Estrogen receptor beta rs1271572 polymorphism and invasive ovarian carcinoma risk: pooled analysis within the Ovarian Cancer Association Consortium

The association of ovarian carcinoma risk with the polymorphism rs1271572 in the estrogen receptor beta (ESR2) gene was examined in 4946 women with primary invasive ovarian carcinoma and 6582 controls in a pooled analysis of ten case-control studies within the Ovarian Cancer Association Consortium (OCAC). All participants were non-Hispanic white women. Odds ratios (ORs) and 95% confidence intervals (CIs) were estimated using unconditional logistic regression adjusted for site and age. Women with the TT genotype were at increased risk of ovarian carcinoma compared to carriers of the G allele (OR = 1.10; 95%; CI: 1.01–1.21; p = 0.04); the OR was 1.09 (CI: 0.99–1.20; p = 0.07) after excluding data from the center (Hawaii) that nominated this SNP for OCAC genotyping A stronger association of rs1271572 TT versus GT/GG with risk was observed among women aged ≤50 years versus older women (OR = 1.35; CI: 1.12–1.62; p = 0.002; p for interaction = 0.02) that remained statistically significant after excluding Hawaii data (OR = 1.34; CI: 1.11–1.61; p = 0.009). No heterogeneity of the association was observed by study, menopausal status, gravidity, parity, use of contraceptive or menopausal hormones, tumor histological type, or stage at diagnosis. This pooled analysis suggests that rs1271572 might influence the risk of ovarian cancer, in particular among younger women.     

Comparison of 6q25 Breast Cancer Hits from Asian and European Genome Wide Association Studies in the Breast Cancer Association Consortium (BCAC)

The 6q25.1 locus was first identified via a genome-wide association study (GWAS) in Chinese women and marked by single nucleotide polymorphism (SNP) rs2046210, approximately 180 Kb upstream of ESR1. There have been conflicting reports about the association of this locus with breast cancer in Europeans, and a GWAS in Europeans identified a different SNP, tagged here by rs12662670. We examined the associations of both SNPs in up to 61,689 cases and 58,822 controls from forty-four studies collaborating in the Breast Cancer Association Consortium, of which four studies were of Asian and 39 of European descent. Logistic regression was used to estimate odds ratios (OR) and 95% confidence intervals (CI). Case-only analyses were used to compare SNP effects in Estrogen Receptor positive (ER+) versus negative (ER−) tumours. Models including both SNPs were fitted to investigate whether the SNP effects were independent. Both SNPs are significantly associated with breast cancer risk in both ethnic groups. Per-allele ORs are higher in Asian than in European studies [rs2046210: OR (A/G) = 1.36 (95% CI 1.26–1.48), p = 7.6×10⁻¹⁴ in Asians and 1.09 (95% CI 1.07–1.11), p = 6.8×10⁻¹⁸ in Europeans. rs12662670: OR (G/T) = 1.29 (95% CI 1.19–1.41), p = 1.2×10⁻⁹ in Asians and 1.12 (95% CI 1.08–1.17), p = 3.8×10⁻⁹ in Europeans]. SNP rs2046210 is associated with a significantly greater risk of ER− than ER+ tumours in Europeans [OR (ER−) = 1.20 (95% CI 1.15–1.25), p = 1.8×10⁻¹⁷ versus OR (ER+) = 1.07 (95% CI 1.04–1.1), p = 1.3×10⁻⁷, p_{heterogeneity} = 5.1×10⁻⁶]. In these Asian studies, by contrast, there is no clear evidence of a differential association by tumour receptor status. Each SNP is associated with risk after adjustment for the other SNP. These results suggest the presence of two variants at 6q25.1 each independently associated with breast cancer risk in Asians and in Europeans. Of these two, the one tagged by rs2046210 is associated with a greater risk of ER− tumours.     

GPFrontend and GPGraphics: graphical analysis tools for genetic association studies

Background  

Most software packages for whole genome association studies are non-graphical, purely text based programs originally designed to run with UNIX-like operating systems. Graphical output is often not intended or supposed to be performed with other command line tools, e.g. gnuplot.     

Hydrophilic compounds in liquids of enzymatic hydrolyzed spruce and pine biomass

This study was focused on organic acids and metals in biofluids of wood. Without seasoning, fresh woods from spruce and bark, phloem, and heartwood from pine were used as materials, which were degraded with either microbes of oyster mushroom, baker’s yeast, or lactic acid bacteria. Due to neutral pH of the fluids, ambient temperature, atmospheric pressure, and short reaction time, native wood microbe populations were supposed to be present. The water content of the fresh woods was 4 to 20%. The study showed that process methodology and experimental conditions affected the generation of lactic, citric, succinic, and adipic acids, which are considered as source chemicals in the biopolymer industry. In addition to the organic acids and metals, the process produced monosaccharides, polysaccharides, and phenolic acids such as benzoic, salicylic, cinnamic, vanillic, tannic, and conifer (ferulic) acids. Concentrations of total acids and acetic and succinic acids in pine fluids from bark, phloem, and heartwood were 58.4 g/kg and 3.5 to 6.9 g/kg, respectively. In spruce, the most dominant acids were l-lactic and l-malic acids. As for metals, Ag and Cr were detected at 0.01-g/kg quantities in pine bark. Alkali metals K, Mg, Sr, and Ca were detected at 10, 8, 1.3, and 4 g/kg, respectively.     

Cytological and histological studies on female gametophyte of Leucojum aestivum (Amaryllidaceae)

In this study, gynoeceum, development of megasporangium, megasporogenesis, megagametogenesis and female gametophyte of Leucojum aestivum were examined cytologically and histologically. Ovules of L. aestivum are of anatropous, bitegmic and crassinucellate type. Inner integument forms the micropyle. Archesporial cell develops directly into a megasporocyte. Embryo sac development is of bisporic Allium type. Filiform apparatus is observed in synergids. Polar nuclei fuse before fertilization to form secondary nucleus near the antipodals.     

High resolution chromosomal microarray analysis in paediatric obsessive-compulsive disorder

Background

Obsessive-Compulsive Disorder (OCD) is a common and chronic disorder in which a person has uncontrollable, reoccurring thoughts and behaviours. It is a complex genetic condition and, in case of early onset (EO), the patients manifest a more severe phenotype, and an increased heritability. Large (>500 kb) copy number variations (CNVs) previously associated with autism and schizophrenia have been reported in OCD. Recently, rare CNVs smaller than 500 kb overlapping risk loci for other neurodevelopmental conditions have also been reported in OCD, stressing the importance of examining CNVs of any size range. The aim of this study was to further investigate the role of rare and small CNVs in the aetiology of EO-OCD.

Methods

We performed high-resolution chromosomal microarray analysis in 121 paediatric OCD patients and in 124 random controls to identify rare CNVs (>50 kb) which might contribute to EO-OCD.

Results

The frequencies and the size of the observed rare CNVs in the patients did not differ from the controls. However, we observed a significantly higher frequency of rare CNVs affecting brain related genes, especially deletions, in the patients (OR?=?1.98, 95% CI 1.02–3.84; OR?=?3.61, 95% CI 1.14–11.41, respectively). Similarly, enrichment-analysis of CNVs gene content, performed with three independent methods, confirmed significant clustering of predefined genes involved in synaptic/brain related functional pathways in the patients but not in the controls. In two patients we detected de-novo CNVs encompassing genes previously associated with different neurodevelopmental disorders (NRXN1, ANKS1B, UHRF1BP1).

Conclusions

Our results further strengthen the role of small rare CNVs, particularly deletions, as susceptibility factors for paediatric OCD.

     

Goldenhar syndrome associated with growth hormone deficiency

Goldenhar syndrome is a rare disorder of unknown etiology. The most frequent findings are vertebral defects, hemifacial microsomia and ear abnormalities. We present an 8-year-old boy with oculo-auriculo-vertebral (Goldenhar) syndrome. He also had a parachute mitral valve and growth hormone deficiency. Parachute mitral valve is a previously unreported finding while growth hormone deficiency was reported just in one case in the literature.     

Antioxidant and free radical scavenging properties of N-acetylcysteine amide (NACA) and comparison with N-acetylcysteine (NAC)

The antioxidant potential of N-acetylcysteine amide (NACA), also known as AD4, was assessed by employing different in vitro assays. These included reducing power, free radical scavenging capacities, peroxidation inhibiting activity through linoleic acid emulsion system and metal chelating capacity, as compared to NAC and three widely used antioxidants, alpha-tocopherol, ascorbic acid and butylated hydroxytoluene (BHT). Of the antioxidant properties that were investigated, NACA was shown to possess higher 2,2-diphenyl-1-picryl-hydrazyl-hydrate (DPPH) radical scavenging ability and reducing power than NAC, at all the concentrations, whereas the scavenging ability of H(2)O(2) differed with concentration. While NACA had greater H(2)O(2) scavenging capacity at the highest concentration, NAC was better than NACA at lower concentrations. NAC and NACA had a 60% and 55% higher ability to prevent beta-carotene bleaching, respectively, as compared to control. The chelating activity of NACA was more than 50% that of the metal chelating capacity of EDTA and four and nine times that of BHT and alpha-tocopherol, respectively. When compared to NACA and NAC; alpha-tocopherol had higher DPPH scavenging abilities and BHT and alpha-tocopherol had better beta-carotene bleaching power. These findings provide evidence that the novel antioxidant, NACA, has indeed enhanced the antioxidant properties of NAC.     

Unconventional serine proteases: variations on the catalytic Ser/His/Asp triad configuration

Serine proteases comprise nearly one-third of all known proteases identified to date and play crucial roles in a wide variety of cellular as well as extracellular functions, including the process of blood clotting, protein digestion, cell signaling, inflammation, and protein processing. Their hallmark is that they contain the so-called "classical" catalytic Ser/His/Asp triad. Although the classical serine proteases are the most widespread in nature, there exist a variety of "nonclassical" serine proteases where variations to the catalytic triad are observed. Such variations include the triads Ser/His/Glu, Ser/His/His, and Ser/Glu/Asp, and include the dyads Ser/Lys and Ser/His. Other variations are seen with certain serine and threonine peptidases of the Ntn hydrolase superfamily that carry out catalysis with a single active site residue. This work discusses the structure and function of these novel serine proteases and threonine proteases and how their catalytic machinery differs from the prototypic serine protease class.