Round Of Polymerase Chain Reaction Research Articles

Nested quantitative real time PCR for detection of occult tumor cells.

Quantification of tumor mRNA markers expressed by occult circulating tumor cells may be of prognostic value in a variety of neoplasms and disease stages. We therefore developed a novel real time nested polymerase chain reaction (PCR) assay to quantify rare transcripts using the light cycler system. Tyrosinase mRNA expressed by melanocytes and melanoma cells was used as a model. Ten-milliliter samples of ethylenediaminetetra-acetate (EDTA) blood from healthy volunteers were spiked with 10-10(4) RVH melanoma cells. Following RNA extraction and cDNA synthesis, a nested PCR with specific primers was performed. Resonance energy transfer between fluorescently labeled hybridization probes specific for the amplified portion of the tyrosinase transcript allowed continuous monitoring of the second round of PCR. The number of preamplification cycles in the first round was varied between 20 and 35. Our results show that nested PCR revealed quantitative data, regardless of the number of cycles used in the first round. The range of real time data can span four logs of target mRNA concentrations (1-10(3) tumor cells/ml of blood) and the x-intercepts of the log phases were always consistent with the amount of transcripts in the sample. These experiments indicate that nested PCR, which is much more sensitive than single-round PCR, is a useful tool for the quantification of rare transcripts--a result with important implications for the study of minimal residual disease. The assay is currently being adapted for other tumor types including leukemias as well as other solid tumors.

Detection of Helicobacter pylori DNA in recurrent aphthous stomatitis tissue by PCR.

Helicobacter pylori is recognised as being an aetiological agent of chronic active gastritis and peptic ulcer disease and has been associated with an increased risk of gastric cancer. The natural reservoir for H. pylori is unknown, although the oral cavity has been the focus of much attention in this respect. Given the histological similarities between gastric and oral ulceration, it seemed prudent to investigate a possible association between H. pylori and recurrent aphthous stomatitis (RAS). In this study, the potential involvement of H. pylori in the aetiology of RAS was investigated using the polymerase chain reaction (PCR). Biopsies from 28 RAS patients were analysed, in addition to 20 oral lichen planus (OLP) and 13 normal biopsies that were used as controls. Genomic DNA was extracted from biopsies, and confirmation of successful extraction of PCR-amplifiable DNA was achieved by carrying out PCR on each DNA sample with nested primers specific for the human beta-haemoglobin gene. PCR identification of H. pylori was carried out using a primer pair specific for the H. pylori 16S ribosomal RNA (rRNA) gene. Two rounds of PCR were carried out to amplify a 295-bp product, and the identity of amplified products was confirmed by DNA sequencing. H. pylori DNA was detected in 3 of 28 (11%) RAS samples but not in any of 20 OLP and 13 normal samples. These results do not support a definitive aetiological role for H. pylori in RAS, although the possibility that H. pylori may be involved in a small proportion of RAS cases cannot be excluded.

Homodimerization via a Leucine Zipper Motif Is Required for Enzymatic Activity of Quiescent Cell Proline Dipeptidase

Homodimerization via a Leucine Zipper Motif Is Required for Enzymatic Activity of Quiescent Cell Proline Dipeptidase

Fetal cells in cervical mucus and maternal blood

Research in developing effective and accurate methods for non-invasive prenatal diagnosis has focused on two main techniques: the retrieval of trophoblast cells from the cervix and the enrichment of fetal erythroblasts from the blood of pregnant women. The isolation of fetal cells by both approaches has permitted the identification of fetal aneuploidies by the use of fluorescence in-situ hybridization (FISH) with appropriate probes, as well as fetal single gene disorders by polymerase chain reaction (PCR). In the latter instance, it has been shown that in order to attain the high degree of specificity required for prenatal diagnosis, it is necessary to analyse single fetal cells isolated by micromanipulation. This practice has permitted the successful characterization of fetal rhesus status, haemoglobinopathies, Duchenné's muscular dystrophy and spinal muscular atrophy, amongst others.Further developments include investigations into whether the diagnostic potential of fetal cells retrieved by either method can be expanded by the possible culturing of such cells, as well as the possibility of performing successive rounds of FISH and PCR by the recycling of isolated fetal cells.A novel observation that our group has made is that the traffic of fetal cells is enhanced in pregnancies affected by the pregnancy related disorder, pre-eclampsia. Our subsequent investigations have shown that this elevation in fetal cell traffic may serve as an early marker for those pregnancies at risk for this disorder.A very recent exciting discovery has been that free extracellular fetal DNA can be detected in the plasma and serum of pregnant women, which may permit the rapid and accurate detection of uniquely fetal loci, such as the fetal rhesus D gene in rhesus D negative pregnant women.

JAB1 Interacts with Both the Progesterone Receptor and SRC-1

JAB1 (Jun activation domain-binding protein-1) has previously been described as a coactivator of AP1 transcription factor. We show here, by yeast and mammalian two-hybrid analyses and by pull-down experiments, that JAB1 also interacts with both the progesterone receptor (PR) and the steroid receptor coactivator 1 (SRC-1) and that it stabilizes PR-SRC-1 complexes. We also show that JAB1 potentiates the activity of a variety of transcription factors known to associate with SRC-1 (nuclear receptors, activator protein-1, and nuclear factor kappaB). This occurs without any modification of PR or SRC-1 concentration. JAB1 is a subunit of a large multiprotein complex that has been called the COP9 signalosome. The latter is present in plant and animal cells and has been shown to be involved in a variety of cellular mechanisms including transcription regulation, cell cycle control, and phosphorylation cascades. We now show that it is also involved in the mechanisms of action of nuclear receptors and of their coactivators.

Frequent T and B Cell Oligoclones in Histologically and Immunophenotypically Characterized Angioimmunoblastic Lymphadenopathy

The identification of clonal rearrangements of T cell receptor (TCR) genes is central to the diagnosis of T cell lymphomas. However, in angioimmunoblastic lymphadenopathy (AILD), first described as a nonneoplastic proliferation associated with immunodeficiency, the heterogeneity of TCR and IgH gene rearrangements suggest that some cases may harbor multiple lymphoid clones. In this study we have isolated DNA from archival paraffin biopsy material from 22 cases of AILD identified on the basis of classical histological and immunohistochemical features with the aim of establishing the occurrence of clones and oligoclones, the frequency of TCR and immunoglobulin heavy chain (IgH) variable (v) gene use, and the relationship of these findings to the presence of Epstein-Barr virus. DNA extracted from the biopsies was amplified using the polymerase chain reaction (PCR) and sequenced to detect functional and nonfunctional gene rearrangements. Epstein-Barr virus-encoded short RNA species (EBERs) were detected using in situ hybridization combined with immunochemistry to identify the phenotype of the Epstein-Barr virus-infected cells. Fifty-seven clonal products were found in 20/22 patients: TCRgamma clonal products were identified in 16/22, TCRbeta clonal products in 16/22 and IgH clonal products in 6/22 cases. Oligoclonal PCR products were seen for TCR in 3/22 and for IgH in 3/22 cases. In one biopsy PCR products from all reactions were polyclonal. Sequence analysis revealed functional TCRgamma, TCRbeta, and IgH sequences in 6/12, 9/11, and 8/8 cases, respectively. Functional TCR and/or IgH oligoclones were detected in 6/20 (30%) cases. In addition, nonfunctional TCR and IgH sequences were found in 11 cases. EBERs were identified in 18/20 cases varying from occasional to 25 to 30% nuclei staining and were associated with both T and B cells, although the majority were of indeterminate phenotype. The presence of EBERs was not associated with all clonal IgH gene rearrangements but was associated with B cell oligoclones. Patterns of gene recombinations indicated that the majority of TCRgamma recombinations used GV1 and GJ1S3/2S3 genes. Six out of eleven cases used TCR BV4S1 or BV2S1 genes associated with various BJ and BD1/2 genes. No common IgH gene usage was identified, but 8 clones had varying degrees of replacement and silent mutations (0.6-10.1%), consistent with B cell clones having undergone somatic mutation in the germinal center, and 3 clones harbored unmutated V genes, consistent with naive B cells. Our data do not support the concept of AILD as a clearly defined peripheral T cell lymphoma (PTCL). Rather, they suggest that AILD as defined by histology and immunohistochemistry is either a heterogeneous entity or represents a lymphoproliferation associated with immunodeficiency in which clonal T cell or B cell proliferation may occur.

Suppression subtractive hybridisation: application in the discovery of novel pharmacological targets.

Suppression subtractive hybridisation (SSH) is a recently developed technology designed for identifying differentially expressed genes. Total cellular RNA isolated from two sources of tissue (such as diseased versus normal) is reverse-transcribed to generate cDNA and subtracted. One critical feature of this technique is the suppression polymerase chain reaction (PCR) in combination with subtraction. To optimnise the subtraction the cDNA is digested with a restriction enzyme to generate small DNA fragments (approximately 500 nucleotides in length). Specially designed DNA adapters are ligated onto one of the cDNA pools (usually the diseased one), which is followed by two rounds of hybridisation and PCR. Since this method is PCR-based, it is sensitive and efficient to identify genes of interest. The discovery of disease-related genes is an important step for the identification of novel therapeutic targets.

Prevalence and phylogenetic characterisation of TT-virus in the blood donor population of Auckland, New Zealand.

TT-virus (TTV, patient initials: T.T.), a novel DNA virus, was first isolated in Japan in 1997 from serum of a patient with post-transfusion hepatitis of unknown aetiology. To date, the contribution of TTV to liver disease remains doubtful. The potential for transmission via blood and blood products makes it essential to establish the prevalence of TTV viraemia in the blood donor population. 413 blood donor serum samples were chosen randomly, the DNA was extracted and TTV-specific DNA amplified by nested polymerase chain reaction (PCR). TTV infection was present in 13 out of 413 (3.15%) blood donors in the Auckland region of New Zealand using a set of primers targeting open reading frame (ORF) 1. These 13 amplification products (264 bp) were sequenced and TTV genotypes determined. Alignment with published TTV sequences showed that seven (53.8%) of the thirteen positive serum samples belonged to genotype 1, five (38.5%) belonged to genotype 2 and one (7.7%) could not be classified as either genotype 1 or 2. One hundred twenty-seven blood donor serum samples were retested with a second set of primers targeting the 5' region of the TTV genome in a single round PCR. Forty-three samples were positive for TTV DNA with these primers resulting in a prevalence of 37%. The data demonstrate that TTV is present among New Zealand blood donors and support the need for further investigation into the natural history of TTV infection.

A widely applicable strategy for single cell genotyping of β‐thalassaemia mutations using DGGE analysis: application to preimplantation genetic diagnosis

Preimplantation genetic diagnosis (PGD) allows the selection of unaffected IVF embryos for transfer in couples that are at risk for transmitting genetic diseases. For monogenic diseases, polymerase chain reaction (PCR)-based diagnosis is usually performed on single blastomeres. In Greece, up to 10 per cent of the population are carriers for β-thalassaemia and related haemoglobinopathies, and more than 20 pathological mutations in the β-globin gene have been described. In this study we report a strategy which includes a first round of PCR, allowing subsequent nested PCR and DGGE analysis for at least 95 per cent of β-thalassaemia major genotypes in the Greek population. The use of DGGE for β-globin genotype analysis is advantageous: it facilitates simultaneous analysis of more than one mutation in a single PCR fragment, it detects the presence of normal alleles and monitors the occurrence of allelic drop-out (ADO) through the expectation that heterozygous samples have more than one electrophoretic band on DGGE analysis. The optimization, accuracy and reliability of the method was evaluated by genotyping 325 single blastomeres, 110 amniocytes and 55 lymphocytes. Results confirmed that PCR efficiency and occurrence of ADO are improved by higher denaturation temperatures in the first cycles of first-round PCR, influenced by the size of the fragment amplified in the first round of PCR and additionally by the quality and type of cells being genotyped. The proposed strategy was accurate and reliable, and thus for application to PGD should ensure the transfer of unaffected embryos. Furthermore it is widely applicable in most of the populations worldwide where β-thalassaemia is common. Copyright © 1999 John Wiley & Sons, Ltd.

A widely applicable strategy for single cell genotyping of β-thalassaemia mutations using DGGE analysis: application to preimplantation genetic diagnosis

Preimplantation genetic diagnosis (PGD) allows the selection of unaffected IVF embryos for transfer in couples that are at risk for transmitting genetic diseases. For monogenic diseases, polymerase chain reaction (PCR)-based diagnosis is usually performed on single blastomeres. In Greece, up to 10 per cent of the population are carriers for beta-thalassaemia and related haemoglobinopathies, and more than 20 pathological mutations in the beta-globin gene have been described. In this study we report a strategy which includes a first round of PCR, allowing subsequent nested PCR and DGGE analysis for at least 95 per cent of beta-thalassaemia major genotypes in the Greek population. The use of DGGE for beta-globin genotype analysis is advantageous: it facilitates simultaneous analysis of more than one mutation in a single PCR fragment, it detects the presence of normal alleles and monitors the occurrence of allelic drop-out (ADO) through the expectation that heterozygous samples have more than one electrophoretic band on DGGE analysis. The optimization, accuracy and reliability of the method was evaluated by genotyping 325 single blastomeres, 110 amniocytes and 55 lymphocytes. Results confirmed that PCR efficiency and occurrence of ADO are improved by higher denaturation temperatures in the first cycles of first-round PCR, influenced by the size of the fragment amplified in the first round of PCR and additionally by the quality and type of cells being genotyped. The proposed strategy was accurate and reliable, and thus for application to PGD should ensure the transfer of unaffected embryos. Furthermore it is widely applicable in most of the populations worldwide where beta-thalassaemia is common.

Variability of polymerase chain reaction detection of the bcl-2-IgH translocation in an international multicentre study

The capacity of the polymerase chain reaction (PCR) to detect very low numbers of cells bearing a t(14;18) translocation has led to its application in assessment of the results of treatment for follicular lymphoma, and suggestions that therapy might be guided by molecular studies. To test the reliability of PCR a collaborative study was undertaken to compare results from different laboratories in Europe and North America. Twenty laboratories with records of publication in molecular diagnostics were sent blood from normal donors with varying numbers of t(14;18)-bearing cells added from a cell line with a translocation in the major breakpoint region (MBR) of the bcl-2 gene. Samples contained 1000, 100, 10, 1 or 0 cells per ml of whole blood and were sent blinded in duplicate. PCR methodology varied widely, with the total number of amplification cycles between 30 and 70, and 13 different primers used for the MBR region. Twelve laboratories used nested PCR and eight single round amplification. The sensitivity of nested and single round PCR was similar at 100 cells/ml but below this the nested method proved significantly more sensitive. The false positive rate was 28%, with 11 samples from 9 laboratories reported as positive when no t(14;18) cells were added. PCR product size and sequence analysis showed that false positives were due to contamination from cell-line DNA rather than background translocations in the donors. There was no significant difference in false positive rates between nested and single round techniques. The polymerase chain reaction to detect bcl-2-IgH rearrangements is presently carried out with widely disparate results. Further effort is required to bring forward a standard PCR protocol which can be re-tested in different laboratories to improve accuracy and reproducibility. The application of quantitative techniques such as real-time PCR may resolve many of the problems presently encountered.

HLA genotyping of 5,000- and 6,000-year-old ancient bones in Japan.

We used polymerase chain reaction (PCR)-based DNA typing to identify HLA class II alleles of two individuals from ancient human remains. Genomic DNAs were isolated from two ancient human skeletons excavated from the Sanganji and Kitakogane sites in the main and northern islands of Japan, respectively. They were archaeologically estimated to be approximately 5,000 and 6,000 years old respectively, representing the remnants from the Jomon era. High molecular weight DNA was extracted by the standard proteinase K-phenol extraction method followed by purification with a Centricon-30 micro concentrator. Several rounds of PCR successfully gave rise to amplification of the HLA-DRB1 and -DQA1 genes. The PCR-restriction fragment length polymorphism (PCR-RFLP) and sequencing based typing (PCR-SBT) methods revealed that those ancient individuals possessed the DRB1 and DQA1 alleles which are highly prevalent among the modern north Asian as well as Japanese populations.

Improvement of sensitivity in HLA-DRB1 typing by semi-nested PCR-RFLP.

A sensitive method of HLA-DRB1 typing was devised using a semi-nested polymerase chain reaction (PCR) followed by a restriction fragment length polymorphism (RFLP) analysis (semi-nested PCR-RFLP method). The first-round amplification (30 cycles) of the semi-nested PCR was performed using DRB generic primer pairs and the second round of PCRs (20 cycles) were performed using DRB1 group-specific primers. The products of the second round PCRs were digested with restriction endonucleases for the typing of HLA-DRB1 alleles. By this method, HLA-DRB1 typing was possible from 10 pg of genomic DNA extracted from lymphocytes and from 0.5 microliter of 1,000 times diluted blood without DNA extraction. HLA-DRB1 alleles could be typed from a 2-mm long bloodstained cotton thread prepared from 10 times diluted blood and from a 2-mm thread of whole blood bloodstains stored at room temperature for 2 years. From the mixture of blood of two individuals with different genotypes, DRB1 alleles of the minor component were detected down to 1/1,000 of the major component. This semi-nested PCR-RFLP method is useful for HLA-DRB1 typing from extremely small amounts of DNA and from mixed samples.

Direct polymerase chain reaction for detection of hepatitis B, C and G virus genomes from serum without nucleic acid extraction—simple, rapid and highly sensitive method

Although hepatitis C virus (HCV) detection by polymerase chain reaction (PCR) assay is now the standard, extensive clinical application has been thwarted by the troublesome procedure, long reaction time and potential for contamination. To overcome these problems, we carried out a PCR assay for the detection of HCV, hepatitis G virus (HGV) and hepatitis B virus (HBV) genomes directly from serum samples without any nucleic acid extraction (direct PCR). The sensitivity of this assay was one chimpanzee-infectious dose of HCV and a 10 −1 chimpanzee-infectious dose of HBV. This result was similar to the sensitivity determined by the conventional PCR. Furthermore, when the detection rate of these genomes in serum samples from chimpanzees and humans is compared, the results matched completely between two different PCR assays. The whole process, including the reverse transcriptase reaction and second round PCR, can be completed within 6 h by the combination of the direct PCR and one-step PCR assay. Our findings indicate that this method is simple, rapid and highly sensitive and could be useful for the screening of blood-borne hepatitis virus infections using serum samples.

Subtracted, Unique-Sequence, In Situ Hybridization : Experimental and Diagnostic Applications

Nonrandom chromosomal aberrations, particularly in cancer, identify pathogenic biological pathways and, in some cases, have clinical relevance as diagnostic or prognostic markers. Fluorescence and colorimetric in situ hybridization methods facilitate identification of numerical and structural chromosome abnormalities. We report the development of robust, unique-sequence in situ hybridization probes that have several novel features: 1) they are constructed from multimegabase contigs of yeast artificial chromosome (YAC) clones; 2) they are in the form of adapter-ligated, short-fragment, DNA libraries that may be amplified by polymerase chain reaction; and 3) they have had repetitive sequences (eg, Alu and LINE elements) quantitatively removed by subtractive hybridization. These subtracted probes are labeled conveniently, and the fluorescence or colorimetric detection signals are extremely bright. Moreover, they constitute a stable resource that may be amplified through at least four rounds of polymerase chain reaction without diminishing signal intensity. We demonstrate applications of subtracted probes for the MYC and EWS oncogene regions, including 1) characterization of a novel EWS-region translocation in Ewing's sarcoma, 2) identification of chromosomal translocations in paraffin sections, and 3) identification of chromosomal translocations by conventional bright-field microscopy.

Genetic studies into inherited and sporadic hemolytic uremic syndrome

Genetic studies into inherited and sporadic hemolytic uremic syndrome

Genetic studies into inherited and sporadic hemolytic uremic syndrome

Hemolytic uremic syndrome (HUS) in adults carries a high morbidity and mortality, and its cause remains unknown despite many theories. Although familial HUS is rare, it affords a unique opportunity to elucidate underlying mechanisms that may have relevance to acquired HUS. We have undertaken a genetic linkage study based on a candidate gene approach. A common area bounded by the markers D1S212 and D1S306, a distance of 26 cM located at 1q32 segregated with the disease (Z max 3.94). We demonstrate that the gene for factor H lies within the region. Subsequent mutation analysis of the factor H gene has revealed two mutations in patients with HUS. In an individual with the sporadic/relapsing form of the disease we have found a mutation comprising a deletion, subsequent frame shift and premature stop codon leading to half normal levels of serum factor H. In one of the three families there is a point mutation in exon 20 causing an arginine to glycine change, which is likely to alter structure and hence function of the factor H protein. Factor H is a major plasma protein that plays a critical regulatory role in the alternative pathway of complement activation. In light of these findings and previous reports of HUS in patients with factor H deficiency, we postulate that abnormalities of factor H may be involved in the etiology of HUS.

Search for Mycobacterium paratuberculosis DNA in orofacial granulomatosis and oral Crohn’s disease tissue by polymerase chain reaction

Background—Although intestinal Crohn’s disease has long been suspected to have a mycobacterial cause, possible mycobacterial involvement in orofacial granulomatosis (OFG) and oral lesions of Crohn’s disease has not yet been...

Comprehensive method for the typing of HLA-A, B, and C alleles by direct sequencing of PCR products obtained from genomic DNA.

Molecular testing is gradually replacing standard typing techniques in the field of HLA because it allows higher resolution, which has significant functional implications. Although several techniques have been so far described for this purpose, the definitive means to determine which alleles are present in a particular sample is to identify their sequence. We describe a simplified method for typing HLA-A, B, and C alleles by direct sequencing of polymerase chain reaction (PCR) products amplified from genomic DNA that could allow large-scale handling of samples for clinical use. The template is the product of a nested PCR. A first round of PCR amplifications from genomic DNA is performed with three different sets of primers, one pair specific for each locus. The PCR products encompass exons 2 and 3, the regions of interest to determine the allele present. These fragments are a mixture of both alleles present in one locus. In a second round of PCRs using the first fragment as template, exons 2 and 3 are separately amplified and simultaneously tailed with sequences corresponding to fluorescent-labeled commercial primers. The sense and antisense sequence of each exon is obtained and compared with a database of all known HLA-A, B, or C alleles. Heterozygous positions are determined and the most probable alleles assigned. This simplified procedure has the practical advantage of allowing high-resolution typing of clinical material by utilizing the same genomic DNA used for standard molecular typing of HLA class I.

Different pattern of interleukin-1β-(IL-1β), interleukin-1 receptor antagonist- (IL-1ra) and interleukin-1 receptor type I- (IL-1R tI) mRNA-expression in single preimplantation mouse embryos at various developmental stages

The interleukin-1 (IL-1) system has been shown to play an important role in human and murine embryo implantation. Recent studies have documented immunohistochemical evidence of interleukin-1β (IL-1β), interleukin-1 receptor antagonist (IL-1ra) and interleukin-1 receptor type I (IL-1R tI) in human preimplantation embryos and protein levels of interleukin-1α (IL-1α), IL-1β and IL1ra in human preimplantation embryo culture fluid have been correlated with successful implantation and pregnancy. Our aim in this study was to detect IL-1β, IL-1ra and IL-1R tI mRNA in single preimplantation mouse embryos and to describe the frequency of positive mRNA-expression at different developmental stages. B6C3F1-mice, 12 weeks old were pregnant mare serum gonadotropin (PMSG)/human chorionic gonadotropin (hCG)-stimulated and mated. Animals were sacrificed at day 0.5, and zygotes were flushed from the tubes and cultured in HAMs-F10 medium. 2-cell- (2C-), 8-cell- (8C-), morula- (M-), early blastocyst- (EB-) and hatching blastocyst- (HB-) stage embryos were examined by one round of reverse transcriptase (RT) followed by two rounds of polymerase chain reaction (PCR) carried out on individual mouse embryos for β-actin (internal standard), IL-1β, IL-1ra and IL-1R tI-mRNAs. The frequencies of positive mRNA-expressions were as follows (2C/8C/M/EB/HB); β-actin: 91/96/100/100/98%; IL-1b: 0/0/2.5/6.25/19; IL-1ra; 0/5/30/41/74% and IL-1R tI: 0/0/10/20/25%. The incidence of IL-1ra mRNA expression increased with developmental stage. IL-1ra mRNA seems to be expressed in a very high percentage (74%) of embryos near the time of implantation, whereas the percentage of IL-1β-mRNA positive embryos is surprisingly low (19%).