PubMeth: a cancer methylation database combining text-mining and expert annotation

Epigenetics, and more specifically DNA methylation is a fast evolving research area. In almost every cancer type, each month new publications confirm the differentiated regulation of specific genes due to methylation and mention the discovery of novel methylation markers. Therefore, it would be extremely useful to have an annotated, reviewed, sorted and summarized overview of all available data. PubMeth is a cancer methylation database that includes genes that are reported to be methylated in various cancer types. A query can be based either on genes (to check in which cancer types the genes are reported as being methylated) or on cancer types (which genes are reported to be methylated in the cancer (sub) types of interest). The database is freely accessible at http://www.pubmeth.org

Diversity in Protein Glycosylation among Insect Species

status: publishe

Ribosome profiling reveals the what, when, where and how of protein synthesis

Ribosome profiling, which involves the deep sequencing of ribosome-protected mRNA fragments, is a powerful tool for globally monitoring translation in vivo. The method has facilitated discovery of the regulation of gene expression underlying diverse and complex biological processes, of important aspects of the mechanism of protein synthesis, and even of new proteins, by providing a systematic approach for experimental annotation of coding regions. Here, we introduce the methodology of ribosome profiling and discuss examples in which this approach has been a key factor in guiding biological discovery, including its prominent role in identifying thousands of novel translated short open reading frames and alternative translation products

Maturation performance, offspring quality and lipid composition of <i>Macrobrachium rosenbergii</i> females fed increasing levels of dietary phospholipids

The effects of increasing levels of dietary phospholipids (PL) on the reproductive performance, egg and larval quality, and lipid composition of females of the freshwater prawn Macrobrachium rosenbergii were investigated. Three isolipidic diets containing similar amounts of highly unsaturated fatty acids but varying levels of PL (0.8, 2.4 and 4.6%) were fed during 180 days to three groups of eight females originating from Thai ponds. No significant differences were observed for fecundity, egg size and hatchability, starved larvae size, and size, survival and tolerance to stress of 8 day-old larvae. Similarly, no major differences in the lipid composition of the midgut gland, ovaries and muscle tissue of females could be detected. Results indicate the lack of need of dietary supplementation of PL for M. rosenbergii broodstock, as previously reported for earlier life stages. It is suggested that the basal level of 0.8% dietary PL was sufficient to meet the dietary demands of the prawn broodstock. The PL requirements of M. rosenbergii broodstock, if any, may be satisfied in commercial feeds through the inclusion of ingredients containing some phospholipids endogenously

Bioinformatics solutions for MS/MS interpretation tailored to the peptidomics field

status: publishe