Classification of the genus Bacillus based on MALDI-TOF MS analysis of ribosomal proteins coded in S10 and spc operons

A rapid bacterial identification method by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) using ribosomal proteins coded in S10 and spc operons as biomarkers, named the S10-GERMS (the S10-spc-alpha operon gene encoded ribosomal protein mass spectrum) method, was applied for the genus Bacillus a Gram-positive bacterium. The S10-GERMS method could successfully distinguish the difference between B. subtilis subsp. subtilis NBRC 13719(T) and B. subtilis subsp. spizizenii NBRC 101239(T) because of the mass difference of 2 ribosomal subunit proteins, despite the difference of only 2 bases in the 16S rRNA gene between them. The 8 selected reliable and reproducible ribosomal subunit proteins without disturbance of S/N level on MALDI-TOF MS analysis, S10, S14, S19, L18, L22, L24, L29, and L30, coded in S10 and spc operons were significantly useful biomarkers for rapid bacterial classification at species and strain levels by the S10-GERMS method of genus Bacillus strains without purification of ribosomal proteins.     

A chlorite-smectite intergrade in soil derived from pyroxene andesite altered hydrothermally in Mt. Kunimidake,Fukui, Central Japan

The interlayered hydroxy-aluminum of a chlorite-smectite intergrade in a dark-red soil derived from a pyroxene andesite altered by hydrothermal action was extracted easily by boiling treatments using both sodium-citrate and ammonium-fluoride solutions. Moreover, this interlayered aluminum was released partially by using a dithionite-citrate-bicarbonate system and an acid ammonium-oxalate solution which were prepared originally for removing the coexistent sesquioxides from soils.     

Root-shoot interaction as a limiting factor of biomass productivity in new tropical rice lines

The objective of the present study was to identify the limiting factors in biomass productivity of new tropical rice lines (panicle weight type) by analyzing the relationship between root and shoot activity. Five field experiments using three new lines, IR65598-112-2, IR65600-42-5-2, and IR68544-29-2-1-3-1-2, and one of the highest-yielding indica rice varieties (panicle number type), IR72, were conducted at the International Rice Research Institute from 1997 to 2002. Specific absorption rate of N (SARN , mg N g^-1 root dry weight d^-1), specific stem sap exudation rate (sap exudation rate, g exudate g^-1 root dry weight 12 h^-1) and specific root respiratory rate (root respiratory rate, μmol O₂ g^-1 root dry weight h^-1) were determined as indices of root activity. Relative growth rate (RGR, mg g^-1 d^-1) was used as an index of shoot activity. Compared with IR72, the new lines showed lower RGR and SAR_N values during the early growth stages. In contrast, during the late growth stages, these activities were higher in the new lines than in IR72. The SAR_B and sap exudation rate showed a linear correlation with RGR at successive growth stages, regardless of the genotypes and growth conditions. These findings indicated that active root-shoot interaction was maintained throughout the growth period in high-yielding tropical rice, including the new lines and IR72. Therefore, it was considered that SAR_N and the sap exudation rate are useful indices of root activity regulating RGR in the new lines. However, the root respiratory rate could not be used for selection, because the relationship between RGR and the root respiratory rate changed with the growth conditions. Our findings support the hypothesis that root and shoot activities during maturation are important factors affecting the productivity of the new lines, which have not yet been able to attain the targeted yield.     

Cloning of the phloem-specific small heat-shock protein from leaves of rice plants

The N-terminal amino-acid sequence of a major rice phloem-sap protein, designated as RPP23, was determined. The complete amino-acid sequence of RPP23 was deduced from the corresponding rice EST- clone and contained an extra 46 amino acids at the N-terminus, that was apparently cleaved off to form mature RPP23 in sieve tubes. RPP23 shared a similarity to plant small heat-shock proteins (smHSPs), though the N-terminal region of RPP23 was distinct from that of known smHSPs. Immunocytological analyses using leaf sections showed that RPP23 was located only in the phloem regions of leaves, and was present in non-stressed plants. In mature leaves, stronger immunocytological signals were detected in sieve elements than in companion cells.     

Microbial distribution and function across wheat rhizosphere with oxamide and ammonium sulfate as N sources

Analysis of the effect of slow-releasing N fertilizers on microbial parameters of the rhizosphere soil is essential for their effective use. This investigation revealed the comparative effects of oxamide and ammonium sulfate as different N sources on some selected microbial parameters as well as the pH in the rhizosphere of wheat (Triticum aestivum cv. Nourin No. 61). The study was conducted on a Japanese upland alluvial soil using a rhizobox system. In the central compartment (CC) of the rhizoboxes treated with oxamide and ammonium sulfate, four wheat seedlings were grown for 53 d. In either of the treatments, the pH of the rhizosphere soil increased with the increase in the distance from the CC. In contrast, nitrate production, bacterial and fungal numbers, microbial biomass nitrogen, and β-acetylglucosaminidase activity decreased with the increase in the distance, with the highest values of the respective parameters being recorded in the CC. However, remarkable changes of these microbial parameters were found within a distance of 1–2 mm from the CC to the distant compartments. Thus the results indicated that pH, bacterial number, and nitrate production were high in the oxamide treatment. In contrast, higher fungal number, microbial biomass N, and .B-acetylglucosaminidase activity were associated with the ammonium sulfate treatment. It was assumed that the significant (p<O.05) effect of the rhizosphere on microbial activities varied with the treatments.     

Correlation of changes in seasonal distribution and catch of red sea bream Pagrus major with winter temperature in the eastern Seto Inland Sea,Japan (1972–2010)

Red sea bream Pagrus major is a commercially important fish in Japan. In eastern Seto Inland Sea (SIS), the catch has increased from 297 tons in 1972 to 2,039 tons in 2010. We examined the relationship, 1972–2010, between increase in catch and winter temperature, based on the catch in February and March and the lowest water temperature at 10 m depth. In 1972–1986, the lowest water temperatures in the inner SIS areas (Osaka Bay, Harima‐nada, and Bisan‐seto) were <8°C, which is physiologically unfavorable for red sea bream. However, in 1987–2010 temperatures were generally ≥8°C. In the inner areas, the catch during winter had been minimal until the early 1980s, presumably because most red sea breams moved to the Kuroshio‐influenced (warmer) Kii Channel area. However, the winter catch in the inner areas of SIS increased from the late 1980s with warm winters. In addition, the catch between April and June, the spawning season, increased in the inner areas from the 1990s, and the catch rate of the inner areas was more than twice higher in the 2000s than in the 1980s. The results suggest that expansion of the distribution area during winter due to warm winter and increase in egg production in the inner areas greatly contributes to the increasing in catch in the eastern SIS.     

Accuracy of imputation of single nucleotide polymorphism marker genotypes from low‐density panels in Japanese Black cattle

Using target and reference fattened steer populations, the performance of genotype imputation using lower‐density marker panels in Japanese Black cattle was evaluated. Population imputation was performed using BEAGLE software. Genotype information for approximately 40 000 single nucleotide polymorphism (SNP) markers by Illumina BovineSNP50 BeadChip was available, and imputation accuracy was assessed based on the average concordance rates of the genotypes, varying equally spaced SNP densities, and the number of individuals in the reference population. Two additional statistics were also calculated as indicators of imputation performance. The concordance rates tended to be lower for SNPs with greater minor allele frequencies, or those located near the ends of the chromosomes. Longer autosomes yielded greater imputation accuracies than shorter ones. When SNPs were selected based on linkage disequilibrium information, relative imputation accuracy was slightly improved. When 3000 and 10 000 equally spaced SNPs were used, the imputation accuracies were greater than 90% and approximately 97%, respectively. These results indicate that combining genotyping using a lower‐density SNP chip with genotype imputation based on a population of individuals genotyped using a higher‐density SNP chip is a cost‐effective and valid approach for genomic prediction.     

Difference Between Tetrodotoxin and Saxitoxins in Accumulation in Puffer Fish Takifugu rubripes Liver Tissue Slices

In vitro accumulation of tetrodotoxin (TTX) and paralytic shellfish toxin (PST) in tiger puffer fish Takifugu rubripes was investigated using liver tissue slices. When T. rubripes liver slices were incubated with Leibovitz’s L-15 medium containing 0.13 mM TTX at 20 °C in air with saturated humidity, they accumulated 21.5 ± 7.3 μg TTX g^?1 liver after the incubation for 12 h and increased to 55.3 ± 8.2 μg TTX g^?1 liver at 48 h. In the incubation of T. rubripes liver slices with 0.13 mM PST-containing medium, PST was detected 6.3 ± 0.9 μg g^?1 liver at 12 h and reached a plateau thereafter. These results reveal the difference between TTX and PST in accumulation in T. rubripes liver tissue slices. To examine the variation in PST accumulation among fish species, the liver tissue slices from tiger puffer fish T. rubripes, parrot-bass Oplegnathus fasciatus and green ling Hexagrammos otakii were incubated at a concentration of 0.027 mM PST. The toxin contents of 3.0 μg g^?1 liver were observed at 8 h regardless of fish species but were not increased subsequently, showing no variety among these three species as to accumulation patterns of PST. It is noted that the tiger puffer fish T. rubripes liver specifically accumulate TTX in preference to PST.