The empirical bias of estimates by restricted maximum likelihood, Bayesian method, and method R under selection for additive, maternal, and dominance models.

Bayesian analysis via Gibbs sampling, restricted maximum likelihood (REML), and Method R were used to estimate variance components for several models of simulated data. Four simulated data sets that included direct genetic effects and different combinations of maternal, permanent environmental, and dominance effects were used. Parents were selected randomly, on phenotype across or within contemporary groups, or on BLUP of genetic value. Estimates by Bayesian analysis and REML were always empirically unbiased in large data sets. Estimates by Method R were biased only with phenotypic selection across contemporary groups; estimates of the additive variance were biased upward, and all the other estimates were biased downward. No empirical bias was observed for Method R under selection within contemporary groups or in data without contemporary group effects. The bias of Method R estimates in small data sets was evaluated using a simple direct additive model. Method R gave biased estimates in small data sets in all types of selection except BLUP. In populations where the selection is based on BLUP of genetic value or where phenotypic selection is practiced mostly within contemporary groups, estimates by Method R are likely to be unbiased. In this case, Method R is an alternative to single-trait REML and Bayesian analysis for analyses of large data sets when the other methods are too expensive to apply.     

ULTRASONOGRAPHIC FEATURES OF DIFFUSE HEPATOCELLULAR DISORDERS IN DAIRY CATTLE

Ultrasonography of the liver was performed in 200 Holstein-Friesian dairy cattle using a 3.5 MHz transducer with a linear array electronic scanner. Liver samples were taken, processed and examined microscopically and the fat occupying rate was calculated. The hepatic ultrasonograms were evaluated according to the presence of bright pattern, dark pattern, deep attenuation, vascular blurring and blurring of edges. Of the 200 animals, 96 had a normal liver, 63 had hydropic degeneration of the liver, 37 had fatty infiltration of the liver, 3 had liver dystrophy and I had hepatic amyloidosis, diagnosed through histopathological examination. Amyloidosis was characterized by bright pattern and blurring of edges. Liver dystrophy had higher percentages of bright pattern and blurring of edges than normal liver. Hydropic degeneration had higher percentages of dark pattern and blurring of edges than normal liver. Fatty infiltration had higher percentages of bright pattern, deep attenuation, vascular blurring and blurring of edges than normal liver. The present results suggest that different ultrasonographic patterns can be observed in various diffuse hepatocellular disorders in dairy cattle     

Flow cytometric analysis of chicken NK activity and its use on the effect of restraint stress

Immune system is organized by the influence of both neural and endocrine systems. NK activity plays an important role in the innate immunity. In this study, we observed the effects of restraint stress on chicken peripheral blood NK activity. Viability of FITC-labeled RP9 was measured with PI after treatment with the effector cells. Chicken peripheral blood CD8alpha+ cells expressed strong cytotoxic activity, in contrast to thrombocytes, while peripheral blood CD3+ CD8alpha+ cells and CD4+ cells had little cytotoxic activity. Con A supernatant enhanced the cytotoxic activity of CD8alpha+ cells. Therefore, it is considered that these cytotoxic activities measured by flow cytometry (FCM) analysis are NK activity. When chickens were exposed to restraint stress, the levels of serum corticosterone increased transiently over a short period of time while the NK activity decreased. The decreased NK activity, however, did not recover to the intact levels for a long time, even once the serum corticosterone levels had recovered. These data indicate that chicken NK activity is able to be measured by flow cytometric analysis and that restraint stress causes severe damage to the chicken NK activity.     

An immunohistochemical study of endocrine cells in the abomasum of vagotomized calf

The effect of thoraco-vagotomy on the distribution and frequency of chromogranin-, serotonin-, somatostatin- and gastrin-immunoreactive cells in the abomasum of the calf were investigated by immunohistochemistry. Calves were vagotomized at 1 week old and sampled 2 and 4 weeks later. The endocrine cells generally decreased in number in vagotomized calves as compared to non-operated control calves. However, the detailed responses of endocrine cells to vagotomy varied depending on the endocrine cell type, region of gastric mucosa, and period after vagotomy. The present result suggests that the vagus nerve has an influence on the intrinsic regulatory system by endocrine cell control in the ruminant abomasum.     

Species identification method for <Emphasis Type="Italic">Scombrops boops</Emphasis> and <Emphasis Type="Italic">Scombrops gilberti</Emphasis> based on polymerase chain reaction-restriction fragment length polymorphism analysis of mitochondrial DNA

ABSTRACT:   Gnomefish Scombrops boops and Scombrops gilberti are commercially important fishes in Japan, but these species are often confused in the markets because of their morphological similarity. To identify these two species, we performed nucleotide sequencing and restriction fragment length polymorphism (RFLP) analysis on 16S ribosomal RNA (rRNA) gene and the control region in mitochondrial DNA. Five and 12 nucleotide substitutions were observed between species in the 777-bp 16S rRNA gene and 471-bp control region, respectively. Diagnostic restriction sites for discriminating between S. boops and S. gilberti were found in the 16S rRNA gene, but not in the control region. Polymerase chain reaction (PCR)–RFLP analysis using two enzymes, Eco NI and Mva I, clearly discriminated between S. boops and S. gilberti identified by meristic characters. The PCR–RFLP analysis identified most of the 168 Scombrops young caught in the coastal waters of the Izu and Miura peninsulas as S. boops , suggesting that S. gilberti juveniles are rare in this area.     

Use of genomic recursions and algorithm for proven and young animals for single‐step genomic BLUP analyses – a simulation study

The purpose of this study was to examine accuracy of genomic selection via single‐step genomic BLUP (ssGBLUP) when the direct inverse of the genomic relationship matrix ( G ) is replaced by an approximation of G ^?1 based on recursions for young genotyped animals conditioned on a subset of proven animals, termed algorithm for proven and young animals (APY). With the efficient implementation, this algorithm has a cubic cost with proven animals and linear with young animals. Ten duplicate data sets mimicking a dairy cattle population were simulated. In a first scenario, genomic information for 20k genotyped bulls, divided in 7k proven and 13k young bulls, was generated for each replicate. In a second scenario, 5k genotyped cows with phenotypes were included in the analysis as young animals. Accuracies (average for the 10 replicates) in regular EBV were 0.72 and 0.34 for proven and young animals, respectively. When genomic information was included, they increased to 0.75 and 0.50. No differences between genomic EBV (GEBV) obtained with the regular G ^?1 and the approximated G ^?1 via the recursive method were observed. In the second scenario, accuracies in GEBV (0.76, 0.51 and 0.59 for proven bulls, young males and young females, respectively) were also higher than those in EBV (0.72, 0.35 and 0.49). Again, no differences between GEBV with regular G ^?1 and with recursions were observed. With the recursive algorithm, the number of iterations to achieve convergence was reduced from 227 to 206 in the first scenario and from 232 to 209 in the second scenario. Cows can be treated as young animals in APY without reducing the accuracy. The proposed algorithm can be implemented to reduce computing costs and to overcome current limitations on the number of genotyped animals in the ssGBLUP method.     

Distribution of a fish pathogen Listonella anguillarum in the Japanese flounder Paralichthys olivaceus hatchery

The present study was undertaken to investigate the distribution of Listonella anguillarum in a Japanese flounder (Paralichthys olivaceus) hatchery. A total of 2704 isolates were obtained from the developing fish, live diets and artificial feeds of Japanese flounder and their rearing water, 439 of which were identified as L. anguillarum by the combining incubation on thiosulfate-citrate-bile salt-sucrose (TCBS) agar at 35 °C overnight with polymerase chain reaction (PCR) detection for the VAH1 hemolysin gene. L. anguillarum was detected in all seven rotifer samples, with densities of 2.5 × 10³ to 4.6 × 10⁶ colony forming units (CFU) g^− 1. Both the analyzed samples of Nannochloropsis oculata contained this bacterium at densities of 1.6 × 10⁴ to 1.4 × 10⁵ CFU g^− 1. L. anguillarum was detected in only one of four samples of Artemia nauplii with a density of 4.8 × 10⁵ CFU g^− 1 (35%) and it was not detected in the two analyzed artificial feed samples. L. anguillarum was detected in 11 of 18 specimens of larval and juvenile Japanese flounder at densities of 5.0 × 10¹ to 7.4 × 10⁵ CFU g^− 1, while it was not detected in the two analyzed egg specimens of Japanese flounder. These results indicate that L. anguillarum associated with the developing Japanese flounder is likely derived from rearing water and live diets such as rotifers. Further, it is strongly suggested that L. anguillarum is a transient bacterium of the intestinal microflora for the Japanese flounder but is a permanently indigenous one for the Japanese flounder hatcheries.     

Influences of Forest Decline on Various Properties of Soils at Mt. Hirugatake, Tanzawa Mountains, Kanto District, Japan

At Mt. Hirugatake in the Tanzawa Mountains, Kanto district, Japan, the deciduous broadleaved forests have rapidly declined. In our previous studies, we reported that the amount of soil organic matter had significantly decreased at the early and final stages of forest decline, and that the soil microbial biomass also showed a large decrease at these stages, suggesting that the composition of soil organic matter might have also changed with forest decline. To clarify the influences of forest decline on the composition of soil organic matter, the amount of humic substances, optical properties of humic acid, and the amount of soil carbohydrates in surface soils at different stages of forest decline were investigated. The amounts of humic acid and fulvic acid decreased to a lesser extent at the early and middle stages of forest decline, and showed a significant decrease at the final stage. As the amount of humin significantly decreased at the early stage, it was plausible that the distinct decrease in the total carbon content of the soil surface horizons at the early stage of forest decline was induced by the decrease in the amount of humin, and at the final stage, by the decrease in the amounts of humic acid and fulvic acid. The amount of soil carbohydrates did not change appreciably with forest decline although the soil organic matter content markedly decreased. It was suggested that most of the carbohydrates in the soil surface horizons were in a stabilized form consisting of complexes with humic substances, metals, and minerals, and would not be affected by the environmental changes associated with forest decline.