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PubMed1999

Culture shock. Molecular methods for diagnosis of infectious diseases.

Nucleic acid detection methods, such as polymerase chain reaction (PCR), can often detect specific microbial pathogens, virulence markers and antimicrobial resistance genes more rapidly and with greater sensitivity and specificity than culture and conventional identification and susceptibility testing. Multiplex PCR can detect multiple genes in a single assay; this capability will be greatly extended by new techniques such as the DNA chip. However, limitations and pitfalls of nucleic detection methods remain.

DNA Primers↗

PubMed2003

[Real-time fluorescent PCR for screening AZFc/DAZ microdeletions on the Y chromosome in male infertility patients].

OBJECTIVE: To develop a real-time fluorescent PCR protocol suitable for the routine screening of AZFc/DAZ microdeletions on the Y chromosome in azoospermic and oligozoospermic male infertility patients. METHODS: A set of real-time fluorescent PCR was established. Eighty-seven azoospermic and ligozoospermic patients undergoing ICSI in the IVF center and 30 azoospermic men undergoing testicular biopsy in the clinic of urology surgery were screened for AZFc/DAZ microdeletions of Y chromosome. RESULTS: Eleven cases (9.4%) of AZFc/DAZ microdeletions were found in 117 cases of azoospermic and oligozoospermic patients by screening of realtime fluorescent PCR. Four cases (6.6%) were found in 61 oligozoospermic patients, and 7 cases (12.5%) were found in 56 azoospermic patients. CONCLUSION: The real-time fluorescent PCR protocol presented in this study is an easy and reliable method for detection of AZFc/DAZ microdeletions on the Y chromosome, which yields identical results to those of the multiplex PCR.

Chromosome Deletion↗

PubMed2001

Mutational analysis of N-ras, p53, p16INK4a, p14ARF and CDK4 genes in primary human malignant mesotheliomas.

Nineteen specimens from primary human malignant mesotheliomas obtained from 19 patients were screened for activating point mutations in the oncogenes N-ras and CDK4 by combined RFLP-PCR/SSCP analysis. In addition, all tumours were screened for deletions and point mutations in the tumour suppressor genes p53, p16INK4a (CDKN2A) and p14ARF (exon-1beta) by combined multiplex-PCR/SSCP analysis. No mutations were found in N-ras, p53 and CDK4. Three tumours displayed homozygous deletion (co-deletion of exons 1, 2 and 3) of p16INK4a. One of them displayed additional homozygous deletion of p14ARF (exon-1beta). Two silent point mutations and 2 polymorphisms were found in p16INK4a in 3 tumours. Our preliminary data indicate that disarrangement of the Rb1 pathway may be involved in mesothelioma formation.

Adult↗

PubMed2001

[Muscular dystrophies detected by immunophenotyping and genotype analysis (mRNA and DNA)].

Complex diagnosis of muscular dystrophies including clinical, bioptical and molecular genetic approaches has been provided in a limited extent in this country. Our group of neurologists, pathologists and geneticists has examined approximately 240 patients suspected of having muscular dystrophies, mostly coming from Southern and Northern Moravia. The patients were sent to the examination most often from departments of neurology and clinical genetics, and less frequently from departments of internal medicine. According to the final diagnosis, the patients were divided into groups: with dystrophinopathies and carriers of dystrophinopathies (DMD/BMD), merosin deficient form of congenital muscular dystrophy, and Emery-Dreifuss muscular dystrophy including the carriers of this disease. Some relatives of patients with dystrophinopathies were also examined using the methods of segregation analysis. High proportion of the DMD/BMD patients can be detected by the methods of molecular genetics. Analysis of mRNA using RT PCR and PTT enables the detection of deletions, duplications, and point mutations in dystrophin gene and encompasses a larger diagnostic scope in comparison with examinations of DNA level by the multiplex PCR method from the peripheral blood which enables only deletion detections. Immunophenotyping of the dystrophin protein plays an important role especially using antibodies against carboxyterminal (DYS2) and rod domain (DYS1) of dystrophin. Deficient sarcolemmal expression of DYS2 and DYS1 reveals unambiguously a pathological dystrophin. On the other hand, less pronounced deficiencies in dystrophin expression in BMD patients and DMD/BMD carriers may not always be detected in muscle biopsies. In this case, it is necessary to supplement the examination by Western blotting and genotype analysis. The examination of patients with clinically diagnosed muscular dystrophy should start with a muscle biopsy which enables the estimation of presence and degree of structural changes. Application of antibodies against the components of DGC and emerin may reveal a deficiency in expression of these proteins. Immunohistochemical examination completed by Western blotting leads to the subsequent molecular genetic analysis of DNA or mRNA. Secondary deficiencies in expression of other DGC proteins are often revealed in muscle biopsies of dystrophinopathies and this fact must be taken into account in the evaluation of immunohistochemical findings. There is a possibility of replacement of invasive muscle biopsy by skin biopsy or buccal mucosal smears in cases of merosin and emerin deficiencies. Commercially available antibodies against merosin, emerin, calpain and sarcoglycans enable extensive identification and detailed classification of muscular dystrophies. Screening of the patients based on the application of methods described and discussed in this report is the task of the forthcoming period.

Adolescent↗

PubMed2004

[Polymorphism and multiplex amplification of 3 X-chromosome specific short tandem repeat loci].

OBJECTIVE: To devise a multiplex PCR system of three X-chromosome specific short tandem repeat (X-STR) loci and study the genetic polymorphism. METHODS: DXS6799, DXS6804 and DXS6854 were amplified simultaneously using a multiplex system and were typed by polyacrylamide gel electrophoresis and silver staining. RESULTS: A total of 262 male and 255 female individuals from Guangdong Han population were tested; each locus showed 7 alleles. 73 haplotypes were detected in the male individuals. The haplotype diversity reached 0.9674. CONCLUSION: The 3 X-STR multiplex system is relatively abundant in polymorphic information for forensic identification and paternity testing.

Chromosome Mapping↗

PubMed2000

Full-length single-gene cDNA libraries: applications in splice variant analysis.

Alternative splicing of pre-mRNA may generate many distinct proteins from a single gene: regulation of alternative exon selection constitutes control of molecular structure downstream of transcription. Identifying natural splice variants among hundreds or thousands of theoretical alternatives, and examining the regulation of exon selection at multiple sites, may require screening many full-length cDNAs. We describe methods for preparing full-length cDNA libraries comprising the splice variants from single genes. The methods employ robust long distance reverse transcription, gene-specific second strand synthesis, long PCR, and cloning: with these methods cDNAs coding full-length open reading frames were prepared for 21 ion channels (1.2-15 kb). Exon combinations in isolated clones are determined by multiplex PCR. Approximately 85% of the clones contain full-length inserts. Screening can detect even rare variants (0.1%) in linear proportion to their abundance in initial mRNA pools. Tissue-specific expression patterns are reproducible. We describe methods for quantifying and minimizing artifactual exon recombination by template switching. These methods can be used to generate thousands of full-length clones of even large transcripts (>8 kb) for the systematic identification of splice variants and the analysis of regulation of alternative exon selection.

Alternative Splicing↗

PubMed2003

Further evidence for sexual reproduction in Rhynchosporium secalis based on distribution and frequency of mating-type alleles.

Rhynchosporium secalis, the causal agent of scald on barley, is thought to be exclusively asexual because no teleomorph has been found. Partial sequences of the HMG-box and alpha-domain of Rhynchosporium secalis isolates were identified and used to develop a PCR assay for the mating-type locus. PCR amplification of only one of these two domains was possible in each strain, suggesting that R. secalis has a MAT organization that is similar to other known heterothallic fungi. A multiplex PCR with primers amplifying either a MAT1-1- or MAT1-2-specific amplicon was used to determine the distribution of mating types in several R. secalis populations. In total, 1101 isolates from Australia, Switzerland, Ethiopia, Scandinavia, California, and South Africa were included in the analysis. Mating types occurred in equal frequencies for most of these populations, suggesting frequency-dependent selection consistent with sexual reproduction. In addition, both mating types were frequently found occupying the same lesion or leaf, providing opportunities for isolates of opposite mating type to interact and reproduce sexually. We propose that R. secalis should be considered a sexual pathogen, although the sexual cycle may occur infrequently in some populations.

Ascomycota↗

PubMed1998

PTEN/MMAC1 is infrequently mutated in pT2 and pT3 carcinomas of the prostate.

Deletion of the q23-24 region of human chromosome 10 is one of the most frequent genetic alterations in prostate cancer, suggesting that inactivation of a tumor suppressor gene in this region is involved in the development or progression of this carcinoma. A candidate gene, PTEN/MMAC1, has been identified from this chromosomal region; mutations of this gene have been found in various advanced tumors and cell lines including those of prostate cancer. To further define the role of PTEN/MMAC1 in the development of prostate cancer and its spectrum of genetic alterations, we analysed 40 pT2 or pT3 prostate tumors for allelic loss, mutations, and homozygous deletions using PCR-based methods. Six tumors showed loss of heterozygosity for one of the ten markers analysed, while one tumor showed loss of two markers. None of the markers within PTEN/MMAC1 was lost. Direct sequencing of PCR amplified exons and intron/exon junctions of all 40 tumors revealed three sequence variants, one of which was a point mutation in exon 9, while the other two were polymorphisms. Using multiplex PCR, no homozygous deletions were detected in any of the neoplasms. Our results showing a low frequency of alterations of PTEN/MMAC1 in pT2 and pT3 prostate cancers suggest that this gene plays an insignificant role in the development of most low stage carcinomas of the prostate.

Adult↗

PubMed2003

[Development of a PCR (polymerase chain reaction) specific for complex Anopheles nili (Theobald) 1904 species in Cameroon ].

The objective of this study was to develop new molecular tools for the identification of members of An. nili group, a malaria vector in Africa. Our strategy was based on the sequence analysis of portions of the rDNA. The ITS2 fragment of An. nili collected in Cameroon was sequenced and compared. The analysis of these sequences has revealed a great variability of ITS2 sequence. Three molecular forms: An. nili typical form, An. nili Oveng form and An. carnevalei were observed within the six morphological types. Specific primers were selected on ITS2 sequence to develop an allele-specific PCR giving 3 size bands. 169 specimens of An. nili collected in Cameroon were successfully tested. This method has been validated on specimens collected in others localities of tropical Africa. The multiplex PCR developed was very sensitive practical and applicable on large scale.

Alleles↗

PubMed2003

Molecular and serological characterization of group a rotavirus isolates obtained from hospitalized children in Goiânia, Brazil, 1998-2000.

Fecal samples positive for rotavirus group A ( n=120) were analyzed by enzyme immunoassay-monoclonal antibody (EIA-MAb) serotyping and/or reverse transcription/multiplex polymerase chain reaction (PCR) amplification to determine the prevalence of the [P] and G genotypes. The most prevalent G genotype/serotype detected was G1 (76.7%), followed by G2 (5.0%). Six samples were characterized as G9 by multiplex PCR, and one sample was characterized as G3 by EIA-MAb. The combinations of [P] and G genotypes found were P[8] and G1 (20.8%), P[6] and G1 (10.8%), P[6] and G9 (4.2%), P[8] and G2 (1.7%), and P[6] and G2 (0.8%). The diversity of rotavirus group A [P] and G genotypes/serotypes reinforces the need for continuous characterization of rotaviruses circulating in populations in Brazil.

Brazil↗

PubMed2003

Applicability of a rapid duplex real-time PCR assay for speciation of Campylobacter jejuni and Campylobacter coli directly from culture plates.

A rapid duplex real-time polymerase chain reaction (PCR) assay for speciation of Campylobacter jejuni and Campylobacter coli using the ABI Prism 7700 sequence detection system (Applied Biosystems) was developed based on two of the genes used in a conventional multiplex PCR. A rapid turnaround time of 3 h was achieved with the use of boiled cell lysates. Applicability of the assay was tested with 6015 random campylobacter strains referred to the Campylobacter Reference Unit, with 97.6% being identified as either C. jejuni or C. coli by this technique. Rapidity, combined with specificity and sensitivity, makes this method for routine campylobacter speciation attractive to any laboratory with a Taqman system.

Campylobacter coli↗

PubMed1992

Two-step polymerase chain reactions and restriction endonuclease analyses detect and differentiate ompA DNA of Chlamydia spp.

Specific and sensitive amplification of major outer membrane protein (MOMP) gene (ompA) DNA sequences of Chlamydia species with various MOMP genotypes was achieved by a two-step polymerase chain reaction (PCR). Degenerate, inosine-containing oligonucleotide primers homologous to the 5' and 3' ends of the translated regions of all chlamydial MOMP genes were used in a PCR to amplify a DNA fragment of approximately 1,120 bp. A portion of this DNA fragment was amplified in a second genus-specific reaction that yielded a DNA fragment of approximately 930 bp. A pair of degenerate oligonucleotide primers homologous to internal sequences of the primary DNA fragment was used in this PCR. This method detected three cognate chlamydial genomes in a background of 1 microgram of unrelated DNA. MOMP genes of 13 representative chlamydial MOMP genotypes of the species C. trachomatis, C. pneumoniae, and C. psittaci were amplified. In a secondary PCR, group-specific detection was achieved by the simultaneous use of one genus-specific primer and three primers derived from different fingerprint regions of three major groups of chlamydiae. This multiplex PCR differentiated the groups by the length of the amplified DNA fragments and detected the simultaneous presence of DNA sequences of the Chlamydia spp. with different MOMP genotypes. Further differentiation as ompA restriction fragment length polymorphism types among all chlamydial strains with the various MOMP genotypes analyzed here was achieved by restriction endonuclease analysis of the secondary PCR products. DNA sequences corresponding to the ompA restriction fragment length polymorphism type B577 of C. psittaci were detected in two of seven milk samples from cases of bovine mastitis.

Animals↗

PubMed1999

Detection and species determination of malaria parasites by PCR: comparison with microscopy and with ParaSight-F and ICT malaria Pf tests in a clinical environment.

A rapid procedure for the diagnosis of malaria infections directly from dried blood spots by PCR amplification was evaluated with samples from 52 patients. Plasmodium infections were identified with a genus-specific primer set, and species differentiation between Plasmodium falciparum and Plasmodium vivax was analyzed by multiplex PCR. The PCR test with any of the three primer sets was able to detect as few as four parasites per microliter by gel electrophoresis or by nonisotopic paper hybridization chromatography. The diagnoses obtained by PCR correlated closely with those obtained by Giemsa staining except for two samples observed to have mixed P. falciparum-P. vivax infections. These were initially missed by microscopic analysis. In comparison with antigen-capture assays for P. falciparum, the PCR assays were able to detect three infections that were missed by the ParaSight-F test. The PCR test was negative for nine ParaSight-F-positive samples and one ICT Malaria Pf-positive sample, and these were confirmed to be false-positive results. The PCR thus gave no false-negative or false-positive results. Patients undergoing antimalarial therapy were also monitored by the PCR assay. Four of seven patients who were PCR positive for P. vivax at the time of discharge were later readmitted to the hospital with a recurrence of P. vivax infection. We would like to propose that PCR is a sensitive and easy method that can serve as a useful addition to microscopy for the diagnosis and the clinical monitoring of treatment of malaria.

Animals↗

PubMed2005

Use of a three-dimensional microarray system for detection of levofloxacin resistance and the mec A gene in Staphylococcus aureus.

We evaluated a novel three-dimensional microarray (Pam Chip microarray) system to detect the presence of levofloxacin-related resistance mutations and the mec A gene. The results were compared to those obtained for 27 Staphylococcus aureus isolates by conventional DNA sequencing or PCR methods. Hybridization and fluorescence detection were performed using an FD 10 system designed for Pam Chip microarray under conditions optimized for each target/probe on the array. In dilution series analysis using multiplex PCR samples, the sensitivity of the microarray was about 10 times greater than that of conventional PCR methods. A high level of data reproducibility was also confirmed in those analyses. Various point mutations in quinolone resistance-determining regions detected by our system corresponded perfectly to the results obtained by conventional DNA sequencing. The results of the mec A gene detection using our system also corresponded to the PCR method; that is, signal/band was detected in all isolates of methicillin-resistant S. aureus, and no signal/band was detected in any isolate of methicillin-susceptible S. aureus. In conclusion, our novel three-dimensional microarray system provided rapid, specific, easy, and reproducible results for the simultaneous detection of levofloxacin resistance and the mec A gene in S. aureus.

Anti-Bacterial Agents↗

PubMed1998

Rapid diagnosis and identification of cross-over sites in patients with glucocorticoid remediable aldosteronism.

Glucocorticoid remediable aldosteronism (GRA) is an autosomal dominant cause of primary aldosteronism and high blood pressure resulting from a chimeric 11beta-hydroxylase/aldosterone synthase gene. Abnormal expression of aldosterone synthase causes primary aldosteronism, which can be inhibited by glucocorticoids. Diagnosis of GRA has depended on the identification of a restriction enzyme product in genomic DNA of affected individuals. Recently, a two-tube long PCR method was described that allowed diagnosis of GRA in a kindred in Australia. A similar long PCR method confirmed the diagnosis of GRA in members of five northeastern Scotland families previously identified by Southern blotting and detected affected members of five GRA families previously identified in Glasgow. A multiplex PCR protocol is described here that allows the control aldosterone synthase amplification and chimeric gene amplification to be carried out in the same tube. We describe the regions of cross-over in each of 10 kindreds identified in Scotland. To identify cross-over regions in each of the kindreds, the chimeric long PCR product was cloned and sequenced. Five cross-over sites were identified ranging from intron 2 to exon 4, indicating the reliability of the method in identifying chimeric genes resulting from different sites of cross-over.

Base Sequence↗

PubMed1999

Maine Caucasian population DNA database using twelve short tandem repeat loci.

A population study of Caucasians residing in Maine was conducted using the AmpF1STR Profiler PCR Amplification Kit and the AmpF1STR Profiler Plus PCR Amplification Kit (Applied Biosystems Division (ABD) of Perkin Elmer, Foster City, CA). The kits contain the reagents necessary to amplify 12 different STR loci and the gender marker Amelogenin using two multiplex PCR, each containing nine STR loci. Thus, there is an overlap of six STR loci. The 12 STR loci are TH01, TPOX, CSF1PO, D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, and D7S820. These loci represent 12 of the 13 core loci selected by the CODIS STR standardization project. Dye-labeled amplification products were separated and detected using the capillary electrophoresis instrument ABI Prism 310 Genetic Analyzer. Allele frequencies were determined for the 12 STR loci. Statistical analysis of the data included Hardy-Weinburg equilibrium (HWE) analysis, pairwise independence testing, power of discrimination (PD), and probability of exclusion (PE).

DNA↗

PubMed1999

The locus for enterocyte effacement (LEE) of enteropathogenic Escherichia coli (EPEC) from dogs and cats.

Enteropathogenic Escherichia coli (EPEC) produce attaching and effacing lesions. The genes responsible for this lesion are clustered on the chromosome forming a 35.5 kilobase pathogenesis island called LEE. The LEE was identified, characterized and completely sequenced from the human EPEC strain E2348/69. The LEE carries genes coding for: a type III secretion system (genes esc and sep), the translocated intimin receptor (gene tir), the outer membrane protein intimin (gene eae) and the E. coli secreted proteins EspA, EspB, and EspD (genes esp). In addition to man and farm animals, EPEC are also isolated from dogs and cats. We studied structurally and functionally the LEE of dog and cat EPEC. First, we used four probes scattered along the LEE to identify the presence of a LEE in canine and feline EPEC isolates. Second, by PCR, we checked the presence of genes homologous to eae, sep, esp, and tir genes in these strains. Third, since the four types of eae and tir genes were described, we developed a multiplex PCR in order to determine the type of eae and tir genes present in each strain. Fourth, we determined by PCR the site of the LEE insertion on the chromosome. Fifth, we tested several of the canine EPEC in their capacity to induce attaching and effacing lesions in the rabbit intestinal loop assay. We can conclude from this study: first, that the a LEE-like structure is present in all tested strains and that it contains genes homologous to esp, sep, tir, and eae genes; second, that there is some preferential associations between the type of eae gene and the type of tir gene present in a strain; third, that the majority of the tested strains contained a LEE located elsewhere on the chromosome in comparison to the human EPEC strain E2348/69; and fourth that dog EPEC were able to induce attaching and effacing lesions in rabbit ileal loop assay.

Adhesins, Bacterial↗

PubMed2003

Idiopathic thrombocytopenic purpura: better therapeutic responses of patients with B- or T-cell clonality than patients without clonality.

Results of recent studies of the pathogenesis of idiopathic thrombocytopenic purpura (ITP) have suggested activated helper T-cells drive B-lymphocytes to produce antibodies. Twenty-eight children and 85 adults with ITP entered this study. We performed polymerase chain reaction (PCR) using framework III variable region (V(H) FRIII)- and joining region (J(H))-specific primers to analyze immunoglobulin heavy-chain gene rearrangement (IgH GR) for B-cell clonality. We used multiplex PCR to analyze T-cell receptor (TCR) gamma-chain gene rearrangement (TCRgamma GR) for T-cell clonality. We diagnosed 10 cases as acute ITP and 97 cases as chronic ITP. The IgH GR result was positive in 77.8% of the acute-form cases and in 58.8% of the chronic-form cases. The TCRgamma GR result was positive in 11.1% of the acute cases and in 10.6% of the chronic cases. There was no difference in frequency of clonality between the acute and chronic forms. After treatment the platelet count normalized in 81.8% (36/44) of the chronic ITP cases with B-cell clonality and in 88.9% (8/9) of the chronic ITP cases with T-cell clonality, compared with a normalized platelet count in 46.2% (12/26) of the chronic ITP cases without clonality. The patients with T- or B-cell clonality appeared to have better therapeutic responses than patients without clonality. In conclusion, T- and B-cell clonality may play a positive role in determining therapeutic response.

Adolescent↗