Polymerase Chain Reaction And Single-strand Conformation Polymorphism Research Articles

Ovine KRTAP36-2: A New Keratin-Associated Protein Gene Related to Variation in Wool Yield.

Keratin-associated proteins (KAPs) are structural components of wool fibres. High-glycine/tyrosine (HGT)-KAPs are a subset of the KAP family, and their abundance in fibres varies. In this study, we report the discovery of an ovine HGT-KAP gene to which we assigned the name KRTAP36-2. Polymerase chain reaction and single-strand conformation polymorphism (PCR-SSCP) analyses revealed four variants of this gene in a screening population of 170 sheep from a variety of breeds. The DNA sequencing of the variants revealed four single-nucleotide polymorphisms (SNPs) and a dinucleotide deletion. Three of these SNPs were in the coding region, and one of these was non-synonymous and potentially led to the amino acid substitution p.Cys27Gly near the middle of the protein. The remaining SNP was located near the putative TATA box, and the di-nucleotide deletion was near the putative transcription initiation site. The effect of this variation in KRTAP36-2 was investigated in 274 Southdown × Merino lambs that were the progeny of five sires. Variation was only found to be associated with wool yield, that is, the proportion of the greasy fleece that remained as clean fleece upon scouring (expressed as a percentage). This may have some value in increasing wool production.

Identification of growth hormone gene variation in exon region at Indonesian Local Cattle based on PCR-SSCP method

Rahmatullah SN, Jakaria, Noor RR. 2016. Identification of growth hormone gene variation in exon region at Indonesian Local Cattle based on PCR-SSCP method. Biodiversitas 17: 492-497. The aim of this study was to identify the polymorphisms of the growth hormone gene (GH) of Indonesian local cattle as well as two exotic cattle, as the outside group, using polymerase chain reaction and single strand conformation polymorphism (PCR-SSCP) and using five primers DNA to identify polymorphism of GH gene. Twenty DNA samples of each Indonesian local cattle, consists of Bali, Pesisir, Madura and Katingan, and ten DNA samples of Simmental and Limousine cattle were used. The results showed that the polymorphism of the GH gene was found in three exons which are exon 1, 2 and 5 for Indonesian local cattle except for the Bali and Madura cattle that showed polymorphism was only at exon 2. Bali and Madura cattle also showed monomorphism in exon 3 and 4. On the other hand, the exotic breed showed the polymorphism in all exons, except for exon 2 in Simmental cattle which was found to be monomorphic.

Prognostic Impact of Nucleophosmin 1 (NPM1) Gene Mutations in Egyptian Acute Myeloid Leukemia Patients

Objective: Somatic mutations of the nucleophosmin gene (NPM1), which alter the subcellular localization of the product, are the most frequent mutations in patients with acute myeloid leukemia. The aim of the study was to assess the prevalence and prognostic impact of NPM1 gene mutations in adult AML patients.Materials and Methods: Polymerase chain reaction and single-strand conformation polymorphism (PCR-SSCP) were used to screen 55 AML patients for mutations of NPM1 gene.Results: NPM1 mutations were found in 12 (21.8%) of 55 patients, significantly associated with higher total leukocytie count, marrow blast percentage (p=0.03 and p=0.02, respectively), and M5 subtype (p<0.001). Patients with NPM1 mutations had significantly higher complete remission rates (p=0.003) and a trend to lower rates of mortality, relapse and refractory disease (p=0.28, p=0.45 and p=0.08, respectively). Survival analysis showed significantly longer disease-free survival (mean 18.635±1.229 versus 11.041±1.250 months, p=0.044) and overall survival (mean 19.810±1.624 versus 12.063±1.244 months, p=0.041) in patients with NPM1 mutations compared with those without. Multivariate analyses confirmed NPM1 mutation as a significant independent predictor for disease-free survival (HR=0.066, p=0.001) and overall survival (HR=0.125, p=0.002).Conclusion: NPM1 mutation is a prognostic factor for a favorable outcome in Egyptian population. This finding is of major clinical importance since it strongly suggests that NPM1 mutations may allow one to divide the heterogeneous patient group of AML into prognostically different subgroups.Conflict of interest:None declared.

PCR-SSCP-based reconstruction of the original fungal flora of heat-processed meat products

Food processing of spoiled meat is prohibited by law, since it is a deception and does not comply with food safety aspects. In general, spoilage of meat is mostly caused by bacteria. However, a high contamination level of fungi could be also found in some meat or meat products with certain preserving conditions. In case that unhygienic meat is used to produce heat processed products, the microorganisms will be deactivated by heat, so that they cannot be detected by a standard cultivation method. Therefore, this study aimed to develop and apply a molecular biological method—polymerase chain reaction and single strand conformation polymorphism (PCR-SSCP)—to reconstruct the original fungal flora of heat processed meat. Twenty primer pairs were tested for their specificity for fungal DNA. Since none of them fully complied with all study criteria (such as high specificity and sensitivity for fungal DNA; suitability of the products for PCR-SSCP) in the matrix “meat”, we designed a new reverse primer, ITS5.8R. The primer pair ITS1/ITS5.8R amplified DNA from all tested fungal species, but not DNA from meat-producing animals or from ingredients of plant origin (spices). For the final test, 32 DNA bands in acrylamide gel from 15 meat products and 1 soy sauce were sequenced—all originating from fungal species, which were, in other studies, reported to contaminate meat e.g. Alternaria alternata, Aureobasidium pullulans, Candida rugosa, C. tropicalis, C. zeylanoides, Eurotium amstelodami and Pichia membranifaciens, and/or spices such as Botrytis aclada, Guignardia mangiferae, Itersonilia perplexans, Lasiodiplodia theobromae, Lewia infectoria, Neofusicoccum parvum and Pleospora herbarum. This confirms the suitability of PCR-SSCP to specifically detect fungal DNA in heat processed meat products, and thus provides an overview of fungal species contaminating raw material such as meat and spices.

Detection of Clonal Rearrangement of the T-cell Receptor Gamma Gene by Polymerase Chain Reaction and Single-strand Conformation Polymorphism (PCR-SSCP).

Background: Diagnosis of T-lymphoid neoplasms frequently requires molecular studies of T-cell receptor (TCR) gene rearrangements. The Southern blot technique traditionally used for these analyses lacks the sensitivity and speed necessary for the routine clinical laboratory. The authors have developed a method using polymerase chain reaction (PCR) amplification with single-strand conformation polymorphism (SSCP) analysis that is rapid, sensitive, and semiautomated. Methods and Results: Polymerase chain reaction of the TCR gamma gene is done with consensus primers to the V and J regions. Amplicons thus include the N region, which serves as a marker of clonal T-cell population. Clonal populations having identical N-region sequences are identified by SSCP analysis, using a semiautomated electrophoresis system with silver staining for gel visualization. A series of 46 DNA samples from normal controls and various hematopoietic malignancies was comparatively analyzed by both Southern blot of the TCR beta locus and PCR-SSCP of the of the TCR gamma gene. The PCR-SSCP technique was rapid and reproducible, and detected clonal T-cell populations constituting 1% of the cell sample: The PCR-SSCP technique detected clones in eight cases that were negative by Southern blot. Conclusions: PCR-SSCP analysis of the TCR gamma gene is a rapid and sensitive method for the detection of clonal T-cell populations.

Types of human papillomavirus revealed in cervical adenocarcinomas after DNA sequencing

In a collection of 173 cervical adenocarcinomas, the prevalence of HPV in relation to the age of women and the distribution of the various oncogenic types of HPV were evaluated. The tumour material was analysed by PCR of the HPV L1 gene followed by direct DNA sequencing and/or the polymerase chain reaction and single-strand conformation polymorphism (PCR-SSCP) technique for the identification and typing of HPV. In 68% (117/173) of the adenocarcinomas, HPV was present. A significant correlation was observed between the prevalence of HPV and age: in women younger than 40 years, HPV was present in 88%, whereas in women 60 years and older, it was found in only 39% (p<0.001). Among the HPV-positive tumours, type 18 predominated (52%) followed by type 16 (35%) and type 45 (7.7%) while other oncogenic types of HPV (31 and 59) were rarely found. HPV 16 was relatively more frequent in older women but this observation was not significant (p=0.06). HPV-typing by PCR and direct DNA sequence analysis is more specific than analysis by PCR-SSCP, especially among the less frequently occurring types of HPV. Our results further show that the prevalence of HPV in women with cervical adenocarcinomas is age-related and that the most frequently occurring types of HPV are 18, followed by 16 and 45. We have concluded that the oncogenic role of HPV in cervical squamous carcinomas and adenocarcinomas is, in some respects, discrepant.

Changes in hypervariable region 1 in patients with chronic hepatitis C of genotype 1b with biochemical response to interferon

Background/aims: The outcome of interferon (IFN) therapy of hepatitis C virus (HCV) infection can be classified as a complete viral response (CR), biochemical response (BR), or no response (NR). Why alanine aminotransferase (ALT) activity decreases in patients with BR despite viral persistence is unknown. Methods: Of 158 patients infected with HCV genotype 1b, all 20 patients with BR and 20 of the 114 patients with NR, matched for viral load to the BR group, were studied. We sequenced nucleotides in the hypervariable region (HVR) of serum HCV RNA, and analyzed quasispecies of this region by the polymerase chain reaction and single-strand conformation polymorphism (PCR-SSCP). Results: In HVR 1, SSCP patterns differed after therapy; the major clone before therapy disappeared with therapy in eight of the 20 BR patients, but in none of the 20 NR patients ( P=0.0033; Fisher's exact test). PCR products of HVR 1 from six patients were cloned before and after therapy, and 40 clones from each patient were sequenced each time. Results of cloning and sequencing were generally consistent with those of SSCP. For the six patients, a major clone could be identified both before and after therapy. In two patients with BR, there were many changes in the amino acid sequence of the major clone after IFN; in one patient with NR, mutations were not found. Conclusion: Changes in the major viral clone with IFN treatment may be related to the decrease in ALT activity in some patients, in spite of the continued presence of HCV RNA.

Restricted T-cell receptor β-chain usage by T cells autoreactive to β2–glycoprotein I in patients with antiphospholipid syndrome

We recently identified CD4(+) T cells that are autoreactive to beta(2)-glycoprotein I (beta(2)GPI) and that promote antiphospholipid antibody production in patients with antiphospholipid syndrome (APS). In this study, T-cell receptor (TCR) beta chains of beta(2)GPI-reactive T cells were examined in 8 beta(2)GPI-responders, including 5 patients with APS and 3 healthy subjects, using polymerase chain reaction and single-strand conformation polymorphism (PCR-SSCP) analysis combined with in vitro stimulation of peripheral blood T cells with recombinant beta(2)GPI. The TCR Vbeta segments that expanded oligoclonally after stimulation with beta(2)GPI varied among responders, but the Vbeta7 and Vbeta8 segments were commonly detected in 6 and 4 beta(2)GPI-responders, respectively. Analysis of the complementarity-determining region 3 sequence of beta(2)GPI-reactive T cells revealed limited diversity, and all Vbeta7(+) TCRs had an amino acid motif of TGxxN/Q or minor variations. The Vbeta8(+) TCRs had another motif, PxAxxD/E. Surprisingly, an identical Vbeta7(+) TCRbeta chain was used by beta(2)GPI-reactive T cells in 3 patients with APS. There was no apparent difference in the TCRbeta usage between APS patients and healthy responders. Some of the Vbeta7(+) TCRs with the TGxxN/Q motif detected by PCR-SSCP analysis were also used by beta(2)GPI-specific CD4(+) T-cell clones responsive to an immunodominant epitope containing the major phospholipid-binding site. Depletion of Vbeta7(+) or Vbeta8(+) T cells from the peripheral blood mononuclear cell cultures significantly inhibited in vitro anti-beta(2)GPI antibody production in response to beta(2)GPI. Our results indicate preferential usage of TCRbeta chains by beta(2)GPI-reactive T cells. These TCRbeta chains can be reasonable targets for TCR-based immunotherapy for patients with APS.

Single-strand conformation polymorphism analysis of the glucose transporter gene GLUT1 in maturity-onset diabetes of the young.

Maturity-onset diabetes of the young (MODY), an autosomal dominant, early-onset form of type-2 diabetes, is caused by mutations in five different genes all leading to defect(s) in the pancreatic beta cell. However, some patients with this form of diabetes do not bear a mutation in any of the known (MODY1-MODY5) loci, a notion prompting the search for new MODY genes. Clinical and genetic data point toward a defect in beta cell function in the majority of patients with MODY, and partners of the glucose-sensing device are reasonable functional candidates. The high-capacity glucose transporter GLUT2 has the ideal kinetic features for performing this task. However, complete GLUT2 deficiency in humans leads to hepato-renal glycogenosis (Fanconi-Bickel syndrome), and heterozygous GLUT2 mutations apparently behave in a recessive manner. Furthermore, in the human beta cell GLUT1 mRNA is predominant when compared to GLUT2 and glucose influx appears to be largely mediated by this low-Km transporter. Thus, we looked for the presence of sequence variants by polymerase chain reaction and single-strand conformation polymorphism (PCR-SSCP) within the GLUT1 gene in 90 Italian pedigrees negative at the search for mutations in glucokinase (MODY2) and hepatocyte nuclear factor-1alpha (MODY3), the two genes responsible for about 60% of MODY cases in Italian children. We found three already described silent mutations and a new single base deletion in position -173 of the 5' regulatory region. The -173de1A variant, which was detected in the heterozygous or homozygous state in 30.8% of MODY patients examined and is located in a Nuclear Factor Y binding sequence, is not associated with hyperglycemia in affected relatives of MODY probands. In conclusion, it appears from these results that the glucose transporter gene GLUT1 is unlikely to play a major role in the etiology of MODY diabetes.

Detection of K-ras point mutations in mesenteric venous blood from colorectal cancer patients by enriched polymerase chain reaction and single-strand conformation polymorphism analysis.

In order to confirm the presence of cancer cells in mesenteric venous blood and to examine their relationship with the occurrence of liver metastases, we attempted to detect K-ras codon 12 point mutations in perioperative mesenteric blood using enriched polymerase chain reaction and single-strand conformation polymorphism (PCR-SSCP) analysis in 25 patients with primary colorectal tumors carrying K-ras point mutations. Among these patients, three with synchronous liver metastases were included. The same K-ras point mutation (substitution of GAT for GGT) was detected in both the blood and the primary tumor in a Dukes' C patient. We confirmed this result by colony hybridization and estimated the tumor-to-normal cell ratio to be 1:400. This patient has no liver metastases two years after surgery and her carcinoembryonic antigen (CEA) level remains normal. We demonstrated that considerable numbers of cancer cells can be found in mesenteric venous blood during colorectal cancer surgery. However, their potential role in the formation of liver metastases remains unclear.

Detection of clonal rearrangement of the t-cell receptor gamma gene by polymerase chain reaction and single-strand conformation polymorphism (PCR-SSCP)

Background: Diagnosis of T-lymphoid neoplasms frequently requires molecular studies of T-cell receptor (TCR) gene rearrangements. The Southern blot technique traditionally used for these analyses lacks the sensitivity and speed necessary for the routine clinical laboratory. The authors have developed a method using polymerase chain reaction (PCR) amplification with single-strand conformation polymorphism (SSCP) analysis that is rapid, sensitive, and semiautomated. Methods and Results: Polymerase chain reaction of the TCR gamma gene is done with consensus primers to the V and J regions. Amplicons thus include the N region, which serves as a marker of clonal T-cell population. Clonal populations having identical N-region sequences are identified by SSCP analysis, using a semiautomated electrophoresis system with silver staining for gel visualization. A series of 46 DNA samples from normal controls and various hematopoietic malignancies was comparatively analyzed by both Southern blot of the TCR beta locus and PCR-SSCP of the of the TCR gamma gene. The PCR-SSCP technique was rapid and reproducible, and detected clonal T-cell populations constituting 1% of the cell sample: The PCR-SSCP technique detected clones in eight cases that were negative by Southern blot. Conclusions: PCR-SSCP analysis of the TCR gamma gene is a rapid and sensitive method for the detection of clonal T-cell populations. (Mol Diagn 1996 Jun;1(2):131-137)

Molecular genetics of glucose-6-phosphate dehydrogenase (G6PD) deficiency in Spain: identification of two new point mutations in the G6PD gene.

In order to explore the nature of glucose-6-phosphate dehydrogenase (G6PD) deficiency in Spain, we have analysed the G6PD gene in 11 unrelated Spanish G6PD-deficient males and their relatives by using the polymerase chain reaction and single-strand conformation polymorphism (PCR-SSCP) analysis combined with a direct PCR-sequencing procedure and PCR-restriction enzyme (RE) analysis. We have identified eight different missense mutations, six of which have been reported in previously described G6PD variants. In nine patients who had presented with acute favism we found the following mutations: G6PD A-376G-202A (four cases), G6PD Union1360T (two cases), G6PD Mediterranean563T (one case) and G6PD Aures143C (one case). In the remaining patient a novel A to G transition was found at nucleotide position 209 which has not been reported in any other ethnic group. This mutation results in a (70) Tyr to Cys substitution and the resulting G6PD variant was biochemically characterized and designated as G6PD Murcia. This new mutation creates a Bsp 1286I recognition site which enabled us to rapidly detect it by PCR-RE analysis. In two patients with chronic non-spherocytic haemolytic anaemia (CNSHA) we found the underlying genetic defects, as had been noted previously, to be located within a cluster of mutations in exon 10. One of them had the T to C transition at nucleotide 1153, causing a (385) Cys to Arg substitution, previously described in G6PD Tomah. The other, previously reported as having a variant called G6PD Clinic, has a G to A transition at nucleotide 1215 that produces a (405) Met to Ile substitution, thus confirming that G6PD Clinic is a new class I variant.

Sensitive detection of p53 gene mutations in esophageal endoscopic biopsy specimens by cell sorting combined with polymerase chain reaction single-strand conformation polymorphism analysis.

For the rapid and sensitive detection of p53 gene mutations in esophageal endoscopic biopsy specimens, we combined cell sorting with the polymerase chain reaction and single‐strand conformation polymorphism (PCR‐SSCP) analysis. Mutations in exons 5–8 of the p53 gene were investigated by FCR‐SSCF analysis using 103 sorted nuclei obtained from each endoscopic biopsy specimen of 16 patients with esophageal cancer. DNAs extracted from their respective surgical specimens were investigated by a conventional method of PCR‐SSCP analysis. Mutations in the biopsy specimens were detected in 6 of the 12 aneuploid tumors but in none of the 4 diploid tumors. After tumor cell enrichment by cell sorting, one mutation in exon 8 became apparent, which could not be detected from the surgical specimen by a conventional method of PCR‐SSCP analysis. This method should improve the sensitivity of detecting p53 gene mutations, and provides additional information concerning the DNA ploidy pattern in the tumors.