Semiconductor-based sequencing of genome-wide DNA methylation states

Methylated DNA immunoprecipitation sequencing (MeDIP-Seq) is a widely used approach to study DNA methylation genome-wide. Here, we developed a MeDIP-Seq protocol compatible with the Ion Torrent semiconductor-based sequencing platform that is low cost, rapid, and scalable. We applied this protocol to demonstrate MeDIP-Seq on the Ion Torrent platform provides adequate coverage of CpG cytosines, the methylation states of which we validated at single-base resolution on the Infinium HumanMethylation450 BeadChip array, and accurately identifies sites of differential DNA methylation. Furthermore, we applied an integrative approach to further investigate and confirm the role of DNA methylation in alternative splicing and to profile 5mC and 5hmC variants of DNA methylation in normal human brain tissue that is localized over distinct genomic regions. These applications of MeDIP-Seq on the Ion Torrent platform have broad utility and add to the current methodologies for profiling genome-wide DNA methylation states in normal and disease conditions.     

Quantitation of cell surface molecules on a differentiating, Ly-1+ B cell lymphoma

The number of molecules expressed on the B cell membrane is known to influence the level of immune responses. However, a careful study of the changes in numbers of cell surface molecules during B cell differentiation has not been undertaken. We have addressed this question by using an inducible B cell lymphoma, CH12. Scatchard analysis was used to quantitate the levels of expression of surface immunoglobulin, major histocompatibility complex-encoded class I and class II molecules, and Ly-1 molecules on these cells during their differentiation in response to lipopolysaccharide (LPS). We found that the density of most molecules on the initial population of CH12 cells was comparable to their densities on small splenic B cells. Upon culture, we could classify the molecules into two groups based on their change in expression. One group, represented by surface immunoglobulin and class II molecules, decreased (surface immunoglobulin) or did not change (class II) in number after LPS stimulation, but increased during culture in the absence of LPS. The second set, represented by class I and Ly-1 molecules, increased after LPS stimulation, but did not change as a result of culture. Although the characteristic behavior of class I and class II molecules was different, concomitant changes were observed in both class I (K and D) molecules, and in both class II (I-A and I-E) molecules.     

Spatial determinants of specificity in insulin action

Insulin is a potent stimulator of intermediary metabolism, however the basis for the remarkable specificity of insulin's stimulation of these pathways remains largely unknown. This review focuses on the role compartmentalization plays in insulin action, both in signal initiation and in signal reception. Two examples are discussed: (1) a novel signalling pathway leading to the phosphorylation of the caveolar coat protein caveolin, and (2) a recently identified scaffolding protein, PTG, involved directly in the regulation of enzymes controlling glycogen metabolism.     

An Attraction Pheromone from Heads of Worker Vespula germanica Wasps

Vespula germanica is a social wasp that efficiently exploits food resources. Odor cues, derived from substances located in wasp heads, have been proved to be central in conspecific attraction in this species. However, it remains unknown whether this attraction is related to foraging or defense responses. In this study we analyze conspecific attraction under two different contexts: at the nest entrance (defense) and under foraging conditions. We also test wasp response with two dosages of head extract and crosschecked the attractiveness of extracts obtained from different populations. We found no evidence of alarm response to head extracts either at the nest entrance or under foraging conditions. Moreover, no differences in attractiveness were found to both doses tested. Head extracts attract similarly in the same or a different population suggesting that conspecific attraction is not restricted to colony nestmates.