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Results for “Nested Genes”

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PubMed1999

Molecular detection of EWS-FLI1 chimeric transcripts in Ewing family tumors by nested reverse transcription-polymerase chain reaction: application to archival paraffin-embedded tumor tissues.

Chromosomal translocations generating unique chimeric genes are highly characteristic of specific sarcomas, and their use as diagnostic markers has been suggested. From a diagnostic pathologic point of view, detection of such cytogenetic or molecular aberrations applicable to routinely processed archival tissue specimens is considered a powerful tool for tumor diagnosis. To assess the feasibility and reliability of the molecular detection of the transcript originating from the chimeric gene in paraffin-embedded tumor specimens, we performed a nested reverse transcription-polymerase chain reaction (RT-PCR)-based assay to detect the EWS-FLI1 chimeric message in a series of Ewing family tumors. Of 24 paraffin-embedded tumor specimens from 23 cases analyzed, the chimeric message was detectable in 20 (83%) specimens from 20 cases (87%) by this nested RT-PCR assay, whereas none of 7 small round cell tumors not from this family (3 alveolar rhabdomyosarcomas, 2 neuroblastomas, 2 malignant lymphomas) showed detectable chimeric messages. In the sequence analysis of the PCR products, the amplified chimeric messages contained the junctions between exon 7 of the EWS gene and any one of exons 5, 6 and 8 of the FLI1 gene. The detection process was usually completed within 3 days, except for the subseqent sequence analysis. Our results endorse the use of this molecular assay as an ancillary technique in the diagnosis of Ewing family tumors using paraffin-embedded material.

Adolescent↗

PubMed2004

Influence of petroleum contamination and biostimulation treatment on the diversity of Pseudomonas spp. in soil microcosms as evaluated by 16S rRNA based-PCR and DGGE.

AIMS: The aim of this study was to apply a group specific PCR system followed by denaturing gradient gel electrophoresis (DGGE) analysis to evaluate the effect of oil contamination and the biostimulation process on the diversity of Pseudomonas populations in soil ecosystems. METHODS AND RESULTS: Direct DNA extraction from biostimulated- and oil-contaminated soil samples was performed. Primers specific for the genus Pseudomonas spp. were used to amplify 16S rRNA genes and then a semi-nested PCR reaction was applied to obtain smaller fragments for comparing the PCR products by DGGE. Whether in bulk, oil-contaminated or biostimulated soils, the DGGE profiles revealed little change in Pseudomonas community throughout the 270 days of experiment. The presence of a few additional bands observed only in treated samples indicated that a bacterial shift occurred with the addition of nutrients and with oil contamination. CONCLUSIONS, SIGNIFICANCE AND IMPACT OF THE STUDY: The combination of semi-nested PCR and DGGE was found to be a rapid and sensitive technique to study the diversity within the genus Pseudomonas and may be suitable for further studies concerning the role of this bacterial group in large-scale oil-contaminated areas.

Ammonium Sulfate↗

PubMed2001

Rapid detection of human fecal Eubacterium species and related genera by nested PCR method.

PCR procedures based on 16S rDNA gene sequence specific for seven Eubacterium spp. and Eggerthella lenta that predominate in the human intestinal tract were developed, and used for direct detection of these species in seven human feces samples. Three species of Eggerthella lenta, Eubacterium rectale, and Eubacterium eligens were detected from seven fecal samples. Eubacterium biforme was detected from six samples. It was reported that E. rectale, E. eligens, and E. biforme were difficult to detect by traditional culture method, but the nested PCR method is available for the detection of these species. This result shows that the nested PCR method utilizing a universal primer pair, followed by amplification with species-specific primers, would allow rapid detection of Eubacterium species in human feces.

Bacteriological Techniques↗

PubMed1999

Human endogenous retrovirus with a high genomic sequence homology with IDDMK(1,2)22 is not specific for Type I (insulin-dependent) diabetic patients but ubiquitous.

AIMS/HYPOTHESIS: It has been reported recently that a novel human endogenous retroviral gene, insulin-dependent diabetes mellitus (IDDM)K(1,2)22, was expressed in the plasma of Type I diabetic patients but not in that of nondiabetic control subjects. This investigation was initiated to determine the specificity of the selective expression of IDDMK(1,2)22 in diabetic patients. METHODS: We isolated the total RNA from the plasma and lymphocytes of 13 new onset Type I diabetic patients and 10 normal control subjects and amplified it by reverse transcriptase polymerase chain reaction. We then determined the presence of IDDMK(1,2)22 with a specific primer set, U3/R-poly(A), used in a recent report and the 5 'SAg/3 'SAg primer set recognizing the putative superantigen encoding the region of the IDDMK(1,2)22 envelope (env) gene. In addition, we carried out nested PCR of the U3/R-poly(A) polymerase chain reaction product using U3N/R primers. RESULTS: We found no difference in the presence of the polymerase chain reaction products between diabetic patients and all nondiabetic subjects tested. Sequencing of the U3/R-poly(A) polymerase chain reaction products showed that the exact sequence of IDDMK(1,2)22 was not present in any of the samples tested, neither in the plasma of diabetic patients nor in that of nondiabetic control subjects. Endogenous retroviral sequences with 90-93% sequence homology to IDDMK(1,2)22 were, however, equally present in both the diabetic and nondiabetic subjects. CONCLUSION/INTERPRETATION: We conclude that a human endogenous retroviral gene with high sequence homology with IDDMK(1,2)22 is not specific for diabetic patients but, rather, is ubiquitous.

Base Sequence↗

PubMed1996

Failure to detect human T-lymphotropic virus type-I proviral DNA in cell lines and tissues from patients with cutaneous T-cell lymphoma.

Previous molecular studies investigating the presence of HTLV-I proviral DNA in cell lines and tissue samples of patients with cutaneous T-cell lymphoma (CTCL) have reported a detection rate ranging from 0-92%. Despite the lack of epidemiologic data linking HTLV-I infection with CTCL, the molecular data still invite speculation regarding the precise role of HTLV-I in the pathogenesis of CTCL. To determine the detection rate of HTLV-I proviral DNA among CTCL patients referred to our medical center, we analyzed Epstein-Barr virus-transformed cell lines established from peripheral blood of seven CTCL patients and 43 tissue samples from 22 patients with different stages of disease. Genomic DNA was polymerase chain reaction-amplified with primers within the HTLV-I tax gene region. Amplification products were probed with nested oligonucleotide probes by Southern blot analysis. No HTLV-I proviral sequences were detected in the samples (0/50). Using HTLV-I/II pol primers, no HTLV-I pol gene sequences were detected. In tissues from one patient, HTLV-II pol and tax gene sequences were detected; however, HTLV-II proviral integration was not detected by Southern blot analysis of the genomic DNA. Our data suggest: (i) HTLV-I does not appear to be a primary etiologic agent in CTCL; and (ii) HTLV-II pol and tax gene sequences can be detected in a minority of CTCL patients, but this does not necessarily imply an etiologic role.

Base Sequence↗

PubMed1992

Use of the polymerase chain reaction to detect Toxoplasma gondii in human blood samples.

AIMS: To assess the value of detecting Toxoplasma gondii in human blood samples using the polymerase chain reaction (PCR). METHODS: Blood samples in lithium heparin were examined from 34 patients with suspected toxoplasmosis, and six healthy volunteers with or without the addition of doubling dilutions of toxoplasma tachyzoites. Products of a nested PCR, using oligonucleotide primers of the B1 gene, were analysed by electrophoresis and stained by ethidium bromide. The primary product was 194 base pairs in length; the nested products were 160 or 97 base pairs. RESULTS: When toxoplasma tachyzoites were added to the leucocytes of six different volunteers, eight to 16 parasites were detected by nested PCR in one experiment and one to four parasites in eight experiments. All nine experiments were negative in samples without added tachyzoites. Of 34 patients, PCR was negative in 13 with recent lymphadenopathy; nine with persisting IgM, including two pregnant patients; four with reactivated infection due to immunodeficiency; and five with no evidence of active infection. Positive PCR results were found in three patients with reactivated infection. There was only one discrepancy between PCR and animal culture results; this was in an immunocompromised patient with a positive PCR and negative culture. CONCLUSIONS: The PCR technique was rapid, sensitive, and specific in human blood samples. Negative PCR results in patients with persisting IgM suggested that the fetus was not at risk, or that treatment was not indicated in myalgic encephalomyelitis-like illness. PCR results in immunocompromised patients permitted appropriate management--no treatment if negative, treatment if positive.

Animals↗

PubMed2007

Identification and characterization of a biomineralization related gene PFMG1 highly expressed in the mantle of Pinctada fucata.

To elucidate the mechanism of nacre biomineralization, the mantle of Pinctada fucata (P. fucata) from the South China Sea was used. Using the mantle cDNA library and the ESTs we have cloned through suppression subtractive hybridization (SSH), ten novel genes including PFMG1 were obtained through nested PCR. Bioinformative results showed that PFMG1 had a high homology (40%) with Onchocerca volvulus calcium-binding protein CBP-1 and had two EF-hand calcium-binding domains from the 81st to the 93rd amino acid and from the 98th to the 133rd amino acid in the deduced amino acid sequence. The results of multitissue RT-PCR and in situ hybridization demonstrated the high expression of PFMG1 in the mantle of P. fucata and confirmed the SSH method. The results of GST-PFMG1 on CaCO3 crystallization showed significant effects on nucleation and precipitation of CaCO3. PFMG1 was cloned into the pcDNA.3.1/myc-HisA vector and was subsequently transfected into MC3T3-E1 cells. RT-PCR revealed upregulation of the marker genes related to cell growth, differentiation, and mineralization, and BMP-2, osterix, and osteopontin were upregulated as a result. This research work suggests that PFMG1 plays an important role in the nacre biomineralization, and the SSH method can pave the way for the bulk cloning and characterization of new genes involved in biomineralization in P. fucata and may accelerate research on the mechanism of pearl formation.

Amino Acid Sequence↗

PubMed1998

PCR sequencing of the spike genes of geographically and chronologically distinct human coronaviruses 229E.

A reverse transcription nested PCR (RT-PCR) sequencing methodology was developed and used to generate sequence data from the spike genes of three geographically and chronologically distinct human coronaviruses 229E. These three coronaviruses were isolated originally from the USA in the 1960s (human coronavirus 229E strain ATCC VR-74), the UK in the 1990s (human coronavirus 229E LRI 281) and Ghana (human coronavirus 229E A162). Upon translation and alignment with the published spike protein sequence of human coronavirus 229E 'LP' (isolated in the UK in the 1970s), it was found that variation within the translated protein sequences was rather limited. In particular, minimal variation was observed between the translated spike protein sequence of human coronaviruses 229E LP and ATCC VR-74 (1/1012 amino acid differences), whilst most variation was observed between the translated spike protein sequence of human coronaviruses 229E LP and A162 (47/1012 amino acid changes). Further, the translated spike protein sequence of human coronavirus 229E A162 showed three clusters of amino acid changes, situated within the 5' half of the translated spike protein sequence.

Adult↗

PubMed2004

Real-time PCR for Chlamydia pneumoniae utilizing the Roche Lightcycler and a 16S rRNA gene target.

Chlamydia pneumoniae (CPN) causes pneumonia in humans, and has emerged as an important respiratory pathogen. There are also established links between CPN infection and coronary artery disease. Traditional culture methods for CPN detection can be time consuming and difficult. There are a variety of molecular-based amplification methods for CPN detection. These methods are more sensitive than culture, but have the disadvantage of being inconsistent and non-comparable across studies. In this paper, we describe the adaptation of the existing primer set CPN 90/CPN91 for use in a real-time PCR assay using the Roche Lightcycler and a Taqman probe. This assay had an analytical sensitivity of between 4 and 0.4 infection-forming units (IFUs)/PCR reaction. A total of 355 samples were tested for validation of the assay. Tested samples included two standardized panels of blinded samples from culture (N = 70), archived specimens consisting of a CPN dilution series, CPN-spiked porcine aortal tissue and endarterectomy specimens (N = 87). The third group consisted of prospectively collected PBMCs from clinical samples (N = 198). Results were compared to nested PCR, which targets the ompA gene of CPN; TETR PCR, which targets the 16S rRNA gene of CPN; or the known result for the sample. Overall, the assay had a sensitivity of 88.5% (69 of 78) and a specificity of 99.3% (275 of 277). This method should prove useful for accurate, high throughput detection of CPN.

Animals↗

PubMed1997

Preimplantation diagnosis of single gene disorders by two-step oocyte genetic analysis using first and second polar body.

Previous work on preimplantation genetic diagnosis (PGD) of single gene disorders by the first polar body (IPB) analysis has demonstrated that the genotype of a considerable number of embryos resulting from heterozygous oocytes cannot be predicted without testing their second PB (IIPB). To overcome this limitation we introduce a two-step DNA analysis of oocytes using both IPB and IIPB to identify hemizygous mutation-free oocytes following the second meiotic division. In the application of the approach to PGD of cystic fibrosis (CF) Delta F-508 mutation, sickle cell disease, and hemophilia B, 80 oocytes were studied by both PBs, resulting in the identification and transfer of 32 homozygous normal embryos. A follow-up genotyping of 52 embryos, resulting from oocytes tested by both IPB and IIPB demonstrated the accuracy of the predicted genotypes. In addition to a nested PCR analysis of the mutant genes in PBs and resulting embryos, simultaneous amplification of different polymorphic markers was performed, demonstrating the reliability of the two-step polar body analysis of oocytes.

Alleles↗

PubMed2000

[Analysis of TCR-gamma gene rearrangement in single H/R-S cells of Hodgkin disease].

OBJECTIVE: To detect the rearrangement of T cell receptor gamma chain gene in single H/R-S cell as an indication of early T lymphocyte differentiation. METHODS: CD30 positive H/R-S cells were isolated with micromanipulator from the frozen sections and analyzed by single-cell PCR. TCR-gamma chain gene rearrangement was detected through semi-nested PCR. In the first round of PCR, a pair of TCR-gamma primers which amplify the segments between Vgamma and Jgamma region (including the N region) of TCR-gamma gene mixing with a pair of beta-globin primers were used. In the second round, only the products positive beta-globin were amplified with the primers for TCR-gamma gene. RESULTS: A 268 bp beta-globin gene specific product was obtained in 24 out of 56 H/R-S cells from 6 cases of Hodgkin's disease. After the first round of PCR, no rearrangement of the TCR-gamma gene was noticed at a single cell level. CONCLUSION: H/R-S cells from the selected cases were not derived from the T-cell lineage but possibly from the B-cell lineage.

Adolescent↗

PubMed1996

Oncogene-related serum proteins and cancer risk: a nested case-control study.

Proto-oncogenes are genes coding for factors involved in cellular growth, reproduction, and differentiation. Cancer results through mutations of proto-oncogenes or through other mechanisms involving the products of proto-oncogenes. This study asks whether serum proteins immunologically related to the products of proto-oncogenes distinguish older men and women who manifest a new cancer during a 2-year follow-up. The authors conducted a nested case-control study that involved 248 men and women selected from a larger group of older (age > or = 65 years) healthy volunteers in a randomized clinical trial of preventive clinical services. Study subjects included 37 with a fatal cancer, 59 non-fatal breast, prostate, colon, or lung cancer, 58 hospitalized with at least one discharge diagnosis that coded to benign neoplasia (International Classification of Diseases, 9th Revision codes 210-239), and 94 randomly selected controls. Using seven monoclonal antibodies prepared against ras, erb-B, FES, myb, and SIS polypeptide sequences, immunoblots detected 17 proteins in serum collected from subjects before the clinical recognition of cancer. Five oncogene-related serum proteins appeared to distinguish older persons who manifested fatal (but not non-fatal) cancer over a brief (2-year) follow-up. Older persons hospitalized with benign neoplasia also had higher levels of these serum proteins. Relative to the 94 control subjects, a 52,000 dalton SIS-related protein (odd ratio (OR) = 5.9, 95% confidence interval (CI) 1.4-24.9) and a 35,000 dalton k-ras-related protein (OR = 11.3, 95% CI 1.2-104) were particularly common in serum from the 37 subjects who manifested a fatal cancer.

Aged↗

PubMed2003

The vitamin K-dependent gamma-glutamyl carboxylase gene contains a TATA-less promoter with a novel upstream regulatory element.

The expression of the vitamin K-dependent gamma-glutamyl carboxylase gene in liver is developmentally regulated. Since the gene product catalyzes an essential post-translational modification of the vitamin K-dependent blood coagulation proteins, the regulation of carboxylase expression is critical for hemostasis. We analyzed the activity of the rat carboxylase gene 5'-regulatory DNA sequences in rat hepatoma cell lines at different states of differentiation. These studies demonstrated that the 2.6-kb 5'-flanking sequence has differentiation-dependent transcriptional activity. Transient gene expression assays, examining the effects of nested deletions and site-directed mutagenesis of putative regulatory sequences, together with electrophoretic mobility shift assays (EMSAs) were used to identify sequences critical for the developmentally regulated transcription of the rat carboxylase gene. We identified a DNA sequence (-76 to -65; GTTCCGGCCTTC) not known to bind to transcription factors, yet which functions as an upstream promoter element. In vivo genomic DNA footprinting confirms the presence of nuclear protein-DNA interactions at this site in the endogenous carboxylase gene in differentiated hepatoma cells. Therefore, this DNA sequence has specific nuclear protein-binding activity and functional properties consistent with a regulatory element that plays a critical role in the developmental expression of the carboxylase gene, and hence the regulation of vitamin K-dependent blood coagulation protein synthesis.

Animals↗

PubMed2004

Phylogeography of surface and cave Astyanax (Teleostei) from Central and North America based on cytochrome b sequence data.

Astyanax fasciatus has become a model organism for the study of regressive and adaptive evolution in cave animals. To fully understand these processes, it is important to have background information on the systematics and phylogeography of surface and cave populations of this species. Here we investigate the phylogeography of A. fasciatus in North and Central America and also the historical biogeography of this region. Phylogenetic analysis of part of the mtDNA cytochrome b gene from 26 surface and nine cave A. fasciatus populations revealed seven major clades, which, in principle, represent geographical patterns of distribution. However, the four strongly eye and pigment reduced cave populations, Piedras, Sabinos, Tinaja, and Curva, form a separate cluster, which is not sister group to the surface populations from the same locality. Similarly the Belizean populations do not cluster with their geographic neighbors from the Yucatan. The analyses indicate that there have been recurrent invasions of surface Astyanax from the south, that were most likely influenced by major climate changes during the Pleistocene. During this period, ancestors of the strongly eye and pigment reduced cave populations were able to survive underground as thermophilic relics when the surface populations became extinct. The high level of genetic divergence among the different clades shows that differing haplotype lineages must have reinvaded the surface waters from the south and/or back-colonized them from residual habitats and also penetrated into the caves. Nested clade analyses show that recurrent gene flow as well as historic processes like past fragmentation and range expansion have influenced current populations of A. fasciatus in Central and North America. Different haplotype clades of the phylogeny are not compatible with the present taxonomy of Astyanax and, therefore, we propose the application of a single systematic unit, called A. fasciatus.

Animals↗

PubMed1991

A nested PCR followed by magnetic separation of amplified fragments for detection of Escherichia coli Shiga-like toxin genes.

The Shiga-like toxin (SLT) I and II genes in cytotoxic Escherichia coli strains were detected using a polymerase chain reaction (PCR) procedure. Identification and differentiation of SLT I and II was carried out using primers giving PCR-generated DNA fragments of different size for the two cytotoxins. A two-step PCR procedure utilizing three primers in a nested configuration for both SLT I and II was combined with magnetic separation to identify the toxin genes in a rapid, specific and sensitive test system designated DIANA (Detection of Immobilized Amplified Nucleic Acid). The first PCR was carried out using standard methods, and the product generated was used as primer in the second PCR. In this procedure one of the primers from the first PCR was used with biotin label, and the second (inner) primer was 32P-labelled. The double-stranded DNA fragments generated containing the two primers, were biotinylated on one 5' end and 32P-labelled on the other 5' end. These fragments were separated from the solution using streptavidin-coated super-paramagnetic microscopic beads. The test could detect and differentiate between SLT I and II in a positive/negative ratio of more than 20. The assay could detect five SLT-positive E. coli organisms in the 5 microliters test sample. The presence of 100-fold more SLT-negative strains in a sample did not adversely affect the test signal.

Bacterial Toxins↗

PubMed1999

Detection of porcine epidemic diarrhea virus using polymerase chain reaction and comparison of the nucleocapsid protein genes among strains of the virus.

Two pairs of PCR primers were designed to perform nested PCR targetting of a 540 bp fragment of the nucleocapsid (N) protein gene (N gene) of porcine epidemic diarrhea virus (PEDV). The N gene of PEDV was amplified with 4 PEDV strains and 11 small intestines of PEDV-infected piglets collected from 2 farms in Kagoshima prefecture, Japan. Nucleotide sequences of the PCR products from a Korean and two Japanese strains (KKN96-1 and S1) of PEDV isolated in 1993 and 1996, respectively, were almost identical. These results suggest that the PCR is an available tool for detection of PEDV from pigs in the field, and that the two Japanese strains (KKN96-1 and S1) were genetically similar to the Korean strain.

Animals↗

PubMed1996

Multiple interspecies transmissions of human and simian T-cell leukemia/lymphoma virus type I sequences.

Using two sets of nucleotide sequences of the human and simian T-cell leukemia/lymphoma virus type I (HTLV-I/STLV-I), one consisting of 522 bp of the env gene from 70 viral strains and the other a 140-bp segment from the pol gene of 52 viral strains, I estimated cladograms based on a statistical parsimony procedure that was developed specifically to estimate within-species gene trees. An extension of a nesting procedure is offered for sequence data that forms nested clades used in hypothesis testing. The nested clades were used to test three hypotheses relating to transmission of HTLV/STLV sequences: (1) Have cross-species transmissions occurred and, if so, how many? (2) In what direction have they occurred? (3) What are the geographic relationships of these transmission events? The analyses support a range of 11-16 cross-species transmissions throughout the history of these sequences. Additionally, outgroup weights were assigned to haplotypes using arguments from coalescence theory to infer directionality of transmission events. Conclusions on geographic origins of transmission events and particular viral strains are inconclusive due to small samples and inadequate sampling design. Finally, this approach is compared directly to results obtained from a traditional maximum parsimony approach and found to be superior at establishing relationships and identifying instances of transmission.

Animals↗

PubMed2003

Comparison of a new quantitative ompA-based real-Time PCR TaqMan assay for detection of Chlamydia pneumoniae DNA in respiratory specimens with four conventional PCR assays.

Chlamydia pneumoniae, an important respiratory pathogen, is difficult to culture, and detection rates by conventional PCRs vary considerably. A new quantitative ompA-based real-time PCR assay based on TaqMan technology for detection of C. pneumoniae in respiratory samples is described, and its performance in terms of sensitivity and reproducibility is compared with those of four published conventional PCRs (one single-step PCR targeting a cloned PstI fragment; two nested PCRs, one targeting the 16S rRNA gene followed by hybridization and the other targeting the ompA gene; and a touchdown enzyme time-release [TETR] PCR also targeting the 16S rRNA gene). Both ompA-based PCRs showed the best analytical sensitivity. All five assays could detect even lower target levels from spiked sputum, with the 16S rRNA assays performing better than the ompA-based nested PCR (10(-6) inclusion-forming units [IFU] were detected in four of four and two of four replicates by the 16S rRNA TETR PCR and the 16S rRNA nested PCR, respectively). In general, the ompA-based real-time protocol produced the most consistent positive results for all replicates tested down to 10(-6) IFU. Eight of 45 patient sputum specimens (18%) were C. pneumoniae DNA positive in at least one of four replicates tested by at least one assay. Without taking into consideration the analytical sensitivity or the reproducibility of the test results, the numbers of C. pneumoniae DNA-positive sputum specimens (n = 8) were four, three, two, two, and one for the 16S rRNA TETR assay, the PstI-based single-step PCR, the ompA-based real-time PCR, the ompA-based nested touchdown PCR, and the 16S rRNA-based nested PCR, respectively. However, the overall rate of concordance of positive results was low. Only one cell culture-positive sputum specimen was positive by four of five assays (14 of 16 replicates; mean cycle threshold value, 25; 10(8) particles/ml of sputum). Thirty-seven specimens were C. pneumoniae negative by all five assays for all replicates tested, as were all negative controls (n = 65 to 100 per testing panel). No PCR inhibitors were detected by real-time PCR or by the 16S rRNA-based nested assay. We confirm that the analytical sensitivity of an assay for the detection of C. pneumoniae does not necessarily predict its ability to detect its target in sputum. A quantitative, fast, and easy-to-handle diagnostic approach such as the ompA-based real-time TaqMan PCR described here might improve the detection of C. pneumoniae in respiratory samples.

Adult↗