Accuracy of imputation of single nucleotide polymorphism marker genotypes from low‐density panels in Japanese Black cattle

Using target and reference fattened steer populations, the performance of genotype imputation using lower‐density marker panels in Japanese Black cattle was evaluated. Population imputation was performed using BEAGLE software. Genotype information for approximately 40 000 single nucleotide polymorphism (SNP) markers by Illumina BovineSNP50 BeadChip was available, and imputation accuracy was assessed based on the average concordance rates of the genotypes, varying equally spaced SNP densities, and the number of individuals in the reference population. Two additional statistics were also calculated as indicators of imputation performance. The concordance rates tended to be lower for SNPs with greater minor allele frequencies, or those located near the ends of the chromosomes. Longer autosomes yielded greater imputation accuracies than shorter ones. When SNPs were selected based on linkage disequilibrium information, relative imputation accuracy was slightly improved. When 3000 and 10 000 equally spaced SNPs were used, the imputation accuracies were greater than 90% and approximately 97%, respectively. These results indicate that combining genotyping using a lower‐density SNP chip with genotype imputation based on a population of individuals genotyped using a higher‐density SNP chip is a cost‐effective and valid approach for genomic prediction.     

The organic acid profiles in the feces of pigs at Brachyspira hyodysenteriae- or B. pilosicoli-positive farms

We observed a significant difference in the organic acid profile of diarrheal feces between pigs infected with and free from pathogenic spirochetes. Diarrhea and loose feces were collected from growing pigs, held at 15 different commercial farms. A total of 106 samples were measured for organic acid concentration by HPLC and were checked for the presence of B. hyodysenteriae and B. pilosicoli by PCR. B. hyodysenteriae was detected in 3 samples collected from one farm. B. pilosicoli was detected in 5 samples collected from another farm. Lower concentrations of iso-butyrate and iso-valerate were likely associated with development of pathogenic spirochete infection.     

Changes in expression and localization of GPRC5B and RARalpha in the placenta and yolk sac during middle to late gestation in mice

The mRNA expression of GPRC5B, an orphan G protein-coupled receptor, is induced by retinoic acid (RA). Because RA plays critical roles in embryonic development, reproductive functions, metabolism and homeostasis, GPRC5B is also considered crucial in these physiological events. We investigated the changes in expression of GPRC5B and RA receptor (RAR) alpha mRNAs and immunohistochemical localization of their proteins in the murine placenta and yolk sac at 13.5, 15.5 and 17.5 days post coitus. Stable levels of GPRC5B and RARalpha mRNAs were detected in the placenta and yolk sac. In the placenta, GPRC5B was present in maternal and fetal vascular endothelial cells, stromal cells, fibroblast-like cells and glycogen cells. A strong reaction to RARalpha was detected in maternal and fetal vascular endothelial cells and stromal cells. The levels of GPRC5B and RARalpha proteins in maternal and fetal vascular endothelial cells decreased with gestation. In the yolk sac, GPRC5B and RARalpha proteins were detected in vascular endothelial cells, but their levels did not change during the gestation period. These findings indicate that GPRC5B is involved in RA-dependent morphogenesis/angiogenesis and regulation of extracellular matrix synthesis in the murine placenta and yolk sac.     

Effect of ovary lipid of skipjack tuna on rat serum components after stress application

Lipid extracted from the ovary of skipjack tuna by the method that we developed is rich in phospholipid-type docosahexaenoic acid. The ovary lipid of skipjack tuna (OLS) was studied for its anti-stress activity in male Wistar rats, focusing on stress-related blood components: recovery from stress was examined after application of water immersion restraint stress. As a result, serum corticosterone (CORT) secretion was inhibited and decreased rapidly after stress application in rats given OLS compared with control rats. As CORT acts as a glucocorticoid, non-esterified fatty acid (NEFA) is expected to increase by stress application. However, the concentration tended to be lower in rats given OLS than in control rats. With respect to OLS concentration, OLS increased serum dehydroepiandrosterone, secretion concentration-dependently. In addition, as with the recovery study, it tended to inhibit the increase in NEFA. These results indicate that OLS may have an anti-stress activity against acute stress.     

Rice cultivation and its environmental conditions in the mediterranean countries I. Climate and physiography in relation to rice cultivation

In order to characterize the rice cultivation in the Mediterranean countries, climate and physiography of rice growing areas in Italy, Spain, and Portugal were studied. In northern Italy rice is extensively cultivated on terraces and fluvial plains of the Po and its tributaries, making use of the supply of water from Alpine glaciers in addition to the relatively abundant rainfalls of the area. In the Iberian peninsula summer climate is so dry that rice is cultivable only where the ratio of catchment area to rice land area is sufficiently large, thus rice lands are practically limited to the floodplains and deltas of the big rivers, such as the Sado and the Tejo in Portugal and the Guadalquivir and the Ebro in Spain.

In order to characterize the rice cultivation in the Mediterranean countries, climate and physiography of rice growing areas in Italy, Spain, and Portugal were studied. In northern Italy rice is extensively cultivated on terraces and fluvial plains of the Po and its tributaries, making use of the supply of water from Alpine glaciers in addition to the relatively abundant rainfalls of the area. In the Iberian peninsula summer climate is so dry that rice is cultivable only where the ratio of catchment area to rice land area is sufficiently large, thus rice lands are practically limited to the floodplains and deltas of the big rivers, such as the Sado and the Tejo in Portugal and the Guadalquivir and the Ebro in Spain.     

Iron uptake in a bicarbonate-resistant cell line of tobacco

Abstract

In alkaline soils, plant growth is impaired mainly by high pH and high concentration of bicarbonates. The bicarbonate concentration increases the pH value, and causes deficiency of iron. A bicarbonate-resistant cell line (BR line) of tobacco (Nicotiana tabacum L. cv. Burley21) was selected by adding excess bicarbonate ions (20 mmol L^?1) to the culture medium. The pH of the medium was buffered 8.0 to 8.3. Under these conditions, about 80% of iron in the medium became insoluble. However, under such conditions, the BR line grew well. In this report, we examined some characteristics of the growth and iron uptake in the BR line under iron-deficient (i.e. high pH or no-iron) condition. At pH 5.8, the Fe³⁺ reduction activity was not significantly different between the non-selected line and the BR line. At pH 8.0, however, the Fe³⁺ reduction activity of the BR line was higher than that of the non-selected line. In no-iron condition, the growth of the non-selected line was markedly reduced after 2 weeks, while the BR line was not affected. The content of malic acid in both lines increased with the medium pH, and the content in the BR line was higher than that in the non-selected line. The BR line was able to adapt to the conditions, which restricted iron uptake, such as high bicarbonate concentration, high pH, and low iron conditions. The high ability of Fe³⁺ reduction was maintained at even high pH conditions. Further, the BR line may be able to improve the utilization of iron in the cells.     

Prevalence of virulent Rhodococcus equi in isolates from soil collected from two horse farms in South Africa and restriction fragment length polymorphisms of virulence plasmids in the isolates from infected foals, a dog and a monkey

The prevalence of virulent Rhodococcus equi in soil isolates from two horse farms in South Africa and nine clinical isolates from six foals, a foal foetus, a dog, and a monkey was investigated. The isolates were tested for the presence of virulence plasmid DNA and 15- to 17-kDa antigens by immunoblotting. Rhodococcus equi was isolated from almost all of the soil samples obtained from the two farms with 5.0 x 10(1) to 3.3 x 10(4) colony forming units per gram of soil. Virulent R. equi was isolated from three soil samples from one of the farms and appeared in 3.8% (three of 80 isolates), but not in any of the 182 isolates from the other farm. Of the three virulent R. equi isolates, one contained an 85-kb type I plasmid and two an 87-kb type I plasmid. Of nine clinical isolates from the foals, foal foetus, dog and monkey, five from the foals were virulent R. equi which expressed the virulence-associated antigens and contained a virulence plasmid 85-kb type I, and were all isolated from cases of pneumonia typical of that induced by R. equi in young foals living in widely separated areas in South Africa. The isolates from the other four foals, the dog and the monkey were avirulent R. equi.     

An investigation of heavy metal exposure and risks to wildlife in the Kafue flats of Zambia

Exposure and ecological risks to heavy metals (copper, zinc, manganese, iron) at Lochnivar and Blue Lagoon National Parks in wildlife dependent on the Kafue river contaminated with mining waste was evaluated. Samples included water, fish, grasses and Kafue Lechwe (Kobus leche kafuensis) liver. At both parks copper ranged from 0.03-0.04 mg/l; 3.0-6.0 mg/kg; 11.0-44.0 mg/kg; trace -199.0 mg/kg; while zinc was 0.01 mg/l; 32.0-82.0 mg/kg; 15.0-21.0 mg/kg; and 52.0-138.0 mg/kg; in water, fish, grasses and lechwe, respectively. Manganese ranges were 0.15-0.16 mg/l; 7.0-18.0 mg/kg; 51.0-145.0 mg/kg; and 40.0-53.0 mg/kg while iron ranges were 0.13-0.14 mg/l; 26.0-134.0 mg/kg; 1766.0-1797.0 mg/kg; and 131.0-856.0 mg/kg; in water, fish, grasses and lechwe, respectively. Levels in all samples except water were high indicating potential for adverse effects.     

Heparin inhibits plaque formation by cell-free Marek's disease viruses in vitro

The mechanisms of Marek's disease virus (MDV) entry to host cells have not yet been analyzed. Heparan sulfate (HS) on the cell surface serves as a receptor for several herpesviruses in mammalian species. In this study, we demonstrated that plaque formation by cell-free MDV is inhibited by the addition of soluble heparin to the cell culture. Moreover, pretreatment of susceptible cells, chicken embryo fibroblasts, with heparinase, partially reduced infectivity of the cell-free MDV. From these results, it was suggested that the MDV entry, at least in the case of cell-free MDV, is dependent on the presence of cell surface glycosaminoglycans, principally HS.     

Bovine leukaemia virus envelope peptides cause immunomodulation in BALB/c mice

Immunomodulatory activity of two bovine leukaemia virus envelope (BLVEnv) derived peptides were examined in BALB/c mice. One is peptide homologous to CKS-17 which is known as a 17-amino acid peptide derived from p15E of feline leukaemia virus (CKS-17/BLV), and the other is an 18-amino acid synthetic peptide of BLV Env 61-78 (pep61). Priming with CKS-17/BLV in vitro, as well as CKS-17, significantly suppressed the mitogen-induced proliferative responses of spleen cells in naive BALB/c mice. In addition, priming of spleen cells with pep61 in vitro and in vivo resulted in suppression of lipopolysaccaride-induced B-cell proliferative response. This suppression was partially due to the basic amino acid sequence in the peptide because if the pep61-derived peptide lacking Arg was used, this inhibitory activity was partially restored. In contrast, pep61 enhanced both concanavalin A-stimulated proliferative response and IL-2 production. These findings showed that pep61 may contribute to the modification of the host immune responses in the course of BLV infection.