scholarly journals Mutation at the Human D1S80 Minisatellite Locus

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Kuppareddi Balamurugan ◽  
Martin L. Tracey ◽  
Uwe Heine ◽  
George C. Maha ◽  
George T. Duncan
Keyword(s):  
Mutation Rate ◽  
Chromosome 1 ◽  
Infinite Allele Model ◽  
Minisatellite Locus ◽  
Repeat Array ◽  
Mutation Model ◽  
Close Proximity ◽  
Stepwise Mutation ◽  
One Step ◽  
The One

Little is known about the general biology of minisatellites. The purpose of this study is to examine repeat mutations from the D1S80 minisatellite locus by sequence analysis to elucidate the mutational process at this locus. This is a highly polymorphic minisatellite locus, located in the subtelomeric region of chromosome 1. We have analyzed 90,000 human germline transmission events and found seven (7) mutations at this locus. The D1S80 alleles of the parentage trio, the child, mother, and the alleged father were sequenced and the origin of the mutation was determined. Using American Association of Blood Banks (AABB) guidelines, we found a male mutation rate of1.04×10-4and a female mutation rate of5.18×10-5with an overall mutation rate of approximately7.77×10-5. Also, in this study, we found that the identified mutations are in close proximity to the center of the repeat array rather than at the ends of the repeat array. Several studies have examined the mutational mechanisms of the minisatellites according to infinite allele model (IAM) and the one-step stepwise mutation model (SMM). In this study, we found that this locus fits into the one-step mutation model (SMM) mechanism in six out of seven instances similar to STR loci.

scholarly journals VNTR allele frequency distributions under the stepwise mutation model: a computer simulation approach.

Genetics ◽  
1993 ◽  
Vol 134 (3) ◽  
pp. 983-993 ◽  
Author(s):  
M D Shriver ◽  
L Jin ◽  
R Chakraborty ◽  
E Boerwinkle
Keyword(s):  
Tandem Repeats ◽  
Repeat Unit ◽  
Allele Size ◽  
Frequency Distributions ◽  
Mutation Model ◽  
Stepwise Mutation ◽  
One Step ◽  
Simulation Results ◽  
Summary Measures ◽  
The One

Abstract Variable numbers of tandem repeats (VNTRs) are a class of highly informative and widely dispersed genetic markers. Despite their wide application in biological science, little is known about their mutational mechanisms or population dynamics. The objective of this work was to investigate four summary measures of VNTR allele frequency distributions: number of alleles, number of modes, range in allele size and heterozygosity, using computer simulations of the one-step stepwise mutation model (SMM). We estimated these measures and their probability distributions for a wide range of mutation rates and compared the simulation results with predictions from analytical formulations of the one-step SMM. The average heterozygosity from the simulations agreed with the analytical expectation under the SMM. The average number of alleles, however, was larger in the simulations than the analytical expectation of the SMM. We then compared our simulation expectations with actual data reported in the literature. We used the sample size and observed heterozygosity to determine the expected value, 5th and 95th percentiles for the other three summary measures, allelic size range, number of modes and number of alleles. The loci analyzed were classified into three groups based on the size of the repeat unit: microsatellites (1-2 base pair (bp) repeat unit), short tandem repeats [(STR) 3-5 bp repeat unit], and minisatellites (15-70 bp repeat unit). In general, STR loci were most similar to the simulation results under the SMM for the three summary measures (number of alleles, number of modes and range in allele size), followed by the microsatellite loci and then by the minisatellite loci, which showed deviations in the direction of the infinite allele model (IAM). Based on these differences, we hypothesize that these three classes of loci are subject to different mutational forces.

scholarly journals EVALUATION OF THE STEPWISE MUTATION MODEL OF ELECTROPHORETIC MOBILITY: COMPARISON OF THE GEL SIEVING BEHAVIOR OF ALLELES AT THE ESTERASE-5 LOCUS OF DROSOPHILA PSEUDOOBSCURA

Genetics ◽  
1977 ◽  
Vol 87 (1) ◽  
pp. 139-157
Author(s):  
George B Johnson
Keyword(s):  
Electrophoretic Mobility ◽  
Drosophila Pseudoobscura ◽  
Conformational Heterogeneity ◽  
Net Charge ◽  
Free Mobility ◽  
Mutation Model ◽  
Protein Properties ◽  
Stepwise Mutation ◽  
The One ◽  
Multiple Variants

ABSTRACT Seven alleles at the esterase-5 locus of Drosophila pseudoobscura appear approximately uniformly spaced on 5% acrylamide gels. Such stepwise "ladders" in mobility have been used to argue for the charge-state model of electrophoretic mobility. To evaluate this interpretation, flies of the seven strains were examined in replicate electrophoresis on polyacrylamide gels of differing pore size, permitting estimation of the relative contributions of charge and of size/conformation to electrophoretic mobility. Six of the seven strains examined proved to be heterogeneous, containing multiple variants that migrate to similar positions on 5% acrylamide gels. In the one strain genetically analyzed to date, the hidden variants segregate in crosses. A total of fourteen variants are detected by this gel sieving analysis, many of them involving apparent conformational differences. Thus, protein properties in addition to net charge appear to play an important role in determining the degree of mobility difference between alleles. Examining estimates of free mobility, uniform charge differences are the rule within conformational classes. However, the superposition of conformational heterogeneity renders interpretation of mobility spacing solely in terms of such charge differences inappropriate.

scholarly journals Estimating the Total Number of Alleles Using a Sample Coverage Method

Genetics ◽  
2001 ◽  
Vol 159 (3) ◽  
pp. 1365-1373 ◽  
Author(s):  
Shu-Pang Huang ◽  
B S Weir
Keyword(s):  
Recurrent Mutation ◽  
Allele Frequencies ◽  
Simulation Studies ◽  
Infinite Allele Model ◽  
Mutation Model ◽  
True Number ◽  
Stepwise Mutation ◽  
Microsatellite Alleles ◽  
Allele Model

Abstract Previously reported methods for estimating the number of different alleles at a single locus in a population have not described a useful general result. Using the number of alleles observed in a sample gives an underestimate for the true number of alleles. The similar problem of estimating the number of species in a population was first investigated in 1943. In this article we use the sample coverage method proposed by Chao and Lee in 1992 to estimate the number of alleles in a population when there are unequal allele frequencies. Simulation studies under the recurrent mutation model show that, for reasonable sample sizes, a significantly better estimate of the true number can be obtained than that using only the observed alleles. Results under the stepwise mutation model and infinite-allele model are presented. Possible applications include improving the characterization of the prior distribution for the allele frequencies, adjusting the estimates of genetic diversity, and estimating the range of microsatellite alleles.

scholarly journals New Methods Employing Multilocus Genotypes to Select or Exclude Populations as Origins of Individuals

Genetics ◽  
1999 ◽  
Vol 153 (4) ◽  
pp. 1989-2000 ◽  
Author(s):  
Jean-Marie Cornuet ◽  
Sylvain Piry ◽  
Gordon Luikart ◽  
Arnaud Estoup ◽  
Michel Solignac
Keyword(s):  
Genetic Distance ◽  
Bayesian Method ◽  
Simulated Data ◽  
Unknown Origin ◽  
Infinite Allele Model ◽  
Multilocus Genotypes ◽  
Mutation Model ◽  
Distance Methods ◽  
Stepwise Mutation ◽  
Time Of Divergence

Abstract A new method for assigning individuals of unknown origin to populations, based on the genetic distance between individuals and populations, was compared to two existing methods based on the likelihood of multilocus genotypes. The distribution of the assignment criterion (genetic distance or genotype likelihood) for individuals of a given population was used to define the probability that an individual belongs to the population. Using this definition, it becomes possible to exclude a population as the origin of an individual, a useful extension of the currently available assignment methods. Using simulated data based on the coalescent process, the different methods were evaluated, varying the time of divergence of populations, the mutation model, the sample size, and the number of loci. Likelihood-based methods (especially the Bayesian method) always performed better than distance methods. Other things being equal, genetic markers were always more efficient when evolving under the infinite allele model than under the stepwise mutation model, even for equal values of the differentiation parameter Fst. Using the Bayesian method, a 100% correct assignment rate can be achieved by scoring ca. 10 microsatellite loci (H ≈ 0.6) on 30–50 individuals from each of 10 populations when the Fst is near 0.1.

scholarly journals Allele frequencies at microsatellite loci: the stepwise mutation model revisited.

Genetics ◽  
1993 ◽  
Vol 133 (3) ◽  
pp. 737-749 ◽  
Author(s):  
A M Valdes ◽  
M Slatkin ◽  
N B Freimer
Keyword(s):  
Mutation Rate ◽  
Microsatellite Loci ◽  
Allele Frequencies ◽  
Stepwise Mutation Model ◽  
Human Populations ◽  
Effective Population ◽  
Allele Size ◽  
Frequency Distributions ◽  
Mutation Model ◽  
Stepwise Mutation

Abstract We summarize available data on the frequencies of alleles at microsatellite loci in human populations and compare observed distributions of allele frequencies to those generated by a simulation of the stepwise mutation model. We show that observed frequency distributions at 108 loci are consistent with the results of the model under the assumption that mutations cause an increase or decrease in repeat number by one and under the condition that the product Nu, where N is the effective population size and u is the mutation rate, is larger than one. We show that the variance of the distribution of allele sizes is a useful estimator of Nu and performs much better than previously suggested estimators for the stepwise mutation model. In the data, there is no correlation between the mean and variance in allele size at a locus or between the number of alleles and mean allele size, which suggests that the mutation rate at these loci is independent of allele size.

A Study on the Rearrangement of Dialkyl 1-Aryl-1-hydroxymethylphosphonates to Benzyl Phosphates

2020 ◽  
Vol 24 (4) ◽  
pp. 465-471 ◽  
Author(s):  
Zita Rádai ◽  
Réka Szabó ◽  
Áron Szigetvári ◽  
Nóra Zsuzsa Kiss ◽  
Zoltán Mucsi ◽  
...  
Keyword(s):  
Quantum Chemical ◽  
Room Temperature ◽  
Phase Transfer ◽  
One Pot ◽  
Substrate Dependence ◽  
Triethylbenzylammonium Chloride ◽  
One Step ◽  
The Pudovik Reaction ◽  
The One ◽  
Solid Liquid

The phospha-Brook rearrangement of dialkyl 1-aryl-1-hydroxymethylphosphonates (HPs) to the corresponding benzyl phosphates (BPs) has been elaborated under solid-liquid phase transfer catalytic conditions. The best procedure involved the use of triethylbenzylammonium chloride as the catalyst and Cs2CO3 as the base in acetonitrile as the solvent at room temperature. The substrate dependence of the rearrangement has been studied, and the mechanism of the transformation under discussion was explored by quantum chemical calculations. The key intermediate is an oxaphosphirane. The one-pot version starting with the Pudovik reaction has also been developed. The conditions of this tandem transformation were the same, as those for the one-step HP→BP conversion.

scholarly journals An evaluation of genetic distances for use with microsatellite loci.

Genetics ◽  
1995 ◽  
Vol 139 (1) ◽  
pp. 463-471 ◽  
Author(s):  
D B Goldstein ◽  
A Ruiz Linares ◽  
L L Cavalli-Sforza ◽  
M W Feldman
Keyword(s):  
Microsatellite Loci ◽  
Phylogenetic Reconstruction ◽  
Genetic Distances ◽  
Stepwise Mutation Model ◽  
Mutation Model ◽  
Stepwise Mutation ◽  
The Difference ◽  
Nei's Distance ◽  
Infinite Alleles Model ◽  
Overall Reliability

Abstract Mutations of alleles at microsatellite loci tend to result in alleles with repeat scores similar to those of the alleles from which they were derived. Therefore the difference in repeat score between alleles carries information about the amount of time that has passed since they shared a common ancestral allele. This information is ignored by genetic distances based on the infinite alleles model. Here we develop a genetic distance based on the stepwise mutation model that includes allelic repeat score. We adapt earlier treatments of the stepwise mutation model to show analytically that the expectation of this distance is a linear function of time. We then use computer simulations to evaluate the overall reliability of this distance and to compare it with allele sharing and Nei's distance. We find that no distance is uniformly superior for all purposes, but that for phylogenetic reconstruction of taxa that are sufficiently diverged, our new distance is preferable.

scholarly journals One-Year Clinical Evaluation of the Bonding Effectiveness of a One-Step, Self-Etch Adhesive in Noncarious Cervical Lesion Therapy

2015 ◽  
Vol 2015 ◽  
pp. 1-5 ◽  
Author(s):  
Babacar Faye ◽  
Mouhamed Sarr ◽  
Khaly Bane ◽  
Adjaratou Wakha Aidara ◽  
Seydina Ousmane Niang ◽  
...  
Keyword(s):  
Clinical Performance ◽  
Retention Rate ◽  
Recall Rate ◽  
Acid Etching ◽  
Significant Difference ◽  
Usphs Criteria ◽  
One Step ◽  
One Year ◽  
The One ◽  
Self Etch

This study evaluated the one-year clinical performance of a one-step, self-etch adhesive (Optibond All-in-One, Kerr, CA, USA) combined with a composite (Herculite XRV Ultra, Kerr Hawe, CA, USA) to restore NCCLs with or without prior acid etching. Restorations performed by the same practitioner were evaluated at baseline and after 3, 6, and 12 months using modified USPHS criteria. At 6 months, the recall rate was 100%. The retention rate was 84.2% for restorations with prior acid etching, but statistically significant differences were observed between baseline and 6 months. Without acid etching, the retention rate was 77%, and no statistically significant difference was noted between 3 and 6 months. Marginal integrity (93.7% with and 87.7% without acid etching) and discoloration (95.3% with and 92.9% without acid etching) were scored as Alpha or Bravo, with better results after acid etching. After one year, the recall rate was 58.06%. Loss of pulp vitality, postoperative sensitivity, or secondary caries were not observed. After one year retention rate was of 90.6% and 76.9% with and without acid conditioning. Optibond All-in-One performs at a satisfactory clinical performance level for restoration of NCCLs after 12 months especially after acid etching.

scholarly journals Building up cyclodextrins from scratch – templated enzymatic synthesis of cyclodextrins directly from maltose

2021 ◽  
Author(s):  
Dennis Larsen ◽  
Sophie R. Beeren
Keyword(s):  
Enzymatic Synthesis ◽  
Combinatorial Libraries ◽  
One Step ◽  
The One ◽  
Kinetic Trapping

Template-induced kinetic trapping of specific cyclodextrins in enzyme-mediated dynamic combinatorial libraries of linear and cyclic α-glucans enables the one-step synthesis of cyclodextrins from maltose in water.

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