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.     

Participation of specific PKC isozymes in the inhibitory effect of ET-1 on progesterone accumulation in cells isolated from early- and mid-phase corpora lutea

Expression of PKC alpha, beta I, beta II, epsilon and micro has been demonstrated in the whole bovine CL with PKC epsilon being differentially expressed as a function of development. In experiment 1 we have investigated the amount of mRNA encoding PKC epsilon at different stages of luteal development (days 1, 4, 10 and 17). In experiment 2, the cellular source of luteal PKC isozymes was determined. Enriched steroidogenic (SC) and endothelial (EC) cells from day-10 CL were used to examine this question by Western blot analysis and immuno-histochemistry. In experiment 3, Western blot analysis was used to examine the ability of ET-1 to activate luteal PKC isozymes in day-10 CL. In experiment 4, the role of luteal PKC isozymes in the ET-1 mediated inhibition of P(4) accumulation in steroidogenic cell cultures from day-4 and day-10 CL was examined. Abundance of PKC epsilon mRNA gradually increased from day-1 to -10 with no further increase on day-17. In experiment 2, PKC epsilon was exclusively detected in SC (LLC and SLC). In contrast, PKC alpha, beta I and beta II were detected in both SC and EC, with EC expressing higher amounts of PKC isozymes. In day-10 CL, ET-1 induced cellular redistribution of PKC alpha, beta I, epsilon but not beta II. Inhibitors specific for conventional PKC isozymes as well as PKC epsilon were able to negate the inhibitory effects of ET-1 on P4 accumulation in the day 10 CL. In the day-4 CL, the inhibitory effect of ET-1 might be mediated via conventional PKC. Thus, an exclusive presence of PKC epsilon in luteal steroidogenic cells, its higher expression along with the ability of ET-1 to stimulate its activation in day-10 CL strongly suggests that this PKC isoform may play an important regulatory role in decreasing P(4) during luteal regression. Inhibition of P(4) by ET-1 in the early CL may be mediated via conventional PKC isozymes.     

Two Hungarian isolates of cucumber mosaic virus from sweet pepper (Capsicum annuum) and melon (Cucumis melo): Identification and antiserum preparation

Two Hungarian virus isolates from sweet pepper (K8) and melon (S4) were identified as cucumber mosaic virus (CMV) on the basis of host plant reactions and serology. The isolates were purified and antisera prepared. Homologous antiserum titers in double-diffusion tests were 256 (K8) and 512 (S4). They were serologically closely related to each other and to other CMV isolates. On the basis of symptoms they belong to different symptomatological groups of CMV; this was supported by serological properties. Sedimentation coefficients were c. 93 S, at 2 mg ml^–1. Purified preparations, stained with 2% uranyl acetate, showed spherical particles. In ELISA purified preparations reacted with each other's antisera.Samenvatting Twee hongaarse virusisolaten uit paprika (K8) en meloen (S4) werden geïdentificeerd als komkommermozaïekvirus (CMV) met behulp van toetsplanten en serologie. Beide isolaten werden gezuiverd en er werden antisera tegen bereid. De homologe titers van de antisera in de agar-geldiffusietoets bedroegen 256 (K8) en 512 (S4). K8 en S4 waren serologisch nauw verwant aan elkaar, evenals aan andere CMV-isolaten. Op grond van hun symptomen op toetsplanten behoren ze tot verschillende symptomatologische groepen van CMV. Dit laatste werd gesteund door de serologische eigenschappen. Beide isolaten hebben een sedimentatiecoëfficiënt van ca 93 S, bij een concentratie van 2 mg ml^–1. Gezuiverde preparaten, gekleurd met 2% uranylacetaat, bleken bolvormige deeltjes te bevatten. In ELISA reageerden gezuiverde preparaten van K8 en S4 met elkaars antisera.     

Contamination of soil with Toxocara eggs in urban (Prague) and rural areas in the Czech Republic

Contamination of soil with feline and canine ascarid eggs in public parks, backyards and sand pits in Prague, Czech Republic was investigated in this work. Soil samples from shelters and rural areas were also collected. The comparison of soil from different areas (urban, rural, backyards and shelters) exhibited significant difference (chi(2)=32.16, d.f.=3 and p<0.0001). The highest rate of contamination (45%) was found in backyards inhabited by feral cats. The eggs of Toxocara spp. were found in 20.4% of parks, 10% of shelters and 5% of rural samples. Mean egg density per sample from Prague parks was 6.2 eggs/100g of soil. In 126 composite samples from children's and pits, the prevalence of Toxocara eggs was 11.90%. The number of eggs in positive samples varied from 2 to 22 (per 100g). A high proportion (46.9%) of eggs was fully embryonated. There was no difference between the sand pits with or without formal exclusion of dogs (chi(2)=0.6, d.f.=1 and p<0.0001).     

Arbovirus isolations from mosquitoes in South Slovakia.

In the years 1973 and 1975 mosquitoes and some other Diptera (Tabanidae, Simuliidae, Hippoboscidae) were tested for virus. 13,924 mosquitoes, 75 horseflies and 60 blackflies were processed in 1973. Five strains of Tahyna virus were isolated from mosquito species Aedes vexans. 3,378 mosquitoes and 12 sheep keds were tested for virus in 1975. Twelve strains of Calovo virus were isolated from Anopheles maculipennis and one strain of Tahyna virus was obtained from Aedes vexans mosquitoes.     

Molecular cloning and expression of kidney‐type glutaminase from common carp (Cyprinus carpio) and its up‐regulation by glutamine in primary culture enterocyte

Glutaminase (GLS) is the key enzyme of glutamine (Gln) metabolism and utilization. In this study, a cDNA encoding GLS protein was identified from common carp Cyprinus carpio intestine. The open reading frame of GLS cDNA encodes a polypeptide of 595 amino acids, which shows a high similarity with its zebrafish Danio rerio counterpart. Bioinformatic analysis showed the protein belongs to kidney‐type GLS. The putative protein has glutaminase domain and ankyrin repeats domain, which are highly conserved among vertebrate orthologues. Real‐time quantitative PCR analysis revealed that the abundance of GLS mRNA was the highest in the white muscle, followed by the brain, eyeball and pituitary. Glutaminase was ubiquitously expressed in all intestinal segments of common carp. The activity of GLS did not distribute uniformly along the entire length of the intestine. In primary culture enterocyte, and the expression of GLS mRNA is up‐regulated quickly and effectively by Gln.