Distribution of a bacterium (γ-1,2,3,4,5,6-hexachlorocyclohexane-decomposing Sphingomonas paucimobilis) among soil aggregates

A great variety of microorganisms lives in soil with a heterogeneous structure. Identification and characterization of microhabitats for survival of individual soil microorganisms are important not only for gaining a better understanding of soil microbial ecology, but also for controling the biological functions of soil such as increase in nitrogen fixation, prevention of soil-borne diseases, and microbial degradation of hazardous waste materials.     

Yield and dry matter dynamics of vegetative and reproductive organs in Japanese and US soybean cultivars

ABSTRACT

Recently, US soybean cultivars have exhibited higher yields than Japanese soybean cultivars. To identify the determinants for this yield difference in reference to dry matter dynamics, recently developed US cultivars and Japanese commercial cultivars were cultivated in drained paddy fields in 2012 and 2013. The total dry matter (TDM) of each cultivar was measured at the initial seed-filling stage (R5), at 30 d after R5, and at maturity (R8). From R5 to R8, the DM of abscised leaves and petioles were measured. The actual HI (with abscised leaves and petioles) and apparent HI (without abscised leaves and petioles) were determined at R8. US soybean cultivars showed higher yields and apparent TDM (without abscised leaves and petioles) than did Japanese cultivars at R8. However, the difference in actual TDM (with abscised leaves and petioles) production was not significant between US and Japanese cultivars at R8. On the other hand, the actual HI was higher in US cultivars than in Japanese cultivars. US cultivars exhibited a higher TDM distribution to the pod before R5 and a higher pod growth rate from R5 to 30 d after R5. US cultivars tended to show greater crop growth rates (CGRs) from R5 to 30 d after R5. The higher yield in US cultivars was associated with the higher actual HI, which was considered attributable to a greater TDM productivity during the seed-filling period and higher DM distribution in the pod before R5.     

Classification and parasitic specialization of blast fungi

Pyricularia oryzae (Magnaporthe oryzae), a causal agent of blast diseases on staple gramineous crops, is a model organism listed as the most important economically and scientifically of the top 10 fungal pathogens by fungal molecular pathologists. Although we are now in an era of genome-enabled analysis, we need to understand the history of the pathogen’s taxonomy, classification, and parasitic specialization in addition to recent research advances. In this review, we focus on these rather fundamental topics. First, the history of classification, including the discovery of its sexual stage and designation, is overviewed. Based on recent results of phylogenetic analysis of Magnaporthaceae isolates, blast fungi are suggested to constitute a robust population that is not congeneric with Magnaporthe salvinii, the type species of Magnaporthe. Second, genetic mechanisms involved in its parasitic specialization into host-specific subgroups and races are outlined. Implications of recent molecular data for resistance breeding are discussed.     

Biochemical and genomic analysis of neoculin compared to monocot mannose-binding lectins

Neoculin occurring in an edible tropical fruit is a heterodimeric protein which has both sweetness and a taste-modifying activity that converts sourness to sweetness. Both the primary and the overall tertiary structures of neoculin resemble those of monocot mannose-binding lectins. This study investigated differences in biochemical properties between neoculin and the lectins. Structural comparison between the mannose-binding sites of lectins and the corresponding regions of neoculin showed that there is at least one amino acid substitution at each site in neoculin, suggesting a reason for the lack of its mannose-binding ability. This was consistent with hemagglutination assay data demonstrating that neoculin had no detectable agglutinin activity. DNA microarray analysis indicated that neoculin had no significant influence on gene expression in Caco-2 cell, whereas kidney bean lectin (Phaseolus vulgaris agglutinin) greatly influenced various gene expressions. These data strongly suggest that neoculin has no lectin-like properties, encouraging its practical use in the food industry.     

Characterization of a Phytophthora mating hormone

Water molds of the genus Phytophthora include many plant pathogens responsible for epidemics such as potato blight and sudden oak death, causing global economic damages. Sexual reproduction is of biological importance in Phytophthora and has been believed to be stimulated by unknown endogenous factors named a hormones. We describe here the chemical characterization of a Phytophthora mating hormone, a1, which was obtained from approximately 2 tons of culture fluid of one mating type of a species and which induced sexual spores on the counter-mating type at a nanogram level.     

Oocyte-specific gene knockdown by intronic artificial microRNAs driven by Zp3 transcription in mice

Conditional knockout technology is a powerful tool for investigating the spatiotemporal functions of target genes. However, generation of conditional knockout mice involves complicated breeding programs and considerable time. A recent study has shown that artificially designed microRNAs (amiRNAs), inserted into an intron of the constitutively expressed gene, induce knockdown of the targeted gene in mice, thus creating a simpler method to analyze the functions of target genes in oocytes. Here, to establish an oocyte-specific knockdown system, amiRNA sequences against enhanced green fluorescent protein (EGFP) were knocked into the intronic sites of the Zp3 gene. Knock-in mice were then bred with EGFP transgenic mice. Our results showed that Zp3-derived amiRNA successfully reduced EGFP fluorescence in the oocytes in a size-dependent manner. Importantly, knockdown of EGFP did not occur in somatic cells. Thus, we present our knockdown system as a tool for screening gene functions in mouse oocytes.     

Manure application has an effect on the carbon budget of a managed grassland in southern Hokkaido,Japan

Abstract

The carbon (C) budget of managed grassland in a cool-temperate region of Japan was estimated using a combination of eddy covariance and the biometric method for five years, to evaluate the effect of manure application. Chemical fertilizer was applied to the fertilizer (F) plot at a rate of 79 ± 20 kg N ha^?1 yr^?1. In the manure (M) plot, dairy cattle manure was applied at a rate of 10 Mg fresh matter ha^?1 yr^?1 (1923 ± 407 kg C ha^?1 yr^?1, 159 ± 68 kg N ha^?1 yr^?1). There was no significant difference in seasonal gross primary production (GPP) and harvest between the treatment plots, indicating that both fertilizer and manure can increase the biomass production. Annual net ecosystem production (NEP) and ecosystem respiration (RE) was significantly different between the treatment plots. The difference in RE, and between M and F plots approximates heterotrophic respiration of manure (RHm), which ranged from 0.9 to 1.3 Mg C ha^?1 yr^?1. Average annual RHm was 1.1 ± 0.4 Mg C ha^?1 yr^?1, and accounted for 56% of the total amount of applied manure C. The annual net biome production (NBP) in the M plot (from 0.0 to 1.5 Mg C ha^?1 yr^?1) was significantly higher than in the F plot (?1.4 to 0.5 Mg C ha^?1 yr^?1). The long-term effect of manure application combined with chemical fertilizer did not reduce grass production compared with chemical fertilizer only; however, manure application decreased the NEP throughout manure decomposition, and long-term manure application enhanced the NBP.     

Habitat shift of ayu Plecoglossus altivelis altivelis in early stages from waters adjacent to the bank to the center of flow in the Shimanto Estuary

ABSTRACT: To clarify the habitats of the ayu in the early stages of development in the Shimanto Estuary, the size and hatching date of the larval and juvenile ayu were examined. Sizes of larvae and juveniles were larger in the center of the flow area than in the waters adjacent to the estuary's banks, which suggests that larvae shift habitat to the center of flow from the waters along the estuary's banks. This shift began at approximately 20 mm body length. However, the resident term in the waters adjacent to the estuary's banks changed with the hatching dates; that is, the early and late-hatched larvae became short and long-term residents, respectively. A similar phenomenon was found also in the juveniles collected in the freshwater section that were migrating upstream. The growth rates of larval ayu in the waters adjacent to the banks tended to decrease with hatching dates. The fluctuations in growth rate with hatching date appear to be a factor leading to the variation of resident term.     

Development and evaluation of a support system for forest education

Field education programs have been conducted throughout the world because learning through experience is an important process in environmental and forest education. We developed a support system for forest education that consists mainly of a Global Positioning System (GPS) and personal digital assistant (PDA). Moreover, field experiments were conducted to evaluate educational efficacy as well as usability of the developed system. Through a post-questionnaire the developed system was highly evaluated in terms of educational efficacy and enjoyment. On the other hand, the questionnaire revealed the need for technical improvements. For example, the drawing function, which involves the use of a stylus pen, was the most poorly evaluated because a drawing could not be partially erased as with an eraser and representation was not sufficiently accurate. In addition, positions where information on nature appeared were sometimes inaccurate due to positional errors caused by using the autonomous GPS. Some participants answered that walking with the developed system was also troublesome due to its shape and size. In fact, they did not feel comfortable about the cables connecting the GPS to the PDA and GPS to its antenna. Although there were some problems with the system, we believe that the field education program was successful because 95% of the participants answered that they would join a similar program again.