Is single-step genomic REML with the algorithm for proven and young more computationally efficient when less generations of data are present?

Efficient computing techniques allow the estimation of variance components for virtually any traditional dataset. When genomic information is available, variance components can be estimated using genomic REML (GREML). If only a portion of the animals have genotypes, single-step GREML (ssGREML) is the method of choice. The genomic relationship matrix (G) used in both cases is dense, limiting computations depending on the number of genotyped animals. The algorithm for proven and young (APY) can be used to create a sparse inverse of G (GAPY~-1) with close to linear memory and computing requirements. In ssGREML, the inverse of the realized relationship matrix (H⁻¹) also includes the inverse of the pedigree relationship matrix, which can be dense with a long pedigree, but sparser with short. The main purpose of this study was to investigate whether costs of ssGREML can be reduced using APY with truncated pedigree and phenotypes. We also investigated the impact of truncation on variance components estimation when different numbers of core animals are used in APY. Simulations included 150K animals from 10 generations, with selection. Phenotypes (h² = 0.3) were available for all animals in generations 1–9. A total of 30K animals in generations 8 and 9, and 15K validation animals in generation 10 were genotyped for 52,890 SNP. Average information REML and ssGREML with G⁻¹ and GAPY~-1 using 1K, 5K, 9K, and 14K core animals were compared. Variance components are impacted when the core group in APY represents the number of eigenvalues explaining a small fraction of the total variation in G. The most time-consuming operation was the inversion of G, with more than 50% of the total time. Next, numerical factorization consumed nearly 30% of the total computing time. On average, a 7% decrease in the computing time for ordering was observed by removing each generation of data. APY can be successfully applied to create the inverse of the genomic relationship matrix used in ssGREML for estimating variance components. To ensure reliable variance component estimation, it is important to use a core size that corresponds to the number of largest eigenvalues explaining around 98% of total variation in G. When APY is used, pedigrees can be truncated to increase the sparsity of H and slightly reduce computing time for ordering and symbolic factorization, with no impact on the estimates.     

Pneumocystis carinii pneumonia in a Cavalier King Charles Spaniel

Pneumocystis carinii pneumonia was diagnosed by postmortem examination of a one-year-old Cavalier King Charles Spaniel with four-week history of dyspnea. Cytologic and histologic examination of lung tissues revealed numerous P. carinii trophozoites and cysts, and P. carinii specific DNA was detected by polymerase chain reaction. The dog showed hypogammagloblinemia and extremely low levels of serum IgG. It was considered that P. carinii pneumonia in this case was associated with an immunodeficient condition which has already been reported in Miniature Dachshunds.     

Molecular cloning of canine thymus and activation-regulated chemokine (TARC) gene and its expression in various tissues

Thymus and activation-regulated chemokine (TARC) is known as a functional ligand for CC chemokine receptor 4 (CCR4), which is selectively expressed on Th2 lymphocytes and induces selective migration of the cells to allergic lesions. In this study, we cloned canine TARC cDNA from canine thymus by RT-PCR with rapid amplification of cDNA ends (RACE) method. The canine TARC clone contained a full-length open reading frame encoding 99 amino acids and included four cysteine residues characteristic to CC chemokine family. The canine TARC cDNA showed 77.5%, 67.4%, and 68.5% amino acid sequence similarity with human, mouse and rat homologues, respectively. Expression of TARC mRNA was detected not only in thymus but also in spleen, lymph node, lung and heart of the various normal dog tissues examined. TARC cDNA clone obtained in this study will be useful for further investigation on allergic diseases in dogs.     

Genetic relationships of fertility traits with test‐day milk yield and fat‐to‐protein ratio in tropical smallholder dairy farms

The test‐day milk fat‐to‐protein ratio (TD‐FPR) could serve as a measure of energy balance status and might be used as a criterion to improve metabolic stability and fertility through genetic selection. Therefore, genetic parameters for fertility traits, test‐day milk yield (TD‐MY) and TD‐FPR, as well as, their relationships during different stages of lactation, were estimated on data collected from 25 968 primiparous Thai dairy crossbred cows. Gibbs sampling algorithms were implemented to obtain (co)variance components using both univariate linear and threshold animal models and bivariate linear‐linear and linear‐threshold animal models with random regression. Average TD‐MY and TD‐FPR were 12.60 and 1.15. Heritability estimates for TD‐MY, TD‐FPR and selected fertility traits ranged from 0.31 to 0.58, 0.17 to 0.19 and 0.02 to 0.05, respectively. Genetic correlations among TD‐FPR and TD‐MY, TD‐FPR and fertility traits, and TD‐MY and fertility traits ranged from 0.05 to ‐0.44, from ‐0.98 to 0.98 and ‐0.22 to 0.79, respectively. Selection for lower TD‐FPR would decrease numbers of inseminations per conception and increase conception at first service and pregnancy within 90 days. In addition, cow selection based only on high milk production has strong effects to prolong days to first service, days open and calving interval.     

Correction to: Dispersion and degradation of environmental DNA from caged fish in a marine environment

Fisheries Science - In the original publication the text in right column of page 330, the sequences of primers were incorrectly published as.     

Correction to: Prevention of hypermelanosis by rearing Japanese flounder Paralichthys olivaceus in net‑lined tanks

Fisheries Science - A correction to this paper has been published: https://doi.org/10.1007/s12562-021-01504-x     

Fire resistance of thick wood-based boards

Thick wood-based boards are used as construction materials for walls and floors in Japan. In this study, fire resistance tests (ISO 834-1) and cone calorimeter tests (ISO 5660-1) were conducted for thick plywood, particleboard, and medium density fiberboard with sample thicknesses of about 28–30mm, and their suitabilities for quasi-fireproof or fire-preventive structures were evaluated. In the ISO 834-1 fire resistance test, the heat-shielding performance (insulation criterion) for walls was evaluated and the results showed that the larger the apparent density of a woodbased board, the higher its insulation performance. The insulation performance of thick wood-based boards in the fire resistance test could be forecast from the results of the cone calorimeter test, especially when the second peak of heat release rate appeared. In the cone calorimeter tests, the surface layer density of the plywood, particleboard, and medium density fiberboard was the dominant parameter for the time to ignition and initial heat release rate. These results indicate that thick wood-based board is a suitable fire-preventive construction material. Part of this study was presented at the Annual Meeting of the Architectural Institute of Japan, Hokkaido, Japan, August 2004     

Kinetics of energy source utilization in Boophilus microplus (Canestrini, 1887) (Acari: Ixodidae) embryonic development

The present work evaluates the kinetics of utilization of the main potential energy sources throughout the embryonic developmental stages of Boophilus microplus. The embryonic development of this arthropod is completed in 21 days. Cellularization of the blastoderm occurs on the 6th day and is rapidly followed by germ band extension and segmentation, whose first signs are visible on the 7th day. Cellularization is typically a maternal-driven process, carried out by molecular determinants deposited in the oocyte during oogenesis. On the other hand, segmentation is of zygotic nature, being the consequence of the synthesis of various components by the growing embryo. The enhancement in total B. microplus RNA was observed after cellularization, corroborating the replacement of maternal-driven processes by embryonic zygotic expression. An abrupt increase in oxygen consumption was observed from cellularization until the 8th day of development. The reduction in dry weight at the same period and the susceptibility of oxygen consumption to KCN suggest that the respiration process is activated during early embryonic development. A marked decrease in total lipid content occurred between the 5th and 7th days of development, suggesting this is the main energy source for cellularization. A major reduction in carbohydrate content occurred later, between the 7th and 9th days, and it could be assigned to the morphological segmentation of the embryo. Although the total amount of proteins remains unchanged from oviposition to hatching, a 15% reduction in vitellin (VT) content was observed before cellularization, up to the 4th day after egglaying. This observation was correlated to the synthesis of new proteins needed to support early embryo development. Additional 20% of VT was consumed thereafter, mainly at the end of embryogenesis, and in this case VT is probably used as energy source to the older embryo. Altogether, these data indicate different energy sources for maternal and zygotic driven processes.     

Age-associated changes of flash visual evoked potentials in dogs

Age-associated changes of visual evoked potentials by flash stimulation (flash VEP) were evaluated in 53 beagle dogs aged from 1- to 15-year-old. Among the components of flash VEP consisted of 3 positive (P1, P2 and P3) and 2 negative (N1 and N2) peaks by 150 msec, the latency of P2 and the later peaks (N2 and P3) were significantly delayed with aging. Both amplitudes of the P2-N2 and N2-P3 also showed a significant correlation with aging. The flash VEP is considered to be an available and useful technique to evaluate not only for visual pathway, but also some disturbance of neurological functions, like as those reported in demented human.     

Characterization of monoclonal antibodies directed against the canine distemper virus nucleocapsid protein

We have established four monoclonal antibodies (MAbs) against the nucleocapsid protein (NP) of canine distemper virus (CDV). A competitive binding assay has revealed that the MAbs are directed against two antigenic domains. An immunofluorescence assay using a series of deletion clones of the NP and an immunoprecipitation assay using the NP have revealed that two of the MAbs recognize the C-terminal region of the NP while the other two recognize the tertiary structure of the N-terminal domain. These MAbs reacted with all eight strains of CDV used in this study, but showed different reactivities against measles virus and rinderpest virus.