Search

Aim: The continental island system comprising Sakhalin, Hokkaido and the southern Kuril Islands (SHSK) in northeastern Asia serves as one of the southernmost habitats for many boreal and arctic organisms, with colonization via land bridges formed during glacial periods. To understand the impacts of past land‐bridge formation under Quaternary climate changes across SHSK, we investigated the demographic history of forest‐dwelling marten species. Location: Sakhalin, Hokkaido and the southern Kuril Islands in northeastern Asia. Taxon: Sable, Martes zibellina (Carnivora, Mustelidae). Methods: We employed multiplexed inter‐simple sequence repeat genotyping by sequencing (MIG‐seq) to obtain genome‐wide single nucleotide polymorphisms (SNPs). We tested possible scenarios of colonization and diversification for SHSK sables using several population genetics approaches including clustering analysis, population tree estimation and approximate Bayesian computation modelling. We also examined haplotype diversity for the mitochondrial ND2 gene. Results: The genetic diversity of the island populations and their affinity for continental populations were found to be higher in the order Sakhalin > Hokkaido > Iturup in both nuclear SNP and mitochondrial DNA analyses. Demographic analyses indicated that the sable migrated repeatedly from the continent, particularly to the neighbouring Sakhalin Island. However, only an earlier colonized lineage has persisted on marginal Iturup Island since the Middle Pleistocene. The stronger effects of repeated migrations and/or isolation influenced by the distance to the continent have shaped the contemporary genetic diversity and differentiation of sable populations in SHSK. Main Conclusions: Genome‐wide and comprehensive sampling approaches demonstrated that the forest‐dwelling sable had long‐term persistence with partial admixture of multiple lineages in SHSK, suggesting the existence of forest corridors and refugia on the islands during the last several glacial periods. The SHSK system of continental islands is valuable for understanding the impacts of Quaternary climate changes on the genetic diversity and evolutionary histories of boreal organisms. [ABSTRACT FROM AUTHOR]

The Japanese archipelago is comprised of four main islands—Hokkaido, Honshu, Shikoku, and Kyushu—which contain high mountainous areas that likely allowed for lineage differentiation and population genetic structuring during the climatic changes of the late Pleistocene. Here, we assess the historical background of the evolutionary dynamics of herbivorous red-backed voles (Myodes) in Japan, examining the evolutionary trends of mitochondrial cytochrome b gene (Cytb) sequence variation. Four apparent signals from rapid expansion events were detected in three species, M. rufocanus and M. rutilus from Hokkaido and M. smithii from central Honshu. Taken together with results from previous studies on Japanese wood mice (Apodemus spp.), three of the expansion events were considered to be associated with predicted bottleneck events at the marine isotope stage (MIS) 4 period, in which glaciers are thought to have expanded extensively, especially at higher elevations. In the late Pleistocene, the possible candidates are transitions MIS 6/5, MIS 4/3, and MIS 2/1, which can be characterized by the cold periods of the penultimate glacial maximum, MIS 4, and the last glacial maximum, respectively. Our data further reveal the genetic footprints of repeated range expansion and contraction in the northern and southern lineages of the vole species currently found in central Honshu, namely M. andersoni and M. smithii , in response to climatic oscillation during the late Pleistocene. The time-dependent evolutionary rates of the mitochondrial Cytb presented here would provide a possible way for assessing population dynamics of cricetid rodents responding to the late Pleistocene environmental fluctuation. [ABSTRACT FROM AUTHOR]

For square contingency tables with ordered categories, there may be some cases that one wants to analyze them by considering collapsed tables with some adjacent categories combined in the original table. This paper proposes three kinds of new models which have the structure of point-symmetry (PS), quasi point-symmetry and marginal point-symmetry for collapsed square tables. This paper also gives a decomposition of the PS model for collapsed square tables. The father's and his daughter's occupational mobility data are analyzed using new models. [ABSTRACT FROM PUBLISHER]

Abstract: This paper provides a new concept based on the Damköhler number (Da) to describe the complete transition behavior found in a flame spread in a solid combustible tube. Through a series of experiments performed with various diameters of the tube, ambient pressure, and oxidizer velocity within a wide range, three combustion modes are observed for the flame spread in a solid fuel tube namely combustion dominated by heat transfer (mode 1), by chemical kinetics (mode 2), and slow combustion sustained under very high blowing conditions (so-called “stabilized combustion”: mode 3). Previous studies on the flame spread in tubes have shown that each transition, from mode 1 to mode 2 (transition 1–2) and from mode 2 to mode 3 (transition 2–3), is characterized by an equivalent velocity and by a friction velocity respectively. Meanwhile, for a flame spread on a fuel plate, it is widely known that both transitions are summarized by the Da. To achieve a comprehensive understanding of the transition characteristics of the combustion modes for the flame spread in the tube, the flame-spread rates under various conditions are experimentally investigated to elucidate the parameters that determine both transitions. First, the authors introduce a laminar friction velocity for the laminar flow region and revealed that transition 2–3 is determined by the laminar and turbulent friction velocity for laminar flow and turbulent flow regime respectively. The correlation between the Da and the friction velocity was experimentally obtained to show that transition 2–3 is consequently determined by the Da. This finding suggests that transition 2–3 corresponds to a blow-off limit that is observed for flame spread on a fuel plate. Second, the same correlation between the non-dimensional flame-spread rate and the Da is obtained, and it clearly showed that the transition 1–2 was determined by the Da. In conclusion, both transition phenomena are physically identical to those observed for on-plate flame spread, except the transition 2–3 occurs instead of the blow-off. [Copyright &y& Elsevier]

The solubility of a nonpolar solute in water is changed upon addition of a salt or cosolvent. Hereafter, "solvent" is formed by water molecules for pure water, by water molecules, cations, and anions for water-salt solution, and by water and cosolvent molecules for water-cosolvent solution. Decrease and increase in the solubility, respectively, are ascribed to enhancement and reduction of the hydrophobic effect. Plenty of experimental data are available for the change in solubility of argon or methane arising from the addition. We show that the integral equation theory combined with a rigid-body model, in which the solute and solvent particles are modeled as hard spheres with different diameters, can reproduce the data for the following items: salting out by an alkali halide and salting in by tetramethylammonium bromide, increase in solubility by a monohydric alcohol, and decrease in solubility by sucrose or urea. The orders of cation or anion species in terms of the power of decreasing the solubility can also be reproduced for alkali halides. With the rigid-body model, the analyses are focused on the roles of entropy originating from the translational displacement of solvent particles. It is argued by decomposing the solvation entropy of a nonpolar solute into physically insightful constituents that the solvent crowding in the bulk is a pivotal factor of the hydrophobic effect: When the solvent crowding in the bulk becomes more serious, the effect is strengthened, and when it becomes less serious, the effect is weakened. It is experimentally known that the thermal stability of a protein is also influenced by the salt or cosolvent addition. The additions which decrease and increase the solubility of a nonpolar solute, respectively, usually enhance and lower the thermal stability. This suggests that the enhanced or reduced hydrophobic effect is also a principal factor governing the stability change. However, urea decreases the solubility but lowers the stability. Bromide and iodide ions decrease the solubility but lower the stability of a protein with a large, positive total charge. In these cases, the urea- or ion-protein van der Waals interaction energy as well as the hydrophobic effect needs to be taken into account in arguing the stability change. We also present a new view on the so-called Hofmeister series: We show how it is expressed when the change in hydrophobic effect dominates and how it is modified when other factors are also influential.

The thermal stability of a protein is lowered by the addition of a monohydric alcohol, and this effect becomes larger as the size of hydrophobic group in an alcohol molecule increases. By contrast, it is enhanced by the addition of a polyol possessing two or more hydroxyl groups per molecule, and this effect becomes larger as the number of hydroxyl groups increases. Here, we show that all of these experimental observations can be reproduced even in a quantitative sense by rigid-body models focused on the entropic effect originating from the translational displacement of solvent molecules. The solvent is either pure water or water-cosolvent solution. Three monohydric alcohols and five polyols are considered as cosolvents. In the rigid-body models, a protein is a fused hard spheres accounting for the polyatomic structure in the atomic detail, and the solvent is formed by hard spheres or a binary mixture of hard spheres with different diameters. The effective diameter of cosolvent molecules and the packing fractions of water and cosolvent, which are crucially important parameters, are carefully estimated using the experimental data of properties such as the density of solid crystal of cosolvent, parameters in the pertinent cosolvent-cosolvent interaction potential, and density of water-cosolvent solution. We employ the morphometric approach combined with the integral equation theory, which is best suited to the physical interpretation of the calculation result. It is argued that the degree of solvent crowding in the bulk is the key factor. When it is made more serious by the cosolvent addition, the solvent-entropy gain upon protein folding is magnified, leading to the enhanced thermal stability. When it is made less serious, the opposite is true. The mechanism of the effects of monohydric alcohols and polyols is physically the same as that of sugars. However, when the rigid-body models are employed for the effect of urea, its addition is predicted to enhance the thermal stability, which conflicts with the experimental fact. We then propose, as two essential factors, not only the solvent-entropy gain but also the loss of protein-solvent interaction energy upon protein folding. The competition of changes in these two factors induced by the cosolvent addition determines the thermal-stability change.

It is of great interest from both scientific and practical viewpoints to theoretically predict the thermal-stability changes upon mutations of a protein. However, such a prediction is an intricate task. Up to now, significantly many approaches for the prediction have been reported in the literature. They always include parameters which are adjusted so that the prediction results can be best fitted to the experimental data for a sufficiently large set of proteins and mutations. The inclusion is necessitated to achieve satisfactorily high prediction performance. A problem is that the resulting values of the parameters are often physically meaningless, and the physicochemical factors governing the thermal-stability changes upon mutations are rather ambiguous. Here, we develop a new measure of the thermal stability. Protein folding is accompanied by a large gain of water entropy (the entropic excluded-volume (EV) effect), loss of protein conformational entropy, and increase in enthalpy. The enthalpy increase originates primarily from the following: The energy increase due to the break of protein-water hydrogen bonds (HBs) upon folding cannot completely be cancelled out by the energy decrease brought by the formation of protein intramolecular HBs. We develop the measure on the basis of only these three factors and apply it to the prediction of the thermal-stability changes upon mutations. As a consequence, an approach toward the prediction is obtained. It is distinguished from the previously reported approaches in the following respects: The parameters adjusted in the manner mentioned above are not employed at all, and the entropic EV effect, which is ascribed to the translational displacement of water molecules coexisting with the protein in the system, is fully taken into account using a molecular model for water. Our approach is compared with one of the most popular approaches, FOLD-X, in terms of the prediction performance not only for single mutations but also for double, triple, and higher-fold (up to sevenfold) mutations. It is shown that on the whole our approach and FOLD-X exhibit almost the same performance despite that the latter uses the adjusting parameters. For multiple mutations, however, our approach is far superior to FOLD-X. Five multiple mutations for staphylococcal nuclease lead to highly enhanced stabilities, but we find that this high enhancement arises from the entropic EV effect. The neglect of this effect in FOLD-X is a principal reason for its ill success. A conclusion is that the three factors mentioned above play essential roles in elucidating the thermal-stability changes upon mutations.