Accuracy of imputation of single nucleotide polymorphism marker genotypes from low‐density panels in Japanese Black cattle          下载免费PDF全文

Shinichiro Ogawa  Hirokazu Matsuda  Yukio Taniguchi  Toshio Watanabe  Akiko Takasuga  Yoshikazu Sugimoto  Hiroaki Iwaisaki 《Animal Science Journal》2016,87(1):3-12

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.  相似文献   

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

Imanishi S  Sugimoto M  Morita M  Kume S  Manabe N 《The Journal of reproduction and development》2007,53(5):1131-1136

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.  相似文献   

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

Ookawa K  Mochizuki K  Sugimoto Y  Suzuki T  Hashizume M  Kitagawa T  Matumoto T  Ito C  Yokogoshi H 《The Journal of veterinary medical science / the Japanese Society of Veterinary Science》2007,69(1):49-54

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.  相似文献   

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     

Takai S  Henton MM  Picard JA  Guthrie AJ  Fukushi H  Sugimoto C 《The Onderstepoort journal of veterinary research》2001,68(2):105-110

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.  相似文献   

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

Syakalima O  Choongo K  Nakazato Y  Onuma M  Sugimoto C  Tsubota T  Fukushi H  Yoshida M  Itagaki T  Yasuda J 《The Journal of veterinary medical science / the Japanese Society of Veterinary Science》2001,63(3):315-318

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.  相似文献   

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

Lee SI  Ohashi K  Sugimoto C  Onuma M 《The Journal of veterinary medical science / the Japanese Society of Veterinary Science》2001,63(4):427-432

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.  相似文献   

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

Kabeya H  Ohashi K  Sugimoto C  Onuma M 《Veterinary immunology and immunopathology》1999,68(1):39-48

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.  相似文献   

Establishment and characterization of a cell line from a chemically-induced mouse hepatoblastoma     

Kobayashi K  Sakairi T  Goto K  Tsuchiya T  Sugimoto J  Mutai M 《The Journal of veterinary medical science / the Japanese Society of Veterinary Science》2000,62(3):263-267

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Infection of bovine immunodeficiency virus and bovine leukemia virus in water buffalo and cattle populations in Pakistan     

Meas S  Seto J  Sugimoto C  Bakhsh M  Riaz M  Sato T  Naeem K  Ohashi K  Onuma M 《The Journal of veterinary medical science / the Japanese Society of Veterinary Science》2000,62(3):329-331

A survey of antibodies to bovine immunodeficiency virus (BIV) known as bovine lentivirus and bovine leukemia virus (BLV) was conducted with samples from water buffalo and cattle populations in Pakistan. A total of 370 water buffaloes and 76 cattle were tested, and 10.3% and 15.8%, respectively, were found positive for anti-BIV p26 antibodies determined by Western blotting, while 0.8% of water buffaloes and no cattle were positive for anti-BLV antibodies determined by immunodiffusion test. BIV-seropositive water buffaloes and cattle were found to have BIV proviral DNA in the peripheral blood mononuclear cells determined by nested polymerase chain reaction. This is the first report of BIV infections in water buffaloes.  相似文献   

Inheritance pattern of chloroplast and mitochondrial genomes in artificial hybrids of Porphyra yezoensis (Rhodophyta)     

Sung-Je Choi  Eun-Jeong Park  Hirotoshi Endo  Yukihiro Kitade  Naotsune Saga 《Fisheries Science》2008,74(4):822-829

ABSTRACT:   To investigate inheritance of chloroplasts and mitochondria (organelles) in the marine red alga Porphyra yezoensis , cleaved amplified polymorphic sequence (CAPS) profiles of the two strains, TU-2 and KGJ, as parental gametophytes and 44 hybrid sporophytes (i.e. female of TU-2 and male of KGJ) were examined. A carbamyl phosphate synthase small subunit gene ( carA ) and ribosomal protein S11 gene ( rps11 )-small subunit ribosomal RNA gene ( rns ) spacer region were used as molecular markers for the chloroplast and mitochondrial DNAs, respectively. Thirty-eight of 44 (86.4%) conchocelis colonies showed maternal banding patterns, five (11.4%) colonies showed biparental bands and one (2.2%) colony showed paternal bands in CAPS analyses both with chloroplast and mitochondrial markers. These results suggest that organelles of P. yezoensis are inherited uniparentally from the female parent.  相似文献