Maternal effect on first-year growth of Hokkaido native foals kept outdoors all year round.

In this study, we investigated maternal effects on the growth of Hokkaido native horses kept outdoors throughout the year. We used the data on body weight (BW), height at withers (HW), heart girth (HG), and cannon circumference (CC) of 517 foals during the first year of life to (1) examine the growth patterns by comparing six linear mixed models and (2) analyze the maternal effect on BW, HW, HG, and CC for each month by estimating variance components. The segmented polynomial third-order regression equation was selected as the best model for all the traits. The estimated proportion of variance components for the effects of the dam were 0.25-0.38 for BW, 0.19-0.28 for HW, 0.19-0.34 for HG, and 0.10-0.21 for CC. A higher effect of the dam compared with that of the sire was observed on BW and HG at all months of age and HW at 0-2 months of age. Therefore, the dam contributed to foal growth not only through half of its heredity but also through the maternal effect derived mainly from its milk. These results provide valuable information for the breeding of Hokkaido native foals.

Changes of sires in a breeding farm enables maintenance of DNA-level genetic variation in a produced herd of Hokkaido Native Horses.

We investigated whether regular changes of the sire in a breeding farm of Hokkaido Native Horses (HKDs) enables the DNA-level genetic variation of the produced animals to be maintained. The genotypes of 31 microsatellite markers were identified and analyzed in 207 animals produced in a breeding farm in which the sire was replaced every 3 to 5 years. The mean allele number indicating the degree of genetic variation was 5.97 and was similar to those reported previously. The mean observed heterozygosity was 0.74 and was higher than the expected heterozygosity, 0.69; FIS was -0.07, indicating that the analyzed animals reflected frequent outbreeding and had maintained genetic variation. Based on genetic structural analysis, the number of genetic subpopulations of the animals was estimated to be as 6, and the majority (more than 50%) of each subpopulation corresponded to the progeny of one of the sires used in the breeding farm; these observations suggested that genetic variation in the analyzed animals reflected the genetic differences among sires. Pedigree records indicated that the average co-ancestry coefficient between sires used in the breeding farm was 0.015 corresponding to second cousin. This level of kinship among sires is acceptable for producing HKDs that maintain genetic variation.

A microarray-based comparative analysis of gene expression profiles in thyroid glands in amphibian metamorphosis: differences in effects between chemical exposure and food restriction.

Tadpoles during metamorphosis are sensitive to chemical exposure as shown in the amphibian metamorphosis assay, which is a method to detect effects of chemicals on the functions of hypothalamus-pituitary-thyroid axis. The present study reports existence of different modes of action between pyriproxyfen (PYR) and 6-propyl-2-thiouracil (PTU) under different feeding conditions based on gene expression profiles (transcriptomics) in the thyroid glands of tadpoles of the African clawed frog, Xenopus laevis. PTU and PYR were exposed to the tadpoles during metamorphosis under normal (fed groups, both of PTU and PRY) and restricted feeding (fasted groups, PTU only) conditions; and effects were compared to control groups. Delayed development based on decreased Nieuwkoop and Faber developmental stage number without any histopathological changes was observed in the control of restricted feeding (control-fasted) group, and the PYR group with reduced food consumption. Clear developmental retardation with typical thyroid histopathological changes was observed in the PTU groups. To find clusters of all samples based on their similarity of expression patterns, hierarchical clustering analysis using selected gene probes was conducted. It revealed gene profiles from samples of the PYR group were quite similar to those of the control-fasted group, followed by the control group with normal feeding (control-fed). The results suggest that key events in the thyroid glands of tadpoles induced by PYR should be quite similar to those of control-fasted, and quite different from those of the PTU groups. Our findings demonstrated the usefulness of transcriptomics, which enabled recognition of the different modes of actions.

Specific alteration of gene expression profile in rats by treatment with thyroid toxicants that inhibit thyroid hormone synthesis.

Transcriptomics technologies have been used for risk assessment of chemicals, mainly to predict the modes of action (MOAs) of chemicals or identify biomarkers. Transcriptomics data may also be helpful to understand MOAs of chemicals at the molecular level in more detail. As an example of the known MOAs, there are two MOAs of thyroid toxicity: inhibition of thyroid hormone synthesis ("direct" effect) and hypermetabolism of thyroid hormone by enzyme induction in liver ("indirect" effect). In the present study, global profiles of gene expression were analyzed in rats treated with chemicals acting directly on the thyroid (thyroid peroxidase inhibitors such as propylthiouracil and methimazole) and chemicals acting indirectly on the thyroid (hepatic enzyme inducers such as phenobarbital and pregnenolone-16α-carbonitrile) using microarrays. Using a subtraction method between these two types of chemicals, we identified characteristic gene expression changes on the thyroid hormone synthesis pathway by direct-acting chemicals. Based on the functions of these genes, alterations of their expression seem to indicate the results of thyroid peroxidase inhibition, and might be helpful in more accurate evaluation of MOAs for thyroid toxicity.

An improved model of predicting hepatocarcinogenic potential in rats by using gene expression data.

Carcinogenicity studies using animals are expensive and time consuming. Therefore, the development of a highly accurate carcinogenicity prediction system to interpret short-term test results would be beneficial. The Ames test is popular for mutagens; however, it cannot detect non-genotoxic carcinogens. Previously, we reported a prediction system using gene expression data obtained from a short-term (28-day) study that screened candidate compounds for testing in long-term carcinogenicity studies. In this study, our system was improved by adding more gene expression data. To establish our new system, we used the data of 93 test compounds (41 hepatocarcinogens and 52 non-hepatocarcinogens). Analysis of liver gene expression data by dividing compounds into 'for training' and 'for test' categories (20 cases assigned randomly) using Support Vector Machine (SVM) identified a set of marker probe sets that could be used to predict hepatocarcinogenicity. The assigned 42 probe sets have included the cancer- or c-Myc-related genes such as Hsp90, Pink1, Hspc111, Fbx29, Hepsin, Syndecan2 and Synbindin. Compared with the older version, the improved system had a higher concordance rate with the training data and a good performance with the external test data.

Toxicogenomics discrimination of potential hepatocarcinogenicity of non-genotoxic compounds in rat liver.

Long-term carcinogenicity testing of a compound is exceedingly time-consuming and costly, and requires many test animals, whereas the Ames test, which is based on the assumption that any substance that is mutagenic may also exert carcinogenic potential, is useful as a short-term screening assay but has major drawbacks. Although, in fact, 90% of compounds that give a positive Ames test cause cancer in laboratory animals, a good proportion of compounds that give a negative Ames test are also carcinogens; that is, there is no good correlation between carcinogenicity and negative Ames test results. As an alternative to these two approaches, we have tried applying toxicogenomics to predict the carcinogenicity of a compound from the gene expression profile induced in vivo. To establish our model, male Sprague-Dawley rats were orally administered test compounds (12 hepatocarcinogens and 26 non-hepatocarcinogens) for 28 days. Analysis of liver gene expression data by Support Vector Machines (SVM) dividing compounds into 'for training' and 'for test' (20 cases assigned randomly) allowed a set of marker genes to be tested for prediction of hepatocarcinogenicity. The developed prediction model was then validated with reference to the concordance rate with training data and test data, and a good performance was obtained. We will have new gene expression data and continue the validation of our model.