for TTV, whereas all second-generation (human protein-free) concentrates were negative for the virus. In 59% of patients treated with either first- or second-generation recombinant factor concentrates, TTV infection developed at some point after the initial infusion. Infection with TTV in these patients before and after treatment did not appear to be clinically important. Thus, first-generation recombinant factor VIII concentrates may contain TTV and the source of the viral contamination may be human albumin.

Blood Transfusion↗
PubMed2003

Campylobacter jejuni contamination on broiler carcasses of C. jejuni-negative flocks during processing in a Japanese slaughterhouse.

At a slaughterhouse, we determined the Campylobacter jejuni status of each broiler flock coming from different farms by culturing cecal contents of representative birds, and examined the prevalence of C. jejuni on carcasses during processing. Then, C. jejuni isolates from the carcasses were typed with RAPD PCR and compared with those from the cecal contents of a C. jejuni-positive flock. C. jejuni was not isolated from the carcasses of C. jejuni-negative flocks processed before the C. jejuni-positive flock, and C. jejuni was isolated from the carcasses of C. jejuni-negative flocks processed after the C. jejuni-positive flock. RAPD PCR type of the isolates from the carcasses of C. jejuni-negative flocks was the same as those from the cecal contents of the previously processed C. jejuni-positive flock. Our results suggest that the carcasses of the C. jejuni-negative flocks were contaminated with C. jejuni strains originating from the intestines of the previously processed C. jejuni-positive flock.

Abattoirs↗
PubMed2001

Integration of genotoxic and population genetic endpoints in biomonitoring and risk assessment.

Genetic ecotoxicology is a multifaceted discipline that examines the effects of xenobiotic compounds on the structure and function of DNA. This paper discusses the role of genetic ecotoxicology in environmental biomonitoring and risk assessment. Genetic ecotoxicology may include somatic effects (e.g., DNA damage) or population genetic effects (changes in genetic diversity or gene frequencies). Traditionally, genetic ecotoxicology studies have focused on either one of these sub-disciplines, but integration of these two approaches would be advantageous for three reasons. First, at the population level, concordant responses between changes in population genetic structure and elevated levels of DNA damage may provide evidence that the population genetic changes are influenced by exposure to genotoxic chemicals. Second, if the frequencies of alleles or other genetic markers differ between genotoxicant-contaminated and reference populations, associations between relative amount of DNA damage and genotype may provide evidence that these changes are due to genotoxicant-induced selection. Third, genetic analysis of gene flow may provide insight into patterns of dispersal that could obscure differences between contaminated and reference populations. In order to demonstrate the application of these ideas, three lines of research are summarized herein. The first is a series of studies that focus on radionuclide-contaminated populations of mosquitofish (Gambusia). This research identified RAPD markers that may be indicative of genetic adaptation to radionuclide stress. Relative amounts of DNA damage among genotypes presented evidence that these markers may be indicators of relative radioresistance. The second study examined DNA damage and population genetic structure in radionuclide-contaminated kangaroo rat (Dipodomys) populations. It was found that between-population differences in genetic diversity paralleled those for DNA damage and relative levels of contamination. Also, population genetic analysis indicated that there was dispersal between contaminated and reference populations, and that between-population differences in the amount of DNA damage could not be detected until this dispersal was taken into account. In the third study, populations of redbreast sunfish (Lepomis auritris) from streams contaminated with complex mixtures of industrial chemicals were examined. It was found that the genetic distances between populations within the contaminated stream corresponded with the relative magnitude of molecular and community-level effects. It was concluded that genetic ecotoxicology could make significant contributions to the fields of environmental biomonitoring and ecological risk assessment, and that integration of genotoxicology and population genetic studies would be a definite advantage toward this end.

Animals↗
PubMedDate not supplied

Acquired immunodeficiency syndrome-associated Kaposi's sarcoma and human herpesvirus 8 DNA detection in serial peripheral blood mononuclear cell samples.

Human herpesvirus 8 (HHV8) DNA was amplified from peripheral blood mononuclear cells (PBMCs) using PCR in 120 HIV-seropositive in- and outpatients who were enrolled in a cohort study between January 1994 and June 1995. Risk factors for HIV infection were homosexuality/bisexuality alone in 64 cases (30 with Kaposi's sarcoma (KS) and 34 without KS, 4 of whom had KS lesions that appeared during follow-up in the cohort), heterosexual contact alone in 32 cases (among whom 1 woman with KS who was the spouse of a bisexual with KS), and transfusion of blood or blood products alone in 24 cases. Three blood samples at 3-4-month intervals were scheduled for each patient. Twenty-five HIV1-seronegative patients served as controls. A total of 47.1% of homo- or bisexual males with KS and 26.7% of homo- or bisexual males without KS had positive HHV8 DNA detection as compared with 21.9% of patients contaminated by heterosexual contact, 8.3% of blood product recipients and 0% of controls. HHV8 DNA detection was intermittent in all but 3 patients according to sequential sampling. Multivariate analysis showed that AIDS-KS was associated with sexual transmission, mainly homo- or bisexual practices and with HHV8 infection assessed by PCR in PBMCs.

Adult↗
PubMed2001

[Cluster analysis of Dendrobium by RAPD and design of specific primer for Dendrobium candidum].

OBJECTIVE: To analyze the genetic relationship of Dendrobium and design a specific primer to differentiate Dendrobium candidum effectively. METHOD: Random amplified polymorphic DNA (RAPD) technique was used to analyze the genetic relationships of 26 species of Dendrobium and one species of Ephemerantha. Dendrogram was constructed by UPGMA. According to the sequence of DNA fragment selected, Sangon 18 primer had been extended from 3' extreme to 20 bp in order to form a specific primer. RESULT AND CONCLUSION: This primer can be used to distinguish Dendrobium candidum from other Dendrobium effectively. Such a technique provides a new way for the identification of Chinese traditional medicines.

Cluster Analysis↗
PubMed1999

Evidence of avian leukosis virus subgroup E and endogenous avian virus in measles and mumps vaccines derived from chicken cells: investigation of transmission to vaccine recipients.

Reverse transcriptase (RT) activity has been detected recently in all chicken cell-derived measles and mumps vaccines. A study of a vaccine manufactured in Europe indicated that the RT is associated with particles containing endogenous avian retrovirus (EAV-0) RNA and originates from the chicken embryonic fibroblasts (CEF) used as a substrate for propagation of the vaccine. We investigated the origin of RT in measles and mumps vaccines from a U.S. manufacturer and confirm the presence of RT and EAV RNA. Additionally, we provide new evidence for the presence of avian leukosis virus (ALV) in both CEF supernatants and vaccines. ALV pol sequences were first identified in particle-associated RNA by amplification with degenerate retroviral pol primers. ALV RNA sequences from both the gag and env regions were also detected. Analysis of hypervariable region 2 of env revealed a subgroup E sequence, an endogenous-type ALV. Both CEF- and vaccine-derived RT activity could be blocked by antibodies to ALV RT. Release of ALV-like virus particles from uninoculated CEF was also documented by electron microscopy. Nonetheless, infectivity studies on susceptible 15B1 chicken cells gave no evidence of infectious ALV, which is consistent with the phenotypes of the ev loci identified in the CEF. PCR analysis of ALV and EAV proviral sequences in peripheral blood mononuclear cells from 33 children after measles and mumps vaccination yielded negative results. Our data indicate that the sources of RT activity in all RT-positive measles and mumps vaccines may not be similar and depend on the particular endogenous retroviral loci present in the chicken cell substrate used. The present data do not support transmission of either ALV or EAV to recipients of the U.S.-made vaccine and provide reassurance for current immunization policies.

Animals↗
PubMed1994

A method for the elimination of false positives generated by the mRNA differential display technique.

The recently described mRNA differential display method provides an attractive tool for the isolation of genes showing regulated expression in a variety of systems. A key step in this technique consists of the isolation of PCR-synthesized radioactive cDNAs corresponding to differentially expressed mRNAs. Here, we show that the purified cDNAs remain contaminated with unrelated cDNA sequences that may lead to the artifactual isolation of false positives in the subsequent steps of the method. A powerful assay for the detection and elimination of this contaminating material, allowing the specific isolation of clones corresponding to the regulated genes identified by the differential display, is provided.

Arabidopsis↗
PubMed1997

Molecular basis, clinical consequences and diagnosis of alpha-1 antitrypsin deficiency.

(1) Deficiency of alpha AT is one of the most common hereditary diseases affecting Caucasians in Europe. The alpha 1AT protein is extremely pleomorphic, and around 90 variants due to mutations have been recognized. The prime functions of alpha 1AT is to inhibit neutrophil elastase, and a proportion of individuals who are deficient in alpha 1AT develop emphysema. The most common deficiency variant (Z) is also associated with liver disease. The main site of alpha 1AT synthesis is in the liver. Not all deficient individuals are affected by lung or liver disease, however, so that other factors (genetic and environmental) are clearly important. (2) Investigation of alpha 1AT status is essential in any child or adult presenting with chronic liver disease. The genetic cause cannot be identified clinically or by any other laboratory investigation. The diagnosis carries important prognostic consequences and is important for other family members. Patients with emphysema should have their Pi type determined, especially if they are under the age of 50, have never smoked or there is a suggestive family history. Asymptomatic individuals who are homozygous type Z should be referred to a chest physician for a clinical and radiological assessment together with lung function tests. (3) Several laboratory tests are available to detect alpha 1AT deficiency, and the choice of test(s) will depend on circumstances. Quantitation of the serum protein is simple and cheap. Because alpha 1AT is an acute phase protein, however, quantitation used in isolation may give false negative results which are clearly unacceptable, particularly in association with paediatric liver disease. Phenotyping by isoelectric focusing requires some experience in distinguishing SZ and ZZ phenotypes, and phenotyping should ideally be used in conjunction with quantitation because heterozygous null phenotypes may appear identical to homozygous normal phenotypes. (4) Prenatal diagnosis is usually performed by DNA analysis of CVS samples obtained at 11-13 weeks. Because of the risk that CVS samples might be contaminated by maternal tissue, assays which are less likely to detect minor contaminants are preferable. At present, use of DNA tests is confined to prenatal diagnosis, but the availability of simple tests and the possibility of unequivocal identification of S and Z alleles means that these tests are likely to find greater use in the near future.

Humans↗
PubMed2006

PCR identification of Salmonella: potential contamination sources from production and postharvest handling of cantaloupes.

Salmonella is one of the most frequently reported etiological agents in outbreaks of foodborne diseases associated with the consumption of cantaloupes. Sensitive and reliable methods for detecting and identifying foodborne microorganisms are needed. The PCR can be used to amplify specific DNA fragments and thus to detect and identify pathogenic bacteria. In this study, a PCR method was used to evaluate the incidence of Salmonella at cantaloupe production, harvest, and packaging steps, and the results were compared with those of the standard method for detection of Salmonella in foods (Mexican NOM-114-SSA1-1994). Salmonella was detected by both standard and PCR methods in 23.5% of the irrigation water samples but only by the PCR method in 9.1% of the groundwater samples, 4.8% of the chlorinated water samples, 16.7% of samples from the hands of packing workers, 20.6% of samples from the packed cantaloupes, and 25.7% of samples from the in-field cantaloupes. With the standard method, Salmonella was found in 8.3% of the crop soil samples. Statistical analysis indicated a significant difference in sensitivity (P < 0.05) between the two methods; the PCR method was 4.3 times more sensitive than the standard method. Salmonella was found at seven of the eight pointsevaluated during the production and postharvest handling of cantaloupe melons.

Consumer Product Safety↗
PubMed1981

DNA synthesis in primary cultures of adult rat hepatocytes in a defined medium: effects of epidermal growth factor, insulin, glucagon, and cyclic-AMP.

Epidermal growth factor (EGF) especially in combination with insulin and glucagon, has been shown to stimulate DNA synthesis in liver cells, both in the whole animal and in cell cultures. As a further development we have found that in primary monolayer cultures of freshly isolated adult rat liver parenchymal cells, in which contamination with nonparenchymal cells was negligible, DNA synthesis was substantially stimulated by these substances. In control cultures, incorporation of [3H]thymidine into DNA and labeling of nuclei in autoradiographs was low. The stimulation by EGF was enhanced by insulin and glucagon, whereas these hormones by themselves exhibited only limited activity. These observations were made in cultures of hepatocytes that were never exposed to serum, even during cell isolation and plating. Hence for stimulation of DNA synthesis under these conditions neither serum factors nor interactions with other types of cells or their products were required. The effects of glucagon were reproduced by substances that elevate intracellular concentration of cyclic-AMP, including cholera toxin, isoproterenol, and methylisobutylxanthine. These various substances, especially EGF, glucagon, or cyclic-AMP, altered the morphological characteristics of the cultures during early stages, promoting cellular spreading and aggregation.

Animals↗
PubMed2002

Evaluation of poliovirus vaccines for pestivirus contamination: non-specific amplification of poliovirus sequences by pan-pestivirus primers.

Two lots of polyvalent live vaccines for human use against poliovirus were tested by reverse transcriptase (RT) and nested PCR for the presence of contaminating pestivirus RNA. By RT-PCR, samples from both lots showed a band of approximately 450 bp instead of 300 bp for the reference pestivirus strain used as positive control. After nested PCR, the template DNA (450 bp product) was not amplified, suggesting non-specificity of the previous amplification. Sequencing analysis confirmed the non-specificity of the 450 bp bands and revealed, respectively, 80 and 77% homology with a region in the VP1 gene of poliovirus type 1 in samples 1 and 2. This suggests that more caution should be taken in interpreting the results obtained by PCR, and that they should be confirmed by nested PCR or sequencing.

Animals↗
PubMed2002

Candida davenportii sp. nov., a potential soft-drinks spoilage yeast isolated from a wasp.

During a survey of yeast ecology in a soft-drinks production facility, a dead wasp was removed from the sampling tap of an external sugar-syrup storage tank. A yeast isolated from the dead wasp was found to be similar, although not identical, in its physiological characteristics to Candida lactis-condensi and Candida stellata. Sequence analysis of the 26S rDNA D1/D2 variable domain revealed that this isolate was most closely related to C stellata, but differed sufficiently in its D1/D2 sequence to indicate that it belonged to a separate species. The yeast species has been named Candida davenportii sp. nov.; the type strain is NCYC 3013T (= CBS 9069T). C davenportii sp. nov. was osmotolerant, moderately preservative-resistant and able to grow in very acidic conditions, i.e. pH 14. This yeast grew well in fruit-containing soft drinks, cola-type beverages and a synthetic soft drink and is therefore a potential cause of spoilage of soft drinks and other sugary food products. Other related yeast species in the same taxonomic clade as C davenportii sp. nov. are also osmotolerant, growing in < 50% (w/v) sugar. Many of these species are associated with insects, specifically bees, bumblebees and leafcutter bees, and many have been reported as the causative agent of spoilage of sugary foods, such as condensed milk, fruit juices and concentrates. It is proposed that C davenportii sp. nov. and other closely related yeasts are primarily associated with Aculeates (bees and wasps). In turn, bees and wasps are attracted by sugary residues in foods such as fruit juices and concentrates, forming the source of infection of these yeasts and thus instigating spoilage.

Animals↗
PubMed2005

Bleeding sap and old wood are the two main sources of contamination of merging organs of vine plants by Xylophilus ampelinus, the causal agent of bacterial necrosis.

The spatial distribution of vine plants contaminated by Xylophilus ampelinus, the agent responsible for bacterial necrosis, was studied over a 5-year period within two vineyards in the Cognac area. Both vineyards were planted with Vitis vinifera cv. Ugni blanc but were different in age and agronomic location. The emission of X. ampelinus in contaminated bleeding sap was observed during vine sprouting. Contaminated bleeding sap is an important source of inoculum for external contamination due to the high susceptibility of young merging shoots to the pathogen. X. ampelinus emission by bleeding sap was not affected by the age of the plants or the location of the vineyards. However, its emission was irregular with time, and it varied between two fruit canes from individual plants and between plants as well as between years. Moreover, the two vineyards appeared to be entirely contaminated. Consequently, the behavior of the pathogen is not predictable. The distribution of the pathogen inside vine plant organs was analyzed through the four growing seasons. The old wood was contaminated throughout the year and constituted a stock inoculum for endophytic contamination of crude sap during the winter and the spring. Despite the fact that most of the young green shoots were contaminated in May, X.ampelinus was not found in green shoots in June and September, refuting the hypothesis of an epiphytic life of the pathogen under natural conditions. Although all plants were entirely contaminated in both vineyards, symptoms were rare and were observed on different plants each year.

Burkholderiaceae↗
PubMed2001

Development of a multiplex polymerase chain reaction assay for detection and differentiation of Staphylococcus aureus in dairy products.

A multiplex polymerase chain reaction (PCR) assay was developed for the detection and differentiation of enterotoxigenic Staphylococcus aureus in dairy products. A solvent extraction procedure was successfully modified for extraction of S. aureus DNA from 10 ml of artificially contaminated skim milk or 20 g cheddar cheese. Primers targeting the enterotoxin C gene (entC) and thermostable nuclease gene (nuc) were used in the multiplex PCR. PCR products were confirmed using restriction fragment length polymorphism analysis. DNA was consistently quantified and amplified by uniplex PCR from 10 CFU/ml of S. aureus in skim milk or 10 CFU/20 g cheddar cheese. The sensitivity of the multiplex PCR was 100 CFU/ml of skim milk or 100 CFU/20 g cheddar cheese. The developed methodology allows presumptive identification and differentiation of enterotoxigenic S. aureus in less than 6 h.

Animals↗
PubMed2006

Sensitive, real-time PCR detects low-levels of contamination by Legionella pneumophila in commercial reagents.

In a real-time PCR assay of Legionella pneumophila (targeting the L. pneumophila-specific mip gene and using SYBR Green dye for DNA detection in conjunction with the iCycler system) we detected as few as 1.3 copies of a mip gene in a 50-microl reaction from serially diluted L. pneumophila genomic DNA. However, cycle threshold (C(T)) were yielded and DNA product detected in our no-template negative controls and the phenomenon persisted when two separate batches of PCR reagents and water from two different biochemical companies were tested. Since L. pneumophila can be widespread in municipal water supplies, the commercial reagents, especially the reagent water (80% of the reaction volume), could be the source of contamination. To test this hypothesis, we treated Millipore Milli-Q water by filtering through a 0.2 microm-pore-size polycarbonate filter to remove bacteria prior to autoclaving. Real-time PCR using this water had no contamination. Our finding is indirect evidence that commercially available purified water can harbor low level contamination by L. pneumophila DNA that has escaped purification processes. This presents a challenge when developing a sensitive DNA-based bacterial detection method if the target organism or its DNA is a common contaminant of necessary reagents.

Colony Count, Microbial↗
PubMed1990

Human immunodeficiency virus integration protein expressed in Escherichia coli possesses selective DNA cleaving activity.

The human immunodeficiency virus (HIV) integration protein, a potential target for selective antiviral therapy, was expressed in Escherichia coli. The purified protein, free of detectable contaminating endonucleases, selectively cleaved double-stranded DNA oligonucleotides that mimic the U3 and the U5 termini of linear HIV DNA. Two nucleotides were removed from the 3' ends of both the U5 plus strand and the U3 minus strand; in both cases, cleavage was adjacent to a conserved CA dinucleotide. The reaction was metal-ion dependent, with a preference for Mn2+ over Mg2+. Reaction selectivity was further demonstrated by the lack of cleavage of an HIV U5 substrate on the complementary (minus) strand, an analogous substrate that mimics the U3 terminus of an avian retrovirus, and an HIV U5 substrate in which the conserved CA dinucleotide was replaced with a TA dinucleotide. Such an integration protein-mediated cleavage reaction is expected to occur as part of the integration event in the retroviral life cycle, in which a double-stranded DNA copy of the viral RNA genome is inserted into the host cell DNA.

Base Sequence↗
PubMed2006

Inhibitor-free DNA for real-time PCR analysis of synovial fluid from horses, cattle and pigs.

The potential of five different commercial DNA isolation methods to remove real-time PCR inhibitors from the synovial fluid of horses, cattle and pigs was investigated. All kits with the exception of one included a silica column-based purification of the DNA. With the fifth kit, DNA purification is achieved by removing contaminating macromolecules by a desalting process. We used a recently developed method based on comparison of the real-time PCR signal of an artificial target incorporated into each PCR reaction in the presence of the isolated DNA from the sample, and in control samples containing water instead of isolated DNA. This was followed by statistical analysis of the data. Inhibition and subsequent reduction of the endpoint fluorescence in the real-time PCR reaction was encountered in many cases. Less frequently, the target copy number in the samples was underestimated. However, we found no experimental evidence of a negative influence of the reduced endpoint fluorescence signal on the detection limit of the real-time PCR assay. All kits tested were useful for analyzing pelleted synovial fluid from horses, cattle and pigs. When analyzing non-pelleted synovial fluid, three kits - two based on silica columns and one employing a desalting process - yielded inhibitor-free DNA for real-time PCR analysis.

Animal Diseases↗