Tug-of-war model for the two-bandit problem: Nonlocally-correlated parallel exploration via resource conservation

We propose a model - the “tug-of-war (TOW) model” - to conduct unique parallel searches using many nonlocally-correlated search agents. The model is based on the property of a single-celled amoeba, the true slime mold Physarum, which maintains a constant intracellular resource volume while collecting environmental information by concurrently expanding and shrinking its branches. The conservation law entails a “nonlocal correlation” among the branches, i.e., volume increment in one branch is immediately compensated by volume decrement(s) in the other branch(es). This nonlocal correlation was shown to be useful for decision making in the case of a dilemma. The multi-armed bandit problem is to determine the optimal strategy for maximizing the total reward sum with incompatible demands, by either exploiting the rewards obtained using the already collected information or exploring new information for acquiring higher payoffs involving risks. Our model can efficiently manage the “exploration-exploitation dilemma” and exhibits good performances. The average accuracy rate of our model is higher than those of well-known algorithms such as the modified ?-greedy algorithm and modified softmax algorithm, especially, for solving relatively difficult problems. Moreover, our model flexibly adapts to changing environments, a property essential for living organisms surviving in uncertain environments.     

A Highlights from MBoC Selection: Dual Functions of Yeast tRNA Ligase in the Unfolded Protein Response: Unconventional Cytoplasmic Splicing of HAC1 Pre-mRNA Is Not Sufficient to Release Translational Attenuation

The unfolded protein response (UPR) is an essential signal transduction to cope with protein-folding stress in the endoplasmic reticulum. In the yeast UPR, the unconventional splicing of HAC1 mRNA is a key step. Translation of HAC1 pre-mRNA (HAC1^u mRNA) is attenuated on polysomes and restarted only after splicing upon the UPR. However, the precise mechanism of this restart remained unclear. Here we show that yeast tRNA ligase (Rlg1p/Trl1p) acting on HAC1 ligation has an unexpected role in HAC1 translation. An RLG1 homologue from Arabidopsis thaliana (AtRLG1) substitutes for yeast RLG1 in tRNA splicing but not in the UPR. Surprisingly, AtRlg1p ligates HAC1 exons, but the spliced mRNA (HAC1ⁱ mRNA) is not translated efficiently. In the AtRLG1 cells, the HAC1 intron is circularized after splicing and remains associated on polysomes, impairing relief of the translational repression of HAC1ⁱ mRNA. Furthermore, the HAC1 5′ UTR itself enables yeast Rlg1p to regulate translation of the following ORF. RNA IP revealed that yeast Rlg1p is integrated in HAC1 mRNP, before Ire1p cleaves HAC1^u mRNA. These results indicate that the splicing and the release of translational attenuation of HAC1 mRNA are separable steps and that Rlg1p has pivotal roles in both of these steps.     

Ecological stoichiometry explains larger-scale facilitation processes by shrubs on species coexistence among understory plants

Plant facilitation (positive plant–plant interactions) strongly influences biodiversity, structure, and dynamics in plant communities, and the topic has received considerable attention among ecologists. Most studies of facilitation processes by shrubs have been conducted at small spatial scales between shrubs and their neighboring species. Yet, we know little about whether facilitation processes by shrubs at a small scale (i.e., a patch scale) also work at a larger scale (i.e., a site scale) in terms of the maintenance of biodiversity. Here, we report that the facilitative effects of shrubs on plant diversity at a larger scale can be explained by changing ecological stoichiometry. The soil fertility showed unimodal shape along shrub cover gradient, suggesting that the facilitative effects of a shrub do not necessarily increase as the shrub develops. The unimodal shape of dependence of plant species richness on shrub cover probably was generated by the unimodal dependence of soil fertility on shrub cover. Soil nutrient enrichment by shrubs shifted low N:P ratios of plant communities with low levels of shrub cover to more balanced N:P ratios at intermediate levels of shrub cover. At the peak N:P ratio along the gradient in shrub cover, the maximum species richness and functional richness were observed, which was consistent with the unimodal relationship predicted by the resource balance hypothesis. Thus, our findings showed that facilitation processes by shrubs at a patch scale also work at a larger scale in terms of the maintenance of biodiversity. Because observed larger-scale facilitation processes are enhanced at some intermediate levels of shrub cover, this study offers practical insight into the need for management practices that allow some intermediate levels of grazing by livestock for optimizing the role of larger-scale facilitation processes in the maintenance of biodiversity and ecosystem functioning in arid and semi-arid rangelands.     

Cross-spatial-scale patterns in the facilitative effect of shrubs and potential for restoration of desert steppe

Facilitation (positive plant–plant interactions) is a potential means to accelerate vegetation restoration in arid areas. Shrubs can accelerate vegetation recovery by means of soil amelioration, but this effect has not been evaluated at large spatial scales or across scales. Here, we examined the facilitative function of shrub change across spatial scales at a desert steppe in Mongolia. Using a high-resolution satellite image, we established five 2500 m² plots in each of three shrub density classes (low, moderate, high) in a desert steppe in Mongolia. To evaluate the facilitative functions of shrubs at multiple spatial scales, we recorded the total number of plant species at three nested spatial scales in each plot: 25, 400, and 2500 m². The facilitative effect of shrubs on plant species richness was more pronounced at larger scales. Denser shrub communities increased plant species diversity at a larger scale. However, the increased taxonomic diversity was not clearly related to increased functional diversity in this system. This scale dependency in species diversity can be explained by the degree to which spatial heterogeneity of habitats within the plots increased as plot size increased. These results support the hypothesis of scale-dependent changes in the balance between facilitation and competition. Therefore, transplanting shrub saplings at high-density and a larger scale could potentially improve the success of vegetation restoration in arid regions.     

Identification of yeast Art5 as a multicopy suppressor for the mitochondrial translocator maintenance protein Tam41

Normal mitochondrial protein import requires multiple translocator complexes in the outer and inner mitochondrial membrane. Tam41 is a peripheral inner membrane protein that is involved in the structural maintenance of the inner membrane translocator the TIM23 complex. Here we identified an arrestin-related protein Art5 as a multicopy suppressor for the Tam41-deficient yeast mutant, which exhibited the deteriorated TIM23 complex and temperature-sensitive growth defects. Overexpression of Art5 suppressed growth defects of tam41Δ cells and partially restored the destabilized TIM23 complex structure in tam41Δ mitochondria, so that the defects in mitochondrial protein import via the TIM23 complex were partially recovered. Deletion of the ART5 gene in turn exhibited synthetic growth defects with the TAM41 deletion. Art5 as a functional partner for Tam41 will provide a starting point to reveal the precise function of Tam41 in the maintenance of the TIM23 complex.     

Growth and survival of <Emphasis Type="Italic">Abies sachalinensis</Emphasis> seedlings for three years after selection harvesting in northern Hokkaido,Japan

Previous studies have indicated that recruitment of Abies sachalinensis, a representative conifer species of northern Japan, decreased following single-tree selection harvesting in stands with dense dwarf bamboo understory. We tested the hypothesis that growth and survival of A. sachalinensis seedlings are reduced by canopy opening in that type of stand. A 0.75 ha study plot was examined, and all the seedlings (defined as trees with height 0.5–2 m) were identified and their shoot extensions measured for three years after single-tree selection harvesting (26% intensity in terms of basal area). The leader extensions of A. sachalinensis seedlings that experienced canopy opening were greatly improved. However, a negative effect on survival was also apparent; nearly 40% of seedlings died at the sites that experienced canopy opening. These results were supported by generalized linear models that examined variations of local harvesting intensity for individual seedlings. Despite the ability of A. sachalinensis to respond rapidly to exposure, some physiological stresses may have appeared, and presumably were amplified by co-occurring dwarf bamboos. With regard to the low seedling density (156 stems ha⁻¹), common in this type of stands, local harvesting intensity in the selection system should be reduced to maintain survival of advanced regeneration, thus sustaining stand structure and composition.     

A high-throughput and generic assay method for the determination of substrate specificities of thermophilic alpha-aminotransferases

For the determination of substrate specificities of thermophilic alpha-aminotransferases (AATs), a novel high-throughput assay method was developed. In this method, a thermophilic omega-aminotransferase (OAT) and a thermophilic aldehyde dehydrogenase (ALDH) are coupled to the AAT reaction. Glutamic acid is used as an amino group donor for the AAT reaction yielding 2-oxoglutalic acid. 2-Oxoglutalic acid produced by the AAT reaction is used as an amino group acceptor in the OAT reaction regenerating glutamic acid. The amino group donor of the OAT reaction is 5-aminopentanoic acid yielding pentanedioic acid semialdehyde which is oxidized by ALDH to pentanedioic acid with concomitant reduction of NADP(+) to NADPH. NADPH thus produced then reduces colorless tetrazolium salt into colored formazan. To construct such a reaction system, the genes for a thermophilic AAT, a thermophilic OAT and a thermophilic ALDH were cloned and expressed in Escherichia coli. These enzymes were subsequently purified and used to determine the activities of AAT for the synthesis of unnatural amino acids. This method allowed the clear detection of the AAT activities as it measures the increase in the absorbance on a low background absorbance reading.     

Fine mapping and allelic dosage effect of <Emphasis Type="Italic">Hwc1</Emphasis>, a complementary hybrid weakness gene in rice

Hybrid weakness is a reproductive barrier that is found in many plant species. In rice, the hybrid weakness caused by two complementary genes, Hwc1 and Hwc2, has been surveyed intensively. However, their gene products and the molecular mechanism that causes hybrid weakness have remained unknown. We performed linkage analyses of Hwc1, narrowed down the area of interest to 60 kb, and identified eight candidate genes. In the F(2) population, in which both Hwc1 and Hwc2 genes were segregated, plants were separable into four classes according to their respective phenotypes: severe type, semi-severe type, F(1) type, and normal type. Severe type plants show such severe symptoms that they could produce only tiny shoot-like structures; they were unable to generate roots. Genetic analyses using closely linked DNA markers of the two genes showed that the symptoms of the F(2) plants were explainable by the genotypes of Hwc1 and Hwc2. Weakness was observed in plants that have both Hwc1 and Hwc2. In Hwc1 homozygote, the symptoms worsened and severe type or semi-severe type plants appeared. Consequently, Hwc1 should have a gene dosage effect and be a semi-dominant gene. The dosage effect of Hwc2 was recognizable, but it was not so severe as that in Hwc1. These results are useful to elucidate the mechanism that causes the hybrid weakness phenomenon and the role of each causal gene in hybrid weakness.     

Inhibition of lipase activities by basic polysaccharide

Basic polysaccharide strongly inhibited the hydrolysis of trioleoylglycerol (TO) emulsified with phosphatidylcholine and taurocholate by either pancreatic lipase or carboxylester lipase. DEAE-Sephadex dose-dependently inhibited the hydrolysis of TO by pancreatic lipase and carboxylester lipase; however, carboxymethyl-Sephadex and Sephadex G-50 did not inhibit the hydrolysis. Polydextrose (PD), a soluble polysaccharide, was a very weak inhibitor of pancreatic lipase. However, when a basic group, a DEAE group, was attached to PD, lipase inhibition by DEAE-PD was increased, and this was dependent on the substitution ratio of DEAE groups. The number of positive charges per PD molecule is important in lipase inhibition. Similar substitution effects were observed with other basic groups, such as piperidinoethyl and 3-triethylamino-2-hydroxypropyl. The natural basic polysaccharide, chitosan, also inhibited pancreatic lipase activity. Gel-filtration experiments suggested that DEAE-PD did not bind strongly to pancreatic lipase. The effect of DEAE-PD on TO hydrolysis by pancreatic lipase was studied using various emulsifiers: DEAE-PD (50 microg/ml) did not inhibit the hydrolysis of TO emulsified with arabic gum, phosphatidylserine, or phosphatidic acid. In vivo, oral administration of DEAE-PD to rats reduced the peak plasma triacylglycerol concentration and increased fecal lipid excretion. These results suggest that basic polysaccharide is able to suppress dietary fat absorption from the small intestine by inhibiting pancreatic lipase activity.