A Molecular Dynamics Study of the Stereoselective Interaction between an Enantiomeric Amino-Acid Ester and an l-Histidine-Containing Catalyst in the Bilayer Membrane

Molecular dynamics simulations were performed to investigate the stereoselective interaction between an enantiomeric amino acid substrate (N-acylated-l-phenylalanine-p-nitrophenyl ester) and an l-histidine-containing dipeptide catalyst (N-(N-benzyloxycarbonyl-l-leucyl)-l-histidine) in the bilayer of cationic surfactants (N,N-bisdodecyl-N,N-dimethylammonium chloride). We found that a catalyst–substrate complex, which had an interamide hydrogen bond, was formed spontaneously in vacuum at 500 K. This complex was found to be stable both in vacuum and in the bilayer membrane for 100 ps at 300 K. The distances between the hydrophobic side chains in the complex were consistent with experimental results. The interamide hydrogen bond was retained in the hydrophobic core of the membrane. These results suggest that the catalyst–substrate complex found in this work is relevant to the stereoselective hydrolysis of the l-enantiomer of the substrate.     

Vibronic attraction energy for superconductivity in the model of Si-containing organic polymers

Superconducting vibronic interaction has been examined for a model of Si-substituted polyacetylene. Large attractive vibronic interaction for the formation of superconducting electron pair has been found for the electron scattering process in between the and in-plane orbitals in silene unit. Doping of holes in these orbitals would be done by extracting electrons from the out-of-plane orbitals as well as from the in-plane orbitals. If stacking of the model polymers is performed in a parallel manner, the interplane electron pairing has also been found to be favorable on account of small Coulombic repulsion.     

Atypical virulence in a type III Toxoplasma gondii strain isolated in Japan

The virulence of a type III Toxoplasma gondii strain isolated in Japan and designated here as TgCatJpGi1/TaJ was examined in mice and micro minipigs in this study. Despite its type III genotype, oral or intraperitoneal inoculation of cysts from it resulted in severe virulence in C57BL/6J and BALB/c mice. In contrast, mice inoculated with a high dose of TgCatJpGi1/TaJ tachyzoites showed no obvious clinical signs of infection, and all of them survived for >21?days post-inoculation. Furthermore, no clinical signs of infection were seen when micro minipigs were inoculated with 900 cysts. Interestingly, our allelic type screening of the virulence-related rop5, rop16, rop17, and rop18 genes, as based on restriction fragment length polymorphism analysis (RFLP), revealed that the RFLP patterns for TgCatJpGi1/TaJ were identical to those from nonvirulent type III parasites. These results suggest that TgCatJpGi1/TaJ possesses an unknown virulence factor or factors.     

Model analysis of the effect of environmental fluctuation on the species replacement pattern of pelagic fishes under interspecific competition

There are two factors affecting long-term fluctuation of planktotrophic pelagic fish: environmental fluctuation and interspecific competition. Long-term catch data of planktotrophic pelagic fishes in Japan suggest that the chub mackerel (species B) was replaced by the sardine (A), A was replaced by the anchovy, Pacific saury and horse mackerel (Group C), and species in group C were replaced by species B. If species A defeats B, B defeats C, and C defeats A in interspecific competitive ability, then the abundance of these three groups fluctuate forever and dominate in the same order. We call this cyclic advantage hypothesis for species replacement. In this model, environmental fluctuation affects the species replacement as a trigger. Environmental fluctuation does not determine the next dominant species but greatly affects when the next replacement occurs.     

The First Symbiont-Free Genome Sequence of Marine Red Alga,Susabi-nori (Pyropia yezoensis)

Nori, a marine red alga, is one of the most profitable mariculture crops in the world. However, the biological properties of this macroalga are poorly understood at the molecular level. In this study, we determined the draft genome sequence of susabi-nori (Pyropia yezoensis) using next-generation sequencing platforms. For sequencing, thalli of P. yezoensis were washed to remove bacteria attached on the cell surface and enzymatically prepared as purified protoplasts. The assembled contig size of the P. yezoensis nuclear genome was approximately 43 megabases (Mb), which is an order of magnitude smaller than the previously estimated genome size. A total of 10,327 gene models were predicted and about 60% of the genes validated lack introns and the other genes have shorter introns compared to large-genome algae, which is consistent with the compact size of the P. yezoensis genome. A sequence homology search showed that 3,611 genes (35%) are functionally unknown and only 2,069 gene groups are in common with those of the unicellular red alga, Cyanidioschyzon merolae. As color trait determinants of red algae, light-harvesting genes involved in the phycobilisome were predicted from the P. yezoensis nuclear genome. In particular, we found a second homolog of phycobilisome-degradation gene, which is usually chloroplast-encoded, possibly providing a novel target for color fading of susabi-nori in aquaculture. These findings shed light on unexplained features of macroalgal genes and genomes, and suggest that the genome of P. yezoensis is a promising model genome of marine red algae.