Evidence for an instructive mechanism of de novo methylation in cancer cells

DNA methylation has a role in the regulation of gene expression during normal mammalian development but can also mediate epigenetic silencing of CpG island genes in cancer and other diseases. Many individual genes (including tumor suppressors) have been shown to undergo de novo methylation in specific tumor types, but the biological logic inherent in this process is not understood. To decipher this mechanism, we have adopted a new approach for detecting CpG island DNA methylation that can be used together with microarray technology. Genome-wide analysis by this technique demonstrated that tumor-specific methylated genes belong to distinct functional categories, have common sequence motifs in their promoters and are found in clusters on chromosomes. In addition, many are already repressed in normal cells. These results are consistent with the hypothesis that cancer-related de novo methylation may come about through an instructive mechanism.     

Toward interoperable bioscience data

To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open 'data commoning' culture. Here we describe the prerequisites for data commoning and present an established and growing ecosystem of solutions using the shared 'Investigation-Study-Assay' framework to support that vision.     

De novo mutations in the actin genes ACTB and ACTG1 cause Baraitser-Winter syndrome

Brain malformations are individually rare but collectively common causes of developmental disabilities. Many forms of malformation occur sporadically and are associated with reduced reproductive fitness, pointing to a causative role for de novo mutations. Here, we report a study of Baraitser-Winter syndrome, a well-defined disorder characterized by distinct craniofacial features, ocular colobomata and neuronal migration defect. Using whole-exome sequencing of three proband-parent trios, we identified de novo missense changes in the cytoplasmic actin-encoding genes ACTB and ACTG1 in one and two probands, respectively. Sequencing of both genes in 15 additional affected individuals identified disease-causing mutations in all probands, including two recurrent de novo alterations (ACTB, encoding p.Arg196His, and ACTG1, encoding p.Ser155Phe). Our results confirm that trio-based exome sequencing is a powerful approach to discover genes causing sporadic developmental disorders, emphasize the overlapping roles of cytoplasmic actin proteins in development and suggest that Baraitser-Winter syndrome is the predominant phenotype associated with mutation of these two genes.     

Genome-wide association analyses identify 13 new susceptibility loci for generalized vitiligo

We previously reported a genome-wide association study (GWAS) identifying 14 susceptibility loci for generalized vitiligo. We report here a second GWAS (450 individuals with vitiligo (cases) and 3,182 controls), an independent replication study (1,440 cases and 1,316 controls) and a meta-analysis (3,187 cases and 6,723 controls) identifying 13 additional vitiligo-associated loci. These include OCA2-HERC2 (combined P = 3.80 × 10(-8)), MC1R (P = 1.82 × 10(-13)), a region near TYR (P = 1.57 × 10(-13)), IFIH1 (P = 4.91 × 10(-15)), CD80 (P = 3.78 × 10(-10)), CLNK (P = 1.56 × 10(-8)), BACH2 (P = 2.53 × 10(-8)), SLA (P = 1.58 × 10(-8)), CASP7 (P = 3.56 × 10(-8)), CD44 (P = 1.78 × 10(-9)), IKZF4 (P = 2.75 × 10(-14)), SH2B3 (P = 3.54 × 10(-18)) and TOB2 (P = 6.81 × 10(-10)). Most vitiligo susceptibility loci encode immunoregulatory proteins or melanocyte components that likely mediate immune targeting and the relationships among vitiligo, melanoma, and eye, skin and hair coloration.     

First-principles investigation on initial stage of 2H-SiC(001) surface oxidation

We present comprehensive first-principles calculations on the initial stages of SiC oxidation by atomic oxygen on the 2H-SiC(001) surface. In order to study the kinetics of oxygen incorporation at the 2H-SiC(001) surface, we investigated adsorption and diffusion of oxygen atoms and SiO₂ nucleation. The adsorption sites, corresponding to the local minima of the potential energy surface (PES) for isolated adatoms, were identified through a comparative study of the adatom binding energy at different locations. We found that the Bridge (siloxane) site is preferred over other adsorption sites. There is no energy barrier at 0K for oxygen insertion into this site. The diffusion energy barriers that the adatom has to overcome when jumping between two adsorption sites were calculated. The premises of silica nucleation were investigated by calculating the modifications of the oxygen atom binding energy due to the interaction with neighboring adatoms. Supported by Snecma Propulsion Solide (Contract FPR No. 0539298A), Natural Science Foundation of China (Grant No 50802076) and Flying Star Program of Northwestern Polytechnical University of China     

The binary Kuiper-belt object 1998 WW31

The recent discovery of a binary asteroid during a spacecraft fly-by generated keen interest, because the orbital parameters of binaries can provide measures of the masses, and mutual eclipses could allow us to determine individual sizes and bulk densities. Several binary near-Earth, main-belt and Trojan asteroids have subsequently been discovered. The Kuiper belt-the region of space extending from Neptune (at 30 astronomical units) to well over 100 AU and believed to be the source of new short-period comets-has become a fascinating new window onto the formation of our Solar System since the first member object, not counting Pluto, was discovered in 1992 (ref. 13). Here we report that the Kuiper-belt object 1998 WW31 is binary with a highly eccentric orbit (eccentricity e approximately 0.8) and a long period (about 570 days), very different from the Pluto/Charon system, which was hitherto the only previously known binary in the Kuiper belt. Assuming a density in the range of 1 to 2 g cm-3, the albedo of the binary components is between 0.05 and 0.08, close to the value of 0.04 generally assumed for Kuiper-belt objects.