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Validation of the multiplex kit genRESMPX-2 for forensic casework analysis.

Validation studies were carried out using the commercially available PCR multiplex system genRESMPX-2. In addition to amelogenin, this system comprises the complete set of eight STR systems which are components of the German DNA database established in 1998 by the Federal Criminal Office of Germany (BKA). The minimum amount of template DNA which gave a complete DNA pattern ranged between 100 pg and 200 pg. Mixed samples could clearly be assigned from ratios between 1:5 (ACTBP2) and 1:20 (VWA, FGA). Experimental investigations with different forensic materials, environmental studies, reproducibility and precision data as well as practical casework analysis revealed that the genRESMPX-2 kit can be regarded as a sensitive, reliable and robust multiplex system even in the case of samples containing limited amounts or degraded DNA.

Animals↗

Extended screening by PCR for seven cry-group genes from field-collected strains of Bacillus thuringiensis.

An extended multiplex PCR method was established to rapidly identify and classify Bacillus thuringiensis strains containing cry (crystal protein) genes toxic to species of Lepidoptera, Coleoptera, and Diptera. The technique enriches current strategies and simplifies the initial stages of large-scale screening of cry genes by pinpointing isolates that contain specific genes or unique combinations of interest with potential insecticidal activities, thus facilitating subsequent toxicity assays. Five pairs of universal primers were designed to probe the highly conserved sequences and classify most (34 of about 60) genes known in the following groups: 20 cry1, 3 cry2, 4 cry3, 2 cry4, 2 cry7, and 3 cry8 genes. The DNA of each positive strain was probed with a set of specific primers designed for 20 of these genes and for cry11A. Twenty-two distinct cry-type profiles were identified from 126 field-collected B. thuringiensis strains. Several of them were found to be different from all published profiles. Some of the field-collected strains, but none of the 16 standard strains, were positive for cry2Ac. Three standard and 38 field-collected strains were positive by universal primers but negative by specific primers for all five known genes of cry7 and cry8. These field-collected strains seem to contain a new gene or genes that seem promising for biological control of insects and management of resistance.

Animals↗

Molecular analysis of mutations at the HPRT and TK loci of human lymphoblastoid cells after combined treatments with 3'-azido-3'-deoxythymidine and 2',3'-dideoxyinosinedagger.

Combinations of antiretroviral drugs that include nucleoside reverse transcriptase inhibitors (NRTIs) are superior to single-agent regimens in treating or preventing HIV infection, but the potential long-term health hazards of these treatments in humans are uncertain. In earlier studies, our group found that coexposure of TK6 human lymphoblastoid cells to 3'-azido-2',3'-dideoxythymidine (AZT) and 2',3'-dideoxyinosine (ddI), the first two NRTIs approved by the FDA as antiretroviral drugs, produced multiplicative synergistic enhancement of DNA incorporation of AZT and mutagenic responses in both the HPRT and TK reporter genes, as compared with single-drug exposures (Meng Q et al. [2000a]: Proc Natl Acad Sci USA 97:12667-12671). The purpose of the current study was to characterize the mutational specificity of equimolar mixtures of 100 microM or 300 microM AZT + ddI at the HPRT and TK loci of exposed cells vs. unexposed control cells, and to compare the resulting mutational spectra data to those previously found in cells exposed to AZT alone (Sussman H et al. [1999]: Mutat Res 429:249-259; Meng Q et al. [2000b]: Toxicol Sci 54:322-329). Molecular analyses of HPRT mutant clones were performed by reverse transcription-mediated production of cDNA, PCR amplification, and cDNA sequencing to define small DNA alterations, followed by multiplex PCR amplification of genomic DNA to define the fractions of deletion events. TK mutants with complete gene deletions were distinguished by Southern blot analysis. The observed HPRT mutational categories included point mutations, microinsertions/microdeletions, splicing-error mutations, and macrodeletions including partial and complete gene deletions. The only significant difference or shift in the mutational spectra for NRTI-treated cells vs. control cells was the increase in the frequency of complete TK gene deletions following exposures (for 3 days) to 300 microM AZT-ddI (P = 0.034, chi-square test of homogeneity); however, statistical analyses comparing the observed mutant fraction values (measured mutant frequency x percent of a class of mutation) between control and NRTI-treated cells for each class of mutation showed that the occurrences of complete gene deletions of both HPRT and TK were significantly elevated over background values (0.34 x 10(-6) in HPRT and 6.0 x 10(-6) in TK) at exposure levels of 100 microM AZT-ddI (i.e., 1.94 x 10(-6) in HPRT and 18.6 x 10(-6) in TK) and 300 microM AZT-ddI (i.e., 5.6 x 10(-6) in HPRT and 34.6 x 10(-6) in TK) (P < 0.05, Mann-Whitney U-statistic). These treatment-related increases in complete gene deletions were consistent with the spectra data for AZT alone (ibid.) and with the known mode of action of AZT and ddI as DNA chain terminators. In addition, cotreatments of ddI with AZT led to substantial absolute increases in the mutant fraction of other classes of mutations, unlike cells exposed solely to AZT [e.g., the frequency of point mutations among HPRT mutants was significantly increased by 130 and 323% over the background value (4.25 x 10(-6)) in cells exposed to 100 and 300 microM AZT-ddI, respectively]. These results indicate that, at the same time that AZT-ddI potentiates therapeutic or prophylactic efficacy, the use of a second NRTI with AZT may confer a greater cancer risk, characterized by a spectrum of mutations that deviates from that produced solely by AZT.

Anti-HIV Agents↗

Presence of phospholipase-D (dly) gene coding for damselysin production is not a pre-requisite for pathogenicity in Photobacterium damselae subsp. damselae.

The presence of the phospholipase-D (dly) gene as pre-requisite for virulence of Photobacterium damselae subsp. damselae for poikilotherm and homoiotherm animals was investigated in a total of 17 strains isolated from fish, shellfish, mammals and seawater. With this aim, we developed two PCR protocols. A simple PCR using primers flanking the almost complete dly gene, and a multiplex-PCR using two sets of primers directed to internal fragments of the dly and 16S rRNA genes. Only six of the 17 Ph. damselae subsp. damselae strains studied harboured the dly gene regardless of their haemolytic activity against sheep or rabbit erythrocytes as well as their virulence for mammals and marine fish. In fact, all strains but one were pathogenic for one or both animals, with LD(50)values ranging from 1x10(3)and 3x10(5)bacteria for turbot, and 2x10(6)and 8x10(7)cells for mice. The PCR results were corroborated in dot blot hybridization experiments employing a DNA probe directed to an internal region of the dly gene. From the data obtained in this work, we can conclude that the presence of the dly gene is not an indicative of the pathogenicity of Ph. damselae subsp. damselae and, therefore, the role of damselysin as the main virulence factor of this marine bacterium for poikilotherm and homoiotherm hosts should be re-evaluated.

Animals↗

A new approach using multiplex long accurate PCR and yeast artificial chromosomes for bacterial chromosome mapping and sequencing.

An efficient approach for structural studies on bacterial chromosomes is presented. It is based on high-resolution PCR map construction by using a multiplex long accurate PCR (MLA PCR) protocol and a YAC clone carrying the region to be mapped as indicator. The high-resolution PCR map of the bacillus subtilis rrnB-dnaB region is presented as an example. Data are also presented on the use of DNA generated by LA PCR for sequencing; they are relevant to LA PCR induced mutations and justify the application of such mapping for sequencing long stretches of bacterial chromosomes.

Bacillus subtilis↗

Detection of and discrimination between gram-positive and gram-negative bacteria in intraocular samples by using nested PCR.

A nested PCR protocol has been developed for the detection of and discrimination between 14 species of gram-positive and -negative bacteria in samples of ocular fluids. First-round PCR with pan-bacterial oligonucleotide primers, based on conserved sequences of the 16S ribosomal gene, was followed by a gram-negative-organism-specific PCR, which resulted in a single 985-bp amplification product, and a multiplex PCR which resulted in two PCR products: a 1,025 bp amplicon (all bacteria) and a 355 bp amplicon (gram-positive bacteria only). All products were detected by gel electrophoresis. The sensitivity of the assay was between 10 fg and 1 pg of bacterial DNA, depending on the species tested, equivalent to between 24 and 4 live bacteria spiked in water. The identification was complete in 3.5 h. The molecular techniques were subsequently applied to four samples of intraocular fluid, (three vitreous and one aqueous) from three patients with clinical signs of bacterial endophthalmitis (test samples) and two samples of vitreous from a patient with chronic intraocular inflammation (control samples). In all culture-positive samples (two of three vitreous and one of one aqueous), a complete concordance was observed between molecular methods and culture results. PCR correctly identified the gram stain classification of the organisms. The bacterial etiology was also identified in a culture-negative patient with clinical history and signs highly suggestive of bacterial endophthalmitis. Furthermore, control samples from a patient with chronic intraocular inflammation remained PCR negative. In summary, this protocol has demonstrated potential as a rapid diagnostic test in confirming the diagnosis of infection and also determining the Gram status of bacteria with high specificity and sensitivity.

Aqueous Humor↗

Expression of cytokine mRNA in canine anal furunculosis lesions.

The pattern of expression of cytokine mRNA in the lesions of anal furunculosis was evaluated in tissue biopsies from 15 dogs, and compared with the pattern in control skin samples from 24 dogs, by reverse-transcriptase PCR using canine cytokine-specific primers and a semi-quantitative multiplex PCR assay. Interleukin-2 (IL-2) was detected in 11 of the 15 affected dogs but in only one of the controls, and interferon-gamma was detected in 14 of the affected dogs but none of the controls. In contrast, IL-4 was detected only in one of the affected dogs. Increased expression of mRNA for IL-1beta, IL-6, tumour necrosis factor alpha, IL-8, IL-10 and transforming growth factor beta1 was detected in the biopsies from the lesions of anal furunculosis relative to the control tissues (P < 0.05).

Animals↗

Identification of single base-pair mutation on uidA gene of Escherichia coli O157:H7 by Peptide Nucleic Acids (PNA) mediated PCR clamping.

Peptide Nucleic Acids (PNA) is a new type of DNA analogue with a peptide backbone. We developed a rapid identification system of Escherichia. coli O157:H7 using PNA mediated PCR clamping. Firstly, we confirmed a single nucleotide alteration in the uidA gene (T93G), which is specific to E. coli O157: H7. We designed forward mutant DNA primer, wild type PNA, and a reverse DNA primer corresponding to the uidA sequence. PCR cycle consisted of four steps including dual annealing temperatures, 57 degrees C and 45 degrees C. Among 20 E. coli strains with various serotypes and 4 neighboring strains, the amplified bands (517 bp) were detected only in E. coli O157:H7 strains. PNA has specifically inhibited the PCR amplification from a wild type uidA gene. We successfully developed a multiplex PCR system, which detects both shigatoxin (stx) and uidA genes at once, to get reliable results by easier and rapid operation. We also analyzed kinetic parameters of PNA/DNA association using surface plasmon resonance and melting temperature using fluorescence resonance energy transfer (FRET). We discussed a selection mechanism of PCR clamping from these results.

Base Pair Mismatch↗

Multiplex reverse transcriptase PCR assay for simultaneous detection of three fish viruses.

A multiplex reverse transcriptase (RT)-PCR assay was developed for the simultaneous detection of three different fish viruses: infectious pancreatic necrosis virus (IPNV), infectious hematopoietic necrosis virus (IHNV), and viral hemorrhagic septicemia virus (VHSV). The sensitivity levels of the multiplex RT-PCR assay were 100, 1, and 32 50% tissue culture infective doses/ml for IPNV, IHNV, and VHSV, respectively.

Animals↗

Combination of immunomagnetic enrichment with multiplex RT-PCR analysis for the detection of disseminated tumor cells.

BACKGROUND: A highly specific and sensitive tumor cell detection assay is reported, which combines immunomagnetic enrichment with multiplex RT-PCR analysis. MATERIALS AND METHODS: The effect on the recovery rate of breast, testicular and colorectal cancer cells using single antibodies and combinations of them for IMS was examined by fluorescence microscopy and multiplex RT-PCR. The clinical utility of a tumor cell detection assay using IMS with multiplex RT-PCR was tested by examination of colorectal cancer blood samples and by comparing the results with CEA serum protein levels. RESULTS: A combination of antibodies for IMS and multiplex RT-PCR analysis proved to be the most sensitive approach for detection of tumor cells in peripheral blood with a detection limit of two tumor cells. The examination of blood of colorectal cancer patients by using a multiplex RT-PCR assay in comparison with CEA serum protein levels indicated a distinct advantage of the former over the latter with respect to a more reliable prediction of an ongoing metastatic process. CONCLUSION: The results indicate that a combination of antibodies for immunomagnetic enrichment with multiplex RT-PCR analysis detects disseminated tumor cells with high sensitivity and specificity, thus indicating a metastatic process several months earlier compared to CEA serum protein level measurements. This assay might be valuable for prognosis in cancer.

Humans↗

Multiplex mutagenically separated PCR: diagnosis of beta-thalassemia and hemoglobin variants.

A rapid and simple method, termed multiplex mutagenically separated PCR (MS-PCR), was developed to detect several molecular defects in the hemoglobin gene in one PCR. This technique, in which different-size allele-specific primers were used, specifically amplified both normal and mutant alleles of the globin gene in the same reaction. Subsequent gel electrophoresis showed at least one of the two allelic products at the same locus or two of the several allelic products of different loci and provided a within-assay quality control for the exclusion of false-negative results. In our study, the four most common beta-thalassemia mutations, together with four other common hemoglobin variants in Chinese, were tested. Using multiplex MS-PCR 6 to 12 primers were added simultaneously into one reaction tube to identify one to four mutations. Not only is this multiplex MS-PCR method reliable and non-isotopic, the results can be obtained in less than one working day.

Alleles↗

Prognostic markers of radiographic progression in early rheumatoid arthritis.

OBJECTIVE: To identify prognostic markers that are predictive of progressive erosive disease in patients with early rheumatoid arthritis (RA). METHODS: The study involved an inception cohort of 111 consecutive patients with RA and a disease duration of <1 year. Patients were treated according to an algorithm designed to avoid overtreatment of mild disease and to accelerate treatment in patients who had continuous disease activity. Patients were evaluated for the presence of clinical and laboratory disease activity markers. We determined the frequency of CD4+,CD28(null) T cells by flow cytometry, HLA-DRB1 gene polymorphisms by polymerase chain reaction (PCR)/sequencing, and 26 single-nucleotide polymorphisms in 19 candidate genes by multiplex PCR and hybridization to an immobilized probe array. Data were analyzed using proportional odds models to identify prognostic markers predictive of erosive progression over 2 years on serial hand/wrist radiographs. RESULTS: After 2 years, disease activity in 52% of the cohort was controlled by treatment with hydroxychloroquine and nonsteroidal agents. Forty-eight percent of the patients did not develop erosions. Older age, presence of erosions at baseline, presence of rheumatoid factor, rheumatoid factor titer, and HLA-DRB1*04 alleles, particularly homozygosity for HLA-DRB1*04, were univariate predictors of radiographic progression. Promising novel markers were the frequency of CD4+,CD28(null) T cells as an immunosenescence indicator, and a polymorphism in the uteroglobin gene. CONCLUSION: Clinical disease activity in patients with early RA can frequently be controlled with nonaggressive treatment, but this is not always sufficient to prevent new erosions. Rheumatoid factor titer, HLA-DRB1 polymorphisms, age, and immunosenescence markers are predictors of poor radiographic outcome. A polymorphism in the uteroglobin gene may identify patients who have a low risk of erosive disease.

Adolescent↗

Polymerase chain reaction-based comprehensive procedure for the analysis of the mutation spectrum at the hypoxanthine-guanine phosphoribosyltransferase locus in Chinese hamster cells.

We have established a comprehensive procedure based on the polymerase chain reaction (PCR) to analyze the molecular spectrum of mutations at the hypoxanthine-guanine phosphoribosyltransferase (hprt) locus in Chinese hamster cells. The procedure includes direct sequencing of PCR-amplified hprt cDNA for locating point mutations in the expressed coding sequences, multiplex PCR amplification of the hprt exons for screening large deletions, and direct sequencing of PCR-amplified hprt exons and their flanking regions for detecting intronic mutations resulting in mRNA splicing errors. Using this procedure, we have identified different types of mutations among a representative collection of spontaneous and induced HPRT-deficient Chinese hamster cell mutants. This procedure is simple, rapid, accurate, and practical for a comprehensive study of the mutation spectrum in a large number of HPRT-deficient Chinese hamster cell mutants.

Animals↗

Identification of bacteriophage types and their carriage in Staphylococcus aureus.

Conserved genomic sequences distinctive of Staphylococcus aureus phage types 3A, 11, 77, 187 and Twort, representative of phage serogroups A, B, F, L and D, were identified and characterized. PCR primers designed for the above sequences were used for development of a multiplex PCR assay which enabled us not only to classify all phages of the International Typing Set plus 16 additional phages, but also to detect prophages in S. aureus genomes. One to four different prophages were unambiguously detected in experimentally lysogenized S. aureus strains, and substantial variation in prophage content was found in 176 S. aureus clinical strains of different provenance. In addition, by using a comparative genomics approach, all the prophages in the S. aureus genomes sequenced to date could be revealed and classified.

DNA Primers↗

Micromachined polymerase chain reaction system for multiple DNA amplification of upper respiratory tract infectious diseases.

This paper presents a micro polymerase chain reaction (PCR) chip for the DNA-based diagnosis of microorganism genes and the detection of their corresponding antibiotic-resistant genes. The micro PCR chip comprises cheap biocompatible soda-lime glass substrates with integrated thin-film platinum resistors as heating/sensing elements, and is fabricated using micro-electro-mechanical-system (MEMS) techniques in a reliable batch-fabrication process. The heating and temperature sensing elements are made of the same material and are located inside the reaction chamber in order to ensure a uniform temperature distribution. This study performs the detection of several genes associated with upper respiratory tract infection microorganisms, i.e. Streptococcus pneumoniae, Haemopilus influenze, Staphylococcu aureus, Streptococcus pyogenes, and Neisseria meningitides, together with their corresponding antibiotic-resistant genes. The lower thermal inertia of the proposed micro PCR chip relative to conventional bench-top PCR systems enables a more rapid detection operation with reduced sample and reagent consumption. The experimental data reveal that the high heating and cooling rates of the system (20 and 10 degrees C/s, respectively) permit successful DNA amplification within 15 min. The micro PCR chip is also capable of performing multiple DNA amplification, i.e. the simultaneous duplication of multiple genes under different conditions in separate reaction wells. Compared with the large-scale PCR system, it is greatly advantageous for fast diagnosis of multiple infectious diseases. Multiplex PCR amplification of two DNA segments in the same well is also feasible using the proposed micro device. The developed micro PCR chip provides a crucial tool for genetic analysis, molecular biology, infectious disease detection, and many other biomedical applications.

Electrophoresis↗

Molecular diagnosis of viral diseases, present trends and future aspects A view from the OIE Collaborating Centre for the Application of Polymerase Chain Reaction Methods for Diagnosis of Viral Diseases in Veterinary Medicine.

The emergence and re-emergence of transboundary animal diseases (TADs), e.g., foot-and-mouth disease, classical swine fever and the highly pathogenic avian influenza strongly indicate the need for the development of powerful and robust new diagnostic methods. The experiences of an OIE-Collaborating Centre and of two EU project consortia are summarised on the diagnostic application of gel-based PCR, general PCR systems, phylogeny, molecular epidemiology, real-time PCR (TaqMan, Molecular Beacons, Primer-Probe Energy Transfer), amplification without thermocycling (Invader), multiplex PCR, nucleic acid extraction and pipetting robotics, automation and quality control, including internal controls. By following the steps of OIE validation, the diagnostic assays are nationally and internationally standardised. The development of padlock probes and microarrays, as well as ultra rapid PCR and sequencing methods is further improving the arsenal of nucleic acid based molecular diagnosis. Further trends of diagnostic development are also mentioned, in order to combat TADs and other viral infections more effectively in the future.

Animals↗

Direct comparison of detection systems used for the development of single-cell genetic tests in preimplantation genetic diagnosis.

PURPOSE: Single-cell polymerase chain reaction (PCR) requires efficient amplification and accurate detection. We compare the accuracy of heteroduplex, fluorescent-fragment, and fluorescent single-strand conformation polymorphism (F-SSCP) analysis as detection systems for analysis of a PCR assay developed for preimplantation genetic diagnosis. METHODS: A single-cell, fluorescent multiplex PCR assay was developed for the cystic fibrosis delta F508 mutation and the short tandem repeat, D21S11. Detection systems were compared by analyzing blinded PCR products. RESULTS: Amplification rates for cystic fibrosis were 89% by heteroduplex and 91% by fragment analysis, while it was 72% for D21S11 by fragment analysis. No difference in allele dropout was detected for cystic fibrosis by any method (2%). Overall accuracy was high, > 97%, although SSCP was the least accurate. CONCLUSIONS: Heteroduplex and fragment analysis proved equal in the diagnosis of a single amplified locus. We determined that fragment analysis allows maximal accuracy of detection and permits analysis of a second loci, controlling for DNA contamination and allelic dropout.

Cystic Fibrosis↗

High frequency of p16INK4A gene alterations in hepatocellular carcinoma.

The tumor suppressor gene p16 (CDKN2/MTS-1/INK4A) is an important component of the cell cycle and inactivation of the gene has been found in a variety of human cancers. In order to investigate the role of p16 gene in the tumorigenesis of hepatocellular carcinoma (HCC), 48 cases of HCC were analysed for p16 alterations by: methylation-specific PCR (MSP) to determine the methylation status of the p16 promoter region; comparative multiplex PCR to detect homozygous deletion; PCR-SSCP and DNA sequencing analysis to identify mutation of the p16 gene. We found high frequency of hypermethylation of the 5' CpG island of the p16 gene in 30 of 48 cases (62.5%) of HCC tumors. Moreover, homozygous deletion at p16 region were present in five of 48 cases (10.4%); and missense mutation were detected in three of 48 cases (6.3%). The overall frequency of p16 alterations, including homozygous deletion, mutation and hypermethylation, in HCC tumors was 70.8% (34 of 48 cases). These findings suggest that: (a) the inactivation of the p16 is a frequent event in HCC; (b) the p16 gene is inactivated by multiple mechanisms including homozygous deletion, promoter hypermethylation and point mutation; (c) the most common somatic alteration of the p16 gene in HCC is de novo hypermethylation of the 5' CpG island; and (d) in contrast to other studies, high frequency of genomic alterations are not uncommon in the 9p21 of the p16 gene. Our results strongly suggest that the p16 gene plays an important role in the pathogenesis of HCC.

Carcinoma, Hepatocellular↗