Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios

Background  

Illumina Infinium whole genome genotyping (WGG) arrays are increasingly being applied in cancer genomics to study gene copy number alterations and allele-specific aberrations such as loss-of-heterozygosity (LOH). Methods developed for normalization of WGG arrays have mostly focused on diploid, normal samples. However, for cancer samples genomic aberrations may confound normalization and data interpretation. Therefore, we examined the effects of the conventionally used normalization method for Illumina Infinium arrays when applied to cancer samples.     

Angiotensin-converting enzyme gene insertion/deletion polymorphism in migraine patients

Background  

The main objective of this study was to investigate the angiotensin converting enzyme (ACE) genotype as a possible risk factor for migraine (both with and without aura) compared to controls. We also wanted to examine whether a clinical response to an ACE inhibitor, lisinopril, or an angiotensin II receptor blocker, candesartan, in migraine prophylaxis was related to ACE genotype.     

Effects of a biologically relevant antioxidant on the dehydrogenative polymerization of coniferyl alcohol

Dehydrogenation polymers (DHPs or synthetic lignins) were synthesized from coniferyl alcohol by enzymatic oxidation in the presence of ascorbic acid to study the potential effects of an antioxidant upon their structure. Specific interunit substructures (beta-O-4', beta-beta', and beta-5') were quantified by 13C NMR, which showed how ascorbic acid altered their amounts compared with control syntheses without this antioxidant, especially by increasing the amount of beta-O-4' substructures. The effect of ascorbic acid increased with its concentration. Surprisingly, no influence on the sizes of the synthetic lignins, as determined by size exclusion chromatography, was observed. The chemistry of this antioxidant effect during dehydrogenative polymerization and the potential biological significance (cell wall lignification) of these observations are discussed.     

Diversity of geometrid moths (Lepidoptera: Geometridae) along an Afrotropical elevational rainforest transect

Geometrid moths were investigated at 26 sites on 9 elevational levels along an elevational transect at Mt. Kilimanjaro (Tanzania), stretching from the fine‐grained mosaic of small agroforest plots with combined cultivation of trees, shrubs and crops at 1650 m through mountain rainforest to heathland at 3300 m. We sampled moths manually at light between 19 : 00 and 22 : 00 in the rainy seasons of March to May and October to January in the years 2000, 2001 and 2002. Along the transect, the composition of moth communities changed from a domination by Sterrhinae and Ennominae to a dominance of Larentiinae with increasing elevation. Overall, alpha diversity was very low compared to other tropical mountain regions. Fisher's alpha showed a maximum of 30 in the agroforest mosaic at 1650 m and decreased to values around 12 in the mountain rainforest. Communities of geometrid moths within the forest belt were significantly dissimilar from communities outside the forest. The diversity patterns on Mt. Kilimanjaro can be related to the young age, island‐like position and history of the mountain. These factors have led to the formation of a homogeneous upper mountain rainforest habitat which in turn houses homogeneous moth communities with a low diversity compared to habitats at lower elevations. Here, a heterogeneous habitat mosaic allowing the intrusion of savannah species into this former forest habitat may account for an increased diversity. In the heath zone above the forest, climatic conditions are very harsh, permitting only few specialists to thrive in this ericaceous woodland. Edge effects were discernible at the forest–heathland boundary where some moth species from heathland invaded the closed forest. At the boundary between agroforest and a forest mosaic of exotic Acacia and Eucalyptus forest plantations and natural mountain forest, diversity values remained low as the dominant species Chiasmia fuscataria accounted for far higher proportions than other dominant species in any of the other habitats.     

Microsatellite Variation in Populations of Atlantic Salmon from North Europe

Our aim was to investigate the level of genetic differentiation in northern European populations of Atlantic salmon, to establish the genetic relationship among major salmon populations in Russia and North Norway, and to compare these to populations from the western Atlantic lineage. Samples were collected along an east—west axis, from Pechora River in Russia to Restigouche River in Quebec, Canada. A total of 439 individual salmon were collected from seven rivers (sample sizes from 50 to 84 individuals). The samples were analysed for variation at four microsatellite loci; Ssa13.37, Ssa14, Ssa171 and Ssa171. Significant differences were found between most of the European populations, and the populations from the Tana and Pechora Rivers were most distinct. The samples from the Rivers Mezenskaya Pizhma and Emtsa in Arkhangelsk oblast in Russia were not significantly different from each other in an exact test of population differences. All other river pairs were significantly different. These results confirmed the deep genetic divergence between American and European salmon populations demonstrated in earlier studies, with alleles specific to continent found in three of the microsatellites.     

Environmental cadmium exposure and forearm bone density

Environmental exposure to cadmium may give rise to osteomalacia combined with renal dysfunction, so called 'Itai-Itai disease', which was endemic in the heavily polluted area in Japan. The main focus of this study was to investigate whether environmental exposure to cadmium is associated with low bone mass in a population living near a smelter. A total of 790 persons (302 males and 488 females), who were all over 35 years old and resided in areas near a lead, zinc and cadmium smelter and in a control area in southeast China, completed a questionnaire, and bone mineral density was measured by SPA-4 single photon absorptiometry at the radius and ulna. Cadmium content of urine was determined by graphite-furnace atomic absorption spectrophotometry as a measure of dose. The present study shows that forearm bone densities were negatively correlated with urinary cadmium excretion (p < 0.001) and forearm bone density decreased linearly with age (p < 0.001) and urinary cadmium (p < 0.01), suggesting a dose-effect relationship between cadmium dose and bone mineral density. Based on the World Health Organization criteria, (bone mineral density < -2.5 SDs below the normal young adult), the prevalence of osteoporosis in women increased from 34.0% in the control area to 51.9% in the heavily polluted area (p < 0.01) among subjects over 50 years old, and the odds ratio value was 2.09 (95% CI: 1.08-4.03) for the highly polluted area compared with the control area. A striking observation in the study was a marked increase of the prevalence of fracture in the cadmium-polluted area in both sexes. It was concluded that environmental exposure to cadmium is associated with an increased loss of bone mineral density in both gender, leading to osteoporosis and increased risk of fractures, especially in the elderly and in females.