Analysis of rice <Emphasis Type="Italic">RNA-dependent RNA polymerase 1</Emphasis> (<Emphasis Type="Italic">OsRDR1</Emphasis>) in virus-mediated RNA silencing after particle bombardment

RNA-dependent RNA polymerases (RDRs) play a key role in various RNA silencing pathways in many organisms. Using the nucleotide sequence of SGS2/SDE1/RDR6 in Arabidopsis as the search query for sequences that flank the insertions of rice retrotransposon Tos17, we selected rice mutant lines (OsRDR1). RT-PCR analysis showed that OsRDR1 mRNA was undetectable in leaves and calli of the mutants, while it was detected in wild type. RNA silencing was induced by particle bombardment to investigate any effects of OsRDR1 on RNA silencing with β-glucuronidase or green fluorescent protein DNA/RNA in the mutant lines. The results showed that RNA silencing was impaired in these mutant lines by inverted repeat (IR) DNA or in vitro transcribed double-stranded RNA. Further, the mutant lines were bombarded with Brome mosaic bromovirus (BMV, a ssRNA virus) or Wheat dwarf geminivirus (WDV, a ssDNA virus), each carrying the IR sequence of a reporter gene. As a result, RNA silencing was impaired by BMV. Interestingly, however, it was not impaired by WDV. Thus we propose that OsRDR1 is required for RNA silencing mediated by Bromovirus, but not by Geminivirus in this system.     

Allometric model of the maximum size–density relationship between stem surface area and stand density

An allometric model of the maximum size–density relationship between mean stem surface area and stand density is proposed, and is fitted to data for even-aged pure stands of Japanese cedar (Cryptomeria japonica D. Don) and Japanese cypress (Chamaecyparis obtusa Endl.). To derive the model, the biomass density was defined as the ratio of the mean stem surface area to the side area of an imaginary column, of which radius and height were equal to the radius of the mean area occupied by a tree and mean tree height, respectively. According to the model, the slope of the maximum size–density relationship on logarithmic coordinates can be estimated from the allometric power relationships of mean tree height and biomass density to mean stem surface area. The resulting slope was −1.089 for the cedar and −0.974 for the cypress. The estimated maximum size–density relationship corresponded well with the combinations of mean stem surface area and stand density for the overcrowded stands of cedar and cypress. The steeper slope for cedar was attributed to the allocation of more resources to height growth compared to cypress. The maximum total stem surface area was approximated to be 1.483 ha/ha for cedar and 0.949 ha/ha for cypress stands. The difference in the maximum total stem surface area between the two species was produced by the characteristics related to tree height and stem biomass packing into space already occupied.     

Geographical variations in the trophic structure of the plankton community along a eutrophic–mesotrophic–oligotrophic transect

The geographical variations in trophic structure of the plankton community, as defined by total and relative carbon biomass of phytoplankton (PP), bacteria (BA), heterotrophic nanoflagellates (HNF), microzooplankton (MZ), and herbivorous (HNZ) and carnivorous net-zooplankton (CNZ), were investigated along an inshore–offshore transect from the innermost part of Osaka Bay to the Pacific Ocean off Kii Channel, Japan, in June 1991. Based on physico-chemical properties of the water and topographical features, the transect was divided into three trophic areas, i.e. eutrophic, mesotrophic and oligotrophic ones. The average carbon biomass of the total plankton community was highest (438 mg m⁻³) in the inshore eutrophic area, and declined steeply offshore (141 and 26.6 mg m⁻³ in the mesotrophic and oligotrophic areas, respectively). In the offshore oligotrophic area, the relative biomass of BA to PP and the relative biomass of small heterotrophs (i.e. BA, HNF and MZ) to the total heterotrophs were higher than in the other areas, indicating that the microbial food chain predominated. In the mesotrophic area, the biomass of HNZ (primarily copepods) was conspicuously high, even higher than that of PP, suggesting that the traditional grazing food chain prevailed. Because of this short food chain, a productive fishing ground is formed there. In the eutrophic area, the biomass of HNZ was much smaller relative to the enormous biomass of PP, indicating that a considerable amount of primary production was not utilized directly by the metazoan zooplankton. However, the relative contribution of the small heterotrophs to the total heterotrophs' biomass was higher in this area, as in the oligotrophic area.     

1H NMR based metabolic profiling in the evaluation of Japanese green tea quality

Classification of tea quality is now mainly performed according to the sensory results by professional tea tasters. However, this evaluation method is inconsistent in differentiating their qualities. A combination of a (1)H NMR technique and a multivariate analysis was introduced to the quality evaluation of green tea by means of a metabolomic technique. A broad range of metabolites were detected by (1)H NMR spectrometry. The principal component analysis (PCA) was used to reduce the complexity of the (1)H NMR spectra data set and provided the quality discrimination result. It offered an extensive clue for classification and quality assessment without any prepurification method. A set of green teas from a Japanese tea contest were analyzed by (1)H NMR to classify the quality with respect to that judged by tea tasters and to conceive a quality prediction model. Metabolic profiling and fingerprinting of (1)H NMR spectra of green teas with different quality were studied. PCA showed a separation between the high- and the low-quality green teas. The taste marker compounds contributing to the discrimination of tea quality were identified. Reliable prediction models were obtained by the partial least-squares projection to latent structure (PLS) analysis together with a preprocessing filter of both orthogonal signal correction (OSC) and a combination between OSC and wavelet transform algorithms.     

Natural habitat contributes more to estuarine fish production than artificial habitat: an example from inter-river comparison in the Ohta River estuaries

Production of juvenile sea bass Lateolabrax japonicus cohorts during the period of post-migration into the Ohta River was compared between a drainage channel (DC) and a natural river (NR) in Hiroshima, southwestern Japan. Freshwater discharge during periods of high precipitation through the DC is controlled to minimize discharge into other rivers which run through the urban area. Juveniles in the DC had been expected to be affected by stronger disturbance in physical properties to their habitat due to higher fluctuations of freshwater discharge. In order to test this hypothesis, cohort-specific growth (G, d^?1) and mortality (M, d^?1) coefficients and the ratio of G to M (G/M as a proxy of juvenile production) were compared between the two rivers. Juvenile vital rates were estimated through (1) repeated sampling at fine time intervals (6–15 days), (2) application of otolith daily increments for cohort identification, and (3) standardization of abundance at age based on the length-dependent catch efficiency of the sampling gear to estimate M more accurately. G (0.012–0.021) did not significantly differ between the DC and NR. M in the DC (0.184–0.239) was significantly higher than in the NR (0.140–0.148) and average ratio of G/M (0.111) in the NR was higher than in the DC (0.082). High mortality due to physical processes (high variability in salinity) was concluded to contribute to the inter-river difference in juvenile production since the differences in prey availability, and vulnerability to predation between the two rivers were minimal.     

Monitoring of chronic wasting disease using real-time quaking-induced conversion assay in Japan

There has been no report on Chronic wasting disease (CWD) cases in Japan to date; however, there is concern about the geographic spread of CWD. To clarify the CWD status in Japan, we conducted CWD monitoring using real-time quaking-induced conversion (RT-QuIC) assay which can detect the low level of CWD prions. A total of 690 obex samples collected from sika deer and Reeves’s muntjac in Hokkaido and Honshu was tested for CWD prions. No CWD-positive cases were found, suggesting that CWD is nonexistent in Japan. Our results also indicate that RT-QuIC assay is useful for continuous monitoring of CWD. Furthermore, nucleotide sequence analysis of the PrP gene revealed sika deer in Japan harbor CWD susceptible allele.     

Off-flavor of red sea bream Pagrus major reared in recirculating aquaculture systems with low salinity is caused by 2-methylisoborneol

Fisheries Science - We detected an earthy/musty off-flavor in the flesh of red sea bream Pagrus major cultured under low saline water conditions using two types of recirculating aquaculture systems...     

Complete sequencing of Tunisian redspotted grouper nervous necrosis virus betanodavirus capsid gene and RNA‐dependent RNA polymerase gene

Finfish nodaviruses (betanodaviruses) can cause highly destructive infections in numerous species of farmed marine fish larvae and juveniles worldwide. The betanodavirus genome consists of two single‐stranded positive‐sense RNA molecules (RNA1 and RNA2). The virus can be classified into four genotypes based on the partial sequences of the coat protein (CP) gene (T2 and T4 regions). Currently, genomic sequence information for RNA1 regions of RNA2 outside of T2 and T4 is less well documented. This study reports on the characterization of the full RNA2 sequence of a Tunisian betanodavirus with a length of 1433 nt, containing a 339 amino acid open‐reading frame encoding the CP, and typing to the redspotted grouper nervous necrosis virus Ia genotype following phylogenetic analysis. The homology of the capsid protein to other betanodaviruses or alphanodaviruses was compared. In addition, a full length RNA1 sequence of 3104 nt encoding a 982 amino acid RNA‐dependent RNA polymerase was obtained.     

Effects of clay on fat necrosis and carcass characteristics in Japanese Black steers

Twenty 10‐month‐old Japanese Black steers were used to evaluate the effects of clay on fat necrosis and carcass characteristics. Ten steers (Clay group) were fed the clay (50 g/day) during 10–30 months of age. The other 10 steers (Control group) were not fed it. There was no significant difference in body weight or average daily gain between the two groups (P > 0.05). The occurrence of fat necrotic mass in the Clay group (30%) was lower (P < 0.05) than that in the Control group (90%) at slaughter. The size of necrotic masses in the Clay group was smaller (P < 0.05) than that in the Control group. There was no significant difference in the marbling score, beef color, Longissimus muscle area or subcutaneous fat thickness between the two groups. These results suggest that the clay prevented the occurrence of fat necrosis and did not affect the carcass characteristics in Japanese Black steers.