Distribution of distances from RBP to amino acid substitutions.

<p>The distances in the three-dimensional structure of HA were measured between RBP and amino acid substitutions occurring on the NGS+ (A and D), NGS− (B and E), and NGS± (C and F) trunk branches for A/H3N2 (A-C) and A/H1N1 (D-F) viruses.</p

Substitution patterns before and after the introduction of oseltamivir in HA1 of A/H3N2 virus.

<p>After dividing the phylogenetic tree of A/H3N2 virus into part I and II, which roughly corresponded to the period before and after the introduction of oseltamivir in humans, respectively, the proportions of charge+ (red bar), charge− (green bar), and charge± (black bar) substitutions in HA1 on the NGS± branches were obtained for part I and II separately. The numbers of amino acid substitutions on the NGS± branches in part I and II are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040422#pone.0040422.s006" target="_blank">Table S2</a>.</p

Presentation_1_Simple Assumptions to Improve Markov Illuminance and Reflectance.pdf

Murray recently introduced a novel computational lightness model, Markov illuminance and reflectance (MIR). MIR is a promising new approach that simulates human lightness processing using a conditional random field (CRF) where natural-scene statistics of reflectance and illumination are implemented. Although MIR can account for various lightness illusions and phenomena, it has limitations, such as the inability to predict reverse-contrast phenomena. In this study, we improved MIR performance by modifying its inference process, the prior on X-junctions, and that on general illumination changes. Our modified model improved predictions for Checkerboard assimilation, the simplified Checkershadow and its control figure, the influence of luminance noise, and White’s effect and its several variants. In particular, White’s effect is a partial reverse contrast that is challenging for computational models, so this improvement is a significant advance for the MIR framework. This study showed the high extensibility and potential of MIR, which shows the promise for further sophistication.</p

Phylogenetic tree of HA for HA-NA available strains of A/H1N1 virus.

<p>The phylogenetic tree was constructed using 998 complete HA-coding nucleotide sequences for HA-NA available strains of A/H1N1 virus. Cluster I and II correspond to those in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040422#pone.0040422.s002" target="_blank">Figure S2</a>. (A) The strain names at exterior nodes were colored according to the net-charge in HA1; red: +14-+16, pink: +12-+13, orange: +10-+11, yellow: +8-+9, right blue: +6-+7, and blue: +4-+5. (B) The strain names at exterior nodes were colored red or orange when they had triple (Gln222, Met234, and Tyr274) or single (Tyr274) amino acid mutation in NA, respectively.</p

Temporal changes in the net-charge and the number of NGS in HA1.

<p>The net-charge (red circles) and the number of NGS (blue circles) in HA1 were plotted against the year of isolation for each strain of (A) A/H3N2 (<i>n</i> = 1,903) and (B) A/H1N1 (<i>n</i> = 723) viruses. The area of the circles is proportional to the frequencies of the strains, with the scales indicated at the corner. The solid and dashed lines represent the average values of the net-charge and the number of NGS in HA1 for the viruses isolated in each year, respectively.</p

Distribution of distances between amino acid substitutions in HA1 occurring on the same NGS± branches.

<p>The distances in the three-dimensional structure of HA between amino acid substitutions occurring on the same NGS± branches were measured for (A) A/H3N2 and (B) A/H1N1 viruses. The red and black bars indicate the proportions of distances between pairs of charge+ and charge− substitutions and other pairs, respectively.</p

Design of the Zinc Ion and Plasmid DNA Co-Delivery System by Poly(1-Vinylimidazole) Derivatives for Myoblast Differentiation

The co-delivery system of zinc ions (Zn2+) and plasmid DNA (pDNA) has been designed by the use of poly(1-vinylimidazole) (PVIm) derivatives for myoblast differentiation. Six PVIm derivatives were synthesized, followed by the optimization of the chemical structure. As a result, methylated and carboxymethylated PVIm (CM-PVIm-Me) delivered the highest amount of Zn2+ ions inside C2C12 myoblast cells. The CM-PVIm-Me also delivered pDNA inside the myoblast cells to exhibit pDNA gene expression which was upregulated by the co-delivered Zn2+ ions. The co-delivered Zn2+ ions were localized in the cell nucleus presumably to affect cellular functions. Actually, the myoblast cells treated with the Zn2+/CM-PVIm-Me/pDNA complexes differentiated to myotubes. These results suggest that the Zn2+ ions delivered by the CM-PVIm-Me inside the cells differentiated myoblasts to myotubes. Our co-delivery system of Zn2+ ion and pDNA without zinc transporter can be a unique tool of regenerative medicine for muscular injury

Compensatory Evolution of Net-Charge in Influenza A Virus Hemagglutinin

<div><p>The propagation of influenza A virus depends on the balance between the activities of hemagglutinin (HA) for binding to host cells and neuraminidase (NA) for releasing from infected cells (HA-NA balance). Since the host cell membrane and the sialic acid receptor are negatively charged, the amino acid substitutions increasing (charge+) and decreasing (charge−) the positive charge of HA subunit 1 (HA1) enhance and reduce, respectively, the binding avidity and affinity. The positive charge of HA1 in human influenza A virus bearing subtype H3N2 (A/H3N2 virus) was observed to have increased during evolution, but the evolutionary mechanism for this observation was unclear because this may disrupt the HA-NA balance. Here we show, from the phylogenetic analysis of HA for human A/H3N2 and A/H1N1 viruses, that the relative frequencies of charge+ and charge− substitutions were elevated on the branches where the number of N-glycosylation sites (NGS) increased and decreased, respectively, compared to those where the number of NGS did not change. On the latter branches, the net-charge of HA1 appeared to have been largely maintained to preserve its structure and function. Since the charge+ and charge− substitutions in HA1 have opposite effects to the gain and loss of NGS on the binding and release of the virus, the net-charge of HA1 may have evolved to compensate for the effect of the gain and loss of NGS, probably through changing the avidity. Apparently, the relative frequency of charge− substitutions in HA1 of A/H3N2 virus was elevated after the introduction of oseltamivir, and that of charge+ substitutions in HA1 of A/H1N1 virus was elevated after the spread of oseltamivir resistance. These observations may also be explained by the compensatory effect of the net-charge in HA1 on the NA activity for keeping the HA-NA balance.</p> </div

Patterns of amino acid substitutions in HA1 on different branches of phylogenetic trees.

<p>The proportions of charge+ (red bar), charge− (green bar), and charge± (black bar) substitutions in HA1 on the trunk, interior, and exterior branches of the NGS+, NGS−, and NGS± branches are indicated for (A) A/H3N2 and (B) A/H1N1 viruses. The number of amino acid substitutions in HA1 is shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040422#pone.0040422.s005" target="_blank">Table S1</a>.</p

Net-charge and number of NGS in HA1 on the trunk branches.

<p>The sums of changes in the net-charge (red line) and the number of NGS (blue line) in HA1 from the root to each node along all trunk branches (A: A/H3N2 virus; C: A/H1N1 virus) and that in the net-charge along NGS± trunk branches (B: A/H3N2 virus; D: A/H1N1 virus) were plotted against the total branch length from the root to the node. The red and blue arrows indicate the trunk branches where gains and losses of NGS occurred in HA1, respectively, with the amino acid positions of NGS.</p