Site-level model–data synthesis of terrestrial carbon fluxes in the CarboEastAsia eddy-covariance observation network: toward future modeling efforts

Based on the model–data comparison at the eddy-covariance observation sites from CarboEastAsia datasets, we report the current status of the terrestrial carbon cycle modeling in monsoon Asia. In order to assess the modeling performance and discuss future requirements for both modeling and observation efforts in Asia, we ran eight terrestrial biosphere models at 24 sites from 1901 to 2010. By analyzing the modeled carbon fluxes against the CarboEastAsia datasets, the strengths and weaknesses of terrestrial biosphere modeling over Asia were evaluated. In terms of pattern and magnitude, the carbon fluxes (i.e., gross primary productivity, ecosystem respiration, and net ecosystem exchange) at the temperate and boreal forest sites were simulated best, whereas the simulation results from the tropical forest, cropland, and disturbed sites were poor. The multi-model ensemble mean values showed lower root mean square errors and higher correlations, suggesting that composition of multiple terrestrial biosphere models would be preferable for terrestrial carbon budget assessments in Asia. These results indicate that the current model-based estimation of terrestrial carbon budget has large uncertainties, and future research should further refine the models to permit re-evaluation of the terrestrial carbon budget.     

Small variation of glucosinolate composition in Japanese cultivars of radish (Raphanus sativus L.) requires simple quantitative analysis for breeding of glucosinolate component

To reveal varietally differing glucosinolate (GSL) contents in radish (Raphanus sativus L.) cultivated in Japan, the total and individual GSLs of 28 cultivars were analyzed using high-performance liquid chromatography. In these cultivars, GSL types including three aliphatic GSLs (glucoraphenin, glucoerucin, and 4-methylthio-3-butenyl GSL (4MTB-GSL)) and three indolyl GSLs (4-hydroxyglucobrassicin, glucobrassicin, and 4-methoxy-glucobrassicin) were detected. No cultivar-specific type of GSL was identified. The dominant GSL was 4MTB-GSL, but its contents differed remarkably: 8.6 μmol/g in ‘Koushin’ to 135.7 μmol/g in ‘Karami 199’. Over about 90% of all GSLs in Japanese radish type are 4MTB-GSL, a higher percentage than in Chinese or European garden radish cultivars. A simple, rapid method for estimating total GSL contents in crude extracts was established because of the small variation of glucosinolate composition in Japanese cultivars. The total GSL content can be estimated using an equation for prediction with absorbance at 425 nm in a mixture of GSL crude extract and palladium (II) chloride solution: Total GSL (μmol/g) = 305.47 × A₄₂₅ − 29.66. Its coefficient of determination (R²) and standard error of prediction (SEP) are 0.968 and 8.052. This method enables total GSL content estimation from more than 200 samples per person per day.     

Close linkage of a blast resistance gene,Pias(t), with a bacterial leaf blight resistance gene,Xa1-as(t), in a rice cultivar ‘Asominori’

It has long been known that a bacterial leaf blight-resistant line in rice obtained from a crossing using ‘Asominori’ as a resistant parent also has resistance to blast, but a blast resistance gene in ‘Asominori’ has not been investigated in detail. In the present study, a blast resistance gene in ‘Asominori’, tentatively named Pias(t), was revealed to be located within 162-kb region between DNA markers YX4-3 and NX4-1 on chromosome 4 and to be linked with an ‘Asominori’ allele of the bacterial leaf blight resistance gene Xa1, tentatively named Xa1-as(t). An ‘Asominori’ allele of Pias(t) was found to be dominant and difference of disease severity between lines having the ‘Asominori’ allele of Pias(t) and those without it was 1.2 in disease index from 0 to 10. Pias(t) was also closely linked with the Ph gene controlling phenol reaction, suggesting the possibility of successful selection of blast resistance using the phenol reaction. Since blast-resistant commercial cultivars have been developed using ‘Asominori’ as a parent, Pias(t) is considered to be a useful gene in rice breeding for blast resistance.     

Histopathology of incidental findings in cynomolgus monkeys ( macaca fascicularis ) used in toxicity studies

The purpose of our publication is to widely communicate pictures of spontaneous findings occurring in cynomolgus monkeys. Focal lymphoplasmacytic infiltration is commonly seen in the general organs. The frequency and severity of these lesions may be influenced by the administration of drugs with an effect on the immune system. Lymphoplasmacytic infiltration in the lamina propria of the stomach is also frequently seen in cynomolgus monkeys, and it is caused mainly by a Helicobacter pylori infection. Various degrees of brown pigments are observed in various organs, and it is possible to distinguish the material of the pigments by its morphological features and site. A focal/segmental glomerular lesion is occasionally seen in a section of the kidney, and the minimal lesion has no influence on the urinalysis. We showed the common glomerular lesions in HE-stained sections, as well as in PAM- or PAS-stained sections, for understanding the details. Young and pubertal monkeys are usually used in toxicity studies; therefore, understanding various maturation stages of the genital system is important. In particular, the female genital system needs to be understood in the morphology, because their cyclic changes are different from other laboratory animals. Thus, we present the normal features of the cyclic changes of the female genital organs. Furthermore, we provide more information on spontaneous findings in cynomolgus monkeys for exact diagnoses in toxicity studies.     

Population structure of pigs determined by single nucleotide polymorphisms observed in assembled expressed sequence tags

We have collected more than 190 000 porcine expressed sequence tags (ESTs) from full‐length complementary DNA (cDNA) libraries and identified more than 2800 single nucleotide polymorphisms (SNPs). In this study, we tentatively chose 222 SNPs observed in assembled ESTs to study pigs of different breeds; 104 were selected by comparing the cDNA sequences of a Meishan pig and samples of three‐way cross pigs (Landrace, Large White, and Duroc: LWD), and 118 were selected from LWD samples. To evaluate the genetic variation between the chosen SNPs from pig breeds, we determined the genotypes for 192 pig samples (11 pig groups) from our DNA reference panel with matrix‐assisted laser desorption ionization time‐of‐flight mass spectrometry. Of the 222 reference SNPs, 186 were successfully genotyped. A neighbor‐joining tree showed that the pig groups were classified into two large clusters, namely, Euro‐American and East Asian pig populations. F‐statistics and the analysis of molecular variance of Euro‐American pig groups revealed that approximately 25% of the genetic variations occurred because of intergroup differences. As the F_IS values were less than the F_ST values_, the clustering, based on the Bayesian inference, implied that there was strong genetic differentiation among pig groups and less divergence within the groups in our samples.     

Commensal bacteria coated by secretory immunoglobulin A and immunoglobulin G in the gastrointestinal tract of pigs and calves

A large amount of secretory immunoglobulin A (S‐IgA) is secreted in the alimentary tract of mammals. It has been reported that S‐IgA coats a portion of commensal intestinal bacteria in human and mouse. However, S‐IgA‐coated bacteria have not been studied in pigs and calves. In this study, we evaluated the distribution of S‐IgA‐coated commensal intestinal bacteria in each portion of the gastrointestinal tracts of pigs and calves. Immunoglobulin G (IgG)‐coated bacteria were also analyzed because a considerable amount of IgG is secreted in the gastrointestinal tracts of pigs, and in particular, calves. S‐IgA‐ or IgG‐coated bacteria were detected in all the segments of the gastrointestinal tracts of pigs and calves. The proportion of S‐IgA‐coated bacteria to total bacteria (i.e. S‐IgA coating ratio) varied in the segments of the gastrointestinal tract in pigs, whereas those of calves were nearly the same throughout the gastrointestinal tract. The S‐IgA and IgG coating ratios were higher in pigs than in calves for all segments of the gastrointestinal tract.     

Carbon balance in a cool–temperate deciduous forest in northern Japan: seasonal and interannual variations, and environmental controls of its annual balance

We monitored variation in seasonal and annual net ecosystem production (NEP), gross primary production (GPP), and ecosystem respiration (R _E) based on 7-year eddy covariance measurements above a cool?Ctemperate deciduous broad-leaved forest (Japanese beech forest). The 7-year means (±SD) of annual NEP, GPP, and R _E were 312?±?64, 1250?±?62, and 938?±?36?g?C?m^?2?year^?1, respectively. Variation in NEP was much larger than variation in GPP and R _E. During the growing season, the main factor controlling carbon balance was air temperature; variation in seasonal integrated NEP was regulated by accumulated air temperature (degree-day) with a significant negative correlation, whereas the seasonal ratio of R _E to GPP was correlated positively with accumulated air temperature. Because the deviation of seasonal NEP was also significantly correlated with seasonal R _E/GPP, NEP was controlled by R _E/GPP, depending on air temperature during the growing season. Seasonal R _E in the defoliation and snow seasons was also important for evaluating the annual carbon balance, because the total number of days in the two seasons was quite large owing to a long snowy winter. In the defoliation and snow seasons, we found defoliation season length was a major factor determining seasonal integrated R _E, illustrating the positive correlation between R _E and defoliation season length. The major factors controlling interannual variations in forest carbon balance are discussed.     

Network simulation modeling of equine infectious anemia in the non-racehorse population in Japan

An equine infectious anemia (EIA) transmission model was developed by constructing a network structure of horse movement patterns in a non-racehorse population. This model was then used to evaluate the effectiveness and efficiency of several EIA surveillance strategies. Because EIA had not been detected in Japan since 1993, it was appropriate to review the current surveillance strategy, which aims to eradicate EIA by intensive testing, and to consider alternative strategies suitable for the current EIA status in Japan.The non-racehorse population was divided into four sectors based on horse usage: the equestrian sector, private owner sector, exhibition sector, and fattening sector. To evaluate the risk of disease spread within and between sectors accompanied by horse movements, a stochastic individual-based network model was developed based on a previous survey of horse movement patterns. Surveillance parameters such as targeting sectors and frequency of testing were added into the model to compare surveillance strategies.The disease spread heterogeneously among sectors. Infection occurred mainly in the equestrian sector; the infection was less disseminated in other sectors. Therefore, we considered that the equestrian sector posed a higher risk of disease dissemination within and between sectors through horse movements. However, surveillance strategies targeting only the equestrian sector were not effective enough for early detection of the disease. Alternatively, targeting horses that moved permanently and those in the private owner sector in addition to the equestrian sector is recommended to achieve effectiveness equivalent to that of the current surveillance. In terms of surveillance efficacy, by increasing the testing interval (once yearly to once every 3 years), this testing scheme could reduce the number of tested horses to 44% of the current surveillance, while maintaining almost equivalent effectiveness. Intensive strategies targeting high-risk populations are considered to enhance effectiveness and efficiency of surveillance. The approach in this study may be helpful in the decision-making process that is involved in setting up strategies for risk-based surveillance.