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Abstract Fluid mixing is crucial in various industrial processes. In this study, focusing on the characteristics that reinforcement learning (RL) is suitable for global-in-time optimization, we propose utilizing RL for fluid mixing optimization of passive scalar fields. For the two-dimensional fluid mixing problem described by the advection–diffusion equations, a trained mixer realizes an exponentially fast mixing without any prior knowledge. The stretching and folding by the trained mixer around stagnation points are essential in the optimal mixing process. Furthermore, this study introduces a physically reasonable transfer learning method of the trained mixer: reusing a mixer trained at a certain Péclet number to the mixing problem at another Péclet number. Based on the optimization results of the laminar mixing, we discuss applications of the proposed method to industrial mixing problems, including turbulent mixing.

Abstract Prevailing directions of seed and pollen dispersal may induce anisotropy of the fine‐scale spatial genetic structure (FSGS), particularly in wind‐dispersed and wind‐pollinated species. To examine the separate effects of directional seed and pollen dispersal on FSGS, we conducted a population genetics study for a dioecious, wind‐pollinated, and wind‐dispersed tree species, Cercidiphyllum japonicum Sieb. et Zucc, based on genotypes at five microsatellite loci of 281 adults of a population distributed over a ca. 80 ha along a stream and 755 current‐year seedlings. A neighborhood model approach with exponential‐power‐von Mises functions indicated shorter seed dispersal (mean = 69.1 m) and much longer pollen dispersal (mean = 870.6 m), effects of dispersal directions on the frequencies of seed and pollen dispersal, and the directions with most frequent seed and pollen dispersal (prevailing directions). Furthermore, the distance of effective seed dispersal within the population was estimated to depend on the dispersal direction and be longest at the direction near the prevailing direction. Therefore, patterns of seed and pollen dispersal may be affected by effective wind directions during the period of respective dispersals. Isotropic FSGS and spatial sibling structure analyses indicated a significant FSGS among the seedlings generated by the limited seed dispersal, but anisotropic analysis for the seedlings indicated that the strength of the FSGS varied with directions between individuals and was weakest at a direction near the directions of the most frequent and longest seed dispersal but far from the prevailing direction of pollen dispersal. These results suggest that frequent and long‐distance seed dispersal around the prevailing direction weakens the FSGS around the prevailing direction. Therefore, spatially limited but directional seed dispersal would determine the existence and direction of FSGS among the seedlings.

Abstract Background Gankyrin (GK) is an oncoprotein which regulates inflammatory responses and its inhibition is considered as a possible anti-inflammatory therapy for inflammatory bowel disease (IBD). Methods In this study, we investigated the role of GK in epithelial cells using mice with intestinal epithelial cell-specific GK deletion in (i) the entire small intestine and colon (Villin-Cre;Gankyrin f/f ) and (ii) the distal intestine and colon (Cdx2-Cre;Gankyrin f/f ). Result Unexpectedly, GK-deficiency in the upper small bowel augmented inflammatory activity compared with control mice when colitis was induced with dextran sodium sulfate. Biochemical analyses have revealed GK-deficiency to have caused reduction in the expression of antimicrobial peptides, α-Defensin-5 and -6, in the upper small bowel. Examination of human samples have further confirmed that the reduction of GK expression in the small bowel is associated with colonic involvement in human Crohn’s disease. Through the sequencing of bacterial 16S rRNA gene amplicons, bacteria potentially deleterious to intestinal homeostasis such as Helicobacter japonicum and Bilophila were found to be over-represented in colitis induced Villin-Cre;Gankyrin f/f mice when compared to Gankyrin f/f control mice under the same condition. Conclusion These results highlight the distinct site dependence of the pro- and anti-inflammatory functions of GK and provide important insights into the pathogenesis of IBD.

Coarse-graining is indispensable for extracting a hierarchy of vortices in fully developed turbulent flow with multiscale nature. In the present study, for a high-Reynolds-number turbulent boundary layer, we employ two simple coarse-graining methods in real space; namely, a Gaussian filter and the combination of the Gaussian filters at two scales. The former corresponds to a low-pass filter of Fourier modes, while the latter corresponds to a band-pass filter. We also examine two different filter widths for the band-pass filter. Then, we show difference in the statistics of the three filtered fields. Since the velocity gradients in turbulence are mainly determined by the smallest-scale motions, vortical structures identified by the second invariant Q of the velocity gradient coarse-grained by the filters are similar. However, there is difference between low- and band-pass filtered fields in the contribution to the enstrophy production rates. This is because the production rates are determined not only by the magnitude of the strain rates but also by the alignment between the vorticity and the stretching direction. In addition, since vortices are not created in the entire system, the conditional sampling by the value of Q is essential to understand the generation mechanism of the hierarchy of vortices. The conditional analysis of the band-pass filtered fields demonstrates that small-scale vortices in the log layer are stretched by twice-larger vortices, whereas they weaken the twice-larger vortices. This observation is consistent with the picture of the energy cascade. We also show that when using the band-pass filter, these conclusions are robust irrespective of the choice of the filter width.

Conifers in northern forests, such as fir and spruce, preferably regenerate on coarse woody debris, including fallen logs, stumps, and snags. In northern Japan, the sub-boreal conifer species Picea jezoensis is completely dependent on coarse woody debris for seedling establishment. To understand the fine-scale spatial genetic structure (FSGS) of this species, a 5-ha plot was established in central Hokkaido, and 531 individual trees were categorized into four life-stages (seedling, sapling, juvenile, and mature) on the basis of age and size. The FSGS of the established seedlings and later growth stages was investigated using 11 nuclear simple sequence repeat loci. A STRUCTURE analysis of seedlings and saplings established on fallen logs revealed that genetically related individuals were spatially localized between adjacent logs. We also found a significant FSGS in early life-stages based on a decline in the kinship coefficient calculated between individuals over shorter to longer spatial distances. Furthermore, the estimation of dispersal kernels indicated the frequent occurrence of short-distance seed dispersal. These results indicated that genetically related seedlings and saplings regenerated on the same or nearby fallen logs. In contrast to the results for the early stages, mature-stage trees showed no significant FSGS. We ran a simulation to examine the hypothesis that the FSGS could be eliminated by demographic thinning during life history processes. We calculated values for simulated offspring generated under three sets of conditions; i.e., by removing (i) inbred individuals, (ii) randomly chosen individuals, and (iii) all individuals on the specific fallen logs. However, the results for the FSGS were significant for all simulated data sets. This indicated that inbreeding depression, stochastic loss, or eradication of establishment sites by local disturbances alone could not explain the lack of FSGS among mature-stage trees. Therefore, it is possible that the colonization history of mature trees present on the study site might differ from that of the current offspring.

ABSTRACT Metagenomics has revealed the existence of numerous uncharacterized viral lineages, which are referred to as viral “dark matter.” However, our knowledge regarding viral genomes is biased toward culturable viruses. In this study, we analyzed 1,600 (1,352 nonredundant) complete double-stranded DNA viral genomes (10 to 211 kb) assembled from 52 marine viromes. Together with 244 previously reported uncultured viral genomes, a genome-wide comparison delineated 617 genus-level operational taxonomic units (OTUs) for these environmental viral genomes (EVGs). Of these, 600 OTUs contained no representatives from known viruses, thus putatively corresponding to novel viral genera. Predicted hosts of the EVGs included major groups of marine prokaryotes, such as marine group II Euryarchaeota and SAR86, from which no viruses have been isolated to date, as well as Flavobacteriaceae and SAR116. Our analysis indicates that marine cyanophages are already well represented in genome databases and that one of the EVGs likely represents a new cyanophage lineage. Several EVGs encode many enzymes that appear to function for an efficient utilization of iron-sulfur clusters or to enhance host survival. This suggests that there is a selection pressure on these marine viruses to accumulate genes for specific viral propagation strategies. Finally, we revealed that EVGs contribute to a 4-fold increase in the recruitment of photic-zone viromes compared with the use of current reference viral genomes. IMPORTANCE Viruses are diverse and play significant ecological roles in marine ecosystems. However, our knowledge of genome-level diversity in viruses is biased toward those isolated from few culturable hosts. Here, we determined 1,352 nonredundant complete viral genomes from marine environments. Lifting the uncertainty that clouds short incomplete sequences, whole-genome-wide analysis suggests that these environmental genomes represent hundreds of putative novel viral genera. Predicted hosts include dominant groups of marine bacteria and archaea with no isolated viruses to date. Some of the viral genomes encode many functionally related enzymes, suggesting a strong selection pressure on these marine viruses to control cellular metabolisms by accumulating genes.

Genome-wide scans for positive selection have become important for genomic medicine, and many studies aim to find genomic regions affected by positive selection that are associated with risk allele variations among populations. Most such studies are designed to detect recent positive selection. However, we hypothesize that ancient positive selection is also important for adaptation to pathogens, and has affected current immune-mediated common diseases. Based on this hypothesis, we developed a novel linkage disequilibrium-based pipeline, which aims to detect regions associated with ancient positive selection across populations from single nucleotide polymorphism (SNP) data. By applying this pipeline to the genotypes in the International HapMap project database, we show that genes in the detected regions are enriched in pathways related to the immune system and infectious diseases. The detected regions also contain SNPs reported to be associated with cancers and metabolic diseases, obesity-related traits, type 2 diabetes, and allergic sensitization. These SNPs were further mapped to biological pathways to determine the associations between phenotypes and molecular functions. Assessments of candidate regions to identify functions associated with variations in incidence rates of these diseases are needed in the future.

To understand the co-existence mechanisms of related species, the recruitment processes of Fagus crenata and F. japonica were censused during 3 and 4 years from emergence, respectively, in a cool-temperate forest in Japan. The distributional properties and the growth traits were compared between two Fagus species. To evaluate the distributional properties, the spatial abundance of seedlings was estimated by a generalized linear model (GLM), with explanatory variables such as topographic variables, light conditions, the presence of dwarf bamboo, and the abundance of the overstory. To evaluate the growth traits under herbivory pressure, both the elongated shoot length and the proportion of recovery from predation (re-growth) were also compared. No spatial segregation and no species-specific differences were detected by GLM, which was consistent throughout the census period. Only F. japonica exhibited a slope-related distribution, while F. crenata exhibited no topographical dependence, indicates the distributional overlaps. For the growth traits, contrasting trends were detected, F. crenata was superior in shoot growth, whereas the proportion of re-growth was higher in F. japonica than F. crenata. We concluded that co-dominance of these species was not attributed to the spatial segregation but to the trade-off between growth and resistance to herbivory.

Subdiffusion is commonly observed in liquids with high density or in restricted geometries, as the particles are constantly pushed back by their neighbors. Since this “cage effect” emerges from many-body dynamics involving spatiotemporally correlated motions, the slow diffusion should be understood not simply as a one-body problem but as a part of collective dynamics, described in terms of space–time correlations. Such collective dynamics are illustrated here by calculations of the two-particle displacement correlation in a system of repulsive Brownian particles confined in a (quasi-)one-dimensional channel, whose subdiffusive behavior is known as the single-file diffusion (SFD). The analytical calculation is formulated in terms of the Lagrangian correlation of density fluctuations. In addition, numerical solutions to the Langevin equation with large but finite interaction potential are studied to clarify the effect of overtaking. In the limiting case of the ideal SFD without overtaking, correlated motion with a diffusively growing length scale is observed. By allowing the particles to overtake each other, the short-range correlation is destroyed, but the long-range weak correlation remains almost intact. These results describe nested space–time structure of cages, whereby smaller cages are enclosed in larger cages with longer lifetimes.

The repertoire of biosynthetic enzymes found in an organism is an important clue for elucidating the chemical structural variations of various compounds. In the case of fatty acids, it is essential to examine key enzymes that are desaturases and elongases, whose combination determine the range of fatty acid structures. We systematically investigated 56 eukaryotic genomes to obtain 275 desaturase and 265 elongase homologs. Phylogenetic and motif analysis indicated that the desaturases consisted of four functionally distinct subfamilies and the elongases consisted of two subfamilies. From the combination of the subfamilies, we then predicted the ability to synthesize six types of fatty acids. Consequently, we found that the ranges of synthesizable fatty acids were often different even between closely related organisms. The reason is that, as well as diverging into subfamilies, the enzymes have functionally diverged within the individual subfamilies. Finally, we discuss how the adaptation to individual environments and the ability to synthesize specific metabolites provides some explanation for the diversity of enzyme functions. This study provides an example of a potent strategy to bridge the gap from genomic knowledge to chemical knowledge.

Environmental genomics can describe all forms of organisms—cellular and viral—present in a community. The analysis of such eco-systems biology data relies heavily on reference databases, e.g., taxonomy or gene function databases. Reference databases of symbiosis sensu lato, although essential for the analysis of organism interaction networks, are lacking. By mining existing databases and literature, we here provide a comprehensive and manually curated database of taxonomic links between viruses and their cellular hosts.

Premise of the study: We developed simple sequence repeat (SSR) markers from expressed sequence tags (ESTs) for Abies firma, a conifer endemic in Japan, to facilitate evaluation of the population genetic structure in this species. Methods and Results: We designed primers for 153 EST-SSRs identified from 486 322 ESTs from A. sachalinensis ESTs, and tested 96 of them for PCR amplification. Thirty-two primers provided clear amplification, and 14 of those 32 displayed clear polymorphic patterns in multiple populations of A. firma and in two closely related species. The number of alleles per locus and mean expected heterozygosity ranged from one to six and 0 to 0.476, respectively. Conclusions: The EST-SSR markers developed in this study may be useful for phylogeography and population genetic studies of A. firma. Successful amplifications were obtained for two other Abies species, suggesting that these markers may also be useful for similar applications in other fir species.