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.     

Identification of bovine serum albumin as an IgE-reactive beef component in a dog with food hypersensitivity against beef

IgE-reactive beef components were examined by an immunoblot analysis using a serum from a dog with food hypersensitivity against beef. The immunoblot analysis revealed a distinct band at approximately 66 kDa and a faint band at approximately 50 kDa. The immunoblot analysis for serum IgE reactivity to bovine serum albumin (BSA) also revealed a positive band at 66 kDa. Serum IgE reactivity to the 66-kDa protein of beef was diminished by pre-incubating the serum sample with BSA. Furthermore, a positive reaction to BSA was detected in intradermal testing in the dog. These results clearly indicated that BSA was an IgE-reactive beef component in the dog with food hypersensitivity against beef.     

Identification of oyster-derived hypotensive peptide acting as angiotensin-I-converting enzyme inhibitor

Angiotensin-I-converting enzyme (ACE) plays a crucial role in the crisis of hypertension. Some peptides that originate from protease hydrolysates are known to suppress ACE activity in vitro and in vivo. Here, we investigated whether trypsin hydrolysate of oyster Crassostrea gigas showed hypotensive activity and ACE inhibition. The hydrolysate significantly suppressed systolic blood pressure and ACE activity in spontaneously hypertensive rats following a one-shot oral administration and a long-term feeding experiment lasting 9 weeks. Each hydrolysate from oyster tissue showed ACE inhibitory activity, indicating the hypotensive effect was due to synergism. One potent ACE inhibitory peptide, Asp-Leu-Thr-Asp-Tyr, was identified from the hydrolysate of the striate muscle, and the peptide exhibited hypotensive activity in vivo. Protease digestion analysis suggested that Asp-Tyr could be the real effector of this penta-peptide in vivo.     

Effects of Aeration, Alum Treatment, Liming, and Organic Matter Application on Phosphorus Exchange between Soil and Water in Aquaculture Ponds at Auburn, Alabama

Application of readily-oxidizable organic substrate to laboratory soil-water systems and fish ponds caused anaerobic conditions in bottom soil and water, and concentrations of soluble reactive phosphorus (SRP) increased. Aeration of ponds increased total phosphorus (TP) concentrations by suspending soil particles in the water, but SRP concentrations declined because of increased oxy- genation of bottom water and soil, Alum [Al₂(SO₄)₃·14H₂O] treatment of ponds reduced SRP and TP concentrations in ponds, but the low concentration of alum used, 20 mg/L, had little residual effect on phosphorus concentration. Application of agricultural limestone at 0.2 kg/m² to ponds with soil pH of 5.5 and Ca²⁺ concentration of 5 mg/L did not affect SRP and TP concentration. Unless pond soils were anaerobic at their surfaces, a condition not acceptable in thermally-unstratified fish ponds, soils released little phosphorus to the water. Strong adsorption of phosphorus by soils in intensive ponds with feeding is beneficial, because removal of phosphorus by aerobic soils is a control on excessive phytoplankton growth. In fertilized ponds, phosphorus must be applied at frequent intervals to replace phosphorus removed from the water by soils.     

Improvement of preservation method for ammonia-oxidizing bacteria by freeze-drying

Long-term preservation of ammonia-oxidizing bacteria had been achieved until now by using the silica gel-freezing method. Recently, the freeze-drying method for the preservation of microorganisms has been widely used, and has been applied to the preservation of ammonia-oxidizing bacteria. The 10% skim milk-l% pyruvate or glutamate ratio was optimum as a dispersion-medium, and the preservation temperature of the freeze-dried cells was effective at -80°C. This method of preservation was found to be considerably more effective than the silica gel-freezing method.     

Molecular and sensory studies on the umami taste of Japanese green tea

Aimed at defining the key drivers for the quality-determining umami taste of a high-grade powdered green tea, called mat-cha, a bioactivity-guided fractionation using solvent extraction, solvent precipitation, preparative chromatographic separations, and human psychophysical experiments was applied on freshly prepared mat-cha. Liquid chromatography-tandem mass spectrometry and one-/two-dimensional nuclear magnetic resonance studies on isolated fractions led to the identification of l-theanine, succinic acid, 3,4,5-trihydroxybenzoic acid (gallic acid), and (1R,2R,3R,5S)-5-carboxy-2,3,5-trihydroxycyclohexyl-3,4,5-trihydroxybenzoate (theogallin) as umami-enhancing compounds in the green tea beverage, and it can be shown by sensory studies that these compounds are able to raise the umami intensity of sodium l-glutamate proportionally.     

Telomere length and telomerase activity in canine mammary gland tumors

OBJECTIVE: To measure telomere length and telomerase activity in naturally occurring canine mammary gland tumors. SAMPLE POPULATION: 27 mammary gland tumor specimens obtained during resection or necropsy and 12 mammary gland tissue specimens obtained from healthy (control) dogs. PROCEDURE: Telomere length in tissue specimens was measured by use of restriction endonuclease digestion and Southern blot analysis. Telomerase activity was measured by use of a telomeric repeat amplification protocol assay. RESULTS: Telomere length in mammary gland tumors ranged from 11.0 to 21.6 kilobase pairs (kbp; mean +/- SEM, 14.5+/-0.5 kbp) but did not differ among tumor types. Telomeres in mammary gland tumors were slightly shorter than in normal tissue specimens, but telomere length could not be directly compared between groups, because mean age of dogs was significantly different between groups. Age was negatively correlated with telomere length in control dogs but was not significantly correlated with length in affected dogs. Telomerase activity was detected in 26 of 27 mammary gland tumors and in 4 of 12 normal tissue specimens. However, telomerase activity and telomere length were not correlated in tumor specimens. CONCLUSIONS AND CLINICAL RELEVANCE: Telomere length is maintained in canine mammary gland tumors regardless of the age of the affected dog. Measurement of telomere length may be a useful tool for monitoring the in vivo effects of telomerase inhibitors in dogs with tumors.