The lack of effectiveness of (−)-epicatechin against alloxan induced diabetes in Wistar rats

(?)-Epicatechin, a naturally occurring flavonoid, has been reported to protect pancreatic beta cells from alloxan-induced diabetes (1) and to stimulate beta cell regeneration when given after alloxan administration (2,3). However, in the present study, we have not been able to confirm these findings. Administration of (?)-epicatechin (100 mg/kg/day for 15 days) beginning three days after alloxan administration (140 mg/kg) had no significant effect on blood glucose levels when compared to alloxan control animals. Another study which failed to demonstrate an antidiabetic effect of (?)-epicatechin (4) has been criticized for not using fresh solutions of (?)-epicatechin because of its instability in aqueous solution (5). We have found, however, that (?)-epicatechin is stable for at least five days based on thin-layer chromatographic analysis and optical rotation measurements.     

Determination of genetic relatedness from low‐coverage human genome sequences using pedigree simulations

We develop and evaluate methods for inferring relatedness among individuals from low‐coverage DNA sequences of their genomes, with particular emphasis on sequences obtained from fossil remains. We suggest the major factors complicating the determination of relatedness among ancient individuals are sequencing depth, the number of overlapping sites, the sequencing error rate and the presence of contamination from present‐day genetic sources. We develop a theoretical model that facilitates the exploration of these factors and their relative effects, via measurement of pairwise genetic distances, without calling genotypes, and determine the power to infer relatedness under various scenarios of varying sequencing depth, present‐day contamination and sequencing error. The model is validated by a simulation study as well as the analysis of aligned sequences from present‐day human genomes. We then apply the method to the recently published genome sequences of ancient Europeans, developing a statistical treatment to determine confidence in assigned relatedness that is, in some cases, more precise than previously reported. As the majority of ancient specimens are from animals, this method would be applicable to investigate kinship in nonhuman remains. The developed software grups (Genetic Relatedness Using Pedigree Simulations) is implemented in Python and freely available.     

Subdivision in an ancestral species creates asymmetry in gene trees

We consider gene trees in three species for which the species tree is known. We show that population subdivision in ancestral species can lead to asymmetry in the frequencies of the two gene trees not concordant with the species tree and, if subdivision is extreme, cause the one of the nonconcordant gene trees to be more probable than the concordant gene tree. Although published data for the human-chimp-gorilla clade and for three species of Drosophila show asymmetry consistent with our model, sequencing error could also account for observed patterns. We show that substantial levels of persistent ancestral subdivision are needed to account for the observed levels of asymmetry found in these two studies.     

Accounting for bias from sequencing error in population genetic estimates

Sequencing error presents a significant challenge to population genetic analyses using low-coverage sequence in general and single-pass reads in particular. Bias in parameter estimates becomes severe when the level of polymorphism (signal) is low relative to the amount of error (noise). Choosing an arbitrary quality score cutoff yields biased estimates, particularly with newer, non-Sanger sequencing technologies that have different quality score distributions. We propose a rule of thumb to judge when a given threshold will lead to significant bias and suggest alternative approaches that reduce bias.     

The use of intraallelic variability for testing neutrality and estimating population growth rate

To better understand the forces affecting individual alleles, we introduce a method for finding the joint distribution of the frequency of a neutral allele and the extent of variability at closely linked marker loci (the intraallelic variability). We model three types of intraallelic variability: (a) the number of nonrecombinants at a linked biallelic marker locus, (b) the length of a conserved haplotype, and (c) the number of mutations at a linked marker locus. If the population growth rate is known, the joint distribution provides the basis for a test of neutrality by testing whether the observed level of intraallelic variability is consistent with the observed allele frequency. If the population growth rate is unknown but neutrality can be assumed, the joint distribution provides the likelihood of the growth rate and leads to a maximum-likelihood estimate. We apply the method to data from published data sets for four loci in humans. We conclude that the Delta32 allele at CCR5 and a disease-associated allele at MLH1 arose recently and have been subject to strong selection. Alleles at PAH appear to be neutral and we estimate the recent growth rate of the European population to be approximately 0.027 per generation with a support interval of (0.017-0.037). Four of the relatively common alleles at CFTR also appear to be neutral but DeltaF508 appears to be significantly advantageous to heterozygous carriers.     

Allele age and a test for selection on rare alleles

An approximate expression for the probability distribution of the age of a neutral allele as a function of its frequency is derived for a population undergoing arbitrary changes in population size. A simple maximum-likelihood estimator of allele age based on frequency is also obtained. The distribution of allele age, combined with a model predicting the extent of intra-allelic variability generated by mutation and recombination, leads to a statistical test of whether a rare allele has experienced natural selection. The test is based on finding whether there is too little or too much intra-allelic variability to be consistent with the observed frequency. The test is applied to the locus, BRCA1, associated with early-onset breast cancer in humans and shows that two common disease-associated alleles (5382insC and 185delAG) appear to have been subject to natural selection.     

A Bayesian method for jointly estimating allele age and selection intensity.

The problem of jointly estimating the intensity of past selection affecting an allele and the allele's age is formulated in a Bayesian framework. The prior distribution of allele age given its frequency is obtained from existing population genetics theory. The prior distribution of selection intensity is assumed to reflect the fact that positive selection on a new mutant is more likely to be weak than strong. The general approach is illustrated by the development of an importance sampling method applicable to low-frequency alleles. This method can be used either when the haplotypes of closely linked marker loci are known or when the lengths of linked ancestral chromosomal segments can be inferred. The method is illustrated with an application to the A-allele of G6PD in Africa. Because changes in allele frequency and recombination are both intrinsically stochastic, there are limits to the accuracy achievable with any method.