Permuted tRNA genes expressed via a circular RNA intermediate in Cyanidioschyzon merolae

A computational analysis of the nuclear genome of a red alga, Cyanidioschyzon merolae, identified 11 transfer RNA (tRNA) genes in which the 3' half of the tRNA lies upstream of the 5' half in the genome. We verified that these genes are expressed and produce mature tRNAs that are aminoacylated. Analysis of tRNA-processing intermediates for these genes indicates an unusual processing pathway in which the termini of the tRNA precursor are ligated, resulting in formation of a characteristic circular RNA intermediate that is then processed at the acceptor stem to generate the correct termini.     

Relative parasitic fitness of isolates of Pyricularia oryzae Cav. with different sensitivities to fungicides

The relative parasitic fitness of isolates of Pyricularia oryzae with different sensitivities to isoprothiolane (di-isopropyl 1,3-dithiolan-2-ylidenemalonate) and IBP (S-benzyl O, O-di-isopropyl phosphorothioate) was studied in the absence of fungicides. Four field isolates (S-1,S-2,MR-1 and MR-2) and two in-vitro mutants (Rvt-1 and Rvt-2) were used for disease epidemics. S-l and S-2 were wild types; MR-1 and MR-2 were sensitive to isoprothiolane and moderately resistant to IBP, and Rvt-1 and Rvt-2 were resistant to both fungicides. Twelve epidemics were made by inoculating rice seedlings with mixed conidial suspensions of two isolates or mutants. The value of relative parasitic fitness (W = 0-1.0) was calculated for each isolate and epidemic. S-l and S-2 were stronger (W = 1.0) than MR-2, Rvt-1 and Rvt-2; but weaker (W = 0.75, 0.73, respectively) than MR-1. MR-1 was strongest among all isolates and mutants used. MR-2 was slightly weaker (W = 0.9-1.0) than S-l and S-2, but stronger than Rvt-1 and Rvt-2. Rvt-1 and Rvt-2 had smaller values of W, ranging from 0.25-0.58, in the epidemics with each field isolate. These results suggest that the proportions of in-vitro mutants do not increase unless intensive selection pressure is given, and would be expected to decrease rapidly after the selection pressure is removed. Isolates moderately resistant to IBP, such as MR-1 and MR-2, however, had high values of W, suggesting that they would increase or would not decrease rapidly in the absence of selection pressure. These results may well explain why isolates highly resistant to isoprothiolane and IBP have seldom been found, and why a large number of isolates moderately resistant to IBP but sensitive to isoprothiolane have been observed in the field.     

Are all three components of conservation agriculture necessary for soil conservation in the Sudan Savanna?

ABSTRACT

Conservation agriculture (CA) as recommended by the Food and Agriculture Organization of the United Nations consists of three components: minimum soil disturbance, soil cover, and crop rotation/association. CA was expected to become an effective countermeasure against water erosion in the Sudan Savanna, but it has not been adopted by local smallholder farmers. As markets for grain legumes (including cowpea) have not been developed in the Sudan Savanna, crop rotation/association should be considered impractical for these farmers. Therefore, we examined whether legume intercropping as a crop rotation/association component is necessary for preventing soil erosion in the Sudan Savanna. Three-year field experiments were conducted in runoff plots at Institute of Environment and Agricultural Research Saria station. The four treatments were conventional practice (full tillage, no sorghum residue mulching, and no intercropping), two-component CA (minimum tillage (MT) and sorghum residue mulching without intercropping), and three-component CA with velvet bean (VB) or pigeon pea (PP) intercropping. It was revealed that: (1) MT and sorghum residue mulching (without intercropping) effectively reduced the annual soil loss by 54% mainly due to the improvement of soil permeability by the boring of termites and wolf spiders found under the sorghum stover mulch; (2) intercropping in combination with MT and crop residue mulching had no effect on soil erosion control mainly because: (a) PP did not survive the long dry season; (b) VB did not serve effectively as a cover crop since soil loss was concentrated at the beginning of the rainy season when VB was still too small; (c) unexpectedly, in combination with MT and crop residue mulching, intercropping with VB did not increase mulch biomass, especially sorghum biomass which prompts the boring of termites and wolf spiders. These results demonstrate that the third component of CA, namely legume intercropping, is not always necessary; rather, the two remaining components – minimum soil disturbance and soil cover – are sufficient for soil conservation in the Sudan Savanna. This finding lightens the burden of adopting CA and thus facilitates its future promotion to the smallholder farmers in the Sudan Savanna.     

Detection of Pythium aphanidermatum in tomato using loop-mediated isothermal amplification (LAMP) with species-specific primers

A loop-mediated isothermal amplification (LAMP) reaction with a primer set designed from the rDNA ITS sequence of P. aphanidermatum was developed. Results of a specificity test using 57 strains of Pythium spp. indicated that the LAMP assay gave no cross reactions in other 39 Pythium species, 11 strains of Phytophthora spp. and eight other soil borne pathogens. The detection limit was 10 fg of genomic DNA, which was ten times the sensitivity of the polymerase chain reaction. The LAMP assay was applied to hydroponic solution samples from tomato fields, and the results were compared to those of the conventional plating method. LAMP was observed to be effective for the specific detection of P. aphanidermatum. Furthermore, P. aphanidermatum was detected directly in tomato roots infected with P. aphanidermatum without DNA extraction. The LAMP method established in this study is a simple, sensitive and rapid tool for the detection of P. aphanidermatum.     

Changes in aboveground and belowground properties during secondary natural succession of a cool-temperate forest in Japan

Forest development in temperate regions is considered to be a global carbon sink. Many studies have examined forest development after harvesting or fire from aboveground (e.g., biomass) or belowground (e.g., soil nutrient) perspectives. However, few studies have explored forest development from both perspectives simultaneously in cool-temperate forests in Japan. In this study, we examined changes over 105 years in both aboveground and belowground components during secondary natural succession. The aboveground biomass increased for 50 years and reached a plateau in a 105-year-old stand. The N mineralization rate increased during succession for 50 years, but showed a decline in the 105-year-old stand due to the decrease in the nitrification rate in late succession. The percent nitrification (i.e., relative contribution of nitrification to N mineralization) decreased significantly with increasing forest stand age. The N mineralization rates had significant relationships with N concentrations of the dominant tree foliage and litter fall and with the amount of litter fall N. Meanwhile, other belowground properties (i.e., soil pH, phenol concentration, soil microbial respiration, and litter mass loss) did not show any significant relationship with forest stand age. This may be because the soil at the study sites was heterogeneous and consisted of Cambisols and Andosols, the latter of which originally has high organic matter content, and thus may have buffered the effect of the aboveground development. These results indicate that belowground N dynamics are more closely associated with aboveground development than other belowground properties in these forests.     

Distribution of minke whales in the Bellingshausen and Amundsen Seas (60°W–120°W), with special reference to environmental/physiographic variables

The relationship between the distribution of minke whales ( Balaenoptera acutorostrata ) in the Bellingshausen and Amundsen Seas (longitude between 60°W and 120°W), and environmental and physiographic variables (sea-surface temperature, sea-ice extension, and sea-floor-slope type), was studied to determine whether these environmental and physical factors affect the distribution and density of minke whales. The analysis was based on sightings data obtained from the 1989/90 and 1982/83 IWC/IDCR cruises. The mean sea-surface temperatures for comparable areas were significantly higher in 1989/90 (2.04°C) than in 1982/83 (1.12°C), and the area where the sea-surface temperature was greater than 1°C in the 1989/90 study was approximately twice that of the 1982/83 study. Additionally, during the surveys, the extent of the sea ice in 1989/90 was less than that in 1982/83, with the mean ice edge about 92.6 km (50 nautical miles; 1 nautical mile ≈1.852 km) farther south in 1989/90 than in 1982/83. This is consistent with the sea ice extent observed in winter, when the sea ice extent was less in 1989 than in 1982. The distribution of minke whales was substantially different between the two surveys, with the density and abundance of minke whales being greater in 1982/83 than in 1989/90. The warmer sea-surface temperatures, fewer cold-water intrusions, and the smaller extent of sea ice in 1989/90 may be related to the difference in distribution of minke whales from 1982/83, possibly owing to the shift in availability of prey.     

Solubility and application effects of African low-grade phosphate rock calcinated with potassium carbonate

This article indicates solubility improvement of African low-grade phosphate rock (PR) through calcination with potassium carbonate. We showed calcination with potassium carbonate made its citric acid solubility up to 100%, and reinforcement of its application effect. In sub-Saharan Africa, although many phosphate deposits have been found, farmers are facing high prices of P fertilizers because of the low solubility of the African PRs. We previously reported PR calcination with Na carbonate improves the solubility, but their application produced limited crop growth, especially in upland conditions. It was speculated soil Na accumulation caused plant growth inhibition. Therefore, we tried to elucidate the effect of calcination with potassium carbonate on PR solubility and its application effects for lowland rice and maize through pot experiments. We used Kodjari PR produced in Burkina Faso for the calcination. Powdered PRs were mixed with K₂CO₃ in five doses to achieve the target K₂O compositions of 200, 250, 300, 350, and 400 g kg^-1. The pelletized PR-K₂CO₃ mixtures were calcined at 900, 1000, 1050, and 1100 °C for 10 min. The pot experiments were conducted for 56 days, monitoring the growth of rice and maize under several application rates. Calcination with K carbonate generated K-rhenanite (KCaPO₄) and kaliophilite (KAlSiO₄), and the solubility reached about 100% in 20 g L^-1 citric acid and about 40% in water. This shows that K carbonates behave like Na carbonate in the solubilization of Kodjari PRs. Although the calcinated Burkina PR (CB) application significantly reduced plant growth when it was applied at an excessive rate, reduced application rates yielded comparable plant growth to that of triple super phosphate (TSP). K carbonate calcination deterred Na accumulation in the soil, and it was effective for plant growth. However, CB easily causes plant damage in excessive application, and it may contain phytotoxicant substances.     

Inhibitory effect of isoprothiolane on metabolism of a phosphoramidate by isolates of Pyricularia oryzae cav. in relation to fungicide sensitivity

The inhibitory effect of isoprothiolane(diisopropyl 1,3-dithiolan-2-ylidenemalonate), a fungicide for rice blast control, on the metabolism of dibutyl N-methyl-N-phenylphosphoramidate (BPA) by 20 isolates of Pyricularia oryzae was examined in relation to sensitivity of the isolates to the reference fungicide IBP(S-benzyl diisopropylphosphorothiolate). The isolates were divided into five groups based on the modes of BPA metabolism and the inhibition of BPA metabolism by isoprothiolane. Every isolate in groups I and II, which was either a field isolate or a stock culture, decomposed BPA rapidly and produced both hydroxylated and N-demethylated BPA as metabolites. BPA decomposition by these isolates was strongly inhibited by isoprothiolane, resulting in the decreased production of both metabolites in group I and of the hydroxylated metabolite in group II. These isolates were almost equally sensitive to isoprothiolane. Isolates in groups III, IV, and V were all obtained from selection of the fungus mutants found growing on media containing isoprothiolane. Isolates in group III, derived by plating large numbers of conidia, did not decompose BPA to any extent. Mutants of groups IV and V were obtained from fast-growing sectors on agar containing isoprothiolane. Both these groups decomposed BPA, but isolates belonging to group IV produced copious amount of N-demethylated BPA whereas isolates in group V did not. BPA metabolism by these in vitro mutants in groups III, IV, and V was not inhibited by isoprothiolane. Thus, the inhibitory effect of isoprothiolane on BPA metabolism was correlated with sensitivity of an isolate to isoprothiolane. The inhibitory effect of IBP on BPA metabolism was not always correlated with the sensitivity of an isolate to IBP.     

Transient uplift after a 17th-century earthquake along the Kuril subduction zone

In eastern Hokkaido, 60 to 80 kilometers above a subducting oceanic plate, tidal mudflats changed into freshwater forests during the first decades after a 17th-century tsunami. The mudflats gradually rose by a meter, as judged from fossil diatom assemblages. Both the tsunami and the ensuing uplift exceeded any in the region's 200 years of written history, and both resulted from a shallow plate-boundary earthquake of unusually large size along the Kuril subduction zone. This earthquake probably induced more creep farther down the plate boundary than did any of the region's historical events.     

Prevalence and characterization of Staphylococcus aureus and enterotoxigenic Staphylococcus aureus in retail raw chicken meat throughout Japan

A total of 444 samples of raw chicken meat (thighs, breasts, wings, livers, gizzards, hearts and ovaries) that retailed at 145 different supermarkets in 47 prefectures in Japan were examined for contamination with Staphylococcus aureus in association with its enterotoxigenicity. S. aureus was isolated from 292 (65.8%) of the samples, and from 131 of the 145 supermarkets. There was no significant difference in the detection rate of S. aureus according to the type of meat examined. About 80% of 714 isolates belonged to the poultry (57.1%) and human biotypes (22.1%). Seventy-eight (21.7%) of 360 isolates were enterotoxigenic and isolated from 78 samples in 53 supermarkets in 31 prefectures. Staphylococcal enterotoxins (SEs) produced were SEB (50 isolates), SEA (14), SEC (8), SED (2), SEA+SEB (2), and SEA+SEC (2). Most of the enterotoxigenic isolates belonged to the human and poultry biotypes, coagulase type VII, VIII or IV, and were lysed by phages of group III. Identical SE types, biotypes, coagulase types and pulsed-field gel electrophoresis (PFGE) patterns were shown in isolates from different types of meat at the same supermarket and from samples taken from different supermarkets in the same prefectures or in isolates from samples obtained from several different prefectures. Among the 50 SEB-producing isolates, 27 yielded three similar PFGE patterns that differed by only a few fragments, suggesting that they were closely related genetically. The three patterns were found in isolates of samples that retailed at 17 supermarkets in 11 prefectures, indicating that they may be disseminated among raw chicken meat in Japan.