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PubMed2005

Semi-nested PCR for detection and typing of bovine Papillomavirus type 2 in urinary bladder and whole blood from cattle with enzootic haematuria.

Bovine Papillomavirus type 2 (BPV-2) and chronic intoxication by bracken fern ingestion were associated with urinary bladder lesions and the clinical signs of enzootic haematuria in adult cattle. Clinically enzootic haematuria is characterized by intermittent haematuria followed by animal death. Enzootic haematuria causes considerable economical impact on extensive cattle breeding worldwide. The demonstration of BPV-2 participation in the etiology of bovine urinary bladder carcinoma by conventional virological methods is not easy and the integrity of epidemiological studies relies on methods that are sensitive and specific for BPV-2 detection and typing. A multiplex-PCR was evaluated for BPV-2 L1 gene and bovine mitochondrial genome ND5 gene (internal control) detection followed by a second round of BPV-2 amplification by a semi-nested PCR (SN-PCR). Six skin papilloma samples were used for PCR technique development. Twenty-two urinary bladder samples from symptomatic (n = 12) and asymptomatic (n = 10, control group) cows and 25 blood samples from cows grazed on enzootic haematuria-endemic (n = 14) and enzootic haematuria-free (n = 11, control group) geographical regions of Parana State, Brazil were analyzed. The SN-PCR detected BPV-2 in seven urinary bladder and 10 whole blood samples collected from cows with enzootic haematuria and in one urinary bladder and one whole blood samples of asymptomatic cows. The specificity of the amplicon was performed by restriction fragment length polymorphism and sequence analysis. The SN-PCR technique developed in this study will make possible the realization of diagnosis and comparative epidemiological studies to evaluate BPV-2 infection rates in cattle, and the association of this infection with bracken fern chronic intoxication in the etiology of enzootic haematuria and opens the possibility of ante mortem studies by lymphocytes analysis.

Animals↗

PubMed2004

[A simple, low-cost and non-invasive method for screening Y microdeletions in infertile men].

OBJECTIVES: Recent investigations showed a high prevalence of Y chromosome microdeletions in men with severely impaired spermatogenesis. Screening for these men is recommended prior to assisted reproduction techniques. The aim of this study was to set up a simple method to detect Y deletion in infertile men. First, we tested the feasibility of cytobrush to collect oral cells as source of DNA. Second, we compared a classic PCR corresponding to European recommendations to the Promega kit. PATIENTS AND METHODS: Seventeen infertile male patients with previously characterized deletions were included in the present study, after fully informed written consent. Both oral cells and blood were used for DNA extraction. A specific DNA extraction protocol was carried out on the buccal cells. The DNAs were tested for Y deletion screening by two different methods. RESULTS: We retrieved between 4 and 10 microg of DNA per brush from buccal cells, allowing several multiplex PCR. The Promega kit detected all the deletions but one: an AZFa deletion was not detected by the two markers of the kit covering this region. In addition, sY130, sY133 and SY153, included in the kit, are not reliable. DISCUSSION AND CONCLUSIONS: Buccal cells represent a convenient substitute for blood in testing for Y microdeletions. Both false negative and false positive results were obtained with Promega Kit. On the opposite, PCR according to the European recommendations allow the accurate detection of Y microdeletion in our 17 cases, at a lower cost.

Chromosomes, Human, Y↗

PubMed2002

Prevalence of circulating Treponema pallidum DNA and RNA in blood donors with confirmed-positive syphilis tests.

BACKGROUND: Although there have been no well-documented cases of transfusion-transmitted syphilis in more than 30 years, serologic tests for syphilis (STS) continues to be required for donated blood. Previously, the methods for detecting viable spirochetes were dependent on the use of the rabbit infectivity test. DNA PCR and RNA RT-PCR were applied to assess the presence of Treponema pallidum DNA or RNA in blood donors with confirmed-positive results in STS. STUDY DESIGN AND METHODS: This case series describes T. pallidum DNA and RNA testing of platelet concentrates prepared from blood donors with reactive results in an automated treponemal screening test and positive test results in the fluorescent treponomal antibody absorption test. The first DNA test was specific for the T. palladium polA gene. The second DNA test was a multiplex PCR using a T. pallidum 47-kDa gene target. The RT-PCR for RNA used T. pallidum 16S rRNA as a template for production of a cDNA target. RESULTS: One hundred sixty-nine samples (including rapid plasma reagin [RPR]+ and RPR-) tested for T. pallidum DNA and/or RNA were negative. CONCLUSIONS: A lack of demonstrable T. pallidum DNA or RNA suggests that blood donors with confirmed-positive results in STS are unlikely to have circulating T. pallidum in their blood and that that their blood is unlikely to be infectious for syphilis.

Adult↗

PubMedDate not supplied

[Genome analysis and primer sets determination for listeria species detection and gene typing].

Computer analysis of listeria genome isolates of sequences from EMBL, GenBank, DDBJ data bases has been made. Variable and highly conservative (homology degree is 90-100% for all known isolates) genes loci iap and listeriolysin (cytolysin) gene locuses have been determined. Primer sets for detection and differentiation of Listeria species by polymerase chain reaction (PCR) were designed by computer and following thermodynamic analysis. Primer sets can provide detection of Listeria monocytogenes, L. ivanovii, L. seeligeri, L. grayi, L. innocua, L. welshimeri and detection of only pathogenic L. monocytogenes and Listeria species with listeriolysin (cytolysin) gene. Differentiation of 6 Listeria species can be done by means of two primer sets for iap and listeriolysin genes. Amplified fragments of listeria species DNA have different amplicon size. Primers melting temperatures selection allows one to carry out listeria species typing by multiplex PCR in a single tube.

Bacterial Proteins↗

PubMed2002

Haemolytic Escherichia coli isolated from dogs with diarrhea have characteristics of both uropathogenic and necrotoxigenic strains.

Twenty-four haemolytic Escherichia coli strains were isolated from dogs with diarrhea. The strains were serotyped and analysed by polymerase chain reaction (PCR) for genes encoding virulence factors associated with E. coli that cause diarrhea in animals. Adhesion antigen production was deduced from haemagglutination experiments. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) of heat extracts was also used as an indication for the production of adhesive structures. The majority of the strains was shown to produce this type of virulence factor. Adhesion and invasion tests of the strains and Caco-2 cells showed that all strains adhered and that two were invasive. The two invasive strains were positive in the intimin PCR and one of them also contained genes encoding CS31A. The PCR for heat stable toxin (ST) was positive in only four strains, as was the presence of F17 fimbrial genes. Surprisingly, 19 strains had intact P fimbrial operons, coding for an adhesin involved in urinary tract infection (UTI). The cytotoxic necrotising factor 1 (CNF1) gene, also mainly found in UTI was likewise detected in these 19 strains. Cytolethal distending toxin (Cdt) genes were found in five strains. The high number of strains positive for CNF1 and P fimbriae prompted us to test the strains in a multiplex PCR used to test E. coli isolated from UTI in various species for 30 virulence associated genes. The data showed that the majority of the diarrhea isolates have virulence factor profiles highly similar to UTI E. coli isolates from dogs. This raises the question whether these isolates are real intestinal pathogens or "innocent bystanders". However, since CNF1 producing necrotoxic E. coli (NTEC) strains isolated from humans, pigs and calves with diarrhea appear to be highly related to our strains, it might be that in dogs this type of isolate is capable of causing not only UTI, but also diarrhea. If this is the case and this type of isolate is "bifunctional", domestic animals likely constitute a reservoir of NTEC strains which can be also pathogenic for humans.

Adhesins, Bacterial↗

PubMed2006

Development of a method for the genetic identification of mussel species belonging to Mytilus, Perna, Aulacomya, and other genera.

Legislation regarding the labeling of processed products is an important issue in the protection of consumer rights. This labeling is especially important in products that cannot be identified on the basis of their morphological characters, because these are removed from the animal in the transformation process. The goal of this study was the identification of mussel species using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) and Forensically Informative Nucleotide Sequencing (FINS) methodologies. The molecular marker selected was 18S rDNA (nuclear small-subunit rDNA gene), which allows identification at the genus level and at the species level in some cases. The genera included in this study were Mytilus, Perna, Aulacomya, Semimytilus, Brachidontes, Choromytilus, and Perumytilus. Different markers were used for genetic identification at the species level. To identify the species included in the genus Perna and Choromytilus, a fragment of ITS 1 (Internal Transcribed Spacer 1) was amplified by multiplex PCR and digested with restrictases. The species of Mytilus were identified by length polymorphism and RFLP of the polyphenolic adhesive protein gene. This methodology was validated with products manufactured in the authors' pilot plant and applied to commercial samples. Therefore, this sequential method can be completely or partially used to determine the mussel genus or species present in any food product.

Animals↗

PubMed2004

Molecular characterization of multidrug-resistant Enterococcus spp. from poultry and dairy farms: detection of virulence and vancomycin resistance gene markers by PCR.

Thirty multidrug-resistant Enterococcus spp. strains, including two from the milk of cows with mastitis, nine from chicken litter and 19 from turkey litter, were isolated. Twenty-five were identified by biochemical methods as E. gallinarum and five as E. faecalis. Most of the isolates were resistant to vancomycin, gentamicin, streptomycin, tetracycline, erythromycin, bacitracin, kanamycin and nalidixic acid but sensitive to ciprofloxacin, sulfamethoxazole, chloramphenicol, ampicillin and ofloxacin. Attempts were made by partial amplification of the gene sequences to detect the vancomycin resistance markers vanA (734-bp), vanB (420-bp), vanC1 (531-bp), and vanC2-C3 (673-bp); virulence markers cylA (427-bp) and cylB (225-bp) for enterococcal cytolysin and a biofilm-forming surface protein (Esp). Individual and multiplex-PCR assays for vancomycin resistance markers revealed the vanC1 gene in 22 E. gallinarum strains. None of the remaining isolates including five E. faecalis strains (MIC=2 microg ml(-1)) and three E. gallinarum strains (MIC=8 microg ml(-1)) had any of the van genes tested. Analysis by pulsed-field gel electrophoresis (PFGE) and a comparison of smaI banding profiles showed 11 different patterns. Probing with a DIG-labeled vanC1 PCR product indicated a common 38.0 kb SmaI DNA fragment in all the E. gallinarum strains harboring the vanC1 gene. The genes cylA and cylB were detected only in one clinical E. gallinarum isolate and two quality control clinical strains of E. faecalis (ATCC 51299 and 29212). None of the virulence factors were found in milk or poultry isolates. Intermediate level resistance to vancomycin in enterococci from the US animal farms was predominantly due to the presence of vanC1 gene.

Animals↗

PubMed1999

Multiple regions of deletion on chromosome arm 13q in head-and-neck squamous-cell carcinoma.

Several lines of evidence suggest that the progression of head-and-neck squamous-cell carcinoma (HNSCC) involves inactivation of at least one and possibly several tumor-suppressor genes on the long arm of chromosome 13. The fact that neither Rb1 nor BRCA2 appears to be inactivated in the majority of head-and-neck cancers suggests that novel tumor-suppressor genes are involved. We have used microsatellite repeat polymorphisms and PCR to detect several distinct minimal regions of deletion on 13q in supraglottic and oral squamous-cell carcinomas. One region maps to 13q34, the second to 13q14.3 and a potential third region, not reported in previous studies, maps to 13q12.1. Overall, 69% of the 145 tumors examined demonstrated allelic loss at one or more loci on 13q. We investigated whether a novel suppressor candidate mapping to 13q14. 3-q21, leukemia-associated gene 1, might also be involved in the progression of squamous-cell carcinomas. Multiplexed PCR revealed homozygous deletion of leu1 in one oral cavity tumor. This suggests that this gene or one nearby may be the actual target of deletions in this region of the chromosome arm.

3-Isopropylmalate Dehydrogenase↗

PubMed1999

A new three allele polymorphism at distal 21q22.3, a region relatively devoid of polymorphic markers. Mutations in brief no. 212. Online.

We amplified 305bp of the 3'UT region of COL18A1 from 62 healthy chromosomes from Caucasian individuals. SSCP analysis of these PCR products allowed us to identify 3 alleles which were confirmed through sequencing analysis and ASO. The heterozigosity found for this polymorphic region is 74.2%, and mendelian inheritance was demonstrated in 5 two/three generation families. This polymorphism, located in a region relatively devoid of microsatellites, will be very useful for linkage analysis, particularly for narrowing down candidate regions for genes mapped in this area.

3' Untranslated Regions↗

PubMed2004

Development of a rapid genotyping method for single nucleotide polymorphisms and its application in cancer studies.

Single nucleotide polymorphisms (SNPs) in cancer-related genes can act as low risk genetic factors for the development of this disease. SNPs have also been shown to influence the efficacy and toxicity of various cytotoxic agents used in the treatment of cancer. Progress in these important areas of cancer research relies upon rapid, inexpensive and accurate means of SNP genotyping. In the present study we describe a fluorescent PCR-based method that utilizes single strand conformation polymorphism (SSCP) analysis to distinguish between different alleles. A real-time DNA fragment analysis platform and ultra-thin, re-useable gels allow short run times and hence a relatively high throughput to be achieved. A standardised procedure for the identification of optimal running conditions for each SNP is presented. We used this fluorescent-SSCP method to genotype SNPs in the MTHFR, p21, cyclin D1, MMP-2, vitamin D receptor, TNF-alpha and IL-6 genes. Multiplex PCR of two SNPs allows up to 500 genotypes per day to be evaluated with 100% accuracy. The low start-up and running costs make this method particularly well suited for SNP genotyping studies that involve up to 1,000 DNA samples.

Base Sequence↗

PubMed2002

Detection and subtyping of swine influenza H1N1, H1N2 and H3N2 viruses in clinical samples using two multiplex RT-PCR assays.

A total of 360 type A swine influenza virus-positive samples including cell culture isolates, nasal swabs or lung tissues along with 30 virus-negative samples were tested for the detection and subtyping of H1N1, H1N2 or H3N2 by two multiplex reverse transcription (RT)-PCR assays. The positive samples had been collected between 1999 and 2001 from pigs with respiratory diseases, and type A influenza virus was isolated and subtyped by hemagglutination inhibition (HI) test at the Minnesota Veterinary Diagnostic Laboratory (MVDL). Two multiplex RT-PCR assays specific for H1 and H3, and N1 and N2 were developed. RT-PCR products with unique sizes characteristic of each subtype of influenza A virus were sequenced, and the sequences were demonstrated to be specific for H1N1, H1N2 or H3N2. Genomic RNAs or DNAs from 12 common swine pathogens other than type A influenza viruses were not amplified when the PCR assays were performed with these primer sets. Positive amplification reaction could be visualized with RNA extracted from up to 10(-5) dilution of each reference virus with original infectivity titer of 10(5) TCID(50)/ml. Of the 360 samples tested, swine influenza virus H1N1, H1N2 and H3N2 were identified in 200, 13 and 139 samples, respectively. The remaining eight samples were positive for both H1N1 and H3N2 viruses. The results of multiplex RT-PCR were 100% in agreement with those of virus isolation. These results demonstrate the usefulness of multiplex RT-PCR for detection and identification of influenza A virus subtypes. The results also indicate an increased occurrence of H1N2 in US swine population.

Animals↗

PubMed2003

Relative mRNA expression of the lactate dehydrogenase A and B subunits as determined by simultaneous amplification and single strand conformation polymorphism. Relation with subunit enzyme activity.

To explore if it is correlated in human tumor cells that the expression of LDH homologous gene and LDH isoenzymes, we used RT-PCR-SSCP technique to measure the relative expression of genes with homologous sequences. The combination of PCR using common primers designed in the highly conserved regions and single-strand conformation polymorphism analysis of the products is used for quantitative determination of the proportions of LDH-A mRNA in human cancer cell lines. The proportion is compared with that of the activities of isoenzymes. The results indicated that the enzyme activity of LDH-A was consistent with mRNA levels in the human tumor cell. The present procedure using a single pair of primers for two fragments can overcome disadvantages in quantitative analysis using multiplex PCR. Template concentrations and PCR cycles did not affect the proportions of LDH-A and LDH-B in the product.

Amino Acid Sequence↗

PubMed2004

Direct detection of bacterial pathogens in brain abscesses by polymerase chain reaction amplification and sequencing of partial 16S ribosomal deoxyribonucleic acid fragments.

OBJECTIVE: To evaluate the feasibility of detecting bacterial pathogens directly from the clinical brain abscess specimens by polymerase chain reaction (PCR) amplification and sequencing of bacterial 16S ribosomal deoxyribonucleic acid (rDNA). METHODS: A total of 14 specimens were tested by both culture and PCR amplification, targeting the full-length or a partial region of 16S rDNA. 16S rDNA is known to be conserved in bacteria. Sequencing of partial-length and full-length 16S rDNA was performed. The sequence data were compared with known sequences of 16S rDNA in the National Center for Biotechnology Information GenBank by using the Basic Local Alignment Search Tool (BLAST) algorithm. The species with the best match of similarity were regarded as the pathogenic species in the samples. We also developed a Streptococcus-specific multiplex PCR analysis for identifying members of the Streptococcus species, the most common pathogen of brain abscesses. RESULTS: The 10 culture-positive specimens were all PCR-positive for partial 16S rDNA, but only seven were positive for full-length 16S rDNA amplification. Bacterial DNA was not detected in the remaining four specimens with a negative culture. Species identification by phenotypes from culture was in agreement with that by sequencing results of partial-length (or full-length) 16S rDNA. The Streptococcus-specific PCR analysis could detect Streptococcus species correctly in one step. CONCLUSION: Bacterial 16S rDNA sequences provide reliable clues to the identification of unknown pathogens. PCR analysis of 16S rDNA and sequencing may identify pathogens to the species level directly from brain abscesses. This approach is rapid and is useful especially in the identification of slow-growing and fastidious organisms.

Adolescent↗

PubMed1998

Identification of 12p as a region of frequent deletion in advanced prostate cancer.

The identification of homozygous deletions in malignant tissue has been a powerful tool for the localization of tumor suppressor genes. Representational difference analysis (RDA) uses selective hybridization and the PCR to isolate regions of chromosomal loss and has facilitated the identification of tumor suppressor genes such as BRCA2 and PTEN. Twenty RDA clones were generated by comparing genomic DNA from a prostate cancer xenograft to the same patient's normal kidney DNA. Southern blot analysis of the tester and driver and of normal and xenograft DNA, using the differential products as probes, showed the homozygous deletion in 16 of 20 RDA clones. The sequence of one of the differential products overlapped HSU59962, a genomic GenBank sequence on chromosome 12p12-13. Multiplex PCR of the xenograft DNA using polymorphic repeats mapped the deletion to a 1-5-cM region on 12p. Genomic DNA isolated from a panel of cryostat microdissected metastatic prostate adenocarcinomas/normal pairs was screened for loss of heterozygosity using the same polymorphic repeats. Loss of heterozygosity was demonstrated in 9 (47%) of 19 patients. This region may contain, or lie in close proximity to, tumor suppressor genes important in the progression and/or initiation of prostate cancer.

Adenocarcinoma↗

PubMed2004

Thirtyfold multiplex genotyping of the p53 gene using solid phase capturable dideoxynucleotides and mass spectrometry.

A mass spectrometry (MS) based multiplex genotyping method using solid phase capturable (SPC) dideoxynucleotides and single base extension (SBE), named the SPC-SBE, has been developed for mutation detection. We report here the simultaneous genotyping of 30 potential point mutation sites in exons 5, 7, and 8 of the human p53 gene in one tube using the SPC-SBE method. The 30 mutation sites, including the most frequently mutated p53 codons, were chosen to explore the high multiplexing scope of the SPC-SBE method. Thirty primers specific to each potential mutation site were designed to yield SBE products with sufficient mass differences. This was achieved by tuning the mass of some primers using modified nucleotides. Genomic DNA was amplified by multiplex PCR to produce amplicons of the three p53 exons. The 30 primers were combined with the PCR products and biotinylated dideoxynucleotides for SBE to generate 3'-biotinylated extension DNA products. These products were then captured by streptavidin-coated magnetic beads, while the unextended primers and other components in the reaction were washed away. The pure extension DNA products were subsequently released from the solid phase and analyzed with MS. We simultaneously genotyped 30 potential mutation sites in the p53 gene from Wilms' tumor, head and neck tumor, and colorectal tumor. Both homozygous and heterozygous genotypes were accurately determined with digital resolution. This is the highest level of multiplex genotyping reported thus far using MS, indicating that the approach might be applicable to screening a repertoire of genotypes in candidate genes as potential disease markers.

Base Sequence↗

PubMed1997

Comparison of primers and optimization of PCR conditions for detection of Cryptosporidium parvum and Giardia lamblia in water.

Eight pairs of published PCR primers were evaluated for the specific detection of Cryptosporidium parvum and Giardia lamblia in water. Detection sensitivities ranged from 1 to 10 oocysts or cysts for purified preparations and 5 to 50 oocysts or cysts for seeded environmental water samples. Maximum sensitivity was achieved with two successive rounds of amplification and hybridization, with oligonucleotide probes detected by chemiluminescence. Primer annealing temperatures and MgCl2 concentrations were optimized, and the specificities of the primer pairs were determined with closely related species. Some of the primers were species specific, while others were only genus specific. Multiplex PCR for the simultaneous detection of Cryptosporidium and Giardia was demonstrated with primers amplifying 256- and 163-bp products from the 18S rRNA gene of Cryptosporidium and the heat shock protein gene of Giardia, respectively. The results demonstrate the potential utility of PCR for the detection of pathogenic protozoa in water but emphasize the necessity of continued development.

Animals↗

PubMed1994

Seasonal incidence and hemoparasite infection rates of Ixodid ticks (Acari: Ixodidae) detached from cattle in Costa Rica.

To determine the tick species hindering the cattle industry in Costa Rica and to assess infection rates of ticks with three important hemoparasite species, cattle were monitored during a period of six months (October 1992-March 1993). Four farms were located in the dry pacific region of the canton of Tilarán and a fifth farm on the slopes of the Poás volcano in a cool tropical cloud-forest ecosystem. On each farm 3 to 5 animals of 6 to 24 months of age were selected at random. All ticks were removed on a monthly basis from the right half side of each animal, while the site of attachment was recorded. Ticks were counted and differentiated according to species, developmental stage and sex. Moreover, engorged female ticks were assayed for the presence of Babesia bigemina, Babesia bovis and Anaplasma marginale using the polymerase chain reaction (PCR) multiplex system. Two species of ticks, Amblyomma cajennense and Boophilus microplus, were encountered on the cattle in the Tilarán region and one species, B. microplus, was detected in the Poás region. Two to ten times as many ticks were encountered in the Tilarán region than in the Poás region, which is in accordance with a stable enzootic protozoan disease situation in the former region and an unstable epizootic situation in the latter region. Nymphal and adult stages of both tick species were present in largest numbers on the ventral parts of the animals. PCR analysis of entire ticks indicated very high infection rates with hemoparasites of veterinary importance. This was in accordance with high seroprevalence rates in the hosts.

Animals↗

PubMed2000

The use of PCR in the diagnosis of hyper-reactive malarial splenomegaly (HMS).

Between August 1997 and September 1998, 14 cases of hyper-reactive malarial splenomegaly (HMS) were diagnosed in the Instituto de Salud Carlos III in Madrid, Spain. These cases, from Equatorial Guinea and Cameroon, were identified using the diagnostic criteria established by Y. M. Fakunle in 1981: gross splenomegaly; high levels of anti-malarial antibodies; IgM in serum at least two standard deviations above the local mean; and clinical and immunological response to antimalarial treatment. Although malarial parasites were only detected in the Giemsa-stained blood films of four of the cases, these four and four others were found to have the DNA of such parasites in their blood when tested using a method based on a semi-nested, multiplex PCR. These result indicate that malarial parasitaemias may be more prevalent in HMS than is usually recognized.

Adult↗