Ethnic differences in the frequency of distribution of serum cholinesterase activity in the Iranian population

One thousand Iranians belonging to 5 different Iranian ethnic groups were tested for butyrylcholinesterase (BChE) activity and phenotype. The phenotype was measured as percent inhibition in the presence of dibucaine. It was found that the Iranian population had an extraordinarily high frequency of the atypical variant of butyrylcholinesterase. 70% to 80% of Iranians carried the atypical mutation (Asp70Gly) on one allele. This contrasts with European and American populations where only 4% carry the atypical allele. The atypical variant of butyrylcholinesterase is known to be associated with prolonged apnea after administration of the muscle relaxants succinylcholine and mivacurium, and is also thought to be associated with abnormal sensitivity to cocaine toxicity. This study demonstrates that the ethnic background of a person has an important role in a person's response to drugs.     

The average frequency of private alleles in a partially isolated population

An analytic model is developed to explore the relationship between gene flow, selection, and genetic drift. We assume that a single copy of a mutant allele appears in a finite, partially isolated population and allow for the effects of immigration, genic selection, and mutation on the frequency of the mutant. Our concern is with the distribution of the mutant's frequency before it either is lost from the population or emigrates. Before either of these events, the allele will be a “private allele” and would be found in only one of several populations in a larger collection. Slatkin [(1985) Evolution 39, 53–65] found several simple properties of private alleles in his simulations. We use the method developed by Karlin and Tavaré [(1980) Genet. Res. 37, 33–46; (1981a), Theor. Pop. Biol. 19, 187–214; (1981b) Theor. Pop. Biol. 19, 215–229] for a model similar to ours to obtain a diffusion equation with a “killing term” and obtain the mean and variance of the mutant's frequency and its expected frequency in samples of a specified size. There is only fair agreement between the analytic results from this model and those from Slatkin's (loc. cit.) simulations. The rescaling method used to obtain the results indicates that if emigration is relatively frequent, the distribution of rare alleles is governed largely by the balance between genetic drift and emigration, with selection, mutation, and immigration playing a lesser role.     

Interference free and simplyfied liquid chromatography-based determination of thiopurine S-methyltransferase activity in erythrocytes

The determination of the thiopurine S-methyltransferase activity (TPMT; EC 2.1.1.67) has become an important issue during thiopurine therapy due to its known genetic polymorphism resulting in a wide range of TPMT activity. Therefore, the standard thiopurine drug regimen is associated with increased hematopoetic toxicity in patients with low or absent TPMT activity, whereas patients with high activity may be insufficiently treated. However, presently available methods are labour intensive and time consuming and tend towards too high or too low enzyme activity due to their methodological approach. The use of instable substrate solutions (6-MP or 6-TG), organic solvents like dimethyl sulfoxide and too high substrate and co-substrate saturation concentrations contribute to this phenomenon. We therefore, established an optimized and fast isocratic HPLC linked TPMT assay based on the enzymatic methylation of mercaptopurine or thioguanine in RBC lysates with S-adenosyl-l-methionine as methyl donor. Unspecific non-enzymatic methylation was not detectable. The recovery of 6-methyl-mercaptopurine was 97-102%, the intra- and interday variation between 1.0 and 5.0%, respectively. The assay dispenses with a time consuming extraction procedure with organic solvents, a heating step, and a gradient elution and is therefore, favourable for clinical routine application. The TPMT activity was measured in 62 untreated children with acute lymphoblastic leucemia at the time of diagnosis (activity = 34.0+/-10.6 nmol/g Hb/h, range: 11.5-55.4 nmol/g Hb/h) and in 12 adult healthy volunteers (62.8+/-7.7 nmol/g Hb/h, range: 48-82 nmol/g Hb/h) reflecting the wide measurable TPMT activity found in erythrocytes.     

In vitro characterization of four novel non-functional variants of the thiopurine S-methyltransferase

Human thiopurine S-methyltransferase (TPMT) is an enzyme responsible for the detoxification of widely used thiopurine drugs such as azathioprine (Aza). Its activity is inversely related to the risk of developing severe hematopoietic toxicity in certain patients treated with standard doses of thiopurines. DNA samples from four leucopenic patients treated with Aza were screened by PCR-SSCP analysis for mutations in the 10 exons of the TPMT gene. Four missense mutations comprising two novel mutations, A83T (TPMT*13, Glu(28)Val) and C374T (TPMT*12, Ser(125)Leu), and two previously described mutations, G430C (TPMT*10, Gly(144)Arg) and T681G (TPMT*7, His(227)Gln) were identified. Using a recombinant yeast expression system, kinetic parameters (K(m) and V(max)) of 6-thioguanine S-methylation of the four TPMT variants were determined and compared to those obtained with wild-type TPMT. This functional analysis suggests that these rare allelic variants are defective TPMT alleles. The His(227)Gln variant retained only 10% of the intrinsic clearance value (V(max)/K(m) ratio) of the wild-type enzyme. The Ser(125)Leu and Gly(144)Arg variants were associated with a significant decrease in intrinsic clearance values, retaining about 30% of the wild-type enzyme, whereas the Glu(28)Val variant produced a more modest decrease (57% of the wild-type enzyme). The data suggest that the sporadic contribution of the rare Glu(28)Val, Ser(125)Leu, Gly(144)Arg, and His(227)Gln variants may account for the occurrence of altered metabolism of TPMT substrates. These findings improve our knowledge of the genetic basis of interindividual variability in TPMT activity and would enhance the efficiency of genotyping methods to predict patients at risk of inadequate responses to thiopurine therapy.     

Analysis and frequency of bovine lymphocyte antigen (BoLA-DRB3) alleles in Iranian Holstein cattle

The bovine lymphocyte antigen (BoLA-DRB3) gene encodes cell surface glycoproteins that initiate immune response by presenting processed antigenic peptides to CD4 T helper cells. DRB3 is the most polymorphic bovine MHC class II gene which encodes the peptide-binding groove. DRB3 gene has been extensively evaluated as a candidate marker for association with various bovine diseases and immunological traits. This study describes genetic variability in the BoLA-DRB3 in Iranian Holstein cattle. This is the first study of the DNA polymorphism of the BoLA-DRB3 gene in Iranian Holstein cattle. Hemi-nested PCR-RFLP method is used for identification the frequency of BoLA-DRB3 alleles. The BoLA-DRB3 locus is highly polymorphic in the studied herd (26 alleles). Almost 67% of the alleles were accounted for four alleles (BoLA-DRB3.2*8, *24, *11 and *16) in Iranian Holstein cattle. The DRB3.2*8 allele frequency (26.6%) was higher than the others. The frequencies of the DRB3.2*54, *37, *36, *28, *25, *14, *13, *10, *1 alleles were lower than 1%. Significant distinctions have been found between Iranian Holstein cattle and other cattle breeds studied. In Iranian Holstein cattle the alleles (BoLA-DRB3.2*22, *2 and *16) associated with a lower risk of cystic ovarian disease in Holstein cattle are found. The alleles associated with the resistance to mastitis and to bovine leukemia virus infection BoLA-DRB3.2*11 and *23 are detected with the frequencies 10.4% and 4.4%, respectively. Thus in the Iranian Holstein cows studied are found alleles which are associated with resistance to various diseases. The method of DNA-typing of animals can be used in agricultural practice for BoLA-DRB3 allele genotyping of cattle in order to reduce spreading of alleles providing susceptibility to mastitis or leukemia in cattle herds.     

The investigation of allele and genotype frequencies of human C3 (rs2230199) in south Iranian population

The complement system is an important mediator of natural and acquired immunity. The complement system genes coding complement proteins have polymorphisms. Hereditary deficiencies of this system predispose to autoimmune conditions such as age-dependent macular degeneration or impairment of immunity against microorganisms. When different populations are compared, the frequency of complement polymorphism shows a very marked geographical distribution. The frequency of the functional polymorphism rs2230199 (Arg80Gly; C > G) in the C3 gene was determined in population from south of Iran (n = 200), using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). One hundred thirty-eight persons (69 %) were homozygous for C allele (CC or SS); fifty-six person (28 %) heterozygote GC (FS) and six people were homozygous for G allele (GG or FF) (3 %). The allele frequency was 82 % for C3S and 18 % for C3F. A distribution of C3C allele frequency in our population is different from the reports of Asians (100 %); Indians (90-98 %); African-American (93 %); Africans (99 %) and south Brazilian (97 %). However, this finding is similar with the findings Caucasian (80-82 %) ( http://www.ncbi.nlm.nih.gov/SNP ); Americans (80 %); Pushtoon, Hazaras, Osbek and Tajik ethnic groups in Afghanistan (88-90 %) and Tunisian population (84 %). Our study confirmed significant inter-ethnic differences in C3 (rs2230199) frequencies between south Iranians and other ethnic groups. The analysis of genetic variation in complement genes is a tool to provide new insights into the evolution of the human immune system.     

Determination of thiopurine S-methyltransferase (TPMT) activity by comparing various normalization factors: reference values for Estonian population using HPLC-UV assay

Thiopurine S-methyltransferase (TPMT; EC 2.1.1.67) is the key enzyme in the metabolism of thiopurine drugs. Determination of TPMT activity has been used for the individualization of thiopurine dose. We developed HPLC-UV assay for the determination of TPMT activity in human erythrocytes using 6-mercaptopurine as a substrate. Various extraction and chromatographic conditions were compared. In-house developed extraction with acetonitrile provided the lowest limit of quantification. TPMT activity was determined in 99 previously genotyped healthy Estonians. TPMT activity was expressed as the formation of 6-methylmercaptopurine ng/ml/h and normalized either to haemoglobin, haematocrit, erythrocyte count or protein content. The receiver-operating characteristic curve analysis revealed similar accuracy values for TPMT activity in predicting heterozygous and wild type individuals for each method of calculation. In healthy Estonians, TPMT activity varied from 21.5 to 129.6 ng/ml/h. For heterozygous individuals (n = 18), TPMT activity was 48.1 +/- 11.7 ng/ml/h. Wild type individuals (n = 81) revealed significantly higher TPMT activity 79.3 +/- 20.7 ng/ml/h (P < 0.001). This sensitive HPLC assay for quantitative determination of TPMT activity could easily be used in clinical settings. Under constant experimental conditions for haemolysate preparation no normalization is required.     

Molecular dynamics simulation of a human thiopurine S-methyltransferase complexed with 6-mercaptopurine model

Human thiopurine S-methyltransferase (TPMT) is an essential protein in 6-mercaptopurine (6MP) drug metabolism. To understand thepharmacogenetics of TPMT and 6MP, X-ray co-crystal structures of TPMT complexes with S-adenosyl-L-methionine (AdoMet) and 6MPare required. However, the co-crystal structure of this complex has not been reported because 6MP is poorly water soluble. We usedmolecular dynamics (MD) simulation to predict the structure of the complex of human TPMT-AdoHcy(CH₂)6MP, where the sulfur atoms ofAdoHcy and 6MP were linked by a CH₂ group. After 1300 picoseconds of MD simulation, the trajectory showed that 6MP was stabilized inthe TPMT active site by formation of non-bonded interactions between 6MP and Phe40, Pro196 and Arg226 side chains of TPMT. Theintersulfur distance between AdoHcy and 6MP as well as the binding modes and the interactions of our TPMT-AdoHcy model areconsistent with those observed in the X-ray crystal structure of murine TPMT-AdoHcy-6MP complex. The predicted binding modes ofAdoHcy and 6MP in our model are consistent with those observed in murine TPMT X-ray crystal structures, which provides structuralinsights into the interactions of TPMT, AdoHcy, and 6MP at the atomic level and may be used as a starting point for further study ofthiopurine drug pharmacogenetics.     

The spatial distribution of transient alleles in a subdivided population: a simulation study

The spatial distributions of newly introducted alleles in a subdivided population are generated using a computer program to model the processes of selection, gene flow and genetic drift. Advantageous, neutral and deleterious alleles are considered, and certain aspects of the patterns generated by new alleles that are ultimately fixed and ultimately lost are examined. To characterize the spatial pattern of rare alleles, the distribution, P(i), the probability that the new allele is found in exactly i local populations before it is lost, is defined and estimated from the simulations. The shape of the P(i) distribution is surprisingly similar for selected and neutral alleles. For advantageous alleles going to fixation, the "wave of advance" is set up quickly, but stochastic effects reduce the wave speed from Fisher's (1937) value. Gene flow is much more effective in dispersing alleles in a two-dimensional array than in one dimension. Long distance gene flow has a much smaller effect in two dimensions than in one dimension.     

Determination of thiopurine S-methyltransferase activity in erythrocytes using 6-thioguanine as substrate and a non-extraction liquid chromatographic technique

A non-extraction high-performance liquid chromatographic (HPLC) method has been developed for the determination of 6-methylthioguanine (6-MTG), as part of the determination of thiopurine S-methyltransferase activity (TPMT) in erythrocytes. Erythrocyte lysate is added to a glass vial containing substrates and incubation buffer, which is then sealed for the rest of the analysis. Enzyme incubation, sample preparation, and analysis are then undertaken without further sample-handling steps. The need for a solvent extraction step has been overcome by heating the incubate to 85 degrees C to stop the enzyme reaction. The heat inactivation step precipitates protein which upon centrifugation forms a thin film in the bottom of the glass vial enabling the supernatant to be injected directly onto the HPLC system. The assay shows excellent precision and recovery with a within-batch imprecision giving a co-efficient of variation of 2.9% (mean=41.5 nmol 6-MTG/gHb/h, n=10) and 5.1% (mean=12.6 nmol 6-MTG/g Hb/h, n=10). The between-batch imprecision gives a co-efficient of variation of 8.2% (mean=11.1 nmol 6-MTG/gHb/h, n=11) and 7.3% (mean=41.0 nmol 6-MTG/gHb/h, n=16). Determination of the TPMT activity in 120 people shows a range of enzyme activity of 11.3-63.8 nmol 6-MTG/gHb/h with a mean and median activity of 34.8 and 34.2 nmol 6-MTG/gHb/h, respectively. TPMT is increasingly used in clinical practice to ensure optimisation of treatment with thioguanine drugs. This direct HPLC method minimises sample-handling, reduces inherent imprecision, the possibility of laboratory error and with the potential for further automation, makes it ideal for use in a regional referral laboratory.     

The distribution of rare alleles

Population geneticists have long been interested in the behavior of rare variants. The definition of a rare variant has been the subject of some debate, centered mainly on whether alleles with small relative frequency should be considered rare, or whether alleles with small numbers should be. We study the behavior of the counts of rare alleles in samples taken from a population genetics model that allows for selection and infinitely-many-alleles mutation structure. We show that in large samples the counts of rare alleles — those represented once, twice, ... — are approximately distributed as a Poisson process, with a parameter that depends on the total mutation rate, but not on the selection parameters. This result is applied to the problem of estimating the fraction of neutral mutations.     

Four human thiopurine s-methyltransferase alleles severely affect protein structure and dynamics

Thiopurine S-methyltransferase (TPMT) metabolizes cytotoxic thiopurine drugs used in the treatment of leukemia and inflammatory bowel disease. TPMT is a major pharmacogenomic target with 23 alleles identified to date. Several of these alleles cause rapid protein degradation and/or aggregation, making it extremely difficult to study the structural impact of the TPMT polymorphisms experimentally. We, therefore, have performed multiple molecular dynamics simulations of the four most common alleles [TPMT*2 (A80P), *3A (A154T/Y240C), *3B (A154T) and *3C (Y240C)] to investigate the molecular mechanism of TPMT inactivation at an atomic level. The A80P polymorphism in TPMT*2 disrupts helix α3 bordering the active site, which breaks several salt-bridge interactions and opens up a large cleft in the protein. The A154T polymorphism is located within the co-substrate binding site. The larger threonine alters the packing of substrate-binding residues (P68, L69, Y166), increasing the solvent exposure of the polymorphic site. This packing rearrangement may account for the complete lack of activity in the A154T mutant. The Y240C polymorphism is located in β-strand 9, distant from the active site. Side-chain contacts between residue 240 and helix α8 are lost in TPMT*3C. Residues 154 and 240 in TPMT*3A are connected through a hydrogen-bonding network. The dual polymorphisms result in a flattened, slightly distorted protein structure and an increase in the thiopurine-binding site solvent accessibility. The two variants that undergo the most rapid degradation in vivo, TPMT*2 and *3A, are also the most deformed in the simulations.     

The distribution of coalescence times and distances between microsatellite alleles with changing effective population size

We investigate the effects of past changes of the effective population size on the present allelic diversity at a microsatellite marker locus. We first derive the analytical expression of the generating function of the joint probabilities of the time to the Most Recent Common Ancestor for a pair of alleles and of their distance (the difference in allele size). We give analytical solutions in the case of constant population size and the geometrical mutation model. Otherwise, numerical inversion allows the distributions to be calculated in general cases. The effects of population expansion or decrease and the possibility to detect an ancient bottleneck are discussed. The method is extended to samples of three and four alleles, which allows investigating the covariance structure of the frequencies f(k) of pairs of alleles with a size difference of k motifs, and suggesting some approaches to the estimation of past demography.     

Plasminogen Activator Inhibitor-1 (PAI-1) gene 4G/5G alleles frequency distribution in the Lebanese population

Plasminogen activator inhibitor-1 (PAI-1) is an inhibitor of fibrinolysis. Increased plasma PAI-1 levels play an essential role in the pathogenesis of cardiovascular risk and other diseases associated with thrombosis. The 4G/5G polymorphism of the PAI-1 promoter region has been extensively studied in different populations. We studied 160 healthy unrelated Lebanese individuals using a reverse hybridization PCR assay to detect the 5G/5G, 4G/5G and, 4G/4G genotypes of the PAI-1 gene and the frequencies of the 4G and 5G alleles. We found that 4G/5G genotype was the most prevalent (45.6%) followed by 5G/5G (36.9%) and 4G/4G (17.5%). The frequencies of the 4G and 5G alleles were calculated to be 0.403 and 0.597, respectively. Compared to other ethnic communities, the Lebanese population was found to harbour a relatively high prevalence of the rare 4G allele. This, in turn, may predispose this population to develop cardiovascular diseases and other thrombotic clinical conditions. This study aids to enhance our understanding of the genetic features of the Lebanese population.     

华南地区人口压力增长对猕猴(Macaca spp.)分布的影响

通过研究本世纪初和现今两个历史时期华南地区猕猴分布、人口和耕地变化发现,猕猴在本世纪初为随机分布,现今已为聚集分布。在现今生产力水平下,180人·km^-2是猕猴分布限量。本世纪初区内有猴分布的县(市)为61%,现今仅为23.47%.21世纪30年代前后预计尚余15.2%县(市)仍有猴分布,主要分布在湘西北、桂西及湘、桂、粤交界的南岭一带,琼西南尚余少数。     

Estimation of the frequency of hexosaminidase a variant alleles in the American Jewish population.

There appear to be several alleles of the hexosaminidase A (HEX A) gene that lead to different clinical syndromes. In addition to the infantile-onset Tay-Sachs disease (TSD), there is a juvenile-onset and an adult-onset form, which are also characterized by low HEX A levels. There are also apparently healthy adults with low HEX A activity. Based primarily on data from population screening for TSD carrier status, we estimate the allele frequency of the combined variant alleles for which data are available to be about 4.5 x 10(-4) and the frequency of adults showing zero HEX A levels (when tested using artificial substrate) to be about 1:67,000. The implications for population screening and prenatal diagnosis are discussed.     

The distribution of homozygosity for four alleles

The stationary density of homozygosity is obtained for a locus with four possible alleles and symmetric mutation between them. As conjectured by F. M. Stewart (1976, Theoret. Pop. Biol. 9, 188-201) this density has spikes at 1/3 and 1/2. The density under heterozygote selection is also given.     

Further evidence for sexual reproduction in Rhynchosporium secalis based on distribution and frequency of mating-type alleles

Rhynchosporium secalis, the causal agent of scald on barley, is thought to be exclusively asexual because no teleomorph has been found. Partial sequences of the HMG-box and alpha-domain of Rhynchosporium secalis isolates were identified and used to develop a PCR assay for the mating-type locus. PCR amplification of only one of these two domains was possible in each strain, suggesting that R. secalis has a MAT organization that is similar to other known heterothallic fungi. A multiplex PCR with primers amplifying either a MAT1-1- or MAT1-2-specific amplicon was used to determine the distribution of mating types in several R. secalis populations. In total, 1101 isolates from Australia, Switzerland, Ethiopia, Scandinavia, California, and South Africa were included in the analysis. Mating types occurred in equal frequencies for most of these populations, suggesting frequency-dependent selection consistent with sexual reproduction. In addition, both mating types were frequently found occupying the same lesion or leaf, providing opportunities for isolates of opposite mating type to interact and reproduce sexually. We propose that R. secalis should be considered a sexual pathogen, although the sexual cycle may occur infrequently in some populations.