In PLoS Computational Biology this week, University of Leeds scientist Stefan Auer led work that studied how nanoparticles affect protein aggregation. Using molecular dynamics simulations of a system of hundreds of peptides over a millisecond timescale, his team showed that the aggregation is a two-phase process. The peptides first assemble on the nanoparticle and then "evolve into highly ordered beta-sheets as their size increases."
Also published in PLoS Computational Biology, researchers at the Max Planck Institute for Dynamics of Complex Technical Systems constructed a "comprehensive qualitative model of the EGFR/ErbB signaling pathway with more than 200 interactions reflecting our current state of knowledge," they say. Using their model in conjunction with high-throughput data, they were able to show inconsistencies in the EGFR/ErbB signaling network in liver biology. Specifically, they say, "Our results strongly suggest that the Rac/Cdc42 induced p38 and JNK cascades are independent of PI3K in both primary hepatocytes and HepG2."
Vamsi Mootha's lab used a computational screen to identify regulators of the human oxidative phosphorylation pathway. Calling their method expression screening, they found that when two candidate genes, CHCHD2 and SLIRP, were silenced with RNAi, there was a noticeable loss of OxPhos enzymatic activity. They also showed that SLIRP "plays an essential role in maintaining mitochondrial-localized mRNA transcripts that encode OxPhos protein subunits," they write in the abstract at PLoS Genetics.
Finally, scientists led by Julius Halaschek-Wiener at the Michael Smith Genome Sciences Centre performed the first "comprehensive analysis of genetic variation in aging-related candidate genes in healthy oldest-old," or people 85 and older. They sequenced 24 candidate healthy aging genes, including those involved in dietary restriction and stress response, and found 935 variants, including 848 SNPs and 87 insertion or deletions. They say that 41 percent of these were not in dbSNP. Their work appears in PLoS One.