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Amano T, Onogi A, Yamada F, Kawai M, Shirai K, Ueda J. Genome-wide association mapping and examination of possible maternal effect for the pace trait of horses. Anim Genet 2018; 49:461-463. [DOI: 10.1111/age.12711] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2018] [Indexed: 11/28/2022]
Affiliation(s)
- T. Amano
- Laboratory of Animal Genetics; Department of Sustainable Agriculture; College of Agriculture, Food and Environment Sciences; Rakuno Gakuen University; Hokkaido 069-0836 Japan
| | - A. Onogi
- Department of Agricultural and Environmental Biology; Graduate School of Agricultural and Life Sciences; The University of Tokyo; Tokyo 113-8657 Japan
| | - F. Yamada
- Field Science Center for Northern Biosphere; Hokkaido University; Hokkaido 056-0141 Japan
| | - M. Kawai
- Field Science Center for Northern Biosphere; Hokkaido University; Hokkaido 056-0141 Japan
| | - K. Shirai
- Hokkaido Native Horse Preservation Association; Hokkaido 063-0804 Japan
| | - J. Ueda
- Laboratory of Animal Genetics; Department of Sustainable Agriculture; College of Agriculture, Food and Environment Sciences; Rakuno Gakuen University; Hokkaido 069-0836 Japan
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Onogi A, Sasaki S, Kobayashi M, Ogino A, Nozaki T, Kurogi K, Yasumori T, Togashi K, Iwata H. A genetic analysis of meat compositions in Japanese Black cattle: Genetic parameters and sex influence. J Anim Breed Genet 2017; 134:373-382. [DOI: 10.1111/jbg.12280] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 04/05/2017] [Indexed: 01/22/2023]
Affiliation(s)
- A. Onogi
- Department of Agricultural and Environmental Biology; Graduate School of Agricultural and Life Sciences; The University of Tokyo; Tokyo Japan
| | - S. Sasaki
- Maebashi Institute of Animal Science; Livestock Improvement Association of Japan, Inc.; Maebashi Japan
| | - M. Kobayashi
- Maebashi Institute of Animal Science; Livestock Improvement Association of Japan, Inc.; Maebashi Japan
| | - A. Ogino
- Maebashi Institute of Animal Science; Livestock Improvement Association of Japan, Inc.; Maebashi Japan
| | - T. Nozaki
- Cattle Breeding Department (beef); Livestock Improvement Association of Japan, Inc.; Tokyo Japan
| | - K. Kurogi
- Maebashi Institute of Animal Science; Livestock Improvement Association of Japan, Inc.; Maebashi Japan
| | - T. Yasumori
- Cattle Breeding Department (beef); Livestock Improvement Association of Japan, Inc.; Tokyo Japan
| | - K. Togashi
- Cattle Breeding Department (beef); Livestock Improvement Association of Japan, Inc.; Tokyo Japan
| | - H. Iwata
- Department of Agricultural and Environmental Biology; Graduate School of Agricultural and Life Sciences; The University of Tokyo; Tokyo Japan
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Atagi Y, Onogi A, Kinukawa M, Ogino A, Kurogi K, Uchiyama K, Yasumori T, Adachi K, Togashi K, Iwata H. Genetic analysis of semen production traits of Japanese Black and Holstein bulls: genome-wide marker-based estimation of genetic parameters and environmental effect trends1. J Anim Sci 2017; 95:1900-1912. [DOI: 10.2527/jas.2016.1186] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Yamamoto E, Matsunaga H, Onogi A, Ohyama A, Miyatake K, Yamaguchi H, Nunome T, Iwata H, Fukuoka H. Efficiency of genomic selection for breeding population design and phenotype prediction in tomato. Heredity (Edinb) 2017; 118:202-209. [PMID: 27624117 PMCID: PMC5234485 DOI: 10.1038/hdy.2016.84] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 07/21/2016] [Accepted: 07/28/2016] [Indexed: 11/09/2022] Open
Abstract
Genomic selection (GS), which uses estimated genetic potential based on genome-wide genotype data for a breeding selection, is now widely accepted as an efficient method to improve genetically complex traits. We assessed the potential of GS for increasing soluble solids content and total fruit weight of tomato. A collection of big-fruited F1 varieties was used to construct the GS models, and the progeny from crosses was used to validate the models. The present study includes two experiments: a prediction of a parental combination that generates superior progeny and the prediction of progeny phenotypes. The GS models successfully predicted a better parent even if the phenotypic value did not vary substantially between candidates. The GS models also predicted phenotypes of progeny, although their efficiency varied depending on the parental cross combinations and the selected traits. Although further analyses are required to apply GS in an actual breeding situation, our results indicated that GS is a promising strategy for future tomato breeding design.
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Affiliation(s)
- E Yamamoto
- Vegetable Breeding and Genome Division, Institute of Vegetable and Tea Science, National Agriculture and Food Research Organization, Tsu, Mie, Japan
| | - H Matsunaga
- Vegetable Breeding and Genome Division, Institute of Vegetable and Tea Science, National Agriculture and Food Research Organization, Tsu, Mie, Japan
| | - A Onogi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, Japan
| | - A Ohyama
- Vegetable Production Technology Division, Institute of Vegetable and Tea Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - K Miyatake
- Vegetable Breeding and Genome Division, Institute of Vegetable and Tea Science, National Agriculture and Food Research Organization, Tsu, Mie, Japan
| | - H Yamaguchi
- Vegetable Breeding and Genome Division, Institute of Vegetable and Tea Science, National Agriculture and Food Research Organization, Tsu, Mie, Japan
| | - T Nunome
- Vegetable Breeding and Genome Division, Institute of Vegetable and Tea Science, National Agriculture and Food Research Organization, Tsu, Mie, Japan
| | - H Iwata
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, Japan
| | - H Fukuoka
- Vegetable Breeding and Genome Division, Institute of Vegetable and Tea Science, National Agriculture and Food Research Organization, Tsu, Mie, Japan
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Atagi Y, Onogi A, Kinukawa M, Ogino A, Kurogi K, Uchiyama K, Yasumori T, Adachi K, Togashi K, Iwata H. Genetic analysis of semen production traits of Japanese Black and Holstein bulls: genome-wide marker-based estimation of genetic parameters and environmental effect trends. J Anim Sci 2017. [DOI: 10.2527/jas2016.1186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Onogi A, Ogino A, Komatsu T, Shoji N, Shimizu K, Kurogi K, Yasumori T, Togashi K, Iwata H. Whole-genome prediction of fatty acid composition in meat of Japanese Black cattle. Anim Genet 2015; 46:557-9. [DOI: 10.1111/age.12300] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2015] [Indexed: 11/30/2022]
Affiliation(s)
- A. Onogi
- Department of Agricultural and Environmental Biology; Graduate School of Agricultural and Life Sciences; The University of Tokyo; Tokyo 113-8657 Japan
| | - A. Ogino
- Maebashi Institute of Animal Science; Livestock Improvement Association of Japan, Inc.; Maebashi 371-0121 Japan
| | - T. Komatsu
- Agricultural Research Center; Ipponmatsu Torigoe Shinjo Yamagata 996-0041 Japan
| | - N. Shoji
- Agricultural Research Center; Ipponmatsu Torigoe Shinjo Yamagata 996-0041 Japan
| | - K. Shimizu
- Maebashi Institute of Animal Science; Livestock Improvement Association of Japan, Inc.; Maebashi 371-0121 Japan
| | - K. Kurogi
- Maebashi Institute of Animal Science; Livestock Improvement Association of Japan, Inc.; Maebashi 371-0121 Japan
| | - T. Yasumori
- Cattle Breeding Department (beef); Livestock Improvement Association of Japan, Inc.; Tokyo 135-0041 Japan
| | - K. Togashi
- Cattle Breeding Department (beef); Livestock Improvement Association of Japan, Inc.; Tokyo 135-0041 Japan
| | - H. Iwata
- Department of Agricultural and Environmental Biology; Graduate School of Agricultural and Life Sciences; The University of Tokyo; Tokyo 113-8657 Japan
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Onogi A, Ogino A, Komatsu T, Shoji N, Simizu K, Kurogi K, Yasumori T, Togashi K, Iwata H. Genomic prediction in Japanese Black cattle: application of a single-step approach to beef cattle. J Anim Sci 2015; 92:1931-8. [PMID: 24782393 DOI: 10.2527/jas.2014-7168] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The implementation of genomic selection for Japanese Black cattle, known for rich marbling of their meat, is now being explored. Although multiple-step methods are often adopted for dairy cattle, they present shortcomings such as bias and loss of information in addition to operational complexity. These can be avoided using single-step genomic BLUP (ssGBLUP) based on the relationship matrix H, which is constructed from the numerator relationship matrix (A) augmented by the genomic relationship matrix (G). This study assessed the use of ssGBLUP for 3 economically important traits in Japanese Black cattle. Three aspects of ssGBLUP that are important for practical use were examined specifically: the mixing proportions of blending G with A, selection of subsets of genotyped animals used for constructing H, and prediction ability for ungenotyped animals. Different mixing proportions were tested to assess the influence of these proportions on variance component estimation and prediction accuracy. For all traits, the highest or nearly highest accuracy was obtained when the adopted mixing proportion provided heritability closest to that inferred based on A. However, the accuracy did not increase greatly under adjustment of the mixing proportion, thereby suggesting that the influence of the mixing proportion on the accuracy was limited. Genotype data of influential bulls showed a greater contribution to accuracy than that of bulls that were less influential. Genotyping animals with phenotypic records increased the accuracy. It can be prioritized over genotyping bulls that are not influential on the population. These results are expected to present good guides to the future expansion of genotyped populations. Even for animals without genotype data but with genotyped sires, ssGBLUP provided more accurate prediction than BLUP did. For both phenotype and breeding value prediction, ssGBLUP provides more accurate prediction than BLUP, suggesting its usefulness in genomic selection in Japanese Black cattle.
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Affiliation(s)
- A Onogi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
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Onogi A, Ogino A, Komatsu T, Shoji N, Simizu K, Kurogi K, Yasumori T, Togashi K, Iwata H. Genomic prediction in Japanese Black cattle: application of a single-step approach to beef cattle. J Anim Sci 2014. [DOI: 10.2527/jas.2013-7168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Oku H, Matsumoto T, Saeki A, Kawamata Y, Chien H, Onogi A, Ikuma K. Bottom-Up Suture in Laparoscopic Myomectomy. J Minim Invasive Gynecol 2011. [DOI: 10.1016/j.jmig.2011.08.318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Onogi A, Naruse K, Sado T, Tsunemi T, Shigetomi H, Noguchi T, Yamada Y, Akasaki M, Oi H, Kobayashi H. Hypoxia inhibits invasion of extravillous trophoblast cells through reduction of matrix metalloproteinase (MMP)-2 activation in the early first trimester of human pregnancy. Placenta 2011; 32:665-670. [PMID: 21764444 DOI: 10.1016/j.placenta.2011.06.023] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 06/10/2011] [Accepted: 06/27/2011] [Indexed: 12/25/2022]
Abstract
During early pregnancy, extravillous trophoblast (EVT) cells are exposed to very low pO(2) values. In this study, we investigated the proteolytic functions and invasiveness of human primary EVT cells under hypoxic conditions to show the early placental pathophysiology. Placental samples (from 5 to 10 weeks gestation) were obtained at termination of pregnancy. Cytotrophoblast cells were separated by Percoll(®) gradient method and cultured on Matrigel(®) to obtain an invasive phenotype (similar to EVT). The invasion capacity (Matrigel-coated invasion assay), migration of the cells (wound healing assay), activity and expression of matrix metalloproteinase (MMP)-2 and tissue inhibitor for MMP (TIMP)-2 (gelatin gel zymography, ELISA, and quantitative RT-PCR), and expression of membrane-type (MT)1-MMP (western blot) were investigated. All cultures (except for quantitative RT-PCR) were performed under 20% oxygen, 5% oxygen, and 5% oxygen with 3 repetitions of 0.1% oxygen hypoxic stimulation for 1 h. Invasion and MMP2 activity of the cells were significantly increased in 20% and decreased in 0.1% oxygen. There was no significant difference in cell migration among the oxygen environments. Concentrations of MMP2 in the supernatant and expression of MT1-MMP were increased in both the 0.1% and 20% oxygen environments. The MMP2 mRNA level was increased after 1-h stimulation with 0.1% oxygen. The TIMP2 concentration was increased only in 20% oxygen, but the mRNA level was decreased in 0.1% oxygen. These results suggested that hypoxia might inhibit the invasive capacity and MMP2 activation of EVT cells in the early first trimester of pregnancy. Decrease in TIMP2 production may reduce the MMP2/TIMP2/MT1-MMP complex and lead to this unique behavior of EVT cells under hypoxic conditions.
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Affiliation(s)
- A Onogi
- Department of Obstetrics and Gynecology, Nara Medical University, 840, Shijo-cho, Kashihara City, 6348521 Nara, Japan
| | - K Naruse
- Department of Obstetrics and Gynecology, Nara Medical University, 840, Shijo-cho, Kashihara City, 6348521 Nara, Japan.
| | - T Sado
- Department of Obstetrics and Gynecology, Nara Medical University, 840, Shijo-cho, Kashihara City, 6348521 Nara, Japan
| | - T Tsunemi
- Department of Obstetrics and Gynecology, Nara Medical University, 840, Shijo-cho, Kashihara City, 6348521 Nara, Japan
| | - H Shigetomi
- Department of Obstetrics and Gynecology, Nara Medical University, 840, Shijo-cho, Kashihara City, 6348521 Nara, Japan
| | - T Noguchi
- Department of Obstetrics and Gynecology, Nara Medical University, 840, Shijo-cho, Kashihara City, 6348521 Nara, Japan
| | - Y Yamada
- Department of Obstetrics and Gynecology, Nara Medical University, 840, Shijo-cho, Kashihara City, 6348521 Nara, Japan
| | - M Akasaki
- Department of Obstetrics and Gynecology, Nara Medical University, 840, Shijo-cho, Kashihara City, 6348521 Nara, Japan
| | - H Oi
- Department of Obstetrics and Gynecology, Nara Medical University, 840, Shijo-cho, Kashihara City, 6348521 Nara, Japan
| | - H Kobayashi
- Department of Obstetrics and Gynecology, Nara Medical University, 840, Shijo-cho, Kashihara City, 6348521 Nara, Japan
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Tanase Y, Morioka S, Niiro E, Onogi A, Shigetomi H, Kawaguchi R, Yoshida S, Furukawa N, Yamada Y, Oi H, Kobayashi H. Atypical Endometriosis of the Ovary: A Description of 2 Cases Treated with Laparoscopic Surgery and Review of the Literature. J Minim Invasive Gynecol 2010. [DOI: 10.1016/j.jmig.2010.08.490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Naruse K, Onogi A, Noguchi T, Sado T, Kitanaka T, Oi H, Kobayashi H. Invasive activities of primary extravillous trophoblast via altered proteinases activity in low oxygen condition. J Reprod Immunol 2010. [DOI: 10.1016/j.jri.2010.06.133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Tanase Y, Komeda S, Onogi A, Kanayama S, Yoshida S, Furukawa N, Yamada Y, Oi H, Kobayashi H. A Rare Case of Huge Ovarian Teratoma Mimicking Omental Cyst Treated with Laparoscopic Surgery. J Minim Invasive Gynecol 2009. [DOI: 10.1016/j.jmig.2009.08.311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Abstract
INRA21 is one of the canine microsatellites recommended for parentage verification by the International Society for Animal Genetics. In Labrador Retrievers, abnormal peak patterns such as three-peak patterns during capillary electrophoresis were frequently observed at INRA21. Pedigree analysis indicated that the abnormal peak patterns were due to inheritable causes, and semiquantitative multiplex (SQM) PCR analysis showed that the abnormal peak patterns were caused by chromosomal duplication. Walking SQM-PCR analysis revealed that the size of the duplicated segment was approximately 1.58 Mb. Genotypes of microsatellites within the duplicated segment indicated that the duplication was an identical-by-descent mutation. This duplication is probably carried by more than half of the dogs in the Japanese population of Labrador Retrievers. The abnormal peak patterns at INRA21 were also observed in German Shorthaired Pointers and Flat-Coated Retrievers. Genotyping analysis of the microsatellites within the duplicated segment in Labrador Retrievers suggested that the abnormal peak patterns observed in the two breeds were due to the duplication inherited from the same ancestor as the duplication of Labrador Retrievers. This study urges attention to the use of INRA21 and shows an example of copy number polymorphisms that are characteristic to dog breeds or lineages.
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Affiliation(s)
- A Onogi
- Maebashi Institute of Animal Science, Livestock Improvement Association of Japan, Inc., Maebashi 371-0121, Japan.
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Nurimoto M, Yoneda K, Onogi A, Kozono Y, Kimura H, Morita M. Two non-amplified alleles at the canine microsatellite AHTh171 locus due to a single nucleotide transition in the primer-binding region. Anim Genet 2005; 36:281-2. [PMID: 15932427 DOI: 10.1111/j.1365-2052.2005.01297.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M Nurimoto
- Maebashi Institute of Animal Science, Livestock Improvement Association of Japan, Inc., Maebashi 371-0121, Japan.
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Nakatsu Y, Yamada K, Ueda J, Onogi A, Ables GP, Nishibori M, Hata H, Takada A, Sawai K, Tanabe Y, Morita M, Daikohara M, Watanabe T. Genetic polymorphisms and antiviral activity in the bovine MX1 gene. Anim Genet 2004; 35:182-7. [PMID: 15147388 DOI: 10.1111/j.1365-2052.2004.01125.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bovine MX1 cDNAs consisting of 2280 bp from 11 animals of five breeds and from a cultured cell line were sequenced and compared with previously reported data. Ten nucleotide substitutions were synonymous mutations, and a single nucleotide substitution at 458 resulted in an amino acid exchange of Ile (ATT) and Met (ATG). A 13-bp deletion-insertion mutation was also found in the 3'-UTR. Based on the nucleotide substitutions found in this study, bovine MX1 cDNA was classified into 11 genotypes. A phylogenetic tree of the 11 genotypes suggested that the genotypes observed in Brahman were a great genetic distance from other genotypes. An 18-bp deletion-insertion variation at position 171 was found to be the result of alternative splicing. The 18-bp deletion-insertion is located at the boundary between exon 3 and intron 3. Permanently transfected 3T3 cell lines expressing bovine MX1 mRNA were established to analyse the antiviral potential against VSVDeltaG*-G infection. Transfected cell clones expressing bovine MX1 mRNA showed a significantly smaller number of cells infected with VSVDeltaG*-G compared with the control cells. These results indicate that the bovine MX1 protein has potent antiviral activity.
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Affiliation(s)
- Y Nakatsu
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
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