Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues

We have identified tens of thousands of short extrachromosomal circular DNAs (microDNA) in mouse tissues as well as mouse and human cell lines. These microDNAs are 200 to 400 base pairs long, are derived from unique nonrepetitive sequence, and are enriched in the 5'-untranslated regions of genes, exons, and CpG islands. Chromosomal loci that are enriched sources of microDNA in the adult brain are somatically mosaic for microdeletions that appear to arise from the excision of microDNAs. Germline microdeletions identified by the "Thousand Genomes" project may also arise from the excision of microDNAs in the germline lineage. We have thus identified a previously unknown DNA entity in mammalian cells and provide evidence that their generation leaves behind deletions in different genomic loci.     

A transdisciplinary research of coastal fisheries co-management: the case of the hairtail <Emphasis Type="Italic">Trichiurus japonicus</Emphasis> trolling line fishery around the Bungo Channel,Japan

Under the coastal fisheries co-management regime in Japan, local fishers play important roles in deciding on and implementing local management measures. Therefore, using the case study of a hairtail trolling line fishery, we conducted a transdisciplinary research with fishers, processors, government officers, etc. Taking social and biological factors into account, we defined management criteria and targets (resource, economic, human community, and local food culture) in collaboration with local fishers. We chartered local fishing vessels to determine parameters that were easily understood by local fishers. We established a local consultative committee comprising fishers, processors, and distributors, and developed a fish distribution strategy to nurture the local hairtail food culture. The integrated effects of various management scenarios were evaluated by the operating model. We found that co-ordinated management by both the trolling line fishery and purse seiners in the neighbouring prefecture was required to achieve targets. Two realistic scenarios are recommended: a conservative scenario that could achieve targets even with few strong year classes, and an adaptive scenario that protects strong year classes, but relies on a higher frequency of these. We shared these results with the local fishers and government officers, which led to actual improvements in management measures.     

Contribution of charcoal to short-term nutrient dynamics after surface fire in the humus layer of a dwarf bamboo-dominated forest

Ecological function of charcoal has been mainly investigated by adding charcoal to soil, which is not fully adequate to understand in situ the role in fire-prone forest ecosystem. To determine in situ effects of charcoal on ecosystem functions, such as nutrient availability, we conducted an experimental burning in a Japanese white birch forest with dense coverage of dwarf bamboo in the understory with or without removal of charcoal. Ammonium-N in the remaining humus layer increased immediately after the burning, but decreased to the level of unburnt plots within 1?month of the burning. Removal of charcoal had no significant effect on the NH₄ ⁺-N dynamics. Although burning did not affect NO₃ ^?-N dynamics during the sampling period, charcoal removal led to a slight increase in NO₃ ^?-N. The available P increased immediately after the burning, but then fell at 1?month after burning. Charcoal inhibited the available P depletion and prolonged the high availability of P. Greater availability of P might be due to the adsorption of phosphate in charcoal pores. Exchangeable Ca and Mg increased gradually; charcoal appeared to extend the period of higher concentration of exchangeable Ca and Mg. Charcoal deriving from fire is a key factor in influencing available nutrient in the humus layer of post-fire forests.     

Seasonality of factors controlling N mineralization rates among slope positions and aspects in cool-temperate deciduous natural forests and larch plantations

This study aimed to evaluate the spatial patterns of soil nitrogen (N) transformations in relation to slope aspect and position, and to investigate the main factors controlling N transformation patterns during both the growing and dormant seasons in cool-temperate deciduous natural forests and larch plantations in eastern Hokkaido, northern Japan. Net rates of N mineralization (NR_minN) and of nitrification (NR_nit) in surface soils on north-facing and lower slopes were higher than those on south-facing and upper slopes, whereas the net rate of ammonium-N production (NR_amm) on south-facing and upper slopes was higher than that on north-facing slopes in both the natural forests and larch plantations. Both NR_minN and NR_nit were higher in the growing than in the dormant season, whereas NR_amm was higher in the dormant season. The soil C/N ratio, water content, soil pH and frequency of freeze–thaw cycles were important variables affecting N transformation patterns in any season. In relation to seasonality, the solar radiation index, daily temperature range and earthworm biomass were important controlling factors only during the growing season, and watershed area and soil N concentration only during the dormant season, suggesting that biological control accompanied with wet–dry events were important factors affecting N transformations during the growing season, but that run-off water and chemical controls were important determinants of spatial variation in N transformations during the dormant season.     

Proton Budgets of Forest Ecosystems on Volcanogenous Regosols in Hokkaido,Northern Japan

The proton budgets of deciduous and coniferous forest ecosystems on volcanogenous regosols in Hokkaido, northern Japan, were studied by measuring the biogeochemical fluxes (atmospheric deposition, canopy leaching, vegetation uptake and leaching from soil) at each site during a three year period. The proton budgets were developed for individual compartments of the ecosystem: vegetation canopy, organic and mineral soil layers. At both sites, atmospheric S deposition was the dominant proton source in the vegetation canopy. In organic horizons, dissociation of weak acids (bicarbonate and/or organic acids) and vegetation uptake of base cations were the dominant proton sources, and the net mineralization of base cations was the dominant proton sink. Atmospheric acid deposition was almost neutralized in the forest canopy and organic horizon. At both sites, weathering and/or ion exchange of base cations and protonation of weak acids (mainly bicarbonate) were the dominant proton sinks in the mineral soil. In both organic and mineral soil, internal proton sources (mainly vegetation uptake of base cations and dissociation of weak acids) exceeded external proton sources, indicating that acid deposition was not the main driving force of soil acidification in the studied forest ecosystems.     

Identification of a novel cytotoxic protein, Cry45Aa, from Bacillus thuringiensis A1470 and its selective cytotoxic activity against various mammalian cell lines

Parasporal inclusion proteins produced by Bacillus thuringiensis strain A1470 exhibit strong cytotoxicity against human leukemic T cells when activated by protease treatment. One of the cytotoxic proteins was separated by anion exchange chromatography and gel filtration chromatography and designated Cry45Aa. Its gene was then expressed in recombinant Escherichia coli, in which the Cry45Aa precursor was accumulated in an inclusion body. It was solubilized in sodium carbonate buffer and processed with proteinase K, and cytotoxic activities of the protein against various mammalian cell lines were evaluated using the 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H tetrazolium bromide assay. The protein exhibited high cytotoxic activity against CACO-2, Sawano, MOLT-4, TCS, and HL60 cells and moderate activity against U-937 DE-4, PC12, and HepG2 cells. On the other hand, the EC50 values against Jurkat, K562, HeLa, A549, Vero, COS-7, NIH3T3, CHO, and four normal tissue cells (human primary hepatocyte cells, UtSMC, MRC-5, and normal T cells) were >2 microg/mL.     

Inhibitory effects of oolong tea polyphenols on pancreatic lipase in vitro

Fifty-four polyphenols isolated from tea leaves were evaluated for their inhibitory activities against pancreatic lipase, the key enzyme of lipid absorption in the gut. (-)-Epigallocatechin 3-O-gallate (EGCG), which is one of major polyphenols in green tea, showed lipase inhibition with an IC50 of 0.349 microM. Moreover, flavan-3-ol digallate esters, such as (-)-epigallocatechin-3,5-digallate, showed higher activities of inhibition on lipase with an IC50 of 0.098 microM. On the other hand, nonesterified flavan-3-ols, such as (+)-catechin, (-)-epicatechin, (+)-gallocatechin, and (-)-epigallocatechin, showed zero and/or the lowest activities against pancreatic lipase (IC50 > 20 microM). These data suggested that the presence of galloyl moieties within the structure was required for enhancement of pancreatic lipase inhibition. It is well-known that flavan-3-ols are polymerized by polyphenol oxidase and/or heating in a manufacturing process of oolong tea. Oolonghomobisflavans A and B and oolongtheanin 3'-O-gallate, which are typical in oolong tea leaves, showed strong inhibitory activities with IC50 values of 0.048, 0.108, and 0.068 microM, respectively, even higher than that of EGCG. The oolong tea polymerized polyphenols (OTPP) were prepared for the assay from oolong tea extract, from which the preparation effectively subtracted the zero and/or less-active monomeric flavan-3-ols by preparative high-performance liquid chromatography. The weight-average molecular weight (Mw) and number-average molecular-weight (Mn) values of OTPP were 2017 and 903, respectively, by using gel permeation choromatography. OTPP showed a 5-fold stronger inhibition against pancreatic lipase (IC50 = 0.28 microg/mL) by comparison with that of the tannase-treated OTPP (IC50 = 1.38 microg/mL). These data suggested that the presence of galloyl moieties within their chemical structures and/or the polymerization of flavan-3-ols were required for enhancement of pancreatic lipase inhibition.     

Intensification of arsenic toxicity to paddy rice by hydrogen sulfide and ferrous iron

Abstract

The phytotoxicity of arsenic to paddy rice was examined by the pot culture method using Utsunomiya grey lowland soil which had received nutrient salts including ammonium sulfate with or without additional rice straw powder as a reducing agent.

By treatment with 50 ppm of arsenic and straw, plant growth was retarded from the beginning of culture, and about 6 weeks later, at the middle of July, small reddish black spots emerged near the tips of expanded green leaves. The spots then increased and spread over the whole leaves resulting in bronzing and final dieback in about the mid-August. On treatment with higher concentrations of arsenic and straw, the plants were more severely injured and died through bronzing at earlier stages. All such dead plants were found to have accumulated abnormally high iron in their leaf tissues. On treatment with lower concentrations of arsenic and straw or in the case of higher arsenic without straw, plant growth and grain yield were reduced with the occurrence of partial bronzing or oranging of leaves and the iron content of the plants was somewhat increased.

These results indicate that arsenic may induce ferrous iron toxicity which intensifies the toxicity of arsenic to paddy rice.     

Nitrous oxide evolved from soil covered with plastic mulch film in horticultural field

Soil solarization practice, in which soil is covered with plastic mulch film and exposed to high temperature prior to crop cultivation, is expected to be an effective method for reducing weeds and pathogenic microorganisms without using agricultural chemicals. Although the production of nitrous oxide (N₂O), a major greenhouse gas, is enhanced in fertilized soil covered with plastic mulch films, its transport route to the atmosphere has not been sufficiently elucidated to date. In this study, we investigated the N₂O evolution from plastic-mulch-film-covered agricultural soil. In a horticultural field where ridge soil was covered with a plastic mulch film after fertilization, we observed significant N₂O flux from the soil surface of the unfertilized furrow between the ridges, indicating the horizontal diffusion of N₂O from the ridge soil covered with the mulch film to the adjacent furrow soil surface. On the other hand, the measurement of the permeance (permeation coefficient) of the plastic mulch film for gaseous N₂O by laboratory experiment revealed that N₂O gradually permeated the mulch film; the permeance increased exponentially with an increase in ambient temperature, indicating possible N₂O emission by permeation through the mulch film under field conditions. In winter, the amount of N₂O emission by permeation through the mulch film was estimated to be lower than that emitted from the furrow soil surface, and it was lower than that in summer. On the other hand, it was estimated to be much higher in summer owing to the higher permeance of the film at high temperatures.