Use of genomic recursions and algorithm for proven and young animals for single‐step genomic BLUP analyses – a simulation study

The purpose of this study was to examine accuracy of genomic selection via single‐step genomic BLUP (ssGBLUP) when the direct inverse of the genomic relationship matrix ( G ) is replaced by an approximation of G ^?1 based on recursions for young genotyped animals conditioned on a subset of proven animals, termed algorithm for proven and young animals (APY). With the efficient implementation, this algorithm has a cubic cost with proven animals and linear with young animals. Ten duplicate data sets mimicking a dairy cattle population were simulated. In a first scenario, genomic information for 20k genotyped bulls, divided in 7k proven and 13k young bulls, was generated for each replicate. In a second scenario, 5k genotyped cows with phenotypes were included in the analysis as young animals. Accuracies (average for the 10 replicates) in regular EBV were 0.72 and 0.34 for proven and young animals, respectively. When genomic information was included, they increased to 0.75 and 0.50. No differences between genomic EBV (GEBV) obtained with the regular G ^?1 and the approximated G ^?1 via the recursive method were observed. In the second scenario, accuracies in GEBV (0.76, 0.51 and 0.59 for proven bulls, young males and young females, respectively) were also higher than those in EBV (0.72, 0.35 and 0.49). Again, no differences between GEBV with regular G ^?1 and with recursions were observed. With the recursive algorithm, the number of iterations to achieve convergence was reduced from 227 to 206 in the first scenario and from 232 to 209 in the second scenario. Cows can be treated as young animals in APY without reducing the accuracy. The proposed algorithm can be implemented to reduce computing costs and to overcome current limitations on the number of genotyped animals in the ssGBLUP method.     

Assessment of water quality in small agricultural ponds in Nara,Japan

Paddy and Water Environment - In Japan, since ancient times, numerous small- to medium-size agricultural ponds have been constructed to irrigate paddy rice fields. Economic growth and urbanization...     

Criterion for estimating humidity control capacity of materials in a room

As a measure of estimating humidity control capacity of materials in an airtight room under sinusoidal temperature variation, we used the Cb value, which is the ratio of the range of variation in relative humidity in a steel box lined with the material of interest to the range in an empty steel box. In order to clarify the factors that affect the Cb value, we focused on both the temperature variation rate and the area that is lined in the box. It was found that changing the rate of temperature variation over one period strongly affected the Cb value, although the amplitude of temperature variation did not. We further noticed that the difference between the time when peak temperature was reached and the time when peak absolute humidity was reached (peak time difference), was found to be useful for estimating the humidity control capacity of materials. Knowing the difference between the phase when peak temperature was reached and the phase when peak absolute humidity was reached (phase angle difference) was also useful. Because the Cb value was affected by both the variation period and the lined area in the box, we can draw a contour diagram of the period and the lined area for materials to give an overview of the humidity control capacity of a material. The materials of primary interest in this study were Japanese cedar and porous ceramics.     

Effect of cropping systems and crop successions on fumonisin levels in corn from Northern Paraná State,Brazil

In this study the effect of different cropping systems and crop successions was evaluated on natural Fusarium sp. contamination and fumonisin levels in corn. The cropping systems consisted of a conventional and no-tillage area cultivated with corn in the summer following either oats or fallow in the winter (2006 and 2007 growing seasons). In addition, the effect of applying nitrogen fertilizer (0, 22.5, 45.0, 90.0 and 90.0 kg ha⁻¹ nitrogen supplemented with potassium oxide) on fumonisin contamination was evaluated in the 2006 growing season. Fusarium sp. was detected in 90% samples in 2006 and in 100% samples in 2007. In both growing seasons, no-till corn following oats showed the highest mean fumonisin levels and differed significantly (P < 0.05) from all the others (2006) and from conventional till corn following either oats or fallow in the winter (2007). Fumonisin levels ranged from 0.13 to 19.52 μg g⁻¹ (mean 6.97 μg g⁻¹) and from 3.70 to 7.75 μg g⁻¹ (mean 6.29 μg g⁻¹) in no-till corn following oats from the 2006 and 2007 growing seasons, respectively. Plots treated with 0 kg ha⁻¹ and 22.5 kg ha⁻¹ nitrogen showed the highest mean fumonisin levels and differed significantly from those with 45.0 and 90 kg ha⁻¹ nitrogen. Fumonisin levels correlated negatively (P < 0.05) with the nitrogen fertilization rates. Although no-till is advantageous from a soil conservation standpoint, it may enhance the potential for fumonisin contamination in corn.     

Identification of odor-active 3-mercapto-3-methylbutyl acetate in volatile fraction of roasted coffee brew isolated by steam distillation under reduced pressure

In a roasted Arabica coffee brew, the potent roasty odor quality compound was identified as 3-mercapto-3-methylbutyl acetate by comparison of its Kovats gas chromatography retention index, mass spectrum, and odor quality to those of the synthetic authentic compound. 3-Mercapto-3-methylbutyl acetate has been identified for the first time in the coffee, and according to the results of the aroma extract dilution analysis, the contribution of this compound to the flavor of the roasted coffee brew varied depending on the degree of the coffee bean roasting. The concentration of this compound in the coffee brews as with 3-mercapto-3-methylbutyl formate increased with an increase in the degree of roasting. However, the slope of the amount of both esters was different, and 3-mercapto-3-methylbutyl acetate hardly increased with a low degree of roasting at more than a 21 luminosity (L)-value, but it rapidly increased when the roasting degree of the coffee beans reached the L-value of 18. These results suggested that the contribution of 3-mercapto-3-methylbutyl acetate to the overall flavor is peculiar to the flavor of the highly roasted coffee.     

Development of an enzyme-linked immunosorbent assay to detect an immunomodulatory alpha-D-glucan-protein complex, MPG-1, in basidiomycete Tricholoma matsutake and related processed foods

We previously isolated a novel immunomodulatory alpha-(1,4)(1,6)(1,2)- d-glucan-protein complex (MPG-1) from mycelia of Tricholoma matsutake in basidiomycetes. In the present study, we raised a polyclonal antibody by immunizing rabbits with MPG-1 and constructed a sandwich enzyme-linked immunosorbent assay (ELISA) system to examine the distribution of MPG-1 among edible mushrooms and related processed foods. The system detected MPG-1 quantitatively at concentrations of more than 10 ng/mL, with a coefficient of variation of less than 10% by intra-assay and interassay precision. Analysis with the system of chemically modified MPG-1 suggested that the sugar moiety was mainly involved in the detection. The system detected MPG-1 in the extracts of the fruiting bodies of T. matsutake but not in those of 34 other basidiomycete species. Moreover, a significant amount of MPG-1 was detected in the extracts of their cultured mycelia. The antigenic structure of MPG-1 was relatively stable in terms of pH and temperature. MPG-1 was detected in processed foods supplemented with T. matsutake. These results suggest that MPG-1 is distributed predominantly in T. matsutake species and that the ELISA system can detect it in processed foods supplemented with T. matsutake.     

Formation mechanism of p-methylacetophenone from citral via a tert-alkoxy radical intermediate

The aim of this study was to clarify the formation mechanism of a potent off-odorant, p-methylacetophenone, from citral under acidic aqueous conditions. An acidic aqueous solution (pH 3.0) containing 10 mg/L of citral was stored at 40 degrees C for 2 weeks. Among the compounds detected in the stored citral solution, 4-(2-hydroxy-2-propyl)benzaldehyde was identified for the first time as a degradation product from citral. The formation of p-methylacetophenone and 4-(2-hydroxy-2-propyl)benzaldehyde behaved the same when antioxidants were added to the citral solution. In addition, both compounds were formed by the Fe(2+)-induced decomposition of 8-hydroperoxy-p-cymene, another compound identified in the stored citral solution. These results suggested that both p-methylacetophenone and 4-(2-hydroxy-2-propyl)benzaldehyde can be formed via the same radical intermediate [p-CH3C6H4C(CH3)2O*] that can be derived from the O-O bond homolysis of 8-hydroperoxy-p-cymene. On the other hand, the degradation of 8-hydroperoxy-p-cymene without Fe2+ under acidic aqueous conditions did not yield p-methylacetophenone and 4-(2-hydroxy-2-propyl)benzaldehyde, but the degradation of citral without Fe2+ did. Therefore, other than the decomposition of 8-hydroperoxy-p-cymene, a mechanism to generate the tert-alkoxy radical intermediate was proposed for the formation of p-methylacetophenone and 4-(2-hydroxy-2-propyl)benzaldehyde in the citral solution.     

Impact of introduced honey bees on native pollination interactions of the endemic Echium wildpretii (Boraginaceae) on Tenerife, Canary Islands

The aim of this study was to investigate effects of introduced honey bees (Apis mellifera) on native pollination interactions of Echium wildpretii ssp. wildpretii in the sub-alpine desert of Tenerife. We selected two study populations, one dominated by honey bees, while the other was visited by many native insects. During peak activity period of insects, nectar was nearly completely depleted in flowers of the first, but not the latter population. Thus, a high abundance of honey bees may have suppressed visitation by native animals due to exploitative competition. Honey bees stayed longer and visited more flowers on the same inflorescence than native bees, thus potentially promoting self-pollination of the plants. Level of seed set and viability was similar in the two study populations. However, we cannot rule out long-term changes in genetic population structure due to changes in gene-flow patterns caused by foraging behaviour of honey bees vs. native flower-visitors.     

Vertical Distribution of Trace Metals in Natural Soil Horizons from Japan Part 2: Effects of Organic Components in Soil

The association of Al, Mn, Fe, Ba, Zn, Cr, Ni, Co and Pb withsoil organic matter (SOM) was investigated in three Japanesesoils. Organically bound metals were assayed by elementalanalysis of a fraction extracted with acidified hydrogenperoxide (H₂O₂) and the humic acid extracted withalkaline reagent, from soil sampled at various depths of solums.A Dystric Cambisol showed higher extractability with acidifiedH₂O₂ for most of the metals than a Humic Andosol and an Orthic Acrisol. A Humic Andosol had more metals associated with humicacid than the other two soils.Cu showed high extractability with acidified H₂O₂ andalso significant association with humic acid, while Pb showedhigh extractability with acidified H₂O₂ but itsassociation with humic acid was relatively low among the metalsinvestigated. As humic acid is highly resistant to weathering,retention of Cu with SOM may last longer than that of Pb.The binding of metals with SOM probably has contributed to theaccumulation of some metals in organic-rich shallow horizons of soil. Such metals were Zn, Cu, Ni and Pb in a Dystric Cambisol,Cu in a Humic Andosol, and Pb and Cu in an Orthic Arisol.