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At least 289 records · Page 16Linked to original sources
PubMed1996

Polymorphisms of the human alpha 2A-adrenergic receptor gene in a Catalan population: description of a new polymorphism in the promoter region.

Alpha 2A-adrenergic receptor polymorphisms were investigated in 55 unrelated Caucasian Catalan individuals. Phenotypes were expressed by alpha 2-adrenoreceptor density and affinity determined by radioligand binding. In addition to the two previously described biallelic restriction fragment length polymorphisms (RFLP) (DraI and Bsu36I) [Hoehe et al 1988; Sun et al 1992], a transition was located in the promoter region of the human alpha 2A-adrenergic receptor using a non-radioisotopic single-strand conformational polymorphism (SSCP) analysis. DNA sequence analysis of this region showed that this transition produces the loss of a HhaI site. In our sample, the estimates of the frequency of this allele was 11% and those of DraI alleles were similar to those reported for other Caucasian populations but different from those observed in Afro-Americans. In addition, frequencies of the Bsu36I alleles in the Catalan population differed from those of Japanese and American White populations. A slight linkage disequilibrium between Bsu36I-DraI was found in our population. No association between phenotypes and RFLP genotypes was observed.

Alleles↗
PubMed1996

Allelic variants of human TCR BV17S1 defined by restriction fragment length polymorphism, single strand conformation polymorphism, and amplification refractory mutation system analyses.

Several human TCR BV gene subfamilies, including BV3, BV14, and BV17S1, are single member genes but are overutilized among activated CD4+ synovial T cells in the rheumatoid arthritis (RA). To define the role of these TCR BV genes in the pathogenesis of disease, it is critical to characterize the genomic organization and the allelic variations of these genes. In this study we describe allelic variations of BV17S1 defined by restriction fragment length polymorphism (RFLP), single strand conformation polymorphism (SSCP), and amplification refractory mutation system (ARMS) analyses. A single nucleotide replacement (C/T) results in an amino acid substitution (F/L) in the leader and distinguishes BV17S1*1 from BV17S1*2. This nucleotide substitution was found to create a BsmAI restriction enzyme recognition site in BV17S1*2. Therefore genotypic analyses can be performed either by the SSCP or RFLP method. The analyses of 75 unrelated individuals show that the frequency for allele BV17S1*1 is 52.7% and for allele BV17S1*2 is 47.3%. Both alleles are functionally expressed and are distributed within CD4+/CD8+ T cell subsets. Another point mutation in the CDR2 region of BV17S1, which results in the amino acid replacement of Gln by His, originally identified form a cDNA clone, has now been confirmed as an allele by ARMS analysis using genomic DNA preparations and designated to as BV17S1*3. Screening of this CDR2 related variant among normal populations indicates that this is a rare allele (1 of 75). Although this variant may be of functional significance, the genotypic analysis and functional studies are difficult due to the low frequency of BV17S1*3. In an attempt to define a correlation between BV17S1 allelic usage and susceptibility to RA, the germline distribution of BV17S1 alleles *1 and *2 has been examined in a small number of RA patients and no skewed usage has been identified.

Alleles↗
PubMed1995

DNA fingerprinting by random amplified polymorphic DNA and restriction fragment length polymorphism is useful for yeast typing.

Random amplified polymorphic DNA (RAPD) analysis was applied to genomic DNA from nineteen yeast strains belonging to the genera Saccharomyces and Zygosaccharomyces. Results obtained with five primers indicated that this technique is a powerful tool for yeast differentiation and identification. The data were consistent with those derived from restriction fragment length polymorphism (RFLP) using two S. cerevisiae DNA probes. We conclude that RAPD fingerprinting, combined with the analysis of RFLP, can provide unambiguous type assignment in yeasts.

DNA, Bacterial↗
PubMed2002

A comprehensive survey for polymorphisms in the bovine IFN-gamma gene reveals a highly polymorphic intronic DNA sequence allowing improved genotyping of Bovinae.

This study aimed to identify interferon-gamma (IFN-gamma) gene variants in cattle for diagnostic purposes. Therefore, the entire bovine IFN-gamma gene (BoIFNG) and 2605 bp of its promoter DNA were sequenced. The BoIFNG DNA sequence conforms to the published part of Bo-IFN-gamma cDNA. Primer extension experiments show the presence of a 5' extension of exon 1 by 42 nucleotides (nt). One SINE element (Bov-A2) is located in the 5'-region, and two SINE elements (Bov-tA, Bov-B) are contained in the 3'-region of BoIFNG. The variants were detected by comparative sequence analysis of PCR amplicons from different bovine species. Four polymorphic mononucleotide repeats are situated in the promoter and in intron 1. Four distinct series of single nucleotide polymorphisms (SNP) were found in functionally important regions of BoIFNG. The region between the two intron 1 microsatellites contains the highest density of SNPs in Bos taurus breeds. One G-T transversion in the coding region of exon 1 causes a Gly(14) to Val(14) exchange in the BoIFNG signal peptide of different bovine species. A G-A transition in exon 2 encodes a Ser(19) to Asn(19) change in the mature protein of the Tibetan yak. Genotyping of randomly sampled Holstein Friesian cows at selected SNPs and of both intron 1 microsatellites revealed two dominant BoIFNG microhaplotypes. The detected SNPs improve the recently reported genotyping system of cattle.

Amino Acid Substitution↗
PubMed2005

Application of NIR spectroscopy in polymorphic analysis: study of pseudo-polymorphs stability.

The accelerated transformation of three azithromycin pseudo-polymorphs (viz. the anhydrous, monohydrate (MH), and dihydrate (DH) forms) at a high temperature and moisture level was examined by near infrared spectroscopy (NIRS). The most marked spectral differences between the pseudo-polymorphs occurred in the 1800-2200 nm region, which corresponds to the first overtone for water. The qualitative analysis of the NIR spectra for the pseudo-polymorphs following storage in a stove at 60 degrees C at 100% relative humidity for 60 days suggests that the crystalline forms (viz. the MH and DH) are stable, whereas the amorphous (anhydrous) form evolves to the DH. This was confirmed by determining the amounts of water and DH present in anhydrous azithromycin and the MH by use of partial least-squares regression (PLSR). The method used to quantify the DH in MH samples was developed and validated in accordance with the standards of the International Conference of Harmonization (ICH) and the European Medicines Agency (EMEA) with a view to its subsequent application by the pharmaceutical industry. The limits of detection (LD) and quantitation (LQ) for the DH in MH provided by the NIRS method were consistent with those obtained by X-ray diffraction (XRD) methodology. This testifies to the accuracy of the proposed method.

Azithromycin↗
PubMed2005

The role of molecular structure in the crystal polymorphism of local anesthetic drugs: crystal polymorphism of local anesthetic drugs, part X.

PURPOSE: This report is the résumé of a comprehensive investigation on the solid-state properties and the crystal polymorphism of the structurally homogenous class of local anesthetic drugs. The goal is to explore the relationship between crystal polymorphism and molecular structural features. METHODS: A salt form (mostly the hydrochloride) as well as the free base of 24 local anesthetics has been characterized by means of thermomicroscopy, differential scanning calorimetry, pycnometry, Fourier transform infrared, Fourier transform Raman, and solid-state NMR spectroscopies, as well as X-ray diffraction methods (single crystal, powder). RESULTS: Based on the thermochemical data, the relative thermodynamic stabilities of the different crystal forms of each polymorphic system were evaluated and visualized as semiquantitative energy/temperature diagrams. CONCLUSION: This study is the first step in recognizing relationships between the structure and the solid-state properties within this limited group of active substances with common structural elements. The results clearly show that there are certain relationships, but, to understand the phenomenological behavior in more detail on a molecular level, more structural information must be collected and analyzed by computational methods.

Adsorption↗
PubMed1997

Polymorphism of sulindac: isolation and characterization of a new polymorph and three new solvates.

The polymorphism of sulindac was investigated. Two polymorphs (I and II) and a new crystalline form (form III) of sulindac were prepared by recrystallization in different solvents. In addition, three new pseudopolymorphs (solvates) from acetone, chloroform, and benzene were obtained, with each containing 1 mol of solvent to 2 mol of sulindac. Different sulindac polymorphs and pseudopolymorphs were characterized by X-ray diffractometry, infrared spectroscopy, differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), and hot-stage microscopy. The transition behavior of the crystalline forms of sulindac, their melting points, and their enthalpies were investigated by DSC. The melting of form II was observed at 184 degrees C, and form I subsequently recrystallized from this melt. Similarly, form III melts at 145 degrees C and then recrystallizes to form I. We also investigated the influence of the crystallization solvent on sulindac crystal shape.

Calorimetry, Differential Scanning↗
PubMed1999

New DNA polymorphisms of human MMH/OGG1 gene: prevalence of one polymorphism among lung-adenocarcinoma patients in Japanese.

MMH/OGG1 is an 8-hydroxyguanine-specific DNA glycosylase/AP-lyase, one of the mutator enzymes for the excision repair of 8-hydroxyguanine. DNA polymorphisms in human MMH/OGG1 gene were newly identified and analyzed to examine a possible association with lung-cancer risk by a population-based study. Polymorphic allele 3 in hMMH/OGG1 exon 1 was significantly prevalent among Japanese patients with adenocarcinoma of the lung [odds ratio (OR): 3.152, 95% confidence interval (CI): 1.266-7.845], indicating that the excision repair of 8-hydroxyguanine may play a role in predisposition to lung cancer.

Adenocarcinoma↗
PubMed1999

Mutation screening of neurofibromatosis type 1 (NF1) exons 28 and 29 with single strand conformation polymorphism (SSCP): five novel mutations, one recurrent transition and two polymorphisms in a panel of 118 unrelated NF1 patients. Mutations in brief no. 229. Online.

Neurofibromatosis type 1 is a clinically variable disorder caused mostly by small mutations within the NF1 gene on chromosome 17q11.2. We used Single Strand Conformation Polymorphism (SSCP) and radioactive sequencing to screen NF1 exons 28 and 29 from 118 unrelated patients, diagnosed with NF1 according to the NIH criteria, identifying five novel and one recurrent germline mutations, two novel polymorphisms and a variant base exchange. All but one cause protein truncation and represent typical NF1 mutations. There are reports that NF1 patients with mutations in exons 28 and 29 could be at greater risk of developing myeloid leukemia. This question was given consideration in this investigation, but none of the children involved have yet shown any symptoms of myeloid leukemia. 4 out of the 6 mutations were de novo.

Codon, Terminator↗
PubMed1999

Detection of mutations and polymorphisms in the p53 tumor suppressor gene by single-strand conformation polymorphism analysis.

Deciphering the genetic mechanisms in cancer development requires analysis of a large number of tumors for consistent genetic alterations. Single-strand conformational polymorphism (SSCP) analysis is a fast and efficient method for detecting mutations, deletions, insertions and loss of alleles. The primary advantage of this method is speed and ability to screen a large number of samples at one time. Here we report the use of the SSCP technique for rapidly screening tumor and normal tissues for mutations and polymorphisms in the p53 tumor suppressor gene. Because the DNA extracted from specific aberrant bands from different samples always give rise to the same nucleotide sequence upon sequencing analysis, the SSCP technique can be used as a diagnostic tool to identify the presence of such genetic alterations without having to spend time on further sequencing analysis.

Genes, p53↗
PubMed2004

High-throughput single nucleotide polymorphism typing by fluorescent single-strand conformation polymorphism analysis with capillary electrophoresis.

In this study, we performed high-throughput and precise single nucleotide polymorphism (SNP) typing by fluorescent capillary electrophoresis single-strand conformation polymorphism (CE-SSCP) analysis. A system composed of a multicapillary DNA analyzer, a newly developed sieving matrix, four different colors of fluorescent labels, and a multiplex polymerase chain reaction (PCR) enabled low-cost and highly reliable SNP typing. Moreover, this system enabled the estimation of SNP allele frequencies using pooled DNA samples, which should be beneficial for large-scale association studies. Thus, fluorescent CE-SSCP analysis is a useful method for large-scale SNP typing.

DNA Fingerprinting↗
PubMed2005

Detection of single nucleotide polymorphisms in coagulation factor XI deficient patients by multitemperature single-strand conformation polymorphism analysis.

Factor XI (FXI) deficiency is a rare inherited disorder which can cause bleeding complications especially in case of hemostatic challenge and/or in tissues with high fibrinolytic activity. A number of causative mutations have been described in FXI deficient individuals which have been detected by various screening methods. In this study, we present the application of the multitemperature single-strand conformation polymorphism analysis (MSSCP) on the FXI gene, a recently developed methodology for the detection of single nucleotide exchanges. We analyzed a total of 217 polymerase chain reaction (PCR) fragments from the promoter region as well as from exons 1-7 and 11-15 and compared the results to automatic fluorescent sequencing. A total of 29 PCR fragments showed single nucleotide exchanges in conventional fluorescent sequencing, representing 10 different mutations (nine missense mutations, one small deletion) and four frequent polymorphisms. With MSSCP electrophoresis at a standard temperature profile (gel temperature 35-20-10 degrees C) we were able to detect 13 of 14 (93%) different nucleotide exchanges in 25 of 29 PCR fragments (86%). Hence, the detection rate for genetic variations in the FXI gene was 86%. To evaluate the reproducibility, MSSCP was performed twice for 174 PCR fragments and the consistency between two electrophoretic runs was 99%. We conclude that the MSSCP is a sensitive, fast, and cost effective screening method for the detection of FXI gene mutations.

DNA Mutational Analysis↗
PubMed2001

Intraspecific variation and host specificity of Entomophthora muscae sensu stricto isolates revealed by random amplified polymorphic DNA, universal primed PCR, PCR-restriction fragment length polymorphism, and conidial morphology.

The intraspecific variations of Entomophthora muscae s. str. associated with particular host species, Musca domestica and Delia radicum, sampled from different localities and different years in Denmark and the variation of E. muscae s. str. originating from different host taxa were investigated. The isolates were compared both by primary spore morphology and by three molecular methods: random amplified polymorphic DNA, universal primed PCR, and PCR-restriction fragment length polymorphism. Analyses of the different molecular data showed the same overall picture and separated E. muscae s. str. into two main groups with all the M. domestica isolates in one group and isolates from D. radicum, Coenosia tigrina, and Pegoplata infirma in the second group. E. muscae s. str. isolates from M. domestica also differ significantly from the rest of the E. muscae s. str. isolates with regard to the morphology of the primary conidia, which were bigger and contained significantly more nuclei per conidium. Several different E. muscae s. str. genotypes were documented and each type was restricted to a single host species, indicating a very high degree of host specificity at or below the level of the subfamily.

Animals↗
PubMed2001

Estimating nucleotide diversity from random amplified polymorphic DNA and amplified fragment length polymorphism data.

A way to estimate the index of nucleotide diversity (pi) from band match frequencies in random amplified polymorphic DNA and amplified fragment length polymorphism data is described. pi is shown to be a simple function of the proportion of mismatched bands between two individuals drawn at random from a population (phi) and the number of discriminating sites in the amplification system. The method is computationally and conceptually simple and avoids some of the assumptions inherent in other approaches: the relationship is independent of the base composition of the target DNA and avoids the bias inherent in estimations of allelic frequencies in dominant systems. Only two individuals from a population are needed to estimate pi. This economy of material suggests utility of this approach in conservation genetics or other fields where obtaining large samples is impractical or undesirable.

Alleles↗
PubMed1995

Sex in Escherichia coli does not disrupt the clonal structure of the population: evidence from random amplified polymorphic DNA and restriction-fragment-length polymorphism.

Analysis of the Escherichia coli population by multilocus enzyme electrophoresis (MLEE) has established its clonal organization, but there is increasing evidence that horizontal DNA transfer occurs in E. coli. We have assessed the genetic structure of the species E. coli and determined the extent to which recombination can affect the clonal structure of bacteria. A panel of 72 E. coli strains from the ECOR collection was characterized by random amplified polymorphic DNA (RAPD) and restriction-fragment-length polymorphism (RFLP) of the ribosomal RNA gene (rrn) regions. These strains have been characterized by MLEE and are assumed to reflect the range of genotypic variation in the species as a whole. Statistical analysis, including factorial analysis of correspondence (FAC) and hierarchical classifications, established that the data obtained with the three genetic markers are mutually corroborative, thus providing compelling evidence that horizontal transfer does not disrupt the clonal organization of the population. However, there is a gradient of correlation between the different classifications which ranges from the highly clonal structure of B2 group strains causing extraintestinal infections in humans to the less-stringent structure of B1 group strains that came mainly from nonprimate mammals. This group (B1) appears to be the framework from which the remaining non-A group strains have emerged. These results indicate that RAPD analysis is well suited to intraspecies characterization of E. coli. Lastly, treating the RAPD data by FAC allowed description of subgroup-specific DNA fragments which can be used, in a strategy comparable to positional cloning, to isolate virulence genes.

Base Sequence↗
PubMed1993

Polymorphisms and linkage disequilibrium in the COL6A1 and COL6A2 gene cluster: novel DNA polymorphisms in the region of a candidate gene for congenital heart defects in Down's syndrome.

The COL6A1 and COL6A2 (collagen VI) gene cluster on chromosome 21 is a candidate region for defects leading to congenital heart anomalies in Down's syndrome. We report a variable number of tandem repeats (VNTR) and a restriction fragment length polymorphism (RFLP) in this gene region, detected using a COL6A1 cDNA probe. Linkage disequilibrium relationships were studied among the RFLPs of this gene cluster. The RFLP reported here shows no significant linkage disequilibrium with any others in the region. It has a polymorphism information content value of 0.27, raising the informativity of the locus.

Chi-Square Distribution↗
PubMed2000

Association studies of 33 single nucleotide polymorphisms (SNPs) in 29 candidate genes for bronchial asthma: positive association a T924C polymorphism in the thromboxane A2 receptor gene.

Although intensive studies have attempted to elucidate the genetic background of bronchial asthma (BA), one of the most common of the chronic inflammatory diseases in human populations, genetic factors associated with its pathogenesis are still not well understood. We surveyed 29 possible candidate genes for this disease for single nucleotide polymorphisms (SNPs), the most frequent type of genetic variation, in genomic DNAs from Japanese BA patients. We identified 33 SNPs, only four of which had been reported previously, among 14 of those genes. We also performed association studies using 585 BA patients and 343 normal controls for these SNPs. Of the 33 SNPs tested, 32 revealed no positive association with BA, but a T924C polymorphism in the thromboxane A2 receptor gene showed significant association (chi2=4.71, P=0.030), especially with respect to adult patients (chi2=6.20, P=0.013). Our results suggest that variants of the TBXA2R gene or some nearby gene(s) may play an important role in the pathogenesis of adult BA.

Alleles↗