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.     

A generic model of thinning and stand density effects on forest growth, mortality and net increment

? For assessing forest thinning effects at large (i.e. continental) scale, data scarcity and technical limitations prevent the application of localized or individual-based thinning models.

? Here we present a simple general framework to analyze and predict the effects of thinning on growth and mortality, including the following stand density development. The effects are modeled in relative terms so that the model can be parameterized based on any thinning experiment that includes an unthinned control, regardless of site conditions and stand age.

? The model was tested against observed thinning effects on growth and mortality from five temperate and boreal species (all species pooled r ² = 0.51). It predicted a maximum increase in net stem biomass increment of 16% and a reduction in density-related mortality of 75% compared to un-thinned conditions at stand densities of around 70% of the maximum (increment optimal density).

? A sensitivity analysis revealed overlapping ranges of near optimal density (net increment within 95% of optimal) among all tested species, suggesting that one thinning scenario can be used for many species. The simple and general formulation of thinning effects based on only five parameters allows easy integration with a wide range of generic forest growth models.

     

Modeling to assess growth respiration of stems inPinus densiflora trees

Multiple regression analyses were applied to the respiration data obtained by an excision method to distinguish between maintenance and growth respiration in stems ofPinus densiflora. Among several types of regression models, a few models showed marked stability of coefficient of growth related respiration that are independent of degrees of correlation between predictors and any combinations of predictors. These models predicted growth respiration as 0.45 g CO₂ g (dry weight)⁻¹. At 15°C, sapwood maintenance respiration rate was estimated to 0.72 mg CO₂ g⁻¹ day⁻¹. These estimates were not different from the results obtained with standing trees.     

Phylogenetic groups and cephalosporin resistance genes of Escherichia coli from diseased food-producing animals in Japan

A total of 318 Escherichia coli isolates obtained from different food-producing animals affected with colibacillosis between 2001 and 2006 were subjected to phylogenetic analysis: 72 bovine isolates, 89 poultry isolates and 157 porcine isolates. Overall, the phylogenetic group A was predominant in isolates from cattle (36/72, 50%) and pigs (101/157, 64.3%) whereas groups A (44/89, 49.4%) and D (40/89, 44.9%) were predominant in isolates from poultry. In addition, group B2 was not found among diseased food-producing animals except for a poultry isolate. Thus, the phylogenetic group distribution of E. coli from diseased animals was different by animal species. Among the 318 isolates, cefazolin resistance (minimum inhibitory concentrations: ≥32 μg/ml) was found in six bovine isolates, 29 poultry isolates and three porcine isolates. Of them, 11 isolates (nine from poultry and two from cattle) produced extended spectrum β-lactamase (ESBL). The two bovine isolates produced bla_CTX-M-2, while the nine poultry isolates produced bla_CTX-M-25 (4), bla_SHV-2 (3), bla_CTX-M-15 (1) and bla_CTX-M-2 (1). Thus, our results showed that several types of ESBL were identified and three types of β-lactamase (SHV-2, CTX-M-25 and CTX-M-15) were observed for the first time in E. coli from diseased animals in Japan.     

The presence of double-stranded RNAs in <Emphasis Type="Italic">Alternaria alternata</Emphasis> Japanese pear pathotype is associated with morphological changes

Strains of the Japanese pear pathotype of Alternaria alternata were screened for double-stranded RNAs (dsRNAs). Four strains had several dsRNAs; strain N18 was associated with several dsRNAs and had impaired growth phenotypes such as irregular mycelium and abnormal pigmentation. We isolated dsRNA-cured isolates from strain N18 by single-conidium isolation. The dsRNA-cured isolates had recovered normal growth and pigmentation. Enlarged vesicles were observed in mycelial cells of the original dsRNA-carrying N18 strain. DAPI nuclear staining revealed regression of the nuclei in dsRNA-carrying N18 cells. These results indicate that the dsRNAs might have negative effects, such as apoptosis-like cell death, on the host fungus.     

Plectosporium blight of monkshood caused by <Emphasis Type="Italic">Plectosporium tabacinum</Emphasis>

Severe blight of potted seedlings of monkshood caused by Plectosporium tabacinum was found in glasshouses in Kagawa Prefecture in southwest Japan in May 2001. Root rot and browning of stem bases were followed by wilting and yellowing of leaves, then blighting of leaves, flower buds and stems. A fungus was isolated from diseased plants and confirmed to cause the disease. The new disease was named “Plectosporium blight of monkshood”.     

Phenolics composition and antioxidant activity of sweet basil (Ocimum basilicum L.)

The antioxidant activity of a methanolic extract of Ocimum basilicum L. (sweet basil) was examined using different in vitro assay model systems. The crude extract was fractionated on a Sephadex LH-20 column, and six fractions were identified. The DPPH scavenging assay system and the oxidation of the soy phosphotidylcholin liposome model system were used to evaluate the antioxidant activity of each fraction. Fraction IV showed the strongest activity followed by fractions V and VI. Phenolic compounds responsible for the antioxidative activity of the fractions were characterized by atmospheric pressure chemical ionization liquid chromatography-mass spectrometry. The major antioxidant compound in fraction IV was confirmed as rosmarinic acid by (1)H NMR and characteristic fragmentations in the mass spectrum. Moreover, the native of antioxidant activity of rosmarinic acid in the liposome system was examined. The results showed that one rosmarinic acid can capture 1.52 radicals, and furthermore, the existence of a synergistic effect between alpha-tocopherol and rosmarinic acid was revealed.