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.     

Effect of carpropamid on secondary infection by rice blast fungus

Carpropamid (WIN™, KTU 3616) provides good control of leaf and panicle blast by ‘one-shot’ nursery-box treatment. It inhibits melanin biosynthesis in appressorial cells of Pyricularia oryzae, making them hyaline. Penetration by infection hyphae from the hyaline appressoria into rice epidermal cells is substantially hindered. In addition, the spread of rice blast spores from primary lesions to the other parts of the plant leading to secondary infection is largely prevented when the plants are treated with carpropamid by spray or water surface application. Secondary infection was simulated in a glass chamber fitted with an ultrasonic humidifier. On treated plants, many blast spores formed in the lesions, but the number of air spora that were dispersed from the lesions decreased significantly. A similar suppression of the spore liberation was observed in vitro when lesions on rice leaf segments, or discs from Pyricularia cultures on oatmeal agar were treated with the chemical. Spores from treated lesions or from the cultures on oatmeal agar amended with the chemical germinated normally and produced well-melanized appressoria on cellophane membranes. In addition, the spores proved to be fully pathogenic towards rice seedlings, producing normal disease symptoms. These results strongly suggest that carpropamid reduces the secondary infection of rice by Pyricularia by specifically hindering spore liberation. © 1999 Society of Chemical Industry     

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.     

Microbiota analysis of Caspian Sea yogurt, a ropy fermented milk circulated in Japan

We analyzed the microbiota of domestic ropy fermented milk, Caspian Sea yogurt (or 'kasupikai yohguruto' in Japanese), circulated in Japan. We collected six varieties from five localities. Lactococcus ( L) lactis ssp. cremoris was isolated from all samples as the dominant strain at levels of 10⁸−10⁹ CFU/g. We show this strain produces an extracellular polysaccharide (EPS) that causes the unique characteristic viscosity of the product. From analysis of the RAPD pattern of 60 bacterial isolates from the six samples, we found that 59 strains from a total of 60 isolates were identical and produced this viscosity. Furthermore, PFGE analysis of representative strains from each sample indicated that the isolates could be classified into four subgroups. This suggests these L. lactis ssp. cremoris strains found in Caspian Sea yogurt may have been slightly mutated during subculture in Japan. In addition, Lactobacillus (L.) sakei ssp. sakei were isolated from three samples; L. plantarum , Gluconoacetobacter sacchari and Acetobacter aceti were isolated from two samples; and L. paracasei , L. kefiri , Leuconostoc ( Leu. ) mesenteroides were isolated from one sample.     

Characteristic upregulation of glucose-regulated protein 78 in an early lesion negative for hitherto established cytochemical markers in rat hepatocarcinogenesis

Previously, we reported α(2)-macroglobulin (α(2)M) to be a novel marker characteristic of rat hepatocellular preneoplastic and neoplastic lesions negative for hitherto well-established markers. In the present study, we further examined other candidate markers with specificity for the same type of lesions. Glutathione S-transferase-placental form (GST-P)-negative hepatocellular altered foci (HAF) were generated using a two-stage (initiation and promotion) carcinogenesis protocol with N,N-diethylnitrosamine (DEN) and either Wy-14,643 or clofibrate, two peroxisome proliferators. Microarray analysis using total RNAs isolated from laser-microdissected GST-P-negative HAF (amphophilic cell foci) and adjacent normal tissues was conducted along with immunohistochemistry and real-time RT-PCR. Staining for glucose-regulated protein 78 (GRP78) was detected in GST-P-negative HAF and hepatocellular adenomas, and slightly increased GRP78 mRNA expression was observed in the lesions by real-time RT-PCR analysis. Thus, an early increase of GRP78 expression in hepatocarcinogenesis is likely a feature of the amphophilic subset of HAF.     

Development of biosensor for measuring oxidative stress of fish

Fisheries Science - To elucidate the dynamics of oxidative stress in fish, it is necessary to know the concentration of superoxide anions as a precursor to various reactive oxygen species in the...     

Cylindrocladium brown leaf spot on Howea belmoreana caused by Calonectria ilicicola (anamorph: Cylindrocladium parasiticum) in Japan

Brown leaf spot disease caused by Cylindrocladium was found on Howea belmoreana on Hachijojima Island, Tokyo, Japan, in December 2001. Typical symptoms were incited after artificial inoculation. A culture of white mycelia, isolated from leaf spot symptoms, produced reddish perithecia of a nectriaceous fungus. Based on morphological and molecular analyses, this fungus was identified as Calonectria ilicicola (anamorph: Cylindrocladium parasiticum). Pathogenicity of this fungus on five plants cultivated on Hachijojima Island was confirmed by artificial inoculation. This report is the first on Cylindrocladium brown leaf spot of H. belmoreana caused by C. ilicicola (anamorph: Cy. parasiticum).