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.     

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.     

Therapeutic effect of anti-TNF-alpha antibody and levofloxacin (LVFX) in a mouse model of enterohemorrhagic Escherichia coli O157 infection

The ability of an anti-TNF-alpha antibody to confer protection against enterohaemorrhagic Escherichia coli (EHEC) O157 was investigated in germfree IQI mice. The use of an antibiotic levofloxacin (LVFX) alone or with the antibody was also studied. Protection included an increase in survival rate. Treatment with the anti-TNF-alpha antibody inhibited the histological signs associated with EHEC infection but did not prevent the colonization of EHEC or production of Shiga toxin (Stx). No clinical signs were observed and EHEC was completely eliminated in the mouse model receiving both anti-TNF-alpha antibody and LVFX. Anti-TNF-alpha antibody suppressed inflammatory cytokine response in the mouse kidney and brain by EHEC infection.     

Silicon content in rice seedlings to protect rice blast fungus at the nursery stage

To control rice blast effectively at the nursery stage, the absolute SiO₂ content necessary for rice plants to resist blast disease was investigated using various rice cultivars and soils. Nine rice cultivars with different complete resistance genes and different degrees of partial resistance were grown on nursery soils amended with silica gel at different rates to change the SiO₂ content of rice plant. The rice seedlings were then inoculated 28 days after sowing with Pyricularia grisea to estimate their blast resistance. In all rice cultivars, the number of lesions was significantly reduced when SiO₂ content increased in the rice seedling; lesions were reduced to 5%–20% of the number on the seedlings grown in soil without silica gel when the seedling SiO₂ content reached 5%. Additionally, the susceptibility to blast disease of rice seedlings grown on eight soils collected from different districts, with varying amounts of silica gel, was compared. The number of lesions decreased significantly when the SiO₂ content in the seedlings reached 5%. These results suggest that SiO₂ content of at least 5% in the rice plant can control this disease at the nursery stage under any conditions.     

Effects of 6-hydroxydopamine on the development of the immune system in chickens

It has been suggested that the sympathetic nervous system communicates with lymphocytes expressing cell surface receptors for neurotransmitters such as norepinephrine (NE), on the basis of the finding that neurotransmitters modify immune responses in mammalian species. We confirmed that chicken lymphocytes in the brusa of Fabricius, thymus and spleen expressed beta-adrenergic receptor (beta-AR) mRNA from embryonic day (E) 10 and that intracellular cAMP level was elevated by NE, suggesting that lymphocytes express functional beta-AR on their surface at an early embryonal stage. To clarify whether the nervous system is involved in the development of the immune system, the effects of 6-hydroxydopamine (6-OHDA), one of sympathectomizing agents, on chicken lymphocytes was investigated. A single injection of 6-OHDA at a dose of 400 microg into a chicken embryo was carried out at E7 or 14 (as referred to E7 group and E14 group, respectively). NE level and the relative proportion of Bu-1a(+), CD4(+) and CD8(+) cells in the spleen of 3-week-old chickens were not altered by 6-OHDA treatment. However, the proliferative responses and expression of IL-2 mRNA in spleen cells cultured with pokeweed mitogen were reduced in E7 group compared with those of control. Furthermore, in CD8(+) spleen cells of E14 group of 3-week-old chickens, the expression of beta-AR mRNA and the relative increase of intracellular cAMP stimulated with NE were significantly decreased. These results suggest that the sympathetic nervous system affects the development of the immune system.     

Protective effects of sugar cane extracts (SCE) on Eimeria tenella infection in chickens

The effects of oral administration of sugar cane extracts (SCE) on Eimeria tenella oocysts infection in chickens were studied with 2 different experiments. In Experiment 1, 3-week-old inbred chickens (MHC; H.B15) were inoculated into the crop with SCE (500 mg/kg/day) for 1 day or 3 consecutive days, and then challenged with E. tenella sporulated oocysts (2 x 10(4) cells/chicken). In Experiment 2, 1-week-old chickens were orally administered SCE at the same dose for 3 consecutive days, and then initially infected with E. tenella sporulated oocysts (2 x 10(3) cells/chicken). At 2 and 3 weeks of age, these chickens were immunized intravenously with the mixed antigens of sheep red blood cells (SRBC) and Brucella abortus (BA). At 4 weeks of age, chickens were challenged with E. tenella sporulated oocysts (1 x 10(5)/chicken). Challenged chickens with E. tenella oocysts showed markedly decreased body weight gain/day, severe hemorrhage and great number of shedding oocysts in feces and high lesion scores. Oral administration of SCE and initial infection with oocysts (2 x 10 (3)/chicken) resulted in a remarkable improvement in body weight gain/day, hemorrhage, the number of shedding oocysts and lesion score, compare to other infected groups. In addition, SCE-inoculated chickens with the initial infection showed a significant increase in antibody responses against SRBC and BA and also improvement in decreased relative proportions of Bu-1a(+) and CD4( )cells in cecal tonsil lymphocytes of E. tenella-challenged chickens. Cecal tissues of chickens administered SCE and initially infected with E. tenella oocysts showed lower numbers of schizonts, gametocytes and oocysts than those of infected control chickens. These results suggest that SCE have immunostimulating and protective effects against E. tenella infection in chickens.