Comparison of morphological and DNA-based techniques for stomach content analyses in juvenile chum salmon <Emphasis Type="Italic">Oncorhynchus keta</Emphasis>: a case study on diet richness of juvenile fishes

To identify the stomach contents of marine organisms, morphological observations are commonly conducted. However, the results obtained by this traditional method are frequently biased, as it is difficult to detect partially digested, soft-bodied organisms. To resolve this, recent studies have used DNA-based (DNA barcoding) analyses to examine the diet breadth of marine organisms. Here, we compared the prey richness of juvenile fishes using morphological observations and DNA-based analyses, with a focus on juvenile chum salmon Oncorhynchus keta. A higher number of prey taxa were successfully identified using DNA-based analyses than morphological observations. However, we also noticed several shortcomings of the DNA-based analyses, as reported in other diet-analysis studies that used molecular techniques. For example, the degree of digestion among prey taxa might have resulted in differential sensitivity to DNA detection. Additionally, several prey taxa could not be precisely identified, as the sequence data for some of the targeted organismal groups are unavailable in public gene databases. Remarkably, it is also possible that DNA-based analyses detected secondary prey, and therefore, the richness of prey taxa was likely overestimated. Thus, dietary analyses of juvenile fishes need to be carefully conducted, considering the respective advantages and disadvantages of DNA-based and morphological techniques.     

Quality Characteristics of Waxy Hexaploid Wheat (Triticum aestivum L.): Properties of Starch Gelatinization and Retrogradation

The viscoelastic properties and molecular structure of the starch isolated from waxy (amylose-free) hexaploid wheat (WHW) (Triticum aestivum L.) were examined. WHW starch generally had lower gelatinization onset temperature, peak viscosity, and setback than the starch isolated from normal hexaploid wheat (NHW). Differential scanning calorimetry (DSC) showed that WHW starch had higher transition temperatures (T_o, T_p, and T_c) and enthalpy (ΔH) than NHW starch. However, when compared on the basis of amylopectin (AP) content, ΔH of WHW starch was almost statistically identical to that of its parental varieties. Typical A-type X-ray diffraction patterns were observed for the starches of WHW and its parental varieties. Somewhat higher crystallinity was indicated for WHW starch. WHW starch was also characterized by having greater retrogradation resistance. The high-performance size-exclusion chromatography (HPSEC) of amylopectin showed that each amylopectin yielded two fractions after debranching. Although WHW amylopectin had somewhat long B chains, little difference was observed in the ratio of Fr.III/ Fr.II between WHW and its parental varieties.     

Seasonal variation of domoic acid in a bivalve Spondylus versicolor in association with that in plankton samples in Nha Phu Bay,Khanh Hoa,Vietnam

Previously we reported that a significant level of domoic acid, a causative toxin for amnesic shellfish poisoning, was detected in bivalves belonging to a genus Spondylus from various tropical Asian countries. These findings indicate that causative plankton species for domoic acid widely distribute in these areas. In the present study, we monitored seasonal change of domoic acid level of Spondylus versicolor in association with that of plankton samples in Nha Phu Bay, Khanh Hoa, Vietnam from December 2004 to October 2005. The toxicity of S. versicolor showed distinct seasonal variation. During the period when domoic acid level of S. versicolor was increasing, a significant level of domoic acid was detected in the plankton samples, showing the correlation between these two parameters. These findings show that plankton causative for domoic acid occurred in the bay, and S. versicolor accumulate domoic acid during a bloom of the toxic plankton by food web transfer.     

Bathymetric distribution of beni-zuwai crab <Emphasis Type="Italic">Chionoecetes japonicus</Emphasis> in the northern part of the Sea of Japan

Surveys of beni-zuwai crab were conducted to clarify the bathymetric distribution and fecundity of beni-zuwai crab populations without the effects of bias due to fisheries. The results were compared with previous ones obtained at the heavily exploited Yamato Bank. Two sites in the northern part of the Sea of Japan, off southwest Hokkaido (200–2500 m deep) and West-Tsugaru Basin (300–1900 m deep), both of which are experiencing low exploitation levels, were surveyed in August to September, 2007. There was an abundance of morphologically immature crabs of both sexes in the depth range 1800–2100 m, and a few occurred at depths >2200 m. Immature crabs of <40 mm carapace width were found to migrate downslope to depths of 1800–2100 m and then to migrate upslope during molting for males and after maturity molting for females. Although data were lacking for depths >2000 m at the West-Tsugaru Basin, these relationships were significant for the pooled data of both localities, and they were similar to the results at the Yamato Bank. Clutch fullness of ovigerous females was negatively correlated with depth, which indicates that the low clutch fullness was not induced by fisheries, although the similar phenomenon observed at the Yamato Bank had previously been considered to be due to fishery effects.     

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.     

Experimental evidence of a pathogenic change caused by homologous recombination between endogenous and introduced dysfunctional Avr-Pita genes in Pyricularia oryzae

To provide experimental evidence that somatic homologous recombination (HR) is involved in the instability and diversification of the avirulence gene Avr-Pita in Pyricularia oryzae, we generated a dysfunctional Avr-Pita homolog and integrated it into strain Hoku-1 containing Avr-Pita. In the transformants, the occurrence of somatic HR events between Avr-Pita and the dysfunctional homolog was confirmed by PCR–RFLP. Germlings from conidia from the HR-positive transformants had lost the avirulence function, which enabled it to infect rice cultivar Yashiromochi containing the corresponding resistant gene Pi-ta. These results suggested that genetic mutation caused by somatic HR is one of the mechanisms responsible for virulence diversity.     

A study on processing of natural fibers by underwater shock wave treatment and its characteristics

Fiber quality is very important for all the steps of the textile area. Underwater shock wave has been utilized for metal, wood, food processing and medical applications and renewed and increased application during the last decade. The main object of this study, is to demonostrate underwater shock wave as a surface treatment of natural fibers such as jute and cotton in form of yarn and to report characterized properties of the treated fibers. The underwater shock wave was generated by the explosion of the detonation fuse in the water tank. The process of bubble generation and expansion inside the water results in the formation of shock wave. Natural fibers were exposed to shock wave treatment depending on the different pressures and detonatinon fuse separation distance. After shock-loading, fibers were selected for physicomechanical and physicochemical tests such as Scaning Elecron Microscopy (SEM) analysis, breaking strength, moisture behavior, permeability and wicking test. The maximum effect with improved moisture content, permeabilty and wicking properties were observed from 100 MPa. The treated fiber showed high performance necessary for use in woven and non woven purpose.     

Effects of delayed first feeding on the survival and growth of tiger grouper,Epinephelus fuscoguttatus (Forsskål, 1775), larvae

The effects of delayed first feeding on the survival and growth of tiger grouper, Epinephelus fuscoguttatus (Forsskål 1775), larvae were examined under controlled conditions. The total length, yolk sac volume, oil globule volume, yolk sac absorption time and nutritional transition period (NTP) of the larvae fed at different first times (0, 6, 12, 18 and 24 h after the mouth opening stage; h AMO) were compared. Larval first feed intake was observed at 54 h after hatching (h AH) at 27.5 ± 0.5 °C. The yolk sac was consumed more rapidly with an increase in delayed first feeding and was significantly different among treatments (P<0.05). Larvae first fed at 0 h AMO had the longest yolk sac absorption (72 h AH) and NTP (20 h) times and had the highest survival and growth rates at the end of the experimental period (360 h AH), being significantly higher (P<0.05) than the other treatments. First mortality was observed at 69 h AH, approximately 2 h after point of no return (PNR) occurred. This study suggests that first feeding of tiger grouper larvae should commence at 0 h AMO for enhancement of larval survival and growth.