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Results for “Molecular polymorphism”

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PubMed2003

Lineage-specific selection in human mtDNA: lack of polymorphisms in a segment of MTND5 gene in haplogroup J.

Human mitochondrial DNA (mtDNA) is a nonrecombining genome that codes for 13 subunits of the mitochondrial oxidative phosphorylation system, 2 rRNAs, and 22 tRNAs. Mutations have accumulated sequentially in mtDNA lineages that diverged tens of thousands of years ago. The genes in mtDNA are subject to different functional constraints and are therefore expected to evolve at different rates, but the rank order of these rates should be the same in all lineages of a phylogeny. Previous studies have indicated, however, that specific regions of mtDNA may have experienced different histories of selection in different lineages, possibly because of lineage-specific interactions or environmental factors such as climate. We report here on a survey for lineage-specific patterns of nucleotide polymorphism in human mtDNA. We calculated molecular polymorphism indices and neutrality tests for classes of functional sites and genes in 837 human mtDNA sequences, compared the results between continent-specific mtDNA lineages, and used two sliding window methods to identify differences in the patterns of polymorphism between haplogroups. A general correlation between nucleotide position and the level of nucleotide polymorphism was identified in the coding region of the mitochondrial genome. Nucleotide diversity in the protein-coding sequence of mtDNA was generally not much higher than that found for many genes in nuclear DNA. A comparison of nonsynonymous/synonymous rate ratios in the 13 protein-coding genes suggested differences in the relative levels of selection between haplogroups, including the European haplogroup clusters. Interestingly, a segment of the MTND5 gene was found to be almost void of segregating sites and nonsynonymous mutations in haplogroup J, which has been associated with susceptibility to certain complex diseases. Our results suggest that there are haplogroup-specific differences in the intensity of selection against particular regions of the mitochondrial genome, indicating that some mutations may be non-neutral within specific phylogenetic lineages but neutral within others.

DNA, Mitochondrial↗

PubMed2006

Phenotypic variation and natural selection at catsup, a pleiotropic quantitative trait gene in Drosophila.

Quantitative traits are shaped by networks of pleiotropic genes . To understand the mechanisms that maintain genetic variation for quantitative traits in natural populations and to predict responses to artificial and natural selection, we must evaluate pleiotropic effects of underlying quantitative trait genes and define functional allelic variation at the level of quantitative trait nucleotides (QTNs). Catecholamines up (Catsup), which encodes a negative regulator of tyrosine hydroxylase , the rate-limiting step in the synthesis of the neurotransmitter dopamine, is a pleiotropic quantitative trait gene in Drosophila melanogaster. We used association mapping to determine whether the same or different QTNs at Catsup are associated with naturally occurring variation in multiple quantitative traits. We sequenced 169 Catsup alleles from a single population and detected 33 polymorphisms with little linkage disequilibrium (LD). Different molecular polymorphisms in Catsup are independently associated with variation in longevity, locomotor behavior, and sensory bristle number. Most of these polymorphisms are potentially functional variants in protein coding regions, have large effects, and are not common. Thus, Catsup is a pleiotropic quantitative trait gene, but individual QTNs do not have pleiotropic effects. Molecular population genetic analyses of Catsup sequences are consistent with balancing selection maintaining multiple functional polymorphisms.

Animals↗

PubMed1995

Properties of statistical tests of neutrality for DNA polymorphism data.

A class of statistical tests based on molecular polymorphism data is studied to determine size and power properties. The class includes Tajima's D statistic as well as the D* and F* tests proposed by Fu and Li. A new method of constructing critical values for these tests is described. Simulations indicate that Tajima's test is generally most powerful against the alternative hypotheses of selective sweep, population bottleneck, and population subdivision, among tests within this class. However, even Tajima's test can detect a selective sweep or bottleneck only if it has occurred within a specific interval of time in the recent past or population subdivision only when it has persisted for a very long time. For greatest power against the particular alternatives studied here, it is better to sequence more alleles than more sites.

Computer Simulation↗

PubMedDate not supplied

[Polymorphism of prolactin in amniotic fluid of women at various times of pregnancy].

The level and molecular forms of prolactin (PRL) in amniotic fluid of pregnant women were investigated at various time of pregnancy with the help of radioimmunoassay, electrophoresis in polyacrylamide gel and immune blotting technique using poly- and monoclonal antibodies to human hypophyseal prolactin (PRL). Changes in the level of immunoreactive PRL in amniotic fluid had the shape of a Gaussian curve with a maximum at 22-29 weeks. Amniotic PRL was characterized by molecular polymorphism. A conclusion has been made that amniotic fluid PRL in pregnancy presents an independent pool of hormones, unrelated to hypophyseal PRL.

Amniotic Fluid↗

PubMed2002

Association of cholecystokinin A receptor gene polymorphism with cholelithiasis and the molecular mechanisms of this polymorphism.

BACKGROUND: The etiology of gallstone formation is multifactorial, and genetic factors are involved. The genetic variations of cholecystokinin A receptor (CCK-AR) in patients having gallstones and the molecular mechanisms of this polymorhpism were examined. The involvement of CCK-AR in gallstone formation was confirmed using CCK-AR gene knockout mice. METHODS: CCK-AR gene expression was determined by Northern transfer analysis in gallbladders with or without gallstones. Genetic variations were determined by Southern blot and by direct sequencing. Molecular mechanisms in terms of the transcriptional activity and methylation status were examined. Finally, we investigated whether gallstone formation was enhanced in CCK-AR gene knockout mice. RESULTS: The gene expression of CCK-AR was significantly decreased in gallbladders with gallstones compared to those without gallstones. No genetic variations were detected in the coding region, but two sequence variations were detected in the promoter region in gallstone patients. However, no significant differences were found for the promoter activities of polymorphic promoter constructs. In contrast, less methylation in the promoter region was related to substantial expression of the CCK-AR gene. Gallstone formation was enhanced in CCK-AR gene knockout mice. The homozygote (GG/TT) polymorphism of the CCK-AR gene showed a significantly higher percentage of body fat. CONCLUSIONS: Deteriorating gallbladder contractions, possibly induced by alterations in the CCK-AR gene, as well as CCK-AR gene polymorphism, promoted gallstone formation.

Adenocarcinoma↗

PubMed1991

Immunogenetics of HLA.

The enormous contributions of Professor Karl Landsteiner are summarized focusing on his discovery of the ABO, MN, and P blood group systems as well as his conceptualization of the hapten concept. The HLA system, the major histocompatibility complex in humans, is discussed from the point of view of its genetic organization, the polymorphism that is recognized by T lymphocytes and the presently defined molecular polymorphism. The structure-function relationship of T cell recognition of class II molecules, based on the known crystallographic structure of an HLA class I molecule, is presented.

Base Sequence↗

PubMed2000

Molecular genetics of RH.

BACKGROUND AND OBJECTIVES: The two Rhesus proteins, RhD and RhCE, constitute one of the clinically most relevant blood group antigen system. In the last two years, the understanding of RH molecular genetics has increased considerably. The state of the current knowledge was briefly summarised. MATERIALS AND METHODS: Recent reviews, original work since 1999 and own results were utilised. RESULTS: The structure of the RH gene locus comprising RHD, RHCE and SMP1 was presented. True RHD genotyping became feasible by establishing the molecular basis of the most prevalent RH haplotype in whites harbouring the RHD gene deletion and of the RHD pseudogene RHD psi in Africans. Molecular and serologic characteristics of weak D and partial D alleles were compared. Closely related alleles for both, weak D and partial D, were collated as examples contributing to the understanding of RH phylogeny. CONCLUSION: The RH gene locus is a model system for molecular polymorphism in clustered genes and suitable for studying molecular evolution in humans. It lends itself for developing molecular diagnostics because its genetics is appropriately complex and challenging; yet the expressed phenotypes have been studied for decades and are well understood. Legal and ethical issues that are rightfully of public concern would not be infringed if RH genotyping will be attempted on a massive scale.

Alleles↗

PubMed2003

Patterns of polymorphism detected in the chloroplast and nuclear genomes of barley landraces sampled from Syria and Jordan.

In order to examine how molecular polymorphism in barley landraces, sampled from five different ecogeographical regions of Syria and Jordan, is organised and partitioned, genetic variability at 21 nuclear and 10 chloroplast microsatellite loci were examined. Chloroplast polymorphism was detected, with most variation being ascribed to differences between the five regions (Fst 0.45) and to within sites within each region (Fst 0.44). Moreover, the distribution of chloroplast polymorphism is structured and not distributed randomly across the barley landraces sampled. From a total of 125 landrace accessions (five lines from each of five sites from each of five regions) genotyped with 21 SSRs a total of 244 alleles were detected, of which 38 were common to the five regions sampled. Most nuclear variation was detected within sites. Significant differentiation between sites (Fst 0.29) was detected with nuclear SSRs and this partially mirrored polymorphism in the chloroplast genome. Strong statistical associations/interaction was also detected between the chloroplast and nuclear SSRs, together with non-random association (linkage disequilibrium) of alleles at both linked and unlinked SSR loci. These results are discussed in the context of adaptation of landraces to the extreme environment, the concept of 'adapted gene complexes' and the exploitation of landraces in breeding programmes.

Analysis of Variance↗

PubMed2003

XRCC3 genetic polymorphism, smoking, and lung carcinoma risk in minority populations.

BACKGROUND: The XRCC3 protein participates in DNA double-strand breaks and recombinational repair. A single C-to-T nucleotide change at codon 241 (Thr241Met) has been identified in the XRCC3 gene. Using a hospital-based case-control approach, the authors studied the XRCC3 polymorphism as a possible genetic risk factor for lung carcinoma in African Americans and Mexican Americans. METHODS: A total of 112 patients with lung carcinoma were frequency matched with 190 control participants on the basis of age, gender, and ethnicity. Polymerase chain reaction-restriction fragment length polymorphism molecular analysis was used successfully to identify the XRCC3 polymorphism in peripheral blood lymphocytes. RESULTS: No significant association between the XRCC3 variant allele polymorphism (odds ratio [OR], 1.25; 95% confidence interval [95% CI], 0.72-2.15) and lung carcinoma risk was noted. However, a significantly increased risk for lung carcinoma (OR, 5.20; 95% CI, 1.59-17.03) was evident in heavy smokers with the variant T-allele genotypes. Furthermore, a joint effect of the T-allele and heavy smoking was observed (OR, 37.31; 95% CI, 11.43-121.72). CONCLUSIONS: The XRCC3 polymorphism appeared to be associated with increased risk of lung carcinoma in certain subgroups. It is plausible that the association is very heavily dependent on the degree of smoking. Further studies with larger sample sizes will be necessary to confirm these findings.

Adult↗

PubMed2006

Genetic variation in Drosophila melanogaster resistance to infection: a comparison across bacteria.

Insects use a generalized immune response to combat bacterial infection. We have previously noted that natural populations of D. melanogaster harbor substantial genetic variation for antibacterial immunocompetence and that much of this variation can be mapped to genes that are known to play direct roles in immunity. It was not known, however, whether the phenotypic effects of variation in these genes are general across the range of potentially infectious bacteria. To address this question, we have reinfected the same set of D. melanogaster lines with Serratia marcescens, the bacterium used in the previous study, and with three additional bacteria that were isolated from the hemolymph of wild-caught D. melanogaster. Two of the new bacteria, Enterococcus faecalis and Lactococcus lactis, are gram positive. The third, Providencia burhodogranaria, is gram negative like S. marcescens. Drosophila genotypes vary highly significantly in bacterial load sustained after infection with each of the four bacteria, but mean loads are largely uncorrelated across bacteria. We have tested statistical associations between immunity phenotypes and nucleotide polymorphism in 21 candidate immunity genes. We find that molecular variation in some genes, such as Tehao, contributes to phenotypic variation in the suppression of only a subset of the pathogens. Variation in SR-CII and 18-wheeler, however, has effects that are more general. Although markers in SR-CII and 18-wheeler explain >20% of the phenotypic variation in resistance to L. lactis and E. faecalis, respectively, most of the molecular polymorphisms tested explain <10% of the total variance in bacterial load sustained after infection.

Animals↗

PubMed1995

Analysis of methicillin-resistant and methicillin-susceptible Staphylococcus aureus by a molecular typing method based on coagulase gene polymorphisms.

A molecular typing method for Staphylococcus aureus based on coagulase gene polymorphisms (coagulase gene typing) was evaluated by examining a total of 240 isolates which comprised 210 methicillin-resistant S. aureus (MRSA) and 30 methicillin-susceptible S. aureus (MSSA) collected from a single hospital. By AluI restriction enzyme digestion of the PCR-amplified 3'-end region of the coagulase gene including 81-bp repeated units, the MRSA and MSSA isolates examined were divided into 6 and 12 restriction fragment length polymorphism (RFLP) patterns, respectively, whereas five patterns were commonly detected in MRSA and MSSA. MRSA isolates that showed a particular RFLP pattern were considered to be predominant in the hospital. Coagulase typing with type-specific antisera was also performed for all S. aureus isolates for comparison. Coagulase types II and VII were most frequently detected and included isolates with four and five different AluI RFLP patterns, respectively, whereas each of the other coagulase types corresponded to a single RFLP pattern. These results indicated that RFLP typing was more discriminatory than serological typing, for typing S. aureus and demonstrated its utility in epidemiologic investigation of S. aureus infection in hospitals.

Bacterial Typing Techniques↗

PubMed1996

Detecting non-neutral heterogeneity across a region of DNA sequence in the ratio of polymorphism to divergence.

Natural selection, in the form of balancing selection or selective sweeps, can result in a decoupling of the amounts of molecular polymorphism and divergence. Thus natural selection can cause some areas of DNA sequence to have greater silent polymorphism, relative to divergence between species, than other areas. It would be useful to have a statistical test for heterogeneity in the polymorphism to divergence ratio across a region of DNA sequence, one that could identify heterogeneity greater than that expected from the neutral processes of mutation, drift, and recombination. The only currently available test requires that a region be arbitrarily divided into sections that are compared with each other, and the subjectivity of this division could be problematic. Here a test is proposed in which runs of polymorphic and fixed sites are counted, where a "run" is a set of one or more sites of one type preceded and followed by the other type. The number of runs is smaller than otherwise expected if polymorphisms are clumped together. By simulating neutral evolution and comparing the observed number of runs to the simulations, a statistical test is possible which does not require any a priori decisions about subdivision.

Animals↗

PubMed2005

The molecular genetics of blood group polymorphism.

Nearly 300 blood group specificities on red cells are known, many of which are polymorphic. The molecular mechanisms responsible for these polymorphisms are diverse, though the majority represent single nucleotide polymorphisms (SNPs) encoding amino acid substitutions. Other mechanisms include the following: gene deletion; single nucleotide deletion and sequence duplication, which introduce reading-frame shifts; nonsense mutation; intergenic recombination between closely-linked genes, giving rise to hybrid genes and hybrid proteins; and a SNP in the promoter region of a blood group gene. Examples of these genetic mechanisms are taken from the ABO, Rh, Kell, and Duffy blood group systems. Null phenotypes, in which no antigens of a blood group system are expressed, are not generally polymorphic, but provide good examples of the effect of inactivating mutations on blood group expression. As natural human 'knock-outs' they provide useful clues to the functions of blood group antigens. Knowledge of the molecular bases to blood group polymorphisms provides a means to predict blood group phenotype from genomic DNA with a high degree of accuracy. This currently has two main applications in transfusion medicine: for determining fetal blood groups to assess whether the fetus is at risk from haemolytic disease; and to determine blood group phenotypes in multiply transfused, transfusion-dependent patients, where serological tests are precluded by the presence of donor red cells. Other applications are being developed for the future.

Blood Group Antigens↗

PubMed2001

Isolation and characterization of polymorphic DNA from Entamoeba histolytica.

An important gap in our understanding of the epidemiology of amebiasis is what determines the outcome of Entamoeba histolytica infections. To investigate the possible existence of invasive and noninvasive strains as one factor, the ability to differentiate individual isolates of E. histolytica is necessary. Two new loci containing internal repeats, locus 1-2 and locus 5-6, have been isolated. Each contains a single repeat block with two types of related direct repeats arranged in tandem. Southern blot analysis suggests that both loci are multicopy and may themselves be arranged in tandem arrays. Three other previously reported, internally repetitive loci containing at least two repeat blocks each with one or more related repeat units were also investigated. PCR was used to study polymorphism at each of these loci, which was detected to various degrees in each case. Variation was seen in the total number of bands obtained per isolate and their sizes. Nucleotide sequence comparison of loci 1-2 and 5-6 in five axenic isolates revealed differences in the number of repeat units, which correlated with the observed PCR product size variation, and in repeat sequence. Use of multiple loci collectively allowed differentiation of a majority of the 13 isolates studied, and we believe that these loci have the potential to be used as polymorphic molecular markers for investigating the epidemiology of E. histolytica and the potential existence of genetically distinct invasive and noninvasive strains.

Animals↗

PubMed1992

Expression of syndecan in transformed mouse keratinocytes.

BACKGROUND: Malignant transformation is frequently associated with altered behavior of cells, a phenomenon that also suggests changes in cell-matrix interactions. We have studied expression of syndecan, a cell surface proteoglycan that binds extracellular matrix components and growth factors, in various chemically transformed mouse keratinocyte cell lines that differ in their morphology and tumorigenicity. EXPERIMENTAL DESIGN: A monoclonal antibody, specific for mouse syndecan, and a cDNA clone for mouse syndecan, were used to detect syndecan in seven different keratinocyte cell lines. The glycosaminoglycan composition of syndecan was studied using differential digestions of heparan sulfate and chondroitin sulfate chains. RESULTS: In general, the tumorigenic cells were found to express lower amounts of syndecan, both at protein and mRNA levels, than the nontumorigenic cells. The most tumorigenic cell line CarC revealed barely detectable syndecan expression. Also, molecular polymorphism of syndecan was observed, as three forms of syndecan with different molecular weights appeared on the surfaces of different keratinocytes. The highly tumorigenic cells, that expressed low amounts of syndecan, expressed syndecan with the largest molecular weight. The different molecular weights were shown to reflect an increased amount of both heparan and chondroitin sulfate chains attached to the core protein. An increased shedding of syndecan ectodomain from the membrane-associated domain was observed in cells that express high amounts of mutated Ha-ras p21. CONCLUSIONS: The results suggest, that transformed epithelial cells can modulate the appearance of syndecan on the cell-surface by at least two ways: (a) by altering its glycosylation or (b) by increasing its shedding from the cell surface. These modulations, together with overall suppression of syndecan expression, could be associated with malignant transformation of keratinocytes.

Animals↗

PubMedDate not supplied

Analysis of B complex polymorphism in Rous sarcoma progressor and regressor chickens with B-G, B-F, and B-L beta probes.

Molecular polymorphism of the B complex was studied in serologically defined B19 haplotypes by use of class I, class II, and class IV probes in Southern blot experiments in chickens. All chickens studied shared identical class IV restriction patterns. In contrast, class I and class II probes revealed six and five subtypes of B19 haplotype, respectively. These subtypes may be resolved in three homozygous genotypes and their corresponding heterozygous combinations. Previous genetic selection allowed us to distinguish two subpopulations in these B19 chickens with regard to the fate of Rous sarcoma virus (RSV)-induced tumors. Molecular genotyping was applied to B19 chickens challenged with RSV in order to determine whether there is a correlation between one of the molecularly defined subtypes and the progressor/regressor phenotypes of the chickens. None of the molecularly defined subtypes correlated with the progressor or regressor phenotype of the challenged birds.

Animals↗

PubMed1982

Two aspects of DNA polymorphism and microheterogeneity: molecular electrostatic potential and steric accessibility.

Polymorphism and microheterogeneity of DNA appear today as being capable of having important biological consequences. This paper presents a synthetic view of two major properties of the main known forms of DNA (A, B, alternating B, C, D and Z), namely their molecular electrostatic potentials and steric accessibilities. Variations in these properties are explained in terms of the conformational changes involved and deductions are drawn concerning their influence on the interactive properties of DNA with external agents.

Base Composition↗

PubMed2003

Clinical description and exclusion of candidate genes in a novel autosomal recessively inherited vitreoretinal dystrophy.

OBJECTIVES: To describe the clinical phenotype of a novel autosomal recessively inherited vitreoretinal dystrophy in one generation of a family originating from eastern Switzerland. METHODS: A clinical study including electroretinographic investigations followed by laboratory-based genetic and molecular analysis. Four affected and 3 unaffected members of the family were examined. Ten candidate regions were tested by linkage analysis with highly polymorphic molecular markers or with intragenic restriction fragment length polymorphisms. RESULTS: Of 8 siblings,4 were affected, showing high myopia with pronounced vitreous liquefaction, retinitis pigmentosa-like retinal degeneration, diffuse retinal pigment epithelium atrophy, macular staphylomata, and premature cataract formation. Strikingly abnormal results on electroretinograms, affecting both the rod and the cone systems, revealed an extensive defect of retinal function, unlike those usually found in pathologic myopia. No extraocular manifestations were observed. Three types of nonsyndromic high myopia, Stickler syndrome I, II, and III, Wagner syndrome, Knobloch syndrome, Goldmann-Favre dystrophy, and multiple vitreoretinopathies were excluded by linkage analysis. CONCLUSIONS: The reported phenotype as well as the results of molecular linkage analysis in the siblings described here suggest an autosomal recessively inherited vitreoretinal dystrophy, which, to our knowledge, has not been described until now.

Aged↗