Evolution and dispersal of mitochondrial DNA haplogroup U5 in Northern Europe: insights from an unsupervised learning approach to phylogeography.

Background: We combined an unsupervised learning methodology for analyzing mitogenome sequences with maximum likelihood (ML) phylogenetics to make detailed inferences about the evolution and diversification of mitochondrial DNA (mtDNA) haplogroup U5, which appears at high frequencies in northern Europe.

Methods: Haplogroup U5 mitogenome sequences were gathered from GenBank. The hierarchal Bayesian Analysis of Population Structure (hierBAPS) method was used to generate groups of sequences that were then projected onto a rooted maximum likelihood (ML) phylogenetic tree to visualize the pattern of clustering.

Impact of electron beam irradiation on the chlorophyll degradation and antioxidant capacity of mango fruit.

At the present, the mechanism of chlorophyll degradation in response to ionizing irradiation in harvested fruits have not been examined. To understand the effect of electron beam (E-beam) irradiation on the chlorophyll degrading pathway in relation to chlorophyll degrading enzymes activity, reactive oxygen species (ROS) and antioxidant capacities of harvested mangoes stored at 13 °C for 16 days were studied. E-beam-treated fruit significantly suppressed the activities of chlorophyll degrading enzymes especially pheophytinase (PPH) and chlorophyll degrading peroxidase (Chl-POX) in the late stage of storage.

X-linked genes and risk of orofacial clefts: evidence from two population-based studies in Scandinavia.

Background: Orofacial clefts are common birth defects of complex etiology, with an excess of males among babies with cleft lip and palate, and an excess of females among those with cleft palate only. Although genes on the X chromosome have been implicated in clefting, there has been no association analysis of X-linked markers.

Methodology/principal Findings: We added new functionalities in the HAPLIN statistical software to enable association analysis of X-linked markers and an exploration of various causal scenarios relevant to orofacial clefts.

Application of a novel hybrid study design to explore gene-environment interactions in orofacial clefts.

Orofacial clefts are common birth defects with strong evidence for both genetic and environmental causal factors. Candidate gene studies combined with exposures known to influence the outcome provide a highly targeted approach to detecting GxE interactions. We developed a new statistical approach that combines the case-control and offspring-parent triad designs into a "hybrid design" to search for GxE interactions among 334 autosomal cleft candidate genes and maternal first-trimester exposure to smoking, alcohol, coffee, folic acid supplements, dietary folate and vitamin A.

Assessing the impact of nicotine dependence genes on the risk of facial clefts: An example of the use of national registry and biobank data.

Background: Maternal smoking during pregnancy has been associated with risk of facial clefts in offspring, but causation has not yet been established. It is possible that the effect of maternal smoking on facial clefts is mediated through genes that are involved in nicotine dependence. Gamma-aminobutyric acid B receptor 2 (), dopa decarboxylase (), and cholinergic receptor nicotinic alpha 4 () are three examples of genes that have previously shown strong associations with nicotine dependence.

Fetal genetic risk of isolated cleft lip only versus isolated cleft lip and palate: a subphenotype analysis using two population-based studies of orofacial clefts in Scandinavia.

Background: Cleft lip only (CLO) and cleft lip and palate (CLP) are commonly regarded as variants of the same defect and traditionally combined to form the single group of cleft lip with or without cleft palate (CL/P) prior to analysis. However, recent data have suggested that at least a subgroup of isolated CLO may be etiologically distinct from isolated CLP.

Methods: To explore fetal genetic risk of isolated CLO separately from isolated CLP, we performed a sub-phenotype analysis using two population-based studies of clefts in Scandinavia.

Maternal genes and facial clefts in offspring: a comprehensive search for genetic associations in two population-based cleft studies from Scandinavia.

Background: Fetal conditions can in principle be affected by the mother's genotype working through the prenatal environment.

Methodology/principal Findings: Genotypes for 1536 SNPs in 357 cleft candidate genes were available from a previous analysis in which we focused on fetal gene effects. After data-cleaning, genotypes for 1315 SNPs in 334 autosomal genes were available for the current analysis of maternal gene effects.

Genetic variants in IRF6 and the risk of facial clefts: single-marker and haplotype-based analyses in a population-based case-control study of facial clefts in Norway.

Mutations in the gene encoding interferon regulatory factor 6 (IRF6) underlie a common form of syndromic clefting known as Van der Woude syndrome. Lip pits and missing teeth are the only additional features distinguishing the syndrome from isolated clefts. Van der Woude syndrome, therefore, provides an excellent model for studying the isolated forms of clefting.