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.     

Atmospheric carbon dioxide concentration within a narrow valley in a forested catchment area

In order to investigate atmospheric carbon dioxide (CO₂) accumulation as a cool air pool in hilly terrain, two-dimensional cross-sectional profile of CO₂ concentration and air temperature was measured for 20 days in summer in a 0.8-ha forested catchment. CO₂ concentration was vertically stratified within the valley, with a slight increase near valley sidewalls compared to the valley center, except during the nights under calm or weak ambient wind conditions. In the daytime, the constantly higher CO₂ concentration at the valley bottom was associated with temperature inversion below the canopy, which could suppress vertical CO₂ dissipation and leaded to vertical stratification, and with limited CO₂ consumption by photosynthesis due to insufficient radiation. In the nighttime, the vertical CO₂ concentration difference within the valley was related to strength of temperature inversion, which was correlated with ambient wind speed. On windy nights, relatively warmer ambient wind covered the cooler valley, to form a temperature inversion, thus confining CO₂ to the lower part of the valley. On calm nights, thermal lapse not the inversion layer resulted from radiative cooling of the canopy, and homogeneous CO₂ concentration within the valley was observed. A large CO₂ storage change within the valley was calculated compared with that of forests on flat terrain. In particular, the vertical change of CO₂ storage calculated with only the center of the valley was much larger than the cross-sectional change of CO₂ storage with the entire valley due to excluding of side parts of the valley with lower CO₂ concentration.     

Evaluation of combustion properties of wood pellets using a cone calorimeter

In this study, the combustion properties of wood pellets were evaluated using a cone calorimeter, which is usually used to verify the fireproof performance of architectural materials. In contrast to the conventional methods including combustion calorimetry and thermogravimetric analysis, a cone calorimeter can estimate various combustion parameters, e.g., changes of heat release rate (HRR), weight decrease during burning process, ignition time, and flame-out and burn-out time as well as combustion heat, in a single experimental run with no pretreatment for sample size reduction. The following results were obtained by the combustion test of Japanese cedar (Cryptomeria japonica) and larch (Larix kaempferi) wood pellets having various volume densities. Ignition time of wood pellet became slower with increasing volume density of the pellets. However, burn-out time was not clearly correlated to volume density. The heat release values measured by cone calorimeter could be comparable to those from the conventional combustion calorimeters, and flaming heat values of the bark pellets were always lower in comparison with pellets made of xylem, although total heat release was almost the same.     

Exclusion of cytoplasmic fragments in flow cytometric analysis of lymph node samples from dogs with lymphoma using membrane-permeable violet laser-excitable DNA-binding fluorescent dye (DyeCycle Violet)

Background: Cytoplasmic fragments derived from fragile neoplastic lymphocytes are common in samples of lymph nodes collected from dogs with lymphoma. These cytoplasmic fragments interfere with accurate gating of target cells and quantification protocols used for flow cytometry because of their variable size and expression of lymphoid cell surface antigens on their membranes. Objective: The aim of this study was to develop a method to efficiently exclude cytoplasmic fragments from flow cytometric analysis of canine lymph nodes in which lymphoma was present. Methods: Single‐cell suspensions of neoplastic cells were prepared from biopsy samples and fine‐needle aspirates of lymph nodes from 23 dogs with lymphoma. Suspensions were stained using a violet laser‐excitable (405 nm) membrane‐permeable DNA‐binding fluorescent dye (DyeCycle Violet [DCV]), incubated with antibodies against CD3, CD5, CD21, CD22, and CD45, and then stained with 7‐amino‐actinomycin D (7‐AAD), an argon‐excitable (488 nm) membrane‐impermeable DNA‐binding fluorescent dye. Multiparameter flow cytometry was used for analysis based on selective uptake and laser‐activated fluorescence of these dyes. Results: Cytoplasmic fragments, which were DCV‐negative and CD45‐positive, and dead cells, which were positive for 7‐AAD, were efficiently separated from neoplastic cells. Conclusion: Staining with DCV is a useful method to improve flow cytometric gating methods and quantitative analyses of lymph node samples from dogs with lymphoma.     

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.     

Orally administered rutin inhibits the gene expression of Th2 cytokines in the gut and lung in aged mice

Rutin is one of the flavonoids derived from plants such as buckwheat and is well known as a powerful antioxidant. To determine whether dietary rutin could modulate mucosal immunity, we examined the gene expression of Th1/Th2 cytokines and the receptors in the gut and lung. Aged (18 months old, 18 M) C3H/HeN female mice were orally administered rutin for 10 days. The small intestine and lung were taken and analyzed by real-time PCR for gene expression. Interleukin (IL)-13 and IL-13Rα2 gene expression was significantly low (P<0.05 respectively) in the small intestine of aged rutin-fed mice. Meanwhile, there was no change in interferon γ gene expression between control and rutin-fed mice. IL-13 gene expression was also downregulated in the lung. To examine the mechanism of the inhibitory effect of rutin on Th2 cytokines in aged mice, intestinal nitric oxide synthase (NOS) expression was evaluated. Rutin inhibited inducible NOS (NOS2) gene expression, but not neuronal NOS and endothelial NOS. Gene analysis of cells collected from the small intestine by laser capture dissection revealed that NOS2 expression was significantly inhibited in crypt regions. Thus, rutin might be effective against a Th2-dominant profile through NOS2 inhibition in aged mice.     

Nutrient and bulk density characteristics of soil profiles in six land use systems along topo-sequences in inland valley watersheds of Ashanti region,Ghana

The bulk density and nutrient distribution in soil profiles as affected by various land use systems were studied. Mean bulk densities of the various soil profiles, 0-20, 20-40, and 4060 cm in the selected five land use systems along the upland / lowland topo-sequences were, 1.26, 1.73, and 1.44 Mg m^-3 for the primary forest (PF) plot in the upland area, 1.13, 1.51, and 1.50 Mg m^-3 for the cacao farm (CP) plot, 1.16, 1.63, and 1.26 Mg m^-3 for the mixed cropping (MC) plot, 1.39, 1.61, and 1.50 Mg m-a for the fallow (Fallow) plot, all three land use systems being in the upland / fringe areas, and 1.46, 1.72, and 1.60 Mg m^-3 for the lowland traditional rice farming (TR) plot, respectively. The very high bulk density of the second layer, especially in the PF plot, may be related to the hardening of the iron / quartz stone layer due to prolonged dry conditions, which may affect plant growth and hydrological cycles in the benchmark inland valley watersheds. The TC contents of the topsoil samples were 43, 32, 24, 26, 18, and 15 g kgm^-1 for the PF, CP, Fallow, MC, TR, and sawah (Sawah) plots, respectively. The C / N ratios of the topsoil samples were 10, 10, 9.8, 9.1, 8.8, and 8.8 for the CP, Fallow, MC, Sawah, TR, and PF plots, respectively, displaying a higher natural fertility, especially for the N supply in the PF plot in the upland area. The available phosphorus levels were low even for the topsoil samples, 1.8 to 3.4 mg kg^-1 for the upland soils while the lowland TR and Sawah plots recorded values of 4.4 and 4.9 mg kg^-1, respectively. The contents of exchangeable K, 0.1-0.4 cmole kg^-1, of the topsoil samples were in the range of those of normal inland valley soils in West Africa. In contrast to the content of available P, although the MC plot showed a depletion, the PF, Fallow, and CP plots showed a replenishment of available K through biological nutrient cycling. The levels of exchangeable Ca and Mg as well as eCEC, were also relatively high compared to those of mean inland valley soils in West Africa. The major component of eCEC was Ex. Ca. The levels of Ex. Ca in the topsoil samples were 11.1, 9.1, 7.8, 4.7, 5.1, and 3.9 cmol_c kg^-1 for the PF, CP, Fallow, MC, TR, and Sawah plots, respectively. The distinctive feature of Ex. Mg was its large distribution in the upper soil profiles in the CP plot, indicating that in the cacao farms, Ex. Mg was enriched, probably due to the high level of Mg in the leaf litter. The lowland soils, normally, should have been enriched in exchangeable bases such as Ca, K, and Mg, leading to a higher eCEC value and higher general fertility through the process of geological fertilization, Le., nutrient flows from upland to lowland areas, as in the case of lowland sawah in monsoon Asia. At the benchmark sites, however, the effects of the geological fertilization process were not evident. This is one of the most important characteristics of West African inland valley watersheds.     

Varietal difference in radiocesium uptake and transfer from radiocesium deposited soils in the genus Amaranthus

Abstract

Within Amaranthaceae, 33 different varieties, including local varieties from Japan, were grown in 2012 in a field in the town of Iino in the Fukushima prefecture, which is located approximately 51 km north of Tokyo Electric Power Company, Fukushima Daiichi Nuclear Power Plant (FDNPP). The contamination level of the soil was 2770 ± 140 Bq kg^?1 dry weight (¹³⁴Cesium (Cs) + ¹³⁷Cs, average ± SE), and the field was also cultivated in 2011. There was a significant varietal difference in the dry weight production, radiocesium accumulation and transfer factor (TF) of radiocesium from the soil to the plant. The ratio of the lowest TF to the highest TF was approximately 3. Because the ratio of ¹³⁷Cs to ¹³³Cs was significantly positive, radiocesium seems to be absorbed in a manner similar to that of ¹³³Cs. It is suggested that the varietal difference in the behavior of radiocesium uptake mainly depends on its genetic background rather than on environmental factors.     

At5g54160 gene encodes <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis> 5-hydroxyconiferaldehyde <Emphasis Type="Italic">O</Emphasis>-methyltransferase

The function of an Arabidopsis thaliana gene, At5g54160 annotated as a caffeic acid O-methyltransferase CAOMT gene was characterized. The recombinant enzyme of this gene (AtOMT1) catalyzed the O-methylation of phenylpropanoid and flavonoid substrates. The specificity constants (k _cat/K _m) for 5-hydroxyconiferaldehyde (5-HCAld) and quercetin were both 0.11 μM⁻¹·min⁻¹. On the other hand, lignins of At5g54160-knockout Arabidopsis mutants lacked syringyl units. In addition, we showed that the gene silencing also resulted in significant accumulation of caffeyl alcohol (CaAlc). These results strongly suggested that At5g54160 gene is involved in syringyl lignin synthesis for the methylation of both 5-hydroxyconiferaldehyde and 3,4-dihydroxyphenyl compound(s). Part of this work was presented at the Annual Meeting of Japan Society for Bioscience, Biotechnology, and Agrochemistry, March 24–27, 2007     

Adsorption,desorption and dissipation of metolachlor in surface and subsurface soils

BACKGROUND: Variations in soil properties with depth influence retention and degradation of pesticides. Understanding how soil properties within a profile affect pesticide retention and degradation will result in more accurate prediction by simulation models of pesticide fate and potential groundwater contamination. Metolachlor is more persistent than other acetanilide herbicides in the soil environment and has the potential to leach into groundwater. Reasonably, information is needed about the dissipation and eventual fate of metolachlor in subsoils. The objectives were to evaluate the adsorption and desorption characteristics and to determine the dissipation rates of metolachlor in both surface and subsurface soil samples. RESULTS: Adsorption of metolachlor was greater in the high‐organic‐matter surface soil than in subsoils. Lower adsorption distribution coefficient (K_ads) values with increasing depth indicated less adsorption at lower depths and greater leaching potential of metolachlor after passage through the surface horizon. Desorption of metolachlor showed hysteresis, indicated by the higher adsorption slope (1/n_ads) compared with the desorption slope (1/n_des). Soils that adsorbed more metolachlor also desorbed less metolachlor. Metolachlor dissipation rates generally decreased with increasing soil depth. The first‐order dissipation rate was highest at the 0–50 cm depth (0.140 week^?1) and lowest at the 350–425 cm depth (0.005 week^?1). Degradation of the herbicide was significantly correlated with microbial activity in soils. CONCLUSION: Metolachlor that has escaped degradation or binding to organic matter at the soil surface might leach into the subsurface soil where it will dissipate slowly and be subject to transport to groundwater. Copyright © 2009 Society of Chemical Industry