Metagenomic analysis using 16S ribosomal RNA genes of a bacterial community in an urban stream,the Tama River,Tokyo

In an effort to determine genus- or species-level taxonomic profiles and diversity of bacterial consortia in the Tama River around urban Tokyo, next-generation sequencing technology targeting a 16S ribosomal RNA (rRNA) gene amplicon was employed. Metagenomic analysis performed by an Ion Personal Genome Machine after sequentially filtering samples through 5-, 0.8- and 0.2-μm filters yielded 1.48 Gb of 16S sequences (average 2.38 M reads/sample). The results indicated that half of the bacterial sequences belonged to Proteobacteria, followed by Bacteroidetes, Actinobacteria and Cyanobacteria. Flavobacterium (Bacteroidetes), possibly including a potential fish pathogen, was the most numerous genera in the Tama River metagenome, and accounted for?~?16% of assigned 16S reads, followed by Mycobacterium. Other dominant bacterial genera including Zoogloea, Sediminibacterium, Hyphomicrobium, Sphingopyxis, Thiothrix and Lysobacter, were thought to be associated with waste water and sludge. MiSeq metagenomic analysis revealed that environmental factors, particularly water temperature, influenced the bacterial composition throughout the year, with a strong negative correlation observed for Proteobacteria and a positive correlation for Bacteroidetes. In terms of bacterial genera, Flavobacterium was positively correlated with temperature, while Polaromonas, Pseudomonas and Bradyrhizobium were negatively correlated with this, suggesting dynamic change in the free-living bacterial population throughout the year and versatile adaptation strategies in relation to environmental factors.     

Relationships among the chalkiness,kernel size and endosperm cell morphology of rice kernels at different spikelet positions within a panicle

The occurrence of chalky kernels in rice is causally related to kernel size and endosperm morphology. This study aimed to investigate the occurrence of chalky kernels by analyzing kernel size, and the number and area of endosperm cells. Spikelets were sampled from upper and middle primary branches and lower secondary branches in a panicle, and divided into four categories: upper, middle, and lower perfect (PF) kernels and lower milky-white (MW) kernels. On the lower secondary branches, there was a higher percentage of chalky kernels, with smaller kernel lengths, widths and thicknesses, than the kernels on the upper and middle primary branches. MW kernels were smaller in size than PF kernels even on the same lower secondary branches. Regardless of grain appearance quality traits, the total areas of endosperm cross sections in lower kernels were significantly smaller than in upper kernels owing to the decreased cell area, and there was a significant negative correlation between the number of cells and average cell area. When the numbers and the areas of cells were analyzed using angular 30° intervals from the line connecting the center point and the dorsal vascular bundle, the MW kernels had significantly less cells than PF kernels near the ventral side at 120–180°. Thus, the decrease in the number of cells near the ventral side was a main causal factor in the decrease in MW kernel widths compared with PF kernel widths, and this suggested that cell division in MW kernels was inhibited at the early grain-filling stage.     

Effects of patch cutting on leaf nitrogen nutrition in hinoki cypress (Chamaecyparis obtusa Endlicher) at different elevations along a slope in Japan

Leaf nitrogen nutrition of hinoki cypress (Chamaecyparis obtusa Endlicher) was investigated at three positions along a slope over a period of 3 years. At each slope position, nitrogen properties were compared in patch-cut plots (0.06–0.09 ha) and uncut control plots (0.04 ha). Nitrogen cycling at the lower slope was characterized by a higher rate of soil nitrogen mineralization, and higher nitrogen concentration in fresh leaves and leaf-litter. The soil nitrogen mineralization rate and fresh-leaf nitrogen concentration in the patch-cut plots were higher than those in the control plots. However, leaf-litter nitrogen concentration did not differ between the patch-cut and control plots. The results suggest that slope position strongly affects leaf nitrogen nutrition of hinoki cypress and soil nitrogen availability. By contrast, patch cutting does not affect leaf-litter nitrogen concentration. These findings indicated that hinoki cypress would not enhance forest nitrogen cycling through changes in leaf-litter nitrogen concentration after patch cutting.     

Tangential and radial shrinkage variation within trees in sugi (<Emphasis Type="Italic">Cryptomeria japonica</Emphasis>) cultivars

The transverse shrinkage variation within trees was examined for five sugi cultivars. The within-tree trends of tangential shrinkage (α _T) were different by cultivar, whereas radial shrinkage (α _R) increased from pith to bark in most cultivars. The tangential/radial shrinkage ratio (α _T/α _R) decreased from pith to bark in most cultivars, because the radial variation of α _R was larger than that of α _T. The cultivars showed significant differences among cultivars in α _T, α _R, and α _T/α _R, but the difference among cultivars for α _T/α _R was smaller. The relationships between transverse shrinkage and microfi bril angle (MFA), basic density (BD), tree ring parameters, and modulus of elasticity were examined. The α _T and α _R showed positive relationships with BD, latewood percentage, latewood density, and modulus of elasticity, and negative relationships with MFA and ring width. The relationships with earlywood density were weak. Sugi exhibited variation in transverse shrinkage within stem and among cultivars, with the variation affected by MFA, density, and tree ring parameters. Part of this article was presented at the 56th Annual Meeting of the Japan Wood Research Society, Akita, Japan, August 2006, and the 57th Annual Meeting of the Japan Wood Research Society, Hiroshima, Japan, August 2007     

Ontogeny of schooling behavior in the oval squid <Emphasis Type="Italic">Sepioteuthis lessoniana</Emphasis>

In contrast to schooling behavior in fish, which is well documented, the schooling behavior of an evolutionary counterpart, squid, has not been adequately described in the literature. In the current study, we investigated the ontogeny of schooling behavior in the oval squid Sepioteuthis lessoniana reared from hatching to about two months of age. During the two months of development, the distance and angle between nearest-neighbor individuals decreased from 5.3 mantle lengths (ML) to 1.8 ML and from 42.7° to 24.2°, respectively. In addition, the swimming distance of individuals in experimental duration decreased from 530.4 to 79.9 ML, and the relative swimming speed also decreased from 17.1 to 4.6 ML/s during the same period, with increasing synchronized hovering of individuals. These observations clearly suggest that oval squid swim randomly until 20 days after hatching, then form a school 30–60 days after hatching with an inter-individual distance of 2.0 ML. At two months after hatching, oval squid individuals swam in a parallel orientation and formed a belt-shaped arrangement, similar to the adult schooling behavior observed in natural populations.     

The membrane‐type estrogen receptor G‐protein‐coupled estrogen receptor suppresses lipopolysaccharide‐induced interleukin 6 via inhibition of nuclear factor‐kappa B pathway in murine macrophage cells

The female sex hormone estrogen exerts anti‐inflammatory effects. The G‐protein‐coupled estrogen receptor (GPER) has been recently identified as a novel membrane‐type estrogen receptor that can mediate non‐genomic estrogenic effects on many cell types. We previously demonstrated that GPER inhibits tumor necrosis factor alpha‐induced expression of interleukin 6 (IL‐6) through repression of nuclear factor‐kappa B (NF‐κB) promoter activity using human breast cancer cells. Although several reports have indicated that GPER suppresses Toll‐like receptor‐induced inflammatory cytokine expression in macrophages, the molecular mechanisms of the inhibition of cytokine production via GPER remain poorly understood. In the present study, we examined GPER‐mediated inhibition of IL‐6 expression induced by lipopolysaccharide (LPS) stimulation in a mouse macrophage cell line. We found that the GPER agonist G‐1 inhibited LPS‐induced IL‐6 expression in macrophage cells, and this inhibition was due to the repression of NF‐κB promoter activity by GPER. G‐1 treatment also decreased the phosphorylation of inhibitor of κB kinases. Among the mitogen‐activated protein kinases, the phosphorylation of c‐jun N‐terminal kinase (JNK) was increased by G‐1. These findings delineate the novel mechanism of the inhibition of LPS‐induced IL‐6 through GPER‐activated JNK‐mediated negative regulation of the NF‐κB pathway in murine macrophage cells, which links anti‐inflammatory effects to estrogen.     

Disparities in activity levels and learning ability between Djungarian hamster (Phodopus sungorus) and Roborovskii hamster (Phodopus roborovskii)

The Djungarian hamster and the Roborovskii hamster belong to the same genus of Phodopus. However, the Djungarian hamster is tame and shows sedative behavior, while Roborovskii hamster is not tame and shows high levels of locomotor activity. Hyperactivity occurs in animals with tameless behavior. Tameness or tamelessness behavior is very important because tameness helps for breeding and controlling as well as it enables a strong human‐animal bond. In the present study, we examined the relationships between activity levels and cognitive function in Djungarian and Roborovskii hamsters. Three types of behavioral tests were performed to analyze their activity levels, memory and leaning ability. The levels of L‐ and D‐amino acids and monoamines in the brain were then determined. Roborovskii hamsters showed significantly higher locomotor activity than Djungarian hamsters. Memory ability was not significantly different between the two hamsters, but Roborovskii hamsters showed lower learning ability. Brain levels of D‐serine which is related to enhancement in memory and learning ability, were significantly higher in Djungarian hamsters, but the reverse was true for brain dopamine and serotonin levels. These results suggest that these differences in brain metabolism may be related to the behavioral differences between the two hamsters.     

Role of perithecia as an inoculum source for stem rot type of pepper root rot caused by Fusarium solani f. sp. piperis (teleomorph: Nectria haematococca f. sp. piperis)

Pepper (Piper nigrum L.) root rot caused by Fusarium solani f. sp. piperis (FSP; teleomorph: Nectria haematococca f. sp. piperis) includes two symptom types called root rot (RR) type and stem rot (SR) type. In this study, the temporal and spatial associations between perithecial formation of FSP and development of SR were investigated in naturally infested fields to verify the hypothesis that ascospores from the perithecia are the major inoculum source of the SR type on vines in the field. In surveys of all vines in two neighboring pepper fields every month from December 2005 to November 2006, I mapped the locations of all vines with perithecia and all vines the SR type. The frequency of vines with perithecia increased during April and May, the late rainy season. In June, the early dry season, the number of vines with SR type greatly increased. The vertical range of perithecial formation on the vines extended to 200 cm in height, but was restricted to 30 cm in the dry season in both fields. The join-count statistics showed a significant spatial association between vines with perithecia and vines with SR type in one field (P = 0.042), while no significant spatial association was recognized in another field. The results suggested that ascospores from perithecia of FSP on pepper vines are likely to be one of the main inoculum sources of the SR type of the disease on adjacent vines, but they may not be the exclusive source.