Subaru telescope observations of Deep Impact

The impact cratering process on a comet is controversial but holds the key for interpreting observations of the Deep Impact collision with comet 9P/Tempel 1. Mid-infrared data from the Cooled Mid-Infrared Camera and Spectrometer (COMICS) of the Subaru Telescope indicate that the large-scale dust plume ejected by the impact contained a large mass (approximately 10(6) kilograms) of dust and formed two wings approximately +/-45 degrees from the symmetric center, both consistent with gravity as the primary control on the impact and its immediate aftermath. The dust distribution in the inner part of the plume, however, is inconsistent with a pure gravity control and implies that evaporation and expansion of volatiles accelerated dust.     

Role for piRNAs and noncoding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus

Genomic imprinting causes parental origin-specific monoallelic gene expression through differential DNA methylation established in the parental germ line. However, the mechanisms underlying how specific sequences are selectively methylated are not fully understood. We have found that the components of the PIWI-interacting RNA (piRNA) pathway are required for de novo methylation of the differentially methylated region (DMR) of the imprinted mouse Rasgrf1 locus, but not other paternally imprinted loci. A retrotransposon sequence within a noncoding RNA spanning the DMR was targeted by piRNAs generated from a different locus. A direct repeat in the DMR, which is required for the methylation and imprinting of Rasgrf1, served as a promoter for this RNA. We propose a model in which piRNAs and a target RNA direct the sequence-specific methylation of Rasgrf1.     

Differential detection of shrimp and crab for food labeling using polymerase chain reaction

Shrimp and crab are well-known as allergenic ingredients. According to Japanese food allergy labeling regulations, shrimp species (including prawns, crayfishes, and lobsters) and crab species must be differentially declared when ≥10 ppm (total protein) of an allergenic ingredient is present. However, the commercial ELISA tests for the detection of crustacean proteins cannot differentiate between shrimp and crab. Therefore, two methods were developed to discriminate shrimp and crab: a shrimp-PCR method with postamplification digestion and a crab-PCR method that specifically amplifies a fragment of the 16S rRNA gene. The sensitivity and specificity of both PCR methods were verified by experiments using DNA extracted from 15 shrimp species, 13 crab species, krill, mysid, mantis shrimp, other food samples (cephalopod, shellfish, and fish), incurred foods, and commercial food products. Both PCR methods could detect 5 pg of DNA extracted from target species and 50 ng of genomic DNA extracted from incurred foods containing 10 ppm (μg/g) total protein of shrimp or crab. The two PCR methods were considered to be specific enough to separately detect species belonging to shrimp and crab. Although false-positive and false-negative results were obtained from some nontarget crustacean species, the proposed PCR methods, when used in conjunction with ELISA tests, would be a useful tool for confirmation of the validity of food allergy labeling and management of processed food safety for allergic patients.     

Characterization of corrinoid compounds from a Japanese black tea (Batabata-cha) fermented by bacteria

A Japanese fermented black tea (Batabata-cha) contained a considerable amount of vitamin B(12) (456 +/- 39 ng per 100 g dry tea leaves and 2.0 +/- 0.3 ng per 100 mL of tea drink). A corrinoid compound was partially purified and characterized from the tea leaves. The patterns of the purified compound by the silica gel 60 thin-layer chromatography and C18 reversed phased high-performance liquid chromatography were identical to those of authentic vitamin B(12). When 20 week old vitamin B(12) deficient rats, which excreted substantial amounts (about 250 mg/day) of methylmalonic acid in urine as an index of vitamin B(12) deficiency, were fed the tea drink (50 mL/day, 1 ng of vitamin B(12)) for 6 weeks, urinary methylmalonic acid excretion (169 +/- 29 mg/day) of the tea drink-supplemented 26 week old rats decreased significantly relative to that (250 +/- 32 mg/day) of the deficient rats. The results indicate that the vitamin B(12) found in the fermented black tea is bioavailable in mammals.     

Humus composition of soils under forest, coffee and arable cultivation in hilly areas of south Sumatra, Indonesia

To understand the effect of land use changes on the composition of humus in tropical soils, samples from land under primary forest, secondary forest, coffee plantation, and arable crops were investigated at three sites in south Sumatra, Indonesia. Total carbon and total nitrogen contents were 1.7 to 4.3 times and 1.1 to 2.8 times greater in the topsoil under primary forest than under the other types of land use. Following change from primary forest to other uses, the proportion of humic acids in the organic matter of the topsoils decreased while that of the fulvic acid fraction increased. Within the range of land uses, differences in the yields of humic acids and fulvic acid fractions were, respectively, larger and smaller than those in total carbon content. The humic acids were classified into the low and middle classes in the degree of humification. Absorption due to the green fraction of humic acids, Pg, was detected in the UV‐visible spectra of almost all the humic acids. No relation was observed between the degree of humification of humic acids or the strength of Pg absorption in their spectra and land use change. The fulvic acid fractions were fractionated on insoluble polyvinylpyrrolidone (PVP) into the adsorbed fractions consisting of humic substances and the non‐adsorbed fractions consisting of non‐humic substances. A positive correlation between the amount of the fulvic acid fraction and the percentage of the PVP‐adsorbed fraction within it indicated that the variation in the amount of the fulvic acid fraction was attributable to acid‐soluble humic substances. The ionization difference spectra of solutions between pH 12 and pH 7 suggested that the chemical structures of the PVP‐adsorbed fulvic acids have been altered by land use change.     

Contribution of Parker and Product indexes to evaluate weathering condition of Yellow Brown Forest soils in Japan

Soil weathering is recognizable through study on physico-chemical characteristics of soil. In this study, Parker, ([(Na)_a / 0.35] + [(Mg)_a / 0.9] + [(K)_a / 0.25] + [(Ca)_a / 0.7]) × 100, and Product, [SiO₂ / (TiO₂ + Fe₂O₃ + SiO₂ + Al₂O₃)] × 100, weathering indexes, originally developed for study on rocks, were tested on Yellow Brown Forest soils from two different regions in Japan. The results showed that the contribution of the mentioned indexes can be used for study on soils weathering. In other word, in a two-dimensional coordination system where the axes are Parker and Product indexes, regarding to the chemical bases of the indexes, initial and lateral products of weathering can be tracked at the same time.

Additionally, the indexes relations with soil color were studied after exposing the samples at a high temperature. Remarkable relationships between a* / b* ratio–parameters of psychometric chromaticness of color in CIE color standard system–and these two weathering indexes demonstrated that a* / b* ratio can be applied reliably to estimate the quantities of Parker and Product indexes in Yellow Brown Forest soils.     

Bacterial community incorporating carbon derived from plant residue in an anoxic non-rhizosphere soil estimated by DNA-SIP analysis

Purpose

Plant residues are one of the main sources of soil organic matter in paddy fields, and elucidation of the bacterial communities decomposing plant residues was important to understand their function and roles, as the microbial decomposition of plant residues is linked to soil fertility. We conducted a DNA stable isotope probing (SIP) experiment to elucidate the bacterial community assimilating 13-carbon (¹³C) derived from plant residue under an anoxic soil condition. In addition, we compared the bacterial community with that under the oxic soil condition, which was elucidated in our previous study (Lee et al. in Soil Biol Biochem 43:814–822, 2011).

Materials and methods

We used the ¹³C-labeled dried rice callus cells as a model of rice plant residue. A paddy field soil was incubated with unlabeled and ¹³C-labeled callus cells. DNA extracted from the soils was subjected to buoyant density gradient centrifugation to fractionate ¹³C-enriched DNA. Then, polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) analysis of bacterial 16S rDNA band patterns and band sequencing method were used to evaluate bacterial community.

Results and discussion

DGGE analysis showed that the band patterns in the ¹³C-enriched fractions were distinctly changed over time, while the changes in the community structure before fractionation were minor. Sequencing of the ¹³C-labeled DGGE bands revealed that Clostridia were a major group in the bacterial communities incorporating the callus-derived carbon although Gram-negative bacteria, and Actinobacteria also participated in the carbon flow from the callus under the anoxic condition. The proportion of Gram-negative bacteria and Actinobacteria increased on 14 days after the onset of incubation, suggesting that the callus was decomposed by diverse bacterial members on this phase. When the bacterial groups incorporating the ¹³C were compared between under anoxic and oxic soil conditions, the composition was largely different under the two opposite conditions. However, some members of Gram-negative bacteria were commonly found under the anoxic and oxic soil conditions.

Conclusions

The majority of bacterial members assimilating the callus carbon was Clostridia in the soil under anoxic conditions. However, several Gram-negative bacterial members, such as Acidobacteria, Bacteroidetes, and Proteobacteria, also participated in the decomposition of callus under anoxic soil conditions. Our study showed that carbon flow into the diverse bacterial members during the callus decomposition and the distinctiveness of the bacterial communities was formed under the anoxic and oxic soil conditions.