Detection of monoclonal integration of bovine leukemia virus proviral DNA as a malignant marker in two enzootic bovine leukosis cases with difficult clinical diagnosis

Monoclonal integration of bovine leukemia virus (BLV) proviral DNA into bovine genomes was detected in peripheral blood from two clinical cases of enzootic bovine leukosis (EBL) without enlargement of superficial lymph nodes. A BLV-specific probe hybridized with 1 to 3 EcoRI and HindIII fragments in these 2 atypical EBL cattle by Southern blotting and hybridization, as well as in 3 typical EBL cattle. The probe also hybridized to a large number of EcoRI and HindIII fragments in 5 cattle with persistent leukosis. These results suggest that the detection of monoclonal integration of BLV provirus into the host genome may serve as a marker of monoclonal proliferation and malignancy in difficult to diagnose EBL cattle.     

Real-time PCR genotyping assay for feline erythrocyte pyruvate kinase deficiency and mutant allele frequency in purebred cats in Japan

Erythrocyte pyruvate kinase (PK) deficiency is an inherited glycolytic erythroenzymopathy caused by mutations of the PKLR gene. A causative mutation of the feline PKLR gene was originally identified in Abyssinian and Somali cats in the U.S.A. In the present study, a TaqMan probe-based real-time PCR genotyping assay was developed and evaluated for rapid genotyping and large-scale screening for this mutation. Furthermore, a genotyping survey was carried out in a population of four popular purebred cats in Japan to determine the current mutant allele frequency. The assay clearly displayed all genotypes of feline PK deficiency, indicating its suitability for large-scale survey as well as diagnosis. The survey demonstrated that the mutant allele frequency in Abyssinian and Somali cats was high enough to warrant measures to control and prevent the disease. The mutant allele frequency was relatively low in Bengal and American Shorthair cats; however, the testing should still be carried out to prevent the spread of the disease. In addition, PK deficiency should always be considered in the differential diagnosis of anemia in purebred cats in Japan as well as worldwide.     

Tooth brushing inhibits oral bacteria in dogs

In this study, scaling, polishing and daily tooth brushing were performed in 20 beagle dogs, and the number of oral bacteria was determined using a bacterial counter. The dogs were randomized into the scaling (S), scaling + polishing (SP), scaling + tooth daily brushing (SB) and scaling + polishing + tooth daily brushing (SPB) groups. Samples were collected from the buccal surface of the maxillary fourth premolars of the dogs immediately after scaling and every week thereafter from weeks 1 to 8. Throughout the study, the number of bacteria was significantly lower in the SB and SPB groups compared with the S group. The findings suggest that daily tooth brushing inhibited oral bacterial growth in the dogs.     

The effect of random and density‐dependent variation in sampling efficiency on variance of abundance estimates from fishery surveys

Abundance indices (AIs) provide information on population abundance and trends over time, while AI variance (AIV) provides information on reliability or quality of the AI. AIV is an important output from surveys and is commonly used in formal assessments of survey quality, in survey comparison studies, and in stock assessments. However, uncertainty in AIV estimates is poorly understood and studies on the precision and bias in survey AIV estimates are lacking. Typically, AIV estimates are “design based” and are derived from sampling theory under some aspect of randomized samples. Inference on population density in these cases can be confounded by unaccounted process errors such as those due to variable sampling efficiency (q). Here, we simulated fish distribution and surveys to assess the effect of q and variance in q on design‐based estimates of AIV. Simulation results show that the bias and precision of AIV depend on the mean q and variance in q. We conclude that to fully evaluate the reliability of AI, both observation error and variability in q must be accounted for when estimating AIV. A decrease in mean q and an increase in the variance in q results in increased bias and decreased precision in survey AIV estimates. These effects are likely small in surveys with mean q ≥ 1. However, for surveys where q ≤ 0.5, these effects can be large. Regardless of the survey type, AIV estimates can be improved with knowledge of q and variance in q.     

Effects of light and microsite conditions on tree size of 6-year-old Cryptomeria japonica planted in a group selection opening

We examined the extent to which direct and indirect measures of light and microsite conditions could explain variation in tree height and diameter at the base of 6-year-old Cryptomeria japonica trees planted in a group selection opening of about 0.32 ha on a steep slope at Shiiba, Miyazaki Prefecture, southern Japan. We first used the gap light index (GLI) and soil thickness (ST) as directly measured indices. For an indirect measure of light, we used a between-cohort competition index (BCI) estimated from the position and total height of residual trees. For indirect measures of microsite, we examined topographic indices (slope, plan and profile curvature, average slope gradient, and relative elevation) derived from digital elevation models (DEMs) with different resolutions ranging from 2 to 10 m. The multiple linear regression using GLI and ST explained about 45% of variation in tree size, while simple regression using only GLI explained about 35%. The contribution of ST was about half of GLI. The multiple regressions using BCI and the topographic indices did not explain any more variation than using BCI alone (R ² of about 0.26). We conclude that microsite conditions with shallower soil and steeper slope have negative effects on tree growth in group selection openings, although the relative importance is smaller than light conditions. More comprehensive studies considering several openings with more heterogeneous topography including different species are needed to generalize our growth prediction using the indirect measures, which are useful for practical forest management.     

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 status of atmospheric concentrations of ammonia in an intensive dairy farming area in central Japan

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Silicon availability in 36 commercial nursery bed soils was evaluated by four methods the phosphate buffer (pH 6.2, 40 mmol L⁻¹), incubation, supernatant and acetate buffer (pH 4.0, 1 mol L⁻¹) Methods. The influence of silicon availability in the nursery bed soils on the silicon uptake of rice Oryza sativa L. cv. Hitomebore seedlings and the effect of silicon fertilizer application were examined in a glass house in 2002.
The results revealed that the best correlation between silicon content in rice seedlings and available silicon in soils was obtained with the phosphate buffer-solution method ( r  = 0.86). More precise evaluation of available silicon was achieved by grouping soils based on these phosphate absorption coefficients (PAC). The correlation coefficients between silicon content in rice seedlings and available silicon in soils were 0.92 and 0.72 for volcanic soils (PAC > 1500) and non volcanic soils (PAC < 1500), respectively.
We concluded that the phosphate buffer method is the most easily adjusted method for estimation of silicon availability in nursery bed soils, and silicon fertilizers should be applied when silicon availability in non-volcanic nursery bed soils goes below 200 mg kg⁻¹, whereas the level is less than 350 mg kg⁻¹ in volcanic soils.     

Low-fidelity homing behaviour of Biwa salmon <Emphasis Type="Italic">Oncorhynchus</Emphasis> sp. landlocked in Lake Biwa as inferred from otolith elemental and Sr isotopic compositions

Biwa salmon Oncorhynchus sp. is endemic to Lake Biwa, Japan, where it is an important commercial and recreational fisheries species. However, no information is currently available on its population structure and migration ecology. Therefore, here we evaluated whether otolith Sr/Ca, Ba/Ca and ⁸⁷Sr/⁸⁶Sr ratios can be used as natural signatures in Biwa salmon and then used these to determine the natal origins of lake-migration-phase individuals and spawning adults, and the homing ability of spawning adults in the Lake Biwa water system. Quadratic discriminant function analysis demonstrated that the lake-migration school comprised individuals with multiple origins, including rivers to the east, west and north of Lake Biwa, and that the homing rate of spawning adults was low (18 out of 80 individuals), with ca. 78% of fish straying into non-natal rivers. However, this straying behaviour was not spatially random, with fish tending to migrate upstream in rivers neighbouring their natal rivers. The high rate of straying in spawning adults is considered important for establishing and maintaining this species, which is highly adapted to life in the Lake Biwa water system where environmental disturbances often occur.