Metagenomic analysis using 16S ribosomal RNA genes of a bacterial community in an urban stream,the Tama River,Tokyo

In an effort to determine genus- or species-level taxonomic profiles and diversity of bacterial consortia in the Tama River around urban Tokyo, next-generation sequencing technology targeting a 16S ribosomal RNA (rRNA) gene amplicon was employed. Metagenomic analysis performed by an Ion Personal Genome Machine after sequentially filtering samples through 5-, 0.8- and 0.2-μm filters yielded 1.48 Gb of 16S sequences (average 2.38 M reads/sample). The results indicated that half of the bacterial sequences belonged to Proteobacteria, followed by Bacteroidetes, Actinobacteria and Cyanobacteria. Flavobacterium (Bacteroidetes), possibly including a potential fish pathogen, was the most numerous genera in the Tama River metagenome, and accounted for?~?16% of assigned 16S reads, followed by Mycobacterium. Other dominant bacterial genera including Zoogloea, Sediminibacterium, Hyphomicrobium, Sphingopyxis, Thiothrix and Lysobacter, were thought to be associated with waste water and sludge. MiSeq metagenomic analysis revealed that environmental factors, particularly water temperature, influenced the bacterial composition throughout the year, with a strong negative correlation observed for Proteobacteria and a positive correlation for Bacteroidetes. In terms of bacterial genera, Flavobacterium was positively correlated with temperature, while Polaromonas, Pseudomonas and Bradyrhizobium were negatively correlated with this, suggesting dynamic change in the free-living bacterial population throughout the year and versatile adaptation strategies in relation to environmental factors.     

Propagation of Asian isolates of canine distemper virus (CDV) in hamster cell lines

Backgrounds

The aim of this study was to confirm the propagation of various canine distemper viruses (CDV) in hamster cell lines of HmLu and BHK, since only a little is known about the possibility of propagation of CDV in rodent cells irrespective of their epidemiological importance.

Methods

The growth of CDV in hamster cell lines was monitored by titration using Vero.dogSLAMtag (Vero-DST) cells that had been proven to be susceptible to almost all field isolates of CDV, with the preparations of cell-free and cell-associated virus from the cultures infected with recent Asian isolates of CDV (13 strains) and by observing the development of cytopathic effect (CPE) in infected cultures of hamster cell lines.

Results

Eleven of 13 strains grew in HmLu cells, and 12 of 13 strains grew in BHK cells with apparent CPE of cell fusion in the late stage of infection. Two strains and a strain of Asia 1 group could not grow in HmLu cells and BHK cells, respectively.

Conclusion

The present study demonstrates at the first time that hamster cell lines can propagate the majority of Asian field isolates of CDV. The usage of two hamster cell lines suggested to be useful to characterize the field isolates biologically.     

First application of PCR-Luminex system for molecular diagnosis of fungicide resistance and species identification of fungal pathogens

Fungicide resistance in plant pathogens is often caused by a single point mutation in a gene encoding fungicide target proteins. Such is the case for resistance to MBI-D (inhibitors of scytalone dehydratase in melanin biosynthesis) fungicides in rice blast fungus (Magnaporthe oryzae), which is caused by a mutation in the scytalone dehydratase gene that results in a replacement of valine with methionine at codon 75 of the fungicide target protein. PCR-Luminex, a novel system developed for high-throughput analysis of single nucleotide polymorphisms (SNPs) was successfully introduced to diagnose MBI-D resistance using specific oligonucleotide probes coupled with fluorescent beads. The PCR-Luminex system was further tested for its potential in identifying species causing Fusarium head blight on wheat. Four major pathogens, Fusarium graminearum (=F. asiaticum), F. culmorum, F. avenaceum, and Microdochium nivale, known to cause the disease, were tested, and the species were identified using the PCR-Luminex method. So far, this report is the first on the application of the DNA-based PCR-Luminex system in the area of crop protection and/or agricultural sciences.     

Culture method and growth characteristics of marine benthic dinoflagellate Ostreopsis spp. isolated from Japanese coastal waters

Blooms of toxic dinoflagellates of the genus Ostreopsis, which is known as a producer of palytoxin (PTX) analogs, may pose a threat to human health in tropical, subtropical, and temperate regions around the world. In the present study, we established a suitable culture method for Ostreopsis spp. isolated from Japanese coastal waters and characterized their growth potential using the method to discuss their bloom dynamics. Each clonal strain of Ostreopsis cf. ovata, Ostreopsis sp.?1, Ostreopsis sp.?5, and Ostreopsis sp.?6 was incubated in 25?×?150?mm test tubes with a flat bottom containing various kinds of medium. Since Ostreopsis spp. strains grew well in IMK and/or f/2 media, we selected these media for cultivation of all the Ostreopsis spp. isolates. Growth rates of O. cf. ovata (0.834?divisions/day), Ostreopsis sp.?1 (0.619?divisions/day), and Ostreopsis sp.?6 (1.04?divisions/day) that produce PTX analogs significantly differed (p?<?0.05) respectively and are clearly higher than those of other reported epiphytic dinoflagellate Gambierdiscus toxicus, Prorocentrum lima, and Coolia monotis cultures, which suggest that these species have ecological advantages to predominate through the algal succession in Japanese coastal waters, resulting in a potential risk to human health in this region.     

Comparison of the amount of thiotrophic symbionts in the deep-sea mussel <Emphasis Type="Italic">Bathymodiolus septemdierum</Emphasis> under different sulfide levels using fluorescent in situ hybridization

Various invertebrates inhabiting hydrothermal vents harbor thiotrophic endosymbionts that provide the host with nutrients and are possibly involved in the detoxification of harmful sulfides. In this study, we first determined the partial 16S rRNA gene sequence of the thiotrophic symbiont of the deep-sea mussel Bathymodiolus septemdierum, a dominant species at hydrothermal vents in the Izu–Ogasawara (Bonin) area. We then designed a new probe, Bsob692, for fluorescent in situ hybridization (FISH) using regions completely conserved among thiotrophic symbionts of all bathymodiolin mussels and established the protocol for FISH to compare the distribution and amount of the symbiont using an image analysis program that is commercially available. We compared fluorescent intensity in the gill of the mussels collected at different sites and found a higher intensity in specimens collected from a site with higher sulfide concentration. We also compared mussels reared in the presence and absence of sulfide and found that the former had a higher fluorescent intensity.     

Quantitative trait loci associated with lodging tolerance in soybean cultivar ‘Toyoharuka’

Lodging tolerance (LT) is an important trait for high yield and combine-harvesting efficiency in soybean [Glycine max (L.) Merr.]. Many previous studies have investigated quantitative trait loci (QTLs) for lodging score (LS) in soybean. Most of the investigated QTLs were located in the proximal region of maturity or growth habit loci. The aim of this study was to identify genetic factors for LT not associated with maturity or growth habit. QTL analysis was performed using a recombinant inbred line (RIL) population derived from a cross between ‘Toyoharuka’ (TH), a lodging-tolerant cultivar, and ‘Toyomusume’ (TM). The genotypes of TH and TM were estimated as both e1e2E3E4 and dt1. The average LS over 4 years was used for QTL analysis, identifying a major and stable QTL, qLS19-1, on chromosome 19. The LS of the near-isogenic line (NIL) with the TH allele at Sat_099, the nearest marker to qLS19-1, was significantly lower than the NIL with the TM allele at that position. The TH allele at Sat_099 rarely had a negative influence on seed yield or other agronomic traits in both NILs and the TM-backcrossed lines. Our results suggest that marker-assisted selection for qLS19-1 is effective for improving LT in breeding programs.     

Growth and age composition of northern shrimp Pandalus eous estimated by multiple length frequency analysis

We examined growth of northern shrimp Pandalus eous in the Sea of Japan, off western Hokkaido, to improve estimations of catch-at-age for stock assessment. Multiple length frequency analysis based on length frequency data collected by a scientific research vessel was conducted to examine length-at-age in the shrimp population. Multi-normal distributions estimated using maximum likelihood indicated a good fit to length distributions. AIC values and regression analyses revealed annual growth variation and a decreasing trend in the length at several age classes in the shrimp population. We revised the method for estimating catch-at-age from the age-conversion table (ACT), which is a simple method for age determination, to age–length keys (ALK) calculated from the results of multiple length frequency analysis. Abundant year classes caught successively year after year could be more easily identified from the catch-at-age data computed using ALK than by using ACT. Our results suggested not only that the mean size of commercial landings fluctuated based on changes in age composition but also that a decrease in the length-at-age in the population influenced the consistent size decrease of commercial landings.     

Disparities in activity levels and learning ability between Djungarian hamster (Phodopus sungorus) and Roborovskii hamster (Phodopus roborovskii)

The Djungarian hamster and the Roborovskii hamster belong to the same genus of Phodopus. However, the Djungarian hamster is tame and shows sedative behavior, while Roborovskii hamster is not tame and shows high levels of locomotor activity. Hyperactivity occurs in animals with tameless behavior. Tameness or tamelessness behavior is very important because tameness helps for breeding and controlling as well as it enables a strong human‐animal bond. In the present study, we examined the relationships between activity levels and cognitive function in Djungarian and Roborovskii hamsters. Three types of behavioral tests were performed to analyze their activity levels, memory and leaning ability. The levels of L‐ and D‐amino acids and monoamines in the brain were then determined. Roborovskii hamsters showed significantly higher locomotor activity than Djungarian hamsters. Memory ability was not significantly different between the two hamsters, but Roborovskii hamsters showed lower learning ability. Brain levels of D‐serine which is related to enhancement in memory and learning ability, were significantly higher in Djungarian hamsters, but the reverse was true for brain dopamine and serotonin levels. These results suggest that these differences in brain metabolism may be related to the behavioral differences between the two hamsters.     

Changes in muscle fiber type and expression of mRNA of myosin heavy chain isoforms in porcine muscle during pre‐ and postnatal development

The purpose of this study is to elucidate developmental changes in muscle fiber type in the pig during pre‐ and postnatal development. For this purpose, we performed a histochemical analysis for myosin adenosine triphosphatase activity to assess muscle fiber type and determined abundances of messenger RNA (mRNA) of myosin heavy chain (MHC) isoforms. Samples of Longissimus dorsi (LD) muscle were taken from fetuses on day 90 of the fetal stage. Further, samples of LD, Rhomboideus and Biceps femoris (B. femoris) muscles were taken from pigs when they were 1, 12, 26, 45 or 75 days old. Expression of MHC 2b mRNA in the LD and the B. femoris muscles rapidly and considerably increased from the late fetal stage to the early postnatal stage and this increase was associated with the development of type 2b fibers at least in the LD muscle. As shown by the rapid and considerable changes in expression of MHC 2b mRNA, it seems that a certain plasticity of muscle fiber type still remains in this developmental stage.