Tree-to-tree and clone-to-clone variations of monoterpenes emitted from needles of hinoki (Chamaecyparis obtusa)

Variations in the composition of low boiling point (LBP) monoterpenes emitted from needle samples of 150 hinoki (Chamaecyparis obtuse) trees (30 strains, each with five clones) native to Shimane Prefecture, Japan, were investigated using a headspace technique. The assays revealed considerable proportional variations especially in the amount of sabinene, which ranged from 24% to 78% of the total LBP monoterpenes. The proportions of α-pinene, myrcene, and limonene negatively correlated with that of sabinene overall. In particular, the proportion of limonene showed clear negative correlation with that of sabinene (r = −0.98). Differences in the proportion of sabinene among five clones in each strain were less than 15% in 22 out of 30 strains, indicating that monoterpene composition is constitutively steady in most strains. In a few strains, however, considerable variation in the composition was observed among clones.     

Phospholipid fatty acid composition of microbiota in the percolating water from a rice paddy microcosm

The microbiota in the percolating water from the plow layer soil in paddy fields was studied based on the composition of phospholipid fatty acids (PLFAs) in a pot experiment. The mean concentrations of PLFAs in the percolating water were 17±5 and 11±4 µg L^-1 in the planted and non-planted pots, respectively. The dominant PLFAs in the percolating water were 16: 0, 16: 1ω7c, 18: 1ω7, 18: 1ω9, il5: 0, and ail5: 0 PLFAs in both the planted and non-planted pots. The dominance percentage of 18: 3ω6c and 17: 1ω8 PLFAs increased at the late stage of rice growth in the planted pots. The percolating water from the planted pots contained in a higher percentage of straight mono-unsaturated PLFAs and a lower percentage of branched-chain PLFAs than that from the non-planted pots. Considerable differences in the PLFA composition in the percolating water were observed between the planted and non-planted treatments and with the duration of the growth period. Principal component analysis indicated that the microbiota in the percolating water was derived from the microbiota in the floodwater and in the plow layer soil. Cluster analysis showed that the similarity of the PLFA composition in the percolating water to the PLFA composition in the plow layer soil was higher than that in the floodwater. The stress factor that was estimated from the trans/cis ratio of 16: 1ω7 PLFA was 0.08±0.04 and 0.14±0.05 in the percolating water from the planted and non-planted pots, respectively, which indicated that the degree of stress on the microbiota in the percolating water from the planted pots was low in a similar way to the degree of stress on the microbiota in the floodwater, while the degree in the percolating water from the non-planted pots was similar to that in the plow layer soil, respectively.     

Assessment of radical scavenging capacity and lipid peroxidation inhibiting capacity of antioxidant

The role of radical scavenging antioxidants against oxidative stress has received much attention, and the antioxidant capacity has been assessed by various methods. Among them, a method that measures the effect of antioxidant on decay of the probe is one of the most widely used methods. The present study was performed to compare the two methods to assess the antioxidant capacity, one to follow the decay of the probe and the other to measure lipid peroxidation products in human plasma. It was shown that the method following probe decay was suitable for assessment of radical scavenging capacity of antioxidant, but not for the capacity to inhibit lipid peroxidation in plasma. This is true whether a hydrophilic or lipophilic probe is used. Such different results arise from the fact that the efficacy of inhibition of lipid peroxidation by antioxidants depends on the fate of antioxidant-derived radical and interaction between antioxidants as well as the capacity of free radical scavenging. Thus, the capacity of antioxidants for inhibition of lipid peroxidation should be assessed from the effect on the extent of oxidation, not from the effect on probe decay.     

Mycoplasma pneumonia of swine (MPS) resistance and immune characteristics of pig lines generated by crossing an MPS pulmonary lesion selected Landrace line and a highly immune capacity selected Large White line

To understand the influence of crossbreeding on Mycoplasma pneumonia of swine (MPS) resistance and immune characteristics, two crossbred lines were characterized. One crossbred line, LaWa, was generated by crossing the MPS pulmonary lesion selected Landrace line (La) and the highly immune‐selected Large White line (Wa). The second crossbred line, LaWb, was generated by crossing the La line and the nonselected Large White line (Wb). The crossbred LbWb line (nonselected Landrace line × nonselected Large White line) and the La line were used as controls. The LaWa and LaWb lines had an intermediate level of MPS lung lesions between La and LbWb lines, although the difference was not statistically significant. After stimulation with sheep red blood cells (SRBCs), the LaWb and LaWa lines showed immune characteristics similar to that of the La line; the number of monocytes in peripheral blood increased, while B cells, T cells, secretion of SRBC‐specific immunoglobulin G, and interleukin (IL)‐13 decreased. Additionally, the number of natural killer (NK) cells and the expression of IL‐4 and IL‐17 were significantly higher in the LaWb and LaWa lines, respectively. These data suggested that crossbreeding of La and Wa lines resulted in the inheritance of some of the selected immune responses.     

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.     

Determination of theaflavins including methylated theaflavins in black tea leaves by solid-phase extraction and HPLC analysis

A quantitative method for four theaflavins and two methylated theaflavin derivatives in black tea leaves was developed by solid-phase extraction and a high-performance liquid chromatographic method with photodiode array detection. The theaflavins in black tea leaves were extracted three times with 40 vol 50% aqueous ethanol (mg dry tea powder/mL) containing 2% ascorbic acid. The ethanol extracts were diluted 4-fold with distilled water. All diluted extracts were directly applied to the solid-phase C18 cartridge column without concentration. The fraction of theaflavins was obtained by 40% ethanol extraction after rinsing with water followed with 15% ethanol extraction. An aliquot of theaflavins after concentration was injected onto an ODS C18 reversed-phase column, and four theaflavins and two methylated theaflavins were sufficiently separated by a linear gradient system using distilled water and acetonitrile with 0.5% acetic acid. This analytical method is sensitive for the determination of a small amount of methylated theaflavins, since various interfering substances produced during the fermentation process were eliminated in advance by solid-phase extraction. Using this analytical method, we also demonstrated that methylated theaflavins were easily produced during the manufacture of black tea.     

Rapid, Micro-Methods to Estimate Plant Silicon Content by Dilute Hydrofluoric Acid Extraction and Spectrometric Molybdenum Method

By treating 0.5 g DW of a plant sample directly with 10 ml of a dilute hydrofluoric acid solution (HF solution, 1.5 M HF—0.6 M HCl), all the silica in plant (as much as 150 mg SiO₂) was dissolved within 1 h. After dilution of the extract with 40 mL of distilled water, the silica in the extract was measured by the spectrometric molybdenum yellow method. The molybdenum yellow method, in which silica in 0.1 mL of the diluted extract can be determined in 8 min, is well suited to rapid, micro-estimations of the silica content in plants. In the micro-modification, the size of the plant sample was reduced to 100 mg DW. The analytical procedure was simple, and the analytical time was less than 2 h. The method can save much labor and time, compared with the gravimetric analysis. The dissolution with HF solution and the molybdenum yellow method were also applied to the measurement of the content of silica separated by acid digestion of rice plants. Excellent agreement in the silica measurement of rice plants was confirmed among the direct extraction method, the gravimetric method and the digestion-separation-dissolution method. In the molybdenum yellow method, the addition of boric acid enabled to mask the interference of hydrofluoric acid, and the least amount of citric acid required for the elimination of phosphorus interference was proposed. In conclusion in this report, recommended methods for the rapid estimation of the silica content in rice plants were presented.     

Control of genic DNA methylation by a jmjC domain-containing protein in Arabidopsis thaliana

Differential cytosine methylation of repeats and genes is important for coordination of genome stability and proper gene expression. Through genetic screen of mutants showing ectopic cytosine methylation in a genic region, we identified a jmjC-domain gene, IBM1 (increase in bonsai methylation 1), in Arabidopsis thaliana. In addition to the ectopic cytosine methylation, the ibm1 mutations induced a variety of developmental phenotypes, which depend on methylation of histone H3 at lysine 9. Paradoxically, the developmental phenotypes of the ibm1 were enhanced by the mutation in the chromatin-remodeling gene DDM1 (decrease in DNA methylation 1), which is necessary for keeping methylation and silencing of repeated heterochromatin loci. Our results demonstrate the importance of chromatin remodeling and histone modifications in the differential epigenetic control of repeats and genes.