Estimating the proportion of resistance alleles from bulk Sanger sequencing, circumventing the variability of individual DNA.

Specimens should be examined as much as possible to obtain a precise estimate of the proportion of resistance alleles in agricultural fields. Monitoring traps that use semiochemicals on sticky sheets are helpful in this regard. However, insects captured by such traps are ordinarily left in the field until collection. Owing to DNA degradation, the amount of DNA greatly varies among insects, causing serious problems in obtaining maximum likelihood estimates and confidence intervals of the proportion of the resistance alleles. We propose a statistical procedure that can circumvent this degradation issue. R scripts for the calculation are provided for readers. We also propose the utilization of a Sanger sequencer. We demonstrate these procedures using field samples of diamide-resistant strains of the diamondback moth, Plutella xylostella (Lepidoptera: Plutellidae). The validity of the assumptions used in the statistical analysis is examined using the same data.

A statistical model for estimating the radiocesium transfer factor from soil to brown rice using the soil exchangeable potassium content.

To reduce radiocesium uptake by rice, large amounts of potassium fertilizer have been applied to paddy fields contaminated by radiocesium released from the Fukushima Dai-ichi Nuclear Power Plant owned by the Tokyo Electric Power Company. The Fukushima Prefectural Government recommended maintenance of the soil exchangeable K content up to 200 mg K kg-1 before conventional fertilization in rice production. We constructed an equation to predict the transfer factor from soil to brown rice using the soil exchangeable K content. This equation was then used to calculate the appropriate soil exchangeable K content, which ensures a low risk (5%) of brown rice exceeding the standard limit (100 Bq kg-1 for grains) established in 2012. The equations were constructed using field data obtained by an investigation (measurement of the 137Cs concentrations in soil and brown rice and measurement of the soil exchangeable K content at harvest) that was performed from 2012 to 2015 in 321 paddy fields distributed all over Fukushima Prefecture. We found that the stochastic fluctuation of the transfer factor approximately follows a lognormal distribution under the given environmental conditions. Four factors are considered in predicting the logarithmic quantity of the transfer factor: (1) the linear influence of the logarithm of the exchangeable K content in soil, (2) the non-linear influence of the logarithm of the exchangeable K content in soil, (3) three districts in the Fukushima Prefecture and (4) the year. The linear model of the logarithm of exchangeable K content in soil was adopted by the RD criterion, which indicates the absolute goodness of models for prediction. The predictive ability of the model increased by 29% after including the logarithm of the exchangeable K content in soil (factor 1), while the predictive ability further increased by 10% after including spatial and temporal information (factors 3 and 4). The validity of the exchangeable K content recommended by the Fukushima Prefectural Government was re-examined using the proposed equations, which indicated that the conventional recommendation was appropriate at 2012 but is not fully appropriate under the current situation in which the radiocesium concentration in soil has decreased.

Effect of Different Silage Storing Conditions on the Oxygen Concentration in the Silo and Fermentation Quality of Rice.

We investigated the effects of different silage storing conditions on the oxygen concentration in the silo and fermentation quality of rice (Oryza sativa L.). Forage rice was ensiled in bottles (with or without space at the bottlemouth, with solid or pinhole cap, and with oxygen scavenger, ethanol transpiration agent, oxygen scavenger and ethanol transpiration agent, or no adjuvant) and stored for 57 days. The oxygen concentration decreased with the addition of the oxygen scavenger and increased with that of the ethanol transpiration agent. The oxygen scavenger facilitated silage fermentation and fungus generation, whereas the ethanol transpiration agent suppressed silage fermentation and fungus generation. However, the combined use of the oxygen scavenger and ethanol transpiration agent facilitated silage fermentation and also suppressed fungus generation. Overall, this study revealed the negative effects of oxygen on the internal silo and the positive effects of the combined use of the oxygen scavenger and ethanol transpiration agent on silage fermentation quality.

Analysis of variations in band positions for normalization in across-gel denaturing gradient gel electrophoresis.

Variation in band position between gels is a well-known problem in denaturing gradient gel electrophoresis (DGGE). However, few reports have evaluated the degree of variation in detail. In this study, we investigated the variation in band positions of DNA samples extracted from soil, normalized using reference positions within marker lanes for DGGE in three organismal (bacterial, fungal, and nematode) conditions. For sample lanes, marker DNA (as a control) and sample DNA were used. The test for normality of distribution showed that the position data of a large percentage of bands were normally distributed but not for certain bands. For the normally-distributed data, their variations [standard deviation of marker bands (SDM) and standard deviation of sample bands (SDS), respectively] were assessed. For all organismal conditions, the degree of within-gel variation were similar between SDMs and SDSs, while between-gel variations in SDSs were larger than those in SDMs. Due to the large effect of between-gel variations, the total variations in SDSs were more varied between sample bands, and the mean variations of all sample bands were higher than those in the markers. We found that the total variation in the fungal and nematode SDSs decreased when the intervals between marker bands were narrowed, suggesting that band interval is important for reducing total variation in normalized band positions. For the non-normally distributed data, the distribution was examined in detail. This study provided detailed information on the variation of band positions, which could help to optimize markers for reducing band position variation, and could aid in the accurate identification of bands in across-gel DGGE analyses.

Changes in the concentration of fumonisins in forage rice during the growing period, differences among cultivars and sites, and identification of the causal fungus.

To clarify the changes in rice fumonisin (FUM) concentrations, we conducted field cultivation of 10 forage rice cultivars and inoculation with fumonisin-producing fungal isolates. We cultivated 10 forage rice cultivars at the NARO Institute of Livestock and Grassland Science and one cultivar at two additional farmland sites in Japan in 2011 and 2012. Fusarium fujikuroi, which primarily infects plants shortly after heading, was inoculated on rice just after heading, and we sampled heads at the yellow-ripe and full-ripe stages to assess FUM concentrations. We found differences among cultivars in the FUM concentration and differences among the sites for the same cultivar, but no cultivar had high levels in leaves and stems. Fusarium fujikuroi was the main fumonisin producer. The FUM concentration in heads increases from <1 to 4760 µg/kg DM after the yellow-ripe stage. To control FUM levels, it is necessary to select low-FUM cultivars and manage the cultivation environment.

Extended key-factor/key-stage analysis for longitudinal data.

Key-factor/key-stage analysis was originally a descriptive approach to analyze life tables. However, this method can be extended to analyze longitudinal data in pharmaceutical experiments. By dividing the variance into components, the extended key-factor/key-stage analysis indicates which factor is influential, and through which stage the factor generates its influence in determining the outcome of treatments. Such knowledge helps us in constructing a class of nonlinear longitudinal models that can be interpretable than linear models. Example SAS programs and R programs are provided for the calculation. Supplemental materials are available for this article. Go to the publisher's online edition of Journal of Biopharmaceutical Statistics to view the supplemental files.

Mating disruption for control of Melanotus okinawensis (Coleoptera: elateridae) with synthetic sex pheromone.

A mating disruption experiment to control Melanotus okinawensis Ohira (Coleoptera: Elateridae) was conducted at a sugarcane (Saccharum spp.) field and a wild Japanese pampas, Miscanthus sinensis Anderss, grassland on Minami-Daito Island (3,057 ha) from 2001 to 2007. The sugarcane field and the pampas grassland were treated with synthetic sex pheromone that evaporated from a polyethylene tube dispenser. The mean total catches obtained by monitoring traps in the sugarcane fields decreased by 96.1% in 2001 from the previous year on Minami-Daito Island. The mean total trap catches in the treated area further decreased by 74.0% from 2001 until 2007 as cumulative effects. Simultaneously, the number of adults captured by hand decreased from 4.7 per sugarcane field in 2001 to 0.5 in 2007 (89.3% reduction), whereas those captured in the untreated area (Miyagi Island) did not show such a decrease. The mating rates were significantly lower in the females captured in the treated area (14.3-71.4%) than those in the untreated area (96.9-100%). However, the amount of the decrease in the trap catches was relatively small at first (39.6% reduction) in the Japanese pampas grassland on the periphery of the Island. This was probably due to the loss of pheromone substance caused by the strong seasonal wind in the periphery. However, mean total trap catches at the periphery also decreased within several years; significant decreases were detected until 2003, 2006, and 2007. These results indicated that the mating disruption effectively reduced an isolated population of M. okinawensis.

Adsorption of herbicidally active degradate 2-(2,4-dichloro-3-methylphenoxy)propanoic acid on an andosol.

The adsorption of 2-(2,4-dichloro-3-methylphenoxy)propanoic acid (DMPA) on the surface horizon of a humus-rich Andosol was examined. To investigate the mechanisms of adsorption, chemically treated Andosols, such as organic matter removed Andosol, organic matter and active metals removed Andosol, and clay minerals of the Andosol, were prepared. Furthermore, humic acid was extracted from the Andosol. The mechanisms of the DMPA adsorption were identified by using those untreated and chemically treated Andosols and the humic acid. The amount of DMPA adsorbed increased with decreasing equilibrium pH value. Active surface hydroxyl groups were identified as the most important soil functional group in DMPA adsorption. The predominant mechanism of DMPA adsorption on the Andosol is a ligand-exchange reaction, in which an active surface hydroxyl on Al and/or Fe is replaced by a carboxylic group of DMPA. A comparative study revealed that the amount of DMPA adsorbed was slightly greater than that of (2,4-dichlorophenoxy)acetic acid (2,4-D), especially at equilibrium pH values below 5. This is because the octanol-water partition coefficient (log Kow) of DMPA in the equilibrium pH range is higher than that of 2,4-D, and SOM participates in the adsorption process through a hydrophobic interaction.