PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Molecular polymorphism”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 451 records · Page 25Linked to original sources
PubMed1997

Clinical relevance of polymorphic markers of arterial thrombosis.

Case-control and cross-sectional studies show that some common molecular variations (polymorphisms) of genes coding for proteins involved in atherosclerosis and thrombosis are often present in subjects who have experienced cerebrovascular or cardiovascular events. The clinical impact of the majority of polymorphic markers is disputed by prospective reports. In contrast, their pathophysiological implications and their role in monitoring parameters that are difficult to be checked by alternative means, are documented by the large majority of the reports. From the evidence available, there may be suggestion for further impact of polymorphic markers in vascular medicine. To substantiate this, new prospective studies that include individuals from different geographical areas and that take into account the statistical power, the informativeness of the markers, the coexistance of established risk factors and the genetic background of the populations analyzed, are urgently needed.

Chromosome Mapping↗
PubMed2001

Simplified method for the detection of apo(a) isoforms.

Apolipoprotein a, is a high molecular weight glycoproteic component of Lp(a), a molecule associated with coronary arterial disease. Apo(a) exhibits considerable size heterogeneity due to variable repetitions of the carbohydrate-containing structural unit, termed kringle. There are five different kringle forms and 10 different kringle 4 types. Apo(a) polymorphism and molecular weight depend on the number of copies of kringle 4 type 2. In this paper we describe a modified 3.75% and 6% discontinuous polyacrylamide gel system and Western-blot technique that shortness the assay time and improves the identification of apo(a) isoforms with a theoretical error of less than 1 kringle. The assay uses a standard curve prepared with five different recombinant apo(a) molecules, detected up to 50 ng of protein in Lp(a), showed a maximal resolution of 2 kringles and, with the use of third degree polynominal regression analysis, had an error of 0.01275. The inter-assay coefficient of variation was 1.7, 2, and 1.4 for the 14 K, 18 K, and 22 K phenotypes, whereas the intra-assay coefficient of variation was 0.32%, 0.18%, and 0.17%, respectively. It is possible that this modified method will diminish the number of putative null alleles so far detected in various studies, but most of all, we are certain that it can be of use in epidemiological studies due to its ease of use, speed, low cost, and enhanced number of samples that can be tested.

Alleles↗
PubMed1992

[Polymorphism of untranscribed spacer rDNA as a molecular genetic marker in population studies of cattle].

Variable polymorphic patterns were detected using EcoRI-SalI fragment of bovine rDNA, including 3'-end of 28S rRNA gene with the adjacent portion of the transcribed spacer, as a probe for hybridization. Some features of these polymorphic patterns are similar to DNA fingerprints detected with the M13 probe. Bovine rDNA spacer polymorphism was used as a molecular genetic marker for population analysis of individual specific patterns of 4 cattle breeds with the help of the Jeffreys' method. It was supposed that the probability of identical fingerprints appearance could be the characteristics of heterogeneity of cattle populations. The observed length of polymorphic gragments ranged from 2000 to 6000 bp. The mean number of fragments per individual for all breeds was 15.05. The probability of identical patterns appearance was very high: from 1.18 x 10(-5) in ajshir's breed to 1.43 x 10(-7) in "white and black"s' breed. So, high probability seems to be dependent on the high allelic frequency and the way of breeding.

Animals↗
PubMed2001

Highly polymorphic short tandem repeat analyses clarify complex molecular test results.

Judicious application of highly polymorphic short tandem repeat (STR) analyses and modification of assay conditions readily distinguished nonparentage from true parentage, with occasional failure to transmit one parentally derived allele. These categories were resolved with a reliability of >99.9%, the standard applied to most DNA evidence presented in a U.S. court of law. While completing a single prenatal diagnosis submitted at 19 weeks gestation, the authors found that one polymorphic grandpaternal allele did not amplify, a duplicate control propositus' DNA sample had been switched by an outside laboratory, and recombination occurred in maternal meiosis within the mutant gene region. In two parentage cases with one available parent, a Y-linked STR or an autosomal STR was modified when transmitted to the offspring. In contrast, some apparently inconsistent results between parental DNA and offspring were resolved by purifying or diluting the original extracted DNA samples. Thus, the source of each complex molecular test result was characterized unambiguously by testing a sufficient number of highly polymorphic STR loci and by purifying or diluting troublesome DNA samples to diminish polymerase chain reaction amplification artifact.

Adult↗
PubMed2003

Low genetic differentiation among seasonal cohorts in Senecio vulgaris as revealed by amplified fragment length polymorphism analysis.

Common groundsel, Senecio vulgaris (Asteraceae), is a highly selfing semelparous ephemeral weed that belongs to the few plant species in central Europe capable of growing, flowering and fruiting all year round. In temperate climates, flowering S. vulgaris cohorts were found to appear up to three times per year. Using amplified fragment length polymorphism (AFLP) molecular markers we examined temporal genetic differentiation among spring, summer and autumn cohorts at each of seven sites located in two regions in Switzerland. Strong genetic differentiation among cohorts may indicate the existence of seasonal races of S. vulgaris, reproductively isolated by nonoverlapping flowering phenologies. Analysis of molecular variance (amova) revealed that < 2.5% of the AFLP variation resided among cohorts within sites, whereas there was significant genetic differentiation among plants from different sites (15.6%) and among individuals within cohorts (81.9%). Significant genetic differentiation was also observed between the two regions. Isolation-by-distance was found on a regional scale, but not on a local scale. Gene flow was estimated to be approximately 15-fold higher among cohorts within sites than among sites. We further found, on average, similar levels of genetic diversity within the three seasonal cohorts. The results of this study demonstrate that season of growth represents a weak barrier for genetic exchange among S. vulgaris populations and does not affect molecular variance. Therefore, there is no evidence for the existence of seasonally specialized races of S. vulgaris. We discuss some implications of the results for the biological control of S. vulgaris using a native rust fungus.

Analysis of Variance↗
PubMed2000

Positional cloning in Arabidopsis. Why it feels good to have a genome initiative working for you.

Positional (or map-based) cloning techniques are widely used to identify the protein products of genes defined by mutation. In Arabidopsis the information generated by the Genome Initiative is giving this approach a decisive boost. A wealth of sequence polymorphisms and molecular markers is now available and can be exploited for fine mapping with technically simple and robust polymerase chain reaction-based methods. As a result it has become possible to complete positional cloning projects in a short time and with relatively little effort.

Arabidopsis↗
PubMed2005

A novel polymorphism in the factor XIII B-subunit (His95Arg): relationship to subunit dissociation and venous thrombosis.

BACKGROUND: Factor (F)XIII B-subunit, which plays a carrier role for zymogen FXIIIA, is highly polymorphic, but the molecular basis for these polymorphisms and their relationship to disease remains unknown. OBJECTIVES: To screen the FXIIIB gene coding region for common variation and analyze possible functional effects. METHODS AND RESULTS: We examined the FXIIIB gene by PCR-SSCP and identified three common single nucleotide polymorphisms: A8259G, C29470T and A30899G. A8259G results in substitution of His95Arg in the second Sushi domain. An FXIII tetramer ELISA was developed to analyze B-subunit dissociation from A-subunit (leading to access to the catalytic site of FXIII). Increased subunit dissociation, 0.51 vs. 0.45 (fraction of total tetramer), was found in plasma from subjects possessing the Arg-allele. However, when the variants were purified to homogeneity and binding was analyzed by steady-state kinetics, no difference was observed. The relationship between His95Arg and venous thrombosis was investigated in 214 patients and 291 controls from Leeds. His/Arg + Arg/Arg genotypes were more frequent in patients than controls (22.4% vs. 15.1%). His95Arg was also investigated in the Leiden Thrombophilia Study, in which a similar difference was observed for 471 patients vs. 472 controls (18.5% vs. 14.0%), for a pooled odds ratio (OR) of 1.5 (CI95 1.1-2.0). CONCLUSIONS: We have identified three FXIIIB polymorphisms, one of which codes for substitution of His95Arg. The Arg95 variant associates with a moderately increased risk for venous thrombosis, and with increased dissociation of the FXIII subunits in plasma, although in vitro steady-state binding between purified subunits was not affected.

Binding Sites↗
PubMed2002

Bioinformatic analysis of the human mu opioid receptor (OPRM1) splice and polymorphic variants.

Mu opioid receptor (OPRM1), a member of the G-protein coupled receptor superfamily, mediates the analgesic and euphoric effects of opioid drugs. The sequences of OPRM1 cDNA and reported splice variants were used to search the public and Celera genomic databases. The matched sequences were analyzed to assemble an OPRM1 genomic contig. Human OPRM1 gene was estimated to span at least 90 kb in the chromosome 6q24-25 region. Four coding exons are separated by 3 introns. While intron 2 has only 773 bp, these databases for the first time provide the precise length of and other information about long introns 1 and 3, containing 50 and 27 kb, respectively. When a consensus exon/intron splice junction at the end of the coding exon 3 was not utilized, it may have resulted in continuous translation of the exon to yield the splice variant OPRM1A. The study did not identify human orthologs of other OPRM1 variants that had been reported for mouse OPRM1, although several proposed exons were found to be included in mouse genomic clones. Single nucleotide polymorphisms in the OPRM1 gene were also analyzed and summarized, which could provide potential polymorphic markers for molecular genetic studies.

Alternative Splicing↗
PubMed1992

Genetic variability in a family of satellite DNAs from tilapia (Pisces: Cichlidae).

We have cloned and sequenced members of a family of satellite DNAs from three genera of the tilapiine tribe of fishes: Oreochromis, Sarotherodon, and Tilapia. The satellite DNAs, visualized as intensely staining bands following electrophoretic separation of EcoRI-digested genomic DNA, consist of three size variants differentially distributed in the various tilapiine species. The sizes of the monomers are approximately 237 bp (type I), 230 bp (type II), and 209 bp (type III). Several cloned monomers were sequenced from Oreochromis niloticus (type III), Oreochromis placidus (types I and II), Sarotherodon galilaeus (type I), Tilapia zillii (type I), and Tilapia rendalli (type I). Comparison of derived consensus sequences for the monomer units of the satellite DNAs revealed sequence identities within and between species that ranged from 89 to 96%. The type II and type III size variants appear to have arisen by deletions of 9 and 29 bp, respectively, within different regions of the type I satellite. Hybridization of a cloned monomer satellite from O. niloticus (type III) to PalI digests of genomic DNA from all three genera detected polymorphic, high molecular weight restriction fragments that produced fingerprint-like patterns. The complexity of these DNA fingerprints varied from one species to another, suggesting a markedly different genomic organization for these polymorphic satellite DNAs.

Animals↗
PubMed1993

Single-strand conformation polymorphism (SSCP) analysis of the molecular pathology of hemophilia B.

In the present study, we report the application of polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) analysis to the screening of seven functionally important factor IX gene (FIX) regions (total length 2.66 kb) in 9 unrelated haemophilia B patients of Portuguese or African origin. In eight of the patients an altered migration pattern of single-stranded DNA was observed. Direct sequencing of the relevant DNA fragments unveiled the following sequence alterations: two novel mutations, namely FIXBarcelos Thr-380-Pro and FIXLousada 9bp insertion at position 31,309 or 31,318; five mutations previously reported in other ethnic groups (FIXPorto Arg-145-His, FIXLuanda Gly-207-Arg, FIXPenafiel Arg-248-Gln, FIXSesimbra Arg-333-Gln, FIXCascais Arg-333-Stop); and a normal variant, G-->T transvertion at position 6,596 in intron 2. We propose hypothetical models for the generation of the 9 bp duplication (FIXLousada). We have performed molecular modeling studies in order to predict the structure of the variant FIX molecules.

Base Sequence↗
PubMed1992

Oligonucleotide genotyping of HLA polymorphism on microtitre plates.

Molecular analysis of mutations and polymorphisms that are of medical importance requires both accuracy and simplicity. In organ transplantation there is a need for an HLA typing procedure that combines the remarkable accuracy of oligonucleotide genotyping with the simplicity of conventional serological typing. We describe a simple semiautomated method of HLA class II typing consisting of an oligonucleotide hybridisation assay done on microtitre plates followed by automatic colorimetric reading. Individual HLA-DR generic typing for 30 DR specificities, including subtypes of DR1, DR2, DR13, DR14, and DR52, is done on a single plate. The entire typing assay can be completed in less than 4 hours. The procedure has been validated on more than a thousand haplotypes in prospective DR typing of kidney transplant patients, leukaemic patients, and their potential donors. The simplicity of this assay makes it suitable for routine laboratory use. It can be applied to genetic testing in general, including the testing of patients with multiple mutations.

Base Sequence↗
PubMed2003

The sequence dependence of fiber organization. A comparative molecular dynamics study of the islet amyloid polypeptide segments 22-27 and 22-29.

Amyloid fiber formation and the possible polymorphism of molecular arrangements depend on the polypeptide length and composition. Here, we seek the chemical clues underlying these processes. Our starting point is based on the experimental observation that some short peptide segments are able to develop fibers that are very similar to those of their original parent proteins. We focus our study on the NFGAILSS peptide, derived from the human islet amyloid polypeptide (residues 22-29). This peptide turned out to be a perfect example, illustrating the fact that the amyloid microscopic organization is highly complex, rather than simply involving hydrogen bond formation. Furthermore, obtaining a reliable molecular model has allowed us to analyze the differences between the amyloid structure we have obtained for this peptide and that obtained for the previously studied, two residues shorter, segment (residues 22-27, NFGAIL). This comparative study yields some clues about chemical events that govern the aggregation of proteins into oriented fibers, such as molecular packing between sheets and the degree of interaction specificity. We characterize the important role played by the hydrophobic and aromatic residues in the inter-sheet association and present new approaches toward the understanding of the nature of events that are likely to take place during fibril formation. These include analysis of interaction patterns derived from specific sheet-associated packing.

Amino Acid Sequence↗
PubMed2003

AACR Special Conference: SNPs, haplotypes, and cancer - applications in molecular epidemiology, Key Biscayne, Florida, USA, 13-17 September 2003.

This American Association for Cancer Research Special Conference brought together scientists with diverse expertise to address issues related to use of appropriate epidemiological, statistical, and laboratory methods to study the genetic epidemiology of cancer. Discussions focused on experiences with association studies using single nucleotide polymorphisms and haplotypes, their limitations, and what is needed to improve on the current 'state of the art'. Various studies were presented in different contexts, ranging from candidate gene studies to whole genome scans, and conducted in prospective cohorts, case-control studies, and other study designs. Common problems such as determining the probability that observed associations are false negative or false positive, the potential effects of admixture, and determining which polymorphisms to examine in which genes and in which populations were examined. Problems specific to haplotype analysis were discussed, with emphasis on haplotype block structures and on how to use haplotypes in analysis. Questions were also posed as to determining the functional relevance of single nucleotide polymorphisms in molecular epidemiology. Finally, future directions, using specific examples, were addressed.

DNA, Neoplasm↗
PubMed1993

Molecular and immunological characterization of a novel polymorphic lipoprotein of Borrelia burgdorferi.

We describe the cloning, expression, and molecular characterization of a novel polymorphic Borrelia burgdorferi lipoprotein recognized by monoclonal antibody LA7. Sequence analysis revealed an open reading frame encoding a 21,866-Da polypeptide (IpLA7). Comparison with other known proteins indicated sequence similarity between IpLA7 signal peptides and those of other prokaryotic lipoproteins, including the immunodominant B. burgdorferi outer surface proteins OspA, OspB, pC, and OspD. Both natural IpLA-7 and recombinant IpLA-7 could be biosynthetically labeled with [3H]palmitate. Upon solubilization of intact B. burgdorferi with the nonionic detergent Triton X-114, IpLA7 was extracted together with other lipoproteins into the detergent phase. Indirect immunolabeling studies indicated that the epitope recognized by monoclonal antibody LA7 is mainly located in the periplasmic space. Two-dimensional gel electrophoresis and immunoblotting confirmed the calculated acidic pI of 5.7 for IpLA-7. The LA7 gene was shown to be species specific and to be located on the linear chromosome of B. burgdorferi. The analysis of 40 individual spirochetal isolates on the basis of restriction fragment length polymorphisms revealed considerable genotypic heterogeneity of LA7 corresponding to that previously found for ospA. Native IpLA-7 and recombinant IpLA-7 were recognized by immune sera from infected mice as well as some human sera derived from infected but healthy donors and may thus prove useful as an additional marker for the serodiagnosis of Lyme disease.

Amino Acid Sequence↗
PubMed1999

Human phenol sulfotransferases SULT1A2 and SULT1A1: genetic polymorphisms, allozyme properties, and human liver genotype-phenotype correlations.

Phenol sulfotransferases (PSTs or phenol SULTs) catalyze the sulfate conjugation of phenolic drugs, xenobiotics, and monoamines. Two human PST isoforms have been defined biochemically, a thermostable (TS), or phenol-preferring, and a thermolabile (TL), or monoamine-preferring form. Pharmacogenetic studies showed that levels of both TS PST activity and TS PST thermal stability (an indirect measure of variation in amino acid sequence) in the platelet were regulated by genetic polymorphisms. Subsequent molecular genetic experiments revealed the existence of three human PST genes, two of which, SULT1A1 and SULT1A2, encode proteins with "TS PST-like" activity. We recently reported common nucleotide polymorphisms for SULT1A1 that are associated with variations in platelet TS PST activity and thermal stability. In the present experiments, we set out to determine whether functionally significant DNA polymorphisms also might exist for SULT1A2, to compare the biochemical properties of all common allozymes encoded by SULT1A2 and SULT1A1, and to study phenol SULT genotype-phenotype correlations in the human liver. We phenotyped 61 human liver biopsy samples for TS PST thermal stability and activity. The open reading frames of SULT1A2 and SULT1A1 then were amplified with the polymerase chain reaction and sequenced for each of these hepatic tissue samples. We observed 13 SULT1A2 alleles that encoded 6 allozymes. These alleles were in linkage disequilibrium with alleles for SULT1A1. Biochemical characterization of common allozymes encoded by both genes suggested that SULT1A1 was primarily responsible for "TS PST phenotype" in the human liver. In summary, both SULT1A2 and SULT1A1 have a series of common alleles encoding enzymes that differ functionally and are associated with individual differences in phenol SULT properties in the liver.

Animals↗