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Wu Z, Dou T, Bai L, Han J, Yang F, Wang K, Han X, Qiao R, Li XL, Li XJ. Genomic prediction and genome-wide association studies for additive and dominance effects for body composition traits using 50 K and imputed high-density SNP genotypes in Yunong-black pigs. J Anim Breed Genet 2024; 141:124-137. [PMID: 37822282 DOI: 10.1111/jbg.12830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/13/2023]
Abstract
Body composition traits are complex traits controlled by minor genes and, in hybrid populations, are impacted by additive and nonadditive effects. We aimed to identify candidate genes and increase the accuracy of genomic prediction of body composition traits in crossbred pigs by including dominance genetic effects. Genomic selection (GS) and genome-wide association studies were performed on seven body composition traits in 807 Yunong-black pigs using additive genomic models (AM) and additive-dominance genomic models (ADM) with an imputed high-density single nucleotide polymorphism (SNP) array and the Illumina Porcine SNP50 BeadChip. The results revealed that the additive heritabilities estimated for AM and ADM using the 50 K SNP data ranged from 0.20 to 0.34 and 0.11 to 0.30, respectively. However, the ranges of additive heritability for AM and ADM in the imputed data ranged from 0.20 to 0.36 and 0.12 to 0.30, respectively. The dominance variance accounted for 23% and 27% of the total variance for the 50 K and imputed data, respectively. The accuracy of genomic prediction improved by 5% on average for 50 K and imputed data when dominance effect were considered. Without the dominance effect, the accuracies for 50 K and imputed data were 0.35 and 0.38, respectively, and 0.41 and 0.43, respectively, upon considering it. A total of 12 significant SNP and 16 genomic regions were identified in the AM, and 14 significant SNP and 21 genomic regions were identified in the ADM for both the 50 K and imputed data. There were five overlapping SNP in the 50 K and imputed data. In the AM, a significant SNP (CNC10041568) was found in both body length and backfat thickness traits, which was in the PLAG1 gene strongly and significantly associated with body length and backfat thickness in pigs. Moreover, a significant SNP (CNC10031356) with a heterozygous dominant genotype was present in the ADM. Furthermore, several functionally related genes were associated with body composition traits, including MOS, RPS20, LYN, TGS1, TMEM68, XKR4, SEMA4D and ARNT2. These findings provide insights into molecular markers and GS breeding for the Yunong-black pigs.
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Affiliation(s)
- Ziyi Wu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Tengfei Dou
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Liyao Bai
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Jinyi Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Feng Yang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xiu-Ling Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xin-Jian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
- Sanya Institute, Hainan Academy of Agricultural Science, Sanya, Hainan, China
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Song C, Zhang Z, Wei Y, Dou Y, Qi K, Li X, Yang F, Li X, Wang K, Qiao R, Han X. Proteomic analysis of boar sperm with differential ability of liquid preservation at 17 °C. Theriogenology 2024; 215:103-112. [PMID: 38029685 DOI: 10.1016/j.theriogenology.2023.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 12/01/2023]
Abstract
Understanding the liquid preservation ability of boar sperm is pivotal for efficient management and breeding of livestock. Although sperm proteins play an important role in semen quality and freezability, how the levels of protein change in boar sperm with different liquid preservation abilities at 17 °C remains unclear. In this study, two groups of boar sperm with extreme difference in liquid preservation ability, namely the good preservation ability (GPA) and the poor preservation ability (PPA) groups, were selected by evaluating sperm motility parameters on the 7th day of liquid preservation at 17 °C. Quantitative proteomics based on tandem mass tag (TMT) labeling was used, sperm proteomic characteristics from two groups were analyzed, and potentially key proteins related to the fluid preservation ability of sperm were identified. A total of 187 differentially expressed proteins (DEPs) were identified among 2791 quantified proteins, including 85 upregulated, and 102 downregulated proteins. Further, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of the DEPs revealed that they were enriched in GO terms associated with response to oxidative stress, enzyme activity related to oxidative stress or redox reactions, and several metabolic activities. The significant KEGG pathways included peroxisome, metabolic pathways, selenocompound metabolism, and collection duct acid secretion. In addition, analysis of protein-protein interactions further identified 8 proteins that could be used as biomarker candidates, including GPX5, GLRX, ENO4, QPCT, BBS7, OXSR1, DHRS4 and AP2S1, which may play an essential role in indicating the liquid preservation ability of boar sperm. These findings in this study provide new insights into the underlying molecular mechanisms of the liquid preservation ability of boar sperm. Moreover, the selected candidate proteins can serve as a reference for evaluating sperm quality or preservation ability in boars and their application in related biotechnologies.
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Affiliation(s)
- Chenglei Song
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zhe Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yilin Wei
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yaqing Dou
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Kunlong Qi
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xiuling Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Feng Yang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xinjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.
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Zheng L, Shi L, Wu X, Hu P, Zhang B, Han X, Wang K, Li X, Yang F, Wang Y, Li X, Qiao R. Advances in Research on Pig Salivary Analytes: A Window to Reveal Pig Health and Physiological Status. Animals (Basel) 2024; 14:374. [PMID: 38338017 PMCID: PMC10854898 DOI: 10.3390/ani14030374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Saliva is an important exocrine fluid that is easy to collect and is a complex mixture of proteins and other molecules from multiple sources from which considerable biological information can be mined. Pig saliva, as an easily available biological liquid rich in bioactive ingredients, is rich in nucleic acid analytes, such as eggs, enzymes, amino acids, sugars, etc. The expression levels of these components in different diseases have received extensive attention, and the analysis of specific proteins, metabolites, and biological compositions in pig saliva has become a new direction for disease diagnosis and treatment. The study of the changes in analytes in pig saliva can provide a new strategy for early diagnosis, prognosis assessment, and treatment of diseases. In this paper, the detection methods and research progress of porcine salivary analytes are reviewed, the application and research progress of porcine salivary analytes in diseases are discussed, and the future application prospect is presented.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (L.Z.); (L.S.)
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Yang ZH, Ye YL, Zhou B, Baba H, Chen RJ, Ge YC, Hu BS, Hua H, Jiang DX, Kimura M, Li C, Li KA, Li JG, Li QT, Li XQ, Li ZH, Lou JL, Nishimura M, Otsu H, Pang DY, Pu WL, Qiao R, Sakaguchi S, Sakurai H, Satou Y, Togano Y, Tshoo K, Wang H, Wang S, Wei K, Xiao J, Xu FR, Yang XF, Yoneda K, You HB, Zheng T. Observation of the Exotic 0_{2}^{+} Cluster State in ^{8}He. Phys Rev Lett 2023; 131:242501. [PMID: 38181133 DOI: 10.1103/physrevlett.131.242501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/05/2023] [Accepted: 11/01/2023] [Indexed: 01/07/2024]
Abstract
We report here the first observation of the 0_{2}^{+} state of ^{8}He, which has been predicted to feature the condensatelike α+^{2}n+^{2}n cluster structure. We show that this state is characterized by a spin parity of 0^{+}, a large isoscalar monopole transition strength, and the emission of a strongly correlated neutron pair, in line with theoretical predictions. Our finding is further supported by the state-of-the-art microscopic α+4n model calculations. The present results may lead to new insights into clustering in neutron-rich nuclear systems and the pair correlation and condensation in quantum many-body systems under strong interactions.
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Affiliation(s)
- Z H Yang
- School of Physics and State Key Laboratory of Nuclear Physics and Technology, Peking University, Beijing 100871, China
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Y L Ye
- School of Physics and State Key Laboratory of Nuclear Physics and Technology, Peking University, Beijing 100871, China
| | - B Zhou
- Key Laboratory of Nuclear Physics and Ion-beam Application (MOE), Institute of Modern Physics, Fudan University, Shanghai 200433, China
- Shanghai Research Center for Theoretical Nuclear Physics, NSFC and Fudan University, Shanghai 200438, China
- Department of Physics, Hokkaido University, 060-0810 Sapporo, Japan
| | - H Baba
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - R J Chen
- Institute of Modern Physics, Chinese Academy of Science, Lanzhou 730000, China
| | - Y C Ge
- School of Physics and State Key Laboratory of Nuclear Physics and Technology, Peking University, Beijing 100871, China
| | - B S Hu
- School of Physics and State Key Laboratory of Nuclear Physics and Technology, Peking University, Beijing 100871, China
| | - H Hua
- School of Physics and State Key Laboratory of Nuclear Physics and Technology, Peking University, Beijing 100871, China
| | - D X Jiang
- School of Physics and State Key Laboratory of Nuclear Physics and Technology, Peking University, Beijing 100871, China
| | - M Kimura
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Department of Physics, Hokkaido University, 060-0810 Sapporo, Japan
- Nuclear Reaction Data Centre, Hokkaido University, 060-0810 Sapporo, Japan
| | - C Li
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - K A Li
- Institute of Modern Physics, Chinese Academy of Science, Lanzhou 730000, China
| | - J G Li
- School of Physics and State Key Laboratory of Nuclear Physics and Technology, Peking University, Beijing 100871, China
| | - Q T Li
- School of Physics and State Key Laboratory of Nuclear Physics and Technology, Peking University, Beijing 100871, China
| | - X Q Li
- School of Physics and State Key Laboratory of Nuclear Physics and Technology, Peking University, Beijing 100871, China
| | - Z H Li
- School of Physics and State Key Laboratory of Nuclear Physics and Technology, Peking University, Beijing 100871, China
| | - J L Lou
- School of Physics and State Key Laboratory of Nuclear Physics and Technology, Peking University, Beijing 100871, China
| | - M Nishimura
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - H Otsu
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - D Y Pang
- School of Physics and Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191, China
| | - W L Pu
- School of Physics and State Key Laboratory of Nuclear Physics and Technology, Peking University, Beijing 100871, China
| | - R Qiao
- School of Physics and State Key Laboratory of Nuclear Physics and Technology, Peking University, Beijing 100871, China
| | - S Sakaguchi
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Department of Physics, Kyushu University, 819-0395 Fukuoka, Japan
| | - H Sakurai
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Y Satou
- Rare Isotope Science Project, Institute for Basic Science, Daejeon 34000, Republic of Korea
| | - Y Togano
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - K Tshoo
- Rare Isotope Science Project, Institute for Basic Science, Daejeon 34000, Republic of Korea
| | - H Wang
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Department of Physics, Tokyo Institute of Technology, 2-12-1 Oh-Okayama, Meguro, Tokyo 152-8551, Japan
| | - S Wang
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - K Wei
- School of Physics and State Key Laboratory of Nuclear Physics and Technology, Peking University, Beijing 100871, China
| | - J Xiao
- School of Physics and State Key Laboratory of Nuclear Physics and Technology, Peking University, Beijing 100871, China
| | - F R Xu
- School of Physics and State Key Laboratory of Nuclear Physics and Technology, Peking University, Beijing 100871, China
| | - X F Yang
- School of Physics and State Key Laboratory of Nuclear Physics and Technology, Peking University, Beijing 100871, China
| | - K Yoneda
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - H B You
- School of Physics and State Key Laboratory of Nuclear Physics and Technology, Peking University, Beijing 100871, China
| | - T Zheng
- School of Physics and State Key Laboratory of Nuclear Physics and Technology, Peking University, Beijing 100871, China
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Han J, Li M, Li X, Liu C, Li XL, Wang K, Qiao R, Yang F, Han X, Li XJ. Effects of microbes in pig farms on occupational exposed persons and the environment. AMB Express 2023; 13:136. [PMID: 38032532 PMCID: PMC10689614 DOI: 10.1186/s13568-023-01631-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
In terms of pig farming, pig gut microbes have a significant effect on farmers and the farm environment. However, it is still unclear which microbial composition is more likely to contribute to this effect. This study collected a total of 136 samples, including pigs' faeces samples, farmers' faeces samples, samples from individuals who had no contact with any type of farm animal (referred to as 'non-exposed' persons), and environmental dust samples (collected from inside and outside pig houses and the farm) from two pig farms, pig farm A and pig farm B. Whereafter, 16S rRNA sequencing and taxonomic composition analysis were performed. According to the study, compared to non-exposed persons, pig farmers had a significantly higher abundance of 7 genera. In addition, the farmers were grouped according to the duration of their occupational exposure, and it was shown that 4 genera, including Turicibacter, Terrisporobacter, and Clostridium_sensu_stricto_1, exhibited a rise in more frequent contact with pigs. As compared to outside the pig house, the environmental dust has a greater concentration of the 3 bacteria mentioned before. Therefore, these 3 microbes can be considered as co-occurring microbes that may exist both in humans and the environment. Also, the 3 co-occurring microbes are involved in the fermentation and production of short-chain fatty acids and their effectiveness decreased as distance from the farm increased. This study shows that the 3 microbes where pig farmers co-occur with the environment come from pig farms, which provides fresh ideas for preventing the spread of microbial aerosols in pig farms and reducing pollution.
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Affiliation(s)
- Jinyi Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Mengyu Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xin Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Chuang Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiu-Ling Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Feng Yang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Xin-Jian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China.
- Sanya Institute, Hainan Academy of Agricultural Science, Sanya, China.
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Zhang L, Zhang S, Yuan M, Zhan F, Song M, Shang P, Yang F, Li X, Qiao R, Han X, Li X, Fang M, Wang K. Genome-Wide Association Studies and Runs of Homozygosity to Identify Reproduction-Related Genes in Yorkshire Pig Population. Genes (Basel) 2023; 14:2133. [PMID: 38136955 PMCID: PMC10742578 DOI: 10.3390/genes14122133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/10/2023] [Accepted: 11/19/2023] [Indexed: 12/24/2023] Open
Abstract
Reproductive traits hold considerable economic importance in pig breeding and production. However, candidate genes underpinning the reproductive traits are still poorly identified. In the present study, we executed a genome-wide association study (GWAS) and runs of homozygosity (ROH) analysis using the PorcineSNP50 BeadChip array for 585 Yorkshire pigs. Results from the GWAS identified two genome-wide significant and eighteen suggestive significant single nucleotide polymorphisms (SNPs) associated with seven reproductive traits. Furthermore, we identified candidate genes, including ELMO1, AOAH, INSIG2, NUP205, LYPLAL1, RPL34, LIPH, RNF7, GRK7, ETV5, FYN, and SLC30A5, which were chosen due to adjoining significant SNPs and their functions in immunity, fertilization, embryonic development, and sperm quality. Several genes were found in ROH islands associated with spermatozoa, development of the fetus, mature eggs, and litter size, including INSL6, TAF4B, E2F7, RTL1, CDKN1C, and GDF9. This study will provide insight into the genetic basis for pig reproductive traits, facilitating reproduction improvement using the marker-based selection methods.
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Affiliation(s)
- Lige Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
| | - Songyuan Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
| | - Meng Yuan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
| | - Fengting Zhan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
| | - Mingkun Song
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
| | - Peng Shang
- Animal Science College, Tibet Agriculture and Animal Husbandry University, Linzhi 860000, China;
| | - Feng Yang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
| | - Xiuling Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
| | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
| | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
| | - Xinjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
| | - Meiying Fang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
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Liu C, Feng H, Han J, Zhou H, Yuan L, Pan H, Wang X, Han X, Qiao R, Yang F, Li X. Effect of L-proline on sperm quality during cryopreservation of boar semen. Anim Reprod Sci 2023; 258:107359. [PMID: 37832280 DOI: 10.1016/j.anireprosci.2023.107359] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/06/2023] [Indexed: 10/15/2023]
Abstract
L-proline has been reported to be useful in semen cryopreservation. However, its use has rarely been reported in the freezing of boar semen. The objective of this study was to evaluate the effects of different concentrations of L-proline (0, 10, 30, 50, and 90 mM) on the quality of boar semen after freezing and thawing. Semen samples from boars (n = 6) were frozen using freezing extenders with added concentrations of L-proline. Total sperm motility, progressive motility, survival time at 37 °C, acrosome integrity, mitochondrial activity, DNA integrity, the content of the lipid peroxidation product malondialdehyde (MDA), total antioxidant capacity (T-AOC) and, expression levels of apoptosis protein (cleaved caspase 3 and Bax) were evaluated after thawing. The results showed that total sperm viability (73.96% vs. 63.58%) and progressive motility (56.88% vs. 47.26%) after thawing were significantly higher in the 10 mM L-proline treatment group than in the control group. The survival time at 37 °C and the total motility of sperm in the 10 mM group within one hour after thawing were significantly higher than in the control group. Acrosome integrity and mitochondrial activity of sperm in the 10 mM group were significantly higher than those in the control, 50 mM, and 90 mM groups. The DNA integrity rate in the 10 mM group was significantly higher than in the control group. The L-proline treatment did not affect sperm MDA content or T-AOC. The expression levels of apoptosis protein (cleaved caspase 3 and Bax) in the 10 mM L-proline supplemented group were lower than those in the control group. In conclusion, the freezing extender containing 10 mM L-proline improved semen quality after freezing and thawing and thus would be a useful reagent for boar semen cryopreservation.
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Affiliation(s)
- Chuang Liu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Henan Agricultural University, China
| | - Haoyi Feng
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Henan Agricultural University, China
| | - Jinyi Han
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Henan Agricultural University, China
| | - Hao Zhou
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Henan Agricultural University, China
| | - Liwei Yuan
- Henan Jingwang Pig Breed Improvement Co. LTD, China
| | - Hongshuang Pan
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Henan Agricultural University, China
| | - Xiaohan Wang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Henan Agricultural University, China
| | - Xuelei Han
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Henan Agricultural University, China
| | - Ruimin Qiao
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Henan Agricultural University, China
| | - Feng Yang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Henan Agricultural University, China.
| | - Xinjian Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Henan Agricultural University, China.
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Qi K, Dou Y, Li C, Liu Y, Song C, Li X, Wang K, Qiao R, Li X, Yang F, Han X. CircGUCY2C regulates cofilin 1 by sponging miR-425-3p to promote the proliferation of porcine skeletal muscle satellite cells. Arch Anim Breed 2023; 66:285-298. [PMID: 38039333 PMCID: PMC10655074 DOI: 10.5194/aab-66-285-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 09/07/2023] [Indexed: 12/03/2023] Open
Abstract
Circular ribonucleic acids (or circRNAs) are an emerging class of endogenous noncoding RNAs that are involved in physiological and pathological processes. Increasing evidence suggests that circRNAs play an important regulatory role in skeletal muscle development and meat quality regulation. In this study, it was found that circGUCY2C exhibits a high expression level in the longissimus dorsi muscle. It shows resistance to RNase R and additionally promotes the mRNA expression of cyclin-dependent kinase 2 (CDK2) and proliferating cell nuclear antigen (PCNA). Specifically, it was observed that the overexpression of circGUCY2C could promote the transition of porcine skeletal muscle satellite cells into the S and G2 phases of the cell cycle and that it regulates the proliferation of porcine skeletal muscle satellite cells. In contrast, miR-425-3p plays the opposite role and has an inhibitory effect on the proliferation of porcine skeletal muscle satellite cells. MiR-425-3p has been described as a target of circGUCY2C; consequently, the depletion of miR-425-3p promoted the proliferation of porcine skeletal muscle satellite cells. CFL1 (cofilin 1) is a target of miR-425-3p, and circGUCY2C upregulated CFL1 expression by inhibiting miR-425-3p. Collectively, our research outcomes demonstrate that circGUCY2C significantly influences the proliferation of porcine skeletal muscle satellite cells by selectively targeting the miR-425-3p-CFL1 axis, and our work partially clarified the role of circGUCY2C in porcine skeletal muscle satellite cells. Thus, the study provides new insight into the function of circGUCY2C and adds to the knowledge of the post-transcriptional regulation of pork quality.
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Affiliation(s)
- Kunlong Qi
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yaqing Dou
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Chenlei Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yingke Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Chenglei Song
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Xinjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiuling Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Feng Yang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
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Qiao R, Li X, Madsen O, Groenen MAM, Xu P, Wang K, Han X, Li G, Li X, Li K. Potential selection for lipid kinase activity and spermatogenesis in Henan native pig breeds and growth shaping by introgression of European genes. Genet Sel Evol 2023; 55:64. [PMID: 37723431 PMCID: PMC10506266 DOI: 10.1186/s12711-023-00841-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 09/12/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND China has one third of the worldwide indigenous pig breeds. The Henan province is one of the earliest pig domestication centers of China (about 8000 years ago). However, the precise genetic characteristics of the Henan local pig breeds are still obscure. To understand the origin and the effects of selection on these breeds, we performed various analyses on lineage composition, genetic structure, and detection of selection sweeps and introgression in three of these breeds (Queshan, Nanyang and Huainan) using genotyping data on 125 Queshan, 75 Nanyang, 16 Huainan pigs and 878 individuals from 43 Eurasian pig breeds. RESULTS We found no clear evidence of ancestral domestic pig DNA lineage in the Henan local breeds, which have an extremely complicated genetic background. Not only do they share genes with some northern Chinese pig breeds, such as Erhualian, Hetaodaer, and Laiwu, but they also have a high admixture of genes from foreign pig breeds (33-40%). Two striking selection sweeps in small regions of chromosomes 2 and 14 common to the Queshan and Nanyang breeds were identified. The most significant enrichment was for lipid kinase activity (GO:0043550) with the genes FII, AMBRA1, and PIK3IP1. Another interesting 636.35-kb region on chromosome 14 contained a cluster of spermatogenesis genes (OSBP2, GAL3ST1, PLA2G3, LIMK2, and PATZ1), a bisexual sterility gene MORC2, and a fat deposition gene SELENOM. Reproduction and growth genes LRP4, FII, and ARHGAP1 were present in a 238.05-kb region on SSC2 under selection. We also identified five loci associated with body length (P = 0.004) on chromosomes 1 and 12 that were introgressed from foreign pig breeds into the Henan breeds. In addition, the Chinese indigenous pig breeds fell into four main types instead of the previously reported six, among which the Eastern type could be divided into two subgroups. CONCLUSIONS Admixture of North China, East China and foreign pigs contributed to high genetic diversity of Henan local pigs. Ontology terms associated with lipid kinase activity and spermatogenesis and growth shaping by introgression of European genes in Henan pigs were identified through selective sweep analyses.
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Affiliation(s)
- Ruimin Qiao
- College of Animal Science, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Xinjian Li
- College of Animal Science, Henan Agricultural University, Zhengzhou, 450046, China
| | - Ole Madsen
- Animal Breeding and Genomics Centre, Department of Animal Sciences, Wageningen University & Research, 6700 HB, Wageningen, The Netherlands
| | - Martien A M Groenen
- Animal Breeding and Genomics Centre, Department of Animal Sciences, Wageningen University & Research, 6700 HB, Wageningen, The Netherlands
| | - Pan Xu
- Jiangsu Agri-Animal Husbandry and Veterinary College, Taizhou, 225300, China
| | - Kejun Wang
- College of Animal Science, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xuelei Han
- College of Animal Science, Henan Agricultural University, Zhengzhou, 450046, China
| | - Gaiying Li
- College of Animal Science, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xiuling Li
- College of Animal Science, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Kui Li
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Qi K, Dou Y, Zhang Z, Wei Y, Song C, Qiao R, Li X, Yang F, Wang K, Li X, Han X. Expression Profile and Regulatory Properties of m6A-Modified circRNAs in the Longissimus Dorsi of Queshan Black and Large White Pigs. Animals (Basel) 2023; 13:2190. [PMID: 37443988 DOI: 10.3390/ani13132190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/21/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
It is well known that N6-methyladenosine (m6A) is the most abundant modification in linear RNA molecules, but many circRNA molecules have now been found to have a wide range of m6A modification sites as well. However, there are few relevant studies and information on the expression profile and functional regulatory properties of m6A-modified circRNAs (m6A-circRNAs) in longissimus dorsi. In this study, a total of 12 putative m6A-circRNAs were identified and characterized in the longissimus dorsi of Queshan Black and Large White pigs-8 of them were significantly more expressed in the longissimus dorsi of Queshan Black than in Large White pigs, while the other 4 were the opposite. These 12 putative m6A-circRNAs were also found to act as miRNA sponge molecules to regulate fat deposition by constructing the ceRNA regulatory network. Enrichment analysis also revealed that the 12 m6A-circRNAs parent genes and their adsorbed miRNA target genes were widely involved in fat deposition and cell proliferation and differentiation-related pathways, such as the HIF-1 signaling pathway, the pentose phosphate pathway, the MAPK signaling pathway, the glycosphingolipid biosynthesis-lacto and neolacto series, and the TNF signaling pathway, suggesting that the analyzed m6A-circRNAs may be largely involved in the formation of pork quality. These results provide new information to study the regulatory properties of m6A-circRNAs in the formation of pork quality.
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Affiliation(s)
- Kunlong Qi
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yaqing Dou
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhe Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yilin Wei
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Chenglei Song
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiuling Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Feng Yang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Xinjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
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Liu Y, Dou Y, Qi K, Li C, Song C, Li X, Li X, Qiao R, Wang K, Han X. Correction to "CircSETBP1 Acts as a MiR-149-5p Sponge to Promote Intramuscular Fat Deposition by Regulating CRTCs". J Agric Food Chem 2023. [PMID: 37290131 DOI: 10.1021/acs.jafc.3c03133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
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Liu Y, Wei Y, Dou Y, Li C, Song C, Zhang Z, Qi K, Li X, Qiao R, Wang K, Li X, Yang F, Han X. Effect of miR-149-5p on intramuscular fat deposition in pigs based on metabolomics and transcriptomics. BMC Genomics 2023; 24:293. [PMID: 37259030 DOI: 10.1186/s12864-023-09382-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 05/15/2023] [Indexed: 06/02/2023] Open
Abstract
As one of the important traits in pig production, meat quality has important research significance and value. Intramuscular fat (IMF) content is one of the most important factors affecting pork quality. Many experimental studies have shown that IMF content is closely related to the flavor, tenderness, and juiciness of pork. Therefore, it is of great significance to study the mechanism of porcine IMF deposition. Previous research indicated that miR-149-5p promoted the proliferation of porcine intramuscular (IM) preadipocytes and decreased their ability to differentiate, albeit the exact mechanism of action is unknown. In vitro, foreign pigs showed increased miR-149-5p expression and reduced fat deposition when compared to Queshan Black pigs. This study conducted metabolomics and transcriptomics analyses of porcine IM preadipocytes overexpressing miR-149-5p to verify their effects on lipid formation. According to metabolomics analysis, the overexpression of miR-149-5p has significantly altered the lipid, organic acid, and organic oxygen metabolites of porcine IM preadipocytes. Specially speaking, it has changed 115 metabolites, including 105 up-regulated and 10 down-regulated ones, as well as the composition of lipid, organic acid, and organic oxygen metabolism-related metabolites. RNA-seq analysis showed that overexpression of miR-149-5p significantly altered 857 genes, of which 442 were up-regulated, and 415 were down-regulated, with enrichment to MAPK, IL-17, PI3K-Akt, and ErbB signaling pathways. We found that overexpression of miR-149-5p inhibited adipogenic differentiation by changing cAMP signaling pathway in porcine IM preadipocytes. In addition, the overexpression of miR-149-5p may affect the transport of Cu2+ by targeting ATP7A and inhibiting adipogenic differentiation. These findings elucidate the regulatory function of miR-149-5p in porcine IM preadipocytes, which may be a key target for controlling pork quality.
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Affiliation(s)
- Yingke Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yilin Wei
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yaqing Dou
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Chenlei Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Chenglei Song
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zhe Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Kunlong Qi
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xinjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xiuling Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Feng Yang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.
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13
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Li C, Zhang Z, Wei Y, Qi K, Dou Y, Song C, Liu Y, Li X, Li X, Wang K, Qiao R, Yang F, Han X. Genome-Wide Analysis of MAMSTR Transcription Factor-Binding Sites via ChIP-Seq in Porcine Skeletal Muscle Fibroblasts. Animals (Basel) 2023; 13:1731. [PMID: 37889674 PMCID: PMC10252000 DOI: 10.3390/ani13111731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/12/2023] [Accepted: 05/17/2023] [Indexed: 10/29/2023] Open
Abstract
Myocyte enhancer factor-2-activating motif and SAP domain-containing transcriptional regulator (MAMSTR) regulates its downstream through binding in its promoter regions. However, its molecular mechanism, particularly the DNA-binding sites, and coregulatory genes are quite unexplored. Therefore, to identify the genome-wide binding sites of the MAMSTR transcription factors and their coregulatory genes, chromatin immunoprecipitation sequencing was carried out. The results showed that MAMSTR was associated with 1506 peaks, which were annotated as 962 different genes. Most of these genes were involved in transcriptional regulation, metabolic pathways, and cell development and differentiation, such as AMPK signaling pathway, TGF-beta signaling pathway, transcription coactivator activity, transcription coactivator binding, adipocytokine signaling pathway, fat digestion and absorption, skeletal muscle fiber development, and skeletal muscle cell differentiation. Lastly, the expression levels and transcriptional activities of PID1, VTI1B, PRKAG1, ACSS2, and SLC28A3 were screened and verified via functional markers and analysis. Overall, this study has increased our understanding of the regulatory mechanism of MAMSTR during skeletal muscle fibroblast development and provided a reference for analyzing muscle development mechanisms.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
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Dou Y, Wei Y, Zhang Z, Li C, Song C, Liu Y, Qi K, Li X, Li X, Qiao R, Wang K, Yang F, Han X. Transcriptome-wide analysis of RNA m 6A methylation regulation of muscle development in Queshan Black pigs. BMC Genomics 2023; 24:239. [PMID: 37142996 PMCID: PMC10161540 DOI: 10.1186/s12864-023-09346-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 04/28/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) refers to the methylation modification of N6 position of RNA adenine, a dynamic reversible RNA epigenetic modification that plays an important regulatory role in a variety of life processes. In this study, we used MeRIP-Seq and RNA-Seq of the longissimus dorsi (LD) muscle of adult (QA) and newborn (QN) Queshan Black pigs to screen key genes with m6A modification involved in muscle growth by bioinformatics analysis. RESULTS A total of 23,445 and 25,465 m6A peaks were found in the whole genomes of QA and QN, respectively. Among them, 613 methylation peaks were significantly different (DMPs) and 579 genes were defined as differentially methylated genes (DMGs). Compared with the QN group, there were 1,874 significantly differentially expressed genes (DEGs) in QA group, including 620 up-regulated and 1,254 down-regulated genes. In order to investigate the relationship between m6A and mRNA expression in the muscle of Queshan Black pigs at different periods, a combined analysis of MeRIP-Seq and RNA-Seq showed that 88 genes were significantly different at both levels. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes results showed that DEGs and DMGs were mainly involved in skeletal muscle tissue development, FoxO signaling pathway, MAPK signaling pathway, insulin signaling pathway, PI3K-Akt signaling pathway, and Wnt signaling pathway. Four DEGs (IGF1R, CCND2, MYOD1 and FOS) and four DMGs (CCND2, PHKB, BIN1 and FUT2), which are closely related to skeletal muscle development, were selected as candidate genes for verification, and the results were consistent with the sequencing results, which indicated the reliability of the sequencing results. CONCLUSIONS These results lay the foundation for understanding the specific regulatory mechanisms of growth in Queshan Black pigs, and provide theoretical references for further research on the role of m6A in muscle development and breed optimization selection.
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Affiliation(s)
- Yaqing Dou
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yilin Wei
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zhe Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Chenlei Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Chenglei Song
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yingke Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Kunlong Qi
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xinjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xiuling Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Feng Yang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.
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15
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Zhang L, Zhang S, Zhan F, Song M, Shang P, Zhu F, Li J, Yang F, Li X, Qiao R, Han X, Li X, Liu G, Wang K. Population Genetic Analysis of Six Chinese Indigenous Pig Meta-Populations Based on Geographically Isolated Regions. Animals (Basel) 2023; 13:ani13081396. [PMID: 37106959 PMCID: PMC10135051 DOI: 10.3390/ani13081396] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/28/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The diversification of indigenous pig breeds in China has resulted from multiple climate, topographic, and human cultural influences. The numerous indigenous pig breeds can be geographically divided into six meta-populations; however, their genetic relationships, contributions to genetic diversity, and genetic signatures remain unclear. Whole-genome SNP data for 613 indigenous pigs from the six Chinese meta-populations were obtained and analyzed. Population genetic analyses confirmed significant genetic differentiation and a moderate mixture among the Chinese indigenous pig meta-populations. The North China (NC) meta-population had the largest contribution to genetic and allelic diversity. Evidence from selective sweep signatures revealed that genes related to fat deposition and heat stress response (EPAS1, NFE2L2, VPS13A, SPRY1, PLA2G4A, and UBE3D) were potentially involved in adaptations to cold and heat. These findings from population genetic analyses provide a better understanding of indigenous pig characteristics in different environments and a theoretical basis for future work on the conservation and breeding of Chinese indigenous pigs.
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Affiliation(s)
- Lige Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Songyuan Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Fengting Zhan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Mingkun Song
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Peng Shang
- Animal Science College, Tibet Agriculture and Animal Husbandry University, Linzhi 860000, China
| | - Fangxian Zhu
- National Animal Husbandry Service, Beijing 100193, China
| | - Jiang Li
- National Supercomputing Center in Zhengzhou, Zhengzhou 450001, China
| | - Feng Yang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiuling Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Xinjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Gang Liu
- National Animal Husbandry Service, Beijing 100193, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
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16
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Zang Z, Qiao R, Zhu Q, Zhou X, Gu W, Han B, Yang R. [Peripheral blood KCNMA1 methylation level is associated with the occurrence and progression of lung cancer]. Nan Fang Yi Ke Da Xue Xue Bao 2023; 43:349-359. [PMID: 37087578 PMCID: PMC10122738 DOI: 10.12122/j.issn.1673-4254.2023.03.03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 04/24/2023]
Abstract
OBJECTIVE To explore the association of KCNMA1 gene methylation levels in peripheral blood with lung cancer. METHODS The methylation levels of 4 CpG sites in KCNMA1 gene were quantitatively detected in 285 patients with lung cancer, 186 age- and sex-matched patients with benign pulmonary nodules and 278 matched healthy control subjects using mass spectrometry (MALDI-TOF-MS). The association of KCNMA1 methylation levels with lung cancer was analyzed using logistic regression models adjusted for covariates. The KCNMA1 methylation levels in different subgroups of lung cancer patients were compared using Mann-Whitney U test. RESULTS In subjects over 55 years and in female subjects, the highest quartile (Q4) vs the lowest quartile (Q1) of KCNMA1_CpG_5 methylation levels were significantly correlated with lung cancer (for subjects over 55 years: OR=2.60, 95% CI: 1.25-5.41, P=0.011; for female subjects: OR=2.09, 95% CI: 1.03?4.26, P=0.042). From Q2 to Q4 of KCNMA1_CpG_5 methylation levels, their correlation with lung cancer became gradually stronger (P=0.003 and 0.038, respectively). In male subjects, the OR of Q4 of KCNMA1_CpG_5 methylation levels was 0.35 in patients with lung cancer as compared with patients with benign nodules (95% CI: 0.16-0.79, P=0.012). KCNMA1_CpG_3 methylation level was significantly lower in invasive adenocarcinoma than in noninvasive adenocarcinoma (P=0.028), and that of KCNMA1_CpG_1 was significantly higher in patients with larger tumors (T2-4) than in those with smaller tumors (T1) (P=0.021). CONCLUSION The change of peripheral blood KCNMA1 methylation level is correlated with the occurrence and development of lung cancer.
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Affiliation(s)
- Z Zang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - R Qiao
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, China
| | - Q Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - X Zhou
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - W Gu
- Department of Clinical Laboratory, Jiangsu Provincial Hospital of Chinese Medicine, Nanjing 210029, China
| | - B Han
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, China
| | - R Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
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Li M, Li X, Liu C, Han J, Han X, Wang K, Qiao R, Yang F, Li XL, Li XJ. Genome-wide association study reveals the candidate genes for reproduction traits in Yunong black pigs. Anim Genet 2023; 54:403-407. [PMID: 36650110 DOI: 10.1111/age.13294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/21/2022] [Accepted: 12/31/2022] [Indexed: 01/19/2023]
Abstract
Enhancing pig reproductive efficiency has the potential to have a significant positive economic impact on the pig business. We collected four reproduction records of 734 Yunong black pigs in this study, including the total number of piglets born (TNB), the number born alive (NBA), the average birth interval of piglets (ABI) and the average birth weight (ABW). A total of 453 Yunong black pigs were genotyped with Porcine 50K SNP BeadChip. Twenty-five SNPs and 35 genomic areas were found to have a substantial impact on the reproductive performance of Yunong black pigs by single-locus GWAS and single-step GWAS (ssGWAS). For the ssGWAS, we found that the two genomic regions (12.67-13.85 and 14.26-15.01 Mb) on Sus scrofa chromosome X were associated with TNB, NBA and ABI. It is worth noting that CNC10110530 and CNC100141254 significantly affected the TNB by both GWAS methods. Finally, we further determined the gene functions by enrichment analysis and a literature search, and identified 28 of them as candidate genes affecting the reproductive performance of Yunong black pigs, including RET, EIF1AX, NELL2, CTPS2, S100G, RBBP7 and PDHA1. This study further promotes understanding of the genetic mechanism of porcine reproductive performance, and also provides more molecular markers for pig breeding.
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Affiliation(s)
- Mengyu Li
- College of Animal Science and Technology, Henan Agricultural University, Henan, Zhengzhou, China
| | - Xin Li
- College of Animal Science and Technology, Henan Agricultural University, Henan, Zhengzhou, China
| | - Chuang Liu
- College of Animal Science and Technology, Henan Agricultural University, Henan, Zhengzhou, China
| | - Jinyi Han
- College of Animal Science and Technology, Henan Agricultural University, Henan, Zhengzhou, China
| | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, Henan, Zhengzhou, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Henan, Zhengzhou, China
| | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, Henan, Zhengzhou, China
| | - Feng Yang
- College of Animal Science and Technology, Henan Agricultural University, Henan, Zhengzhou, China
| | - Xiu-Ling Li
- College of Animal Science and Technology, Henan Agricultural University, Henan, Zhengzhou, China
| | - Xin-Jian Li
- College of Animal Science and Technology, Henan Agricultural University, Henan, Zhengzhou, China
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Li C, Han J, Duan D, Liu C, Han X, Wang K, Qiao R, Li XL, Li XJ. Lymphoid enhancer binding factor 1 is associated with nose color in Yunong black pigs. Anim Genet 2023; 54:398-402. [PMID: 36649734 DOI: 10.1111/age.13292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 11/11/2022] [Accepted: 12/31/2022] [Indexed: 01/19/2023]
Abstract
Yunong black pig is an indigenous black pig breed being cultivated that has a pure black whole body. However, some individuals appear with a white spot on the nose. We performed case-control association studies and FST approaches in 76 animals with nose color records (26 white-nosed pigs vs. 50 black-nosed pigs) by Illumina Porcine SNP50 BeadChip data. In total, 76 SNPs, which included 2 genome-wide significant SNPs and 18 chromosome-wide suggestive SNPs, were identified by association study. The top-ranked 0.1% windows of FST results as signals under selection and 24 windows were selected. The lymphoid enhancer binding factor 1 was identified as candidate gene with strong signal in analyses of genome-wide association study and FST in black- and white-nosed pigs. Overall, our findings provide evidence that nose color is a heritable trait influenced by many loci. The results contribute to expand our understanding of pigmentation in pigs and provide SNP markers for skin color and related traits selection in Yunong black pigs. Additional research on the genetic link between nose pigmentation is needed.
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Affiliation(s)
- Cong Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Jinyi Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Dongdong Duan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Chuang Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xiu-Ling Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xin-Jian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
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19
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Song C, Chang L, Wang B, Zhang Z, Wei Y, Dou Y, Qi K, Yang F, Li X, Li X, Wang K, Qiao R, Han X. Seminal plasma metabolomics analysis of differences in liquid preservation ability of boar sperm. J Anim Sci 2023; 101:skad392. [PMID: 38006391 PMCID: PMC10718801 DOI: 10.1093/jas/skad392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 11/23/2023] [Indexed: 11/27/2023] Open
Abstract
The preservation of semen is pivotal in animal reproduction to ensure successful fertilization and genetic improvement of livestock and poultry. However, investigating the underlying causes of differences in sperm liquid preservation ability and identifying relevant biomarkers remains a challenge. This study utilized liquid chromatography-mass spectrometry (LC-MS) to analyze the metabolite composition of seminal plasma (SP) from two groups with extreme differences in sperm liquid preservation ability. The two groups namely the good liquid preservation ability (GPA) and the poor preservation ability (PPA). The aim was to explore the relationship between metabolite composition in SP and sperm liquid preservation ability, and to identify candidate biomarkers associated with this ability of sperm. The results revealed the identification of 756 metabolites and 70 differentially expressed metabolites (DEM) in the SP from two groups of boar semen with differing liquid preservation abilities at 17 °C. The majority of identified metabolites in the SP belonged to organic acids and derivatives as well as lipids and lipid-like molecules. The DEM in the SP primarily consisted of amino acids, peptides, and analogs. The Kyoto Encyclopedia of Genes and Genomes analysis also demonstrated that the DEM are mainly concentrated in amino acid synthesis and metabolism-related pathways (P < 0.05). Furthermore, eleven key metabolites were identified and six target amino acids were verified, and the results were consistent with the non-targeted metabolic analysis. These findings indicated that amino acids and their associated pathways play a potential role in determining boar sperm quality and liquid preservation ability. D-proline, arginine, L-citrulline, phenylalanine, leucine, DL-proline, DL-serine, and indole may serve as potential biomarkers for early assessment of boar sperm liquid preservation ability. The findings of this study are helpful in understanding the causes and mechanisms of differences in the liquid preservation ability of boar sperm, and provide valuable insights for improving semen quality assessment methods and developing novel extenders or protocols.
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Affiliation(s)
- Chenglei Song
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Lebin Chang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Bingjie Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhe Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yilin Wei
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yaqing Dou
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Kunlong Qi
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Feng Yang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiuling Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Xinjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
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20
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Qiao R, Zhang M, Zhang B, Li X, Han X, Wang K, Li X, Yang F, Hu P. Population genetic structure analysis and identification of backfat thickness loci of Chinese synthetic Yunan pigs. Front Genet 2022; 13:1039838. [PMID: 36437945 PMCID: PMC9681789 DOI: 10.3389/fgene.2022.1039838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/26/2022] [Indexed: 11/10/2022] Open
Abstract
Yunan is a crossed lean meat pig breed in China. Backfat thickness is the gold standard for carcass quality grading. However, over 14 years after breed registration, the backfat of Yunan thickened and the consistency of backfat thickness decreased. Meanwhile, no genetic study has been ever performed on Yunan population. So, in this study we collected all the 120 nucleus individuals of Yunan and recorded six backfat traits of them, carried out population genetic structure analysis, selection signals analysis and genome-wide association study of Yunan pigs with the help of their founder population Duroc and Chinese native Huainan pigs, to determine the genomic loci on backfat of Yunan. Genetic diversity indexes suggested Yunan pigs had no inbreeding risk while population genetic structure showed they had few molecular pedigrees and were stratified. A total of 71 common selection signals affecting growth and fat deposition were detected by FST and XP-CLR methods. 34 significant loci associated with six backfat traits were detected, among which a 1.40 Mb region on SSC4 (20.03–21.43 Mb) were outstanding as the strong region underlying backfat. This region was common with the results of selection signature analysis, former reported QTLs for backfat and was common for different kinds of backfat traits at different development stage. ENPP2, EXT1 and SLC30A8 genes around were fat deposition related genes and were of Huainan pig’s origin, among which Type 2 diabetes related gene SLC30A8 was the most reasonable for being in a 193.21 Kb haplotype block of the 1.40 Mb region. Our results had application value for conservation, mating and breeding improvement of backfat thickness of Yunan pigs and provided evidence for a human function gene might be reproduced in pigs.
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Affiliation(s)
- Ruimin Qiao
- *Correspondence: Ruimin Qiao, ; Panyang Hu, hpy9809.@163.com
| | | | | | | | | | | | | | | | - Panyang Hu
- *Correspondence: Ruimin Qiao, ; Panyang Hu, hpy9809.@163.com
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Liu Y, Dou Y, Qi K, Li C, Song C, Li X, Li X, Qiao R, Wang K, Han X. CircSETBP1 Acts as a MiR-149-5p Sponge to Promote Intramuscular Fat Deposition by Regulating CRTCs. J Agric Food Chem 2022; 70:12841-12851. [PMID: 36165804 DOI: 10.1021/acs.jafc.2c05697] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Circular RNAs (circRNAs) appear to be crucial in the process of adipogenesis according to mounting data. CircSETBP1 is a newly discovered circRNA associated with adipogenesis. Sequencing verification and RNase R treatment have confirmed the circular nature of circSETBP1 in porcine tissue. The precise function and mechanism of circSETBP1 in adipocyte biology are still unclear. Cell counting kit-8 (CCK8), Oil red O staining, and quantitative real-time polymerase chain reaction (qRT-PCR) were employed in this investigation to reveal the functions of circSETBP1 and miR-149-5p in the growth and development of porcine intramuscular (IM) preadipocytes. CircSETBP1 overexpression accelerated cell differentiation while reducing cell proliferation. The opposite outcome was produced by overexpressing miR-149-5p. Meanwhile, circSETBP1 down-regulated the expression of miR-149-5p and miR-149-5p restrained the expression of CRTC1/CRTC2. CircSETBP1 was directly targeted by miR-149-5p, and CRTC1/CRTC2 were the target genes of miR-149-5p using bioinformatic analysis, the dual-Luciferase reporter system, and qRT-PCR. In conclusion, circSETBP1 controls the proliferation and differentiation of porcine IM preadipocytes and 3T3-L1 cells by regulating the miR-149-5p/CRTCs axis. The results of this study not only illuminate the molecular mechanism of circSETBP1/miR-149-5p involved in the deposition of porcine intramuscular fat (IMF), but they also provide a significant theoretical reference for raising quality of pork.
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Affiliation(s)
- Yingke Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yaqing Dou
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Kunlong Qi
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Chenlei Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Chenglei Song
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Xinjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiuling Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
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22
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Zhang M, Zhang C, Hu P, Shi L, Ju M, Zhang B, Li X, Han X, Wang K, Li X, Qiao R. Comprehensive analysis of mitogenome of native Henan pig breeds with 58 worldwide pig breeds. Anim Genet 2022; 53:803-813. [PMID: 36071602 DOI: 10.1111/age.13261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/27/2022]
Abstract
Mitochondria follow non-Mendelian maternal inheritance, and thus can be used to compare genetic diversity and infer the expansion and migration between animal populations. Based on the mitochondrial DNA sequences of 58 pig breeds from Asia, Europe, Oceania, and America, we observed a distinct division of Eurasian pig species into two main Haplogroups (A and B), with the exception of the Berkshire and Yorkshire breeds. Oceanian pigs were much more similar to European and American pigs in Haplogroup A. Additionally, native Chinese pigs exhibited the most abundant genetic polymorphisms and occupied the centre of Haplogroup B. Miyazaki (Japan) and Siberia (Russia) are two distant and disconnected regions; however, most pigs from these regions were clustered into a subcluster, while native pigs from Korea clustered into a second subcluster. This study is the first to report that pigs from Thailand and Vietnam had haplotypes similar to those of Henan, where the earliest evidence of domestic pigs was found from the Yellow River Basin of North China. Local Henan pig breeds are related to many Asian breeds while still having their own mutation identity, such as g.314 delins T>AC/AT/C of the 12S rRNA gene in Yuxi. Some pigs from Palawan, Itbayat, and Batan Islands of the Philippines and Lanyu Island of China were distinct from other Asian pigs and clustered together into Haplogroup C. These findings show that the complexity of domestication of worldwide pig breeds and mitochondria could reflect genetic communication between pig breeds due to geographical proximity and human activities.
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Affiliation(s)
- Menghao Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Chen Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shanxi, China
| | - Panyang Hu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Lidan Shi
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Mingming Ju
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Ben Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xinjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xiuling Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
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23
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Chen J, Wu Z, Chen R, Huang Z, Han X, Qiao R, Wang K, Yang F, Li XJ, Li XL. Identification of Genomic Regions and Candidate Genes for Litter Traits in French Large White Pigs Using Genome-Wide Association Studies. Animals (Basel) 2022; 12:ani12121584. [PMID: 35739920 PMCID: PMC9219640 DOI: 10.3390/ani12121584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/09/2022] [Accepted: 06/17/2022] [Indexed: 11/16/2022] Open
Abstract
The reproductive traits of sows are one of the important economic traits in pig production, and their performance directly affects the economic benefits of the entire pig industry. In this study, a total of 895 French Large White pigs were genotyped by GeneSeek Porcine 50K SNP Beadchip and four phenotypic traits of 1407 pigs were recorded, including total number born (TNB), number born alive (NBA), number healthy piglets (NHP) and litter weight born alive (LWB). To identify genomic regions and genes for these traits, we used two approaches: a single-locus genome-wide association study (GWAS) and a single-step GWAS (ssGWAS). Overall, a total of five SNPs and 36 genomic regions were identified by single-locus GWAS and ssGWAS, respectively. Notably, fourof all five significant SNPs were located in 10.72–11.06 Mb on chromosome 7, were also identified by ssGWAS. These regions explained the highest or second highest genetic variance in the TNB, NBA and NHP traits and harbor the protein coding gene ENSSSCG00000042180. In addition, several candidate genes associated with litter traits were identified, including JARID2, PDIA6, FLRT2 and DICER1. Overall, these novel results reflect the polygenic genetic architecture of the litter traits and provide a theoretical reference for the following implementation of molecular breeding.
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24
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Yu L, Xu J, Qiao R, Han B, Zhong H, Zhong R. 148P Pathological stage N1 limited-stage small-cell lung cancer patients can benefit from surgical resection. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.02.179] [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] Open
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25
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Li C, Duan D, Xue Y, Han X, Wang K, Qiao R, Li XL, Li XJ. An association study on imputed whole-genome resequencing from high-throughput sequencing data for body traits in crossbred pigs. Anim Genet 2022; 53:212-219. [PMID: 35026054 DOI: 10.1111/age.13170] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 10/20/2021] [Accepted: 12/24/2021] [Indexed: 12/12/2022]
Abstract
Body traits are important economic factors in the pig industry. Genome-wide association studies (GWASs) have been widely applied using high-density genotype data to detect QTL in pigs. The aim of the present study was to detect the genetic variants significantly associated with body traits in crossbred pigs using the Illumina Porcine SNP50 BeadChip and imputed whole-genome sequence data. A set of seven body traits - body length, body height, chest circumference, cannon bone circumference, leg buttock circumference, back fat thickness and loin muscle depth - were measured. Moderate to high heritabilities were obtained for most traits (from 0.14 to 0.46), and significant genetic and phenotypic correlations among them were observed. GWAS identified 714 significantly associated SNPs located at 39 regions on all autosomes for body traits, and a total of seven functionally related candidate genes: PIK3CD, HOXA, PCGF2, CHST11, COL2A1, BMI1 and OSR2. Functional enrichment analysis revealed that candidate genes were enriched in the estrogen signaling pathway, embryonic skeletal system morphogenesis and embryonic skeletal system development. These results aim to uncover the genetic mechanisms underlying body development and marker-assisted selection programs focusing on body traits in pigs.
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Affiliation(s)
- Cong Li
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Dongdong Duan
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yahui Xue
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xuelei Han
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Kejun Wang
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Ruimin Qiao
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xiu-Ling Li
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xin-Jian Li
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, Henan, China
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26
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Ju M, Wang X, Li X, Zhang M, Shi L, Hu P, Zhang B, Han X, Wang K, Li X, Zhou L, Qiao R. Effects of Litter Size and Parity on Farrowing Duration of Landrace × Yorkshire Sows. Animals (Basel) 2021; 12:ani12010094. [PMID: 35011200 PMCID: PMC8749871 DOI: 10.3390/ani12010094] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/24/2021] [Accepted: 12/29/2021] [Indexed: 01/21/2023] Open
Abstract
Simple Summary Litter size is an important economic trait in pigs. Improving the number born alive is an important breeding goal of the pig husbandry. A shorter farrowing duration is welcome for facilitating the management and sows’ health. Therefore, the aim of this study was to explore the effect of litter size and parity on farrowing duration, to determine whether a shorter length of farrowing duration could be considered as a breeding parameter in pig breeding. Our results showed the total number born had no significant relation with farrowing duration, but number of stillbirths increased with the prolongation of farrowing duration and decrease of live litter size if farrowing duration was longer than 240–300 min. Different parities sows had little difference in the same farrowing duration interval except for gilts. A shorter farrowing duration within 300 min might be considered in pig breeding without worrying about the decreasing of live litter size or the negative effect of parity. Abstract Litter size has increased and farrowing duration has also prolonged in recent years. The aim of this study was to analyze the effect of litter size and parity on farrowing duration (FAR) to estimate the possibility of selecting a short farrowing duration. We recorded 32,200 parturitions of 8420 Landrace × Yorkshire sows, determined farrowing duration, litter size, parity, gestation length. Results showed that total number of born (TNB) and parity obeyed a cubic (p = 0.0004, p = 0.004) relationship while number born alive (NBA) and number born dead (NBD) obeyed a linear (p = 0.0239, p = 0.0035) relationship with FAR. Gestation length obeyed a linear (p = 0.02) relationship with FAR. FAR of sows with stillbirth was longer than that of sows without stillbirth. Stillbirth rate increased rapidly from about 2% to 4%, especially when FAR was over 240 min. FAR gradually prolonged with the parities. FAR of 7th parity sows was longer than that of 1st~6th parity sows (p < 0.05), but different parity sows had little difference in the same FAR interval except for gilts. Results indicated it was possible and necessary to consider FAR into pig breeding without worrying about decreasing of live litter size or negative effect of parity if FAR was shorter than 300 min.
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Affiliation(s)
- Mingming Ju
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (M.J.); (X.W.); (X.L.); (M.Z.); (L.S.); (P.H.); (B.Z.); (X.H.); (K.W.); (X.L.)
| | - Xiaonv Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (M.J.); (X.W.); (X.L.); (M.Z.); (L.S.); (P.H.); (B.Z.); (X.H.); (K.W.); (X.L.)
| | - Xinjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (M.J.); (X.W.); (X.L.); (M.Z.); (L.S.); (P.H.); (B.Z.); (X.H.); (K.W.); (X.L.)
| | - Menghao Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (M.J.); (X.W.); (X.L.); (M.Z.); (L.S.); (P.H.); (B.Z.); (X.H.); (K.W.); (X.L.)
| | - Lidan Shi
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (M.J.); (X.W.); (X.L.); (M.Z.); (L.S.); (P.H.); (B.Z.); (X.H.); (K.W.); (X.L.)
| | - Panyang Hu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (M.J.); (X.W.); (X.L.); (M.Z.); (L.S.); (P.H.); (B.Z.); (X.H.); (K.W.); (X.L.)
| | - Ben Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (M.J.); (X.W.); (X.L.); (M.Z.); (L.S.); (P.H.); (B.Z.); (X.H.); (K.W.); (X.L.)
| | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (M.J.); (X.W.); (X.L.); (M.Z.); (L.S.); (P.H.); (B.Z.); (X.H.); (K.W.); (X.L.)
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (M.J.); (X.W.); (X.L.); (M.Z.); (L.S.); (P.H.); (B.Z.); (X.H.); (K.W.); (X.L.)
| | - Xiuling Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (M.J.); (X.W.); (X.L.); (M.Z.); (L.S.); (P.H.); (B.Z.); (X.H.); (K.W.); (X.L.)
| | - Lisheng Zhou
- College of Animal Science, Qingdao Agricultural University, Qingdao 266109, China;
| | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (M.J.); (X.W.); (X.L.); (M.Z.); (L.S.); (P.H.); (B.Z.); (X.H.); (K.W.); (X.L.)
- Correspondence:
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Qi K, Liu Y, Li C, Li X, Li X, Wang K, Qiao R, Han X. Construction of circRNA-related ceRNA networks in longissimus dorsi muscle of Queshan Black and Large White pigs. Mol Genet Genomics 2021; 297:101-112. [PMID: 34792645 DOI: 10.1007/s00438-021-01836-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 11/06/2021] [Indexed: 11/24/2022]
Abstract
Circular RNA (circRNA) is a class of non-coding RNA (ncRNA) that plays an important regulatory role in various biological processes of the organisms and has a major function in muscle growth and development. However, its molecular mechanisms of how it regulates pork quality remain unclear at present. In this study, we compared the longissimus dorsi (LD) muscle expression profiles of Queshan Black (QS) and Large White (LW) pigs to explore the role of circRNAs in meat quality using transcriptome sequencing. A total of 62 differentially expressed circRNAs (DECs), including 46 up- and 16 down-regulated, 39 differentially expressed miRNAs (DEmiRNAs), including 21 up- and 18 down-regulated and 404 differentially expressed mRNAs (DEMs), including 174 up- and 230 down-regulated were identified, and most circRNAs were composed of exons. Our results indicated that the DEC parent genes and DEMs were enriched in the positive regulation of fast-twitch skeletal muscle fiber contraction, relaxation of skeletal muscle, regulation of myoblast proliferation, AMPK signaling pathway, Wnt and Jak-STAT signaling pathway. Furthermore, circSETBP1/ssc-miR-149/PIK3CD and circGUCY2C/ssc-miR-425-3p/CFL1 were selected by constructing the competitive endogenous RNA (ceRNA) regulatory network, circSETBP1, circGUCY2C, PIK3CD and CFL1 had low expression level in QS, while ssc-miR-149 and ssc-miR-425-3p had higher expression level than LW, our analysis revealed that circSETBP1, circGUCY2C, ssc-miR-149, ssc-miR-425-3p, PIK3CD and CFL1 were associated with lipid regulation, cell proliferation and differentiation, so the two ceRNAs regulatory networks may play an important role in regulating intramuscular fat (IMF) deposition, thereby affecting pork quality. In conclusion, we described the gene regulation by the circRNA-miRNA-mRNA ceRNA networks by comparing QS and LW pigs LD muscle transcriptome, and the two new circRNA-associated ceRNA regulatory networks that could help to elucidate the formation mechanism of pork quality. The results provide a theoretical basis for further understanding the genetic mechanism of meat quality formation.
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Affiliation(s)
- Kunlong Qi
- College of Animal Science and Technology, Henan Agricultural University, No.218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, China
| | - Yingke Liu
- College of Animal Science and Technology, Henan Agricultural University, No.218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, China
| | - Chenlei Li
- College of Animal Science and Technology, Henan Agricultural University, No.218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, China
| | - Xinjian Li
- College of Animal Science and Technology, Henan Agricultural University, No.218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, China
| | - Xiuling Li
- College of Animal Science and Technology, Henan Agricultural University, No.218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, No.218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, China
| | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, No.218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, China
| | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, No.218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, China.
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Roychoudhury S, Zhuo Z, Qiao R, Wan L, Liang Y, Pan F, Chuang YD, Prendergast D, Yang W. Controlled Experiments and Optimized Theory of Absorption Spectra of Li Metal and Salts. ACS Appl Mater Interfaces 2021; 13:45488-45495. [PMID: 34529403 DOI: 10.1021/acsami.1c11970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Investigation of Li metal and ionic compounds through experimental and theoretical spectroscopy has been of tremendous interest due to their prospective applications in Li-metal and Li-ion batteries. Li K-edge soft X-ray absorption spectroscopy (sXAS) provides the most direct spectroscopic characterization; unfortunately, due to the low core-level energy and the highly reactive surface, Li-K sXAS of Li metal has been extremely challenging, as evidenced by many controversial reports. Here, through controlled and ultra-high energy resolution experiments of two kinds of in situ prepared samples, we report the intrinsic Li-K sXAS of Li-metal that displays a prominent leading peak that has not been revealed before. Furthermore, theoretical simulations show that, due to the low number of valence electrons in Li, the Li-K sXAS is strongly affected by the response of the valence electrons to the core hole. We successfully reproduce the Li-K sXAS by state-of-the-art calculations with considerations of a number of relevant parameters such as temperature, energy resolution, and, especially, contributions from transitions which are forbidden in the single-particle treatment. Such a comparative experimental and theoretical investigation is further extended to a series of Li ionic compounds, which highlight the importance of considering the total and single-particle energies for obtaining an accurate alignment of the spectra. Our work provides the first reliable Li-K sXAS of the Li metal surface with advanced theoretical calculations. The experimental and theoretical results provide a critical benchmark for studying Li chemistry in both metallic and ionic states.
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Affiliation(s)
- Subhayan Roychoudhury
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley California 94720, United States
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley California 94720, United States
| | - Zengqing Zhuo
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley California 94720, United States
| | - Ruimin Qiao
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley California 94720, United States
| | - Liwen Wan
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Yufeng Liang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley California 94720, United States
| | - Feng Pan
- School of Advanced Materials, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yi-de Chuang
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley California 94720, United States
| | - David Prendergast
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley California 94720, United States
| | - Wanli Yang
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley California 94720, United States
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29
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Li X, Han X, Sun C, Li G, Wang K, Li X, Qiao R. Analysis of mRNA and Long Non-Coding RNA Expression Profiles in Developing Yorkshire Pig Spleens. Animals (Basel) 2021; 11:ani11102768. [PMID: 34679790 PMCID: PMC8532824 DOI: 10.3390/ani11102768] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/16/2021] [Accepted: 09/18/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary Epidemic disease is a prominent problem in intensive pig production. The spleen is a blood bank and the largest immune organ, and most of the diseases in pig farms will be reflected as spleen abnormality. The results showed how the mRNA–lncRNA expression profiles in Yorkshire spleens varied with age (seven, 90, and 180 days after birth). Our study shows that 90 days after birth the gene-expression profile of pig spleen no longer changes significantly. The results are helpful for a better understanding of the transcriptome and functional genomics of spleen tissue in farm animals and could provide reference for precision pig disease research and prevention and control in pig farms. Abstract Epidemic diseases cause great economic loss in pig farms each year; some of these diseases are characterized mainly in the spleen, but mRNA and lncRNA (long non-coding RNA) expression networks in developing Yorkshire pig spleens remain obscure. Here, we profiled the systematic characters of mRNA and lncRNA repertoires in three groups of spleens from nine Yorkshire pigs, each three aged at seven days, 90 days, and 180 days. By using a precise mRNA and lncRNA identification pipeline, we identified 19,647 genes and 219 known and 3219 putative lncRNA transcripts; 1729 genes and 64 lncRNAs therein were found to express differentially. The gene expression characteristics of genes and lncRNAs were found to be basically fixed before 90 days after birth. Three large gene expression modules were detected. The enrichment analyses of differentially expressed genes and the potential target genes of differentially expressed lncRNAs both displayed the crucial roles of up-regulation in immune activation and hematopoiesis, and down-regulation in cell replication and division in 90 days and 180 days compared to seven days. ENSSSCT00000001325 was the only lncRNA transcript that existed in the three groups. CDK1, PCNA, and PLK were detected to be node genes that varied with age. This study contributes to a further understanding of mRNA and lncRNA expression in different developmental pig spleens.
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30
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Yun W, Sechadri S, Spink I, Qiao R, Lewis S. Holistically optimized laboratory XAS systems. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321094484] [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: 11/10/2022] Open
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31
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Wang K, Zhang L, Duan D, Qiao R, Li X, Li X, Han X. Genomic Analysis Reveals Human-Mediated Introgression From European Commercial Pigs to Henan Indigenous Pigs. Front Genet 2021; 12:705803. [PMID: 34220966 PMCID: PMC8249855 DOI: 10.3389/fgene.2021.705803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 05/24/2021] [Indexed: 11/13/2022] Open
Abstract
Introgression of genetic features from European pigs into Chinese pigs was reported possibly contributing to improvements in productivity traits, such as feed conversion efficiency and body size. However, the genomic differences from European pigs and the potential role of introgression in Henan indigenous pigs remains unclear. In this study, we found significant introgression from European pigs into the genome of Chinese indigenous pigs, especially in Henan indigenous pigs. The introgression in Henan indigenous pigs, particularly in the Nanyang black pig, was mainly derived from Duroc pigs. Most importantly, we found that the NR6A1, GPD2, and CSRNP3 genes were introgressed and reshaped by artificial selection, and these may have contributed to increases in pig body size and feed conversion efficiency. Our results suggest that human-mediated introgression and selection have reshaped the genome of Henan pigs and improved several of their desired traits. These findings contribute to our understanding of the history of Henan indigenous pigs and provide insights into the genetic mechanisms affecting economically important traits in pig populations.
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Affiliation(s)
- Kejun Wang
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, China
| | - Lige Zhang
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, China
| | - Dongdong Duan
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, China
| | - Ruimin Qiao
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, China
| | - Xiuling Li
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, China
| | - Xinjian Li
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, China
| | - Xuelei Han
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, China
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32
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Alemanno F, An Q, Azzarello P, Barbato FCT, Bernardini P, Bi XJ, Cai MS, Catanzani E, Chang J, Chen DY, Chen JL, Chen ZF, Cui MY, Cui TS, Cui YX, Dai HT, D'Amone A, De Benedittis A, De Mitri I, de Palma F, Deliyergiyev M, Di Santo M, Dong TK, Dong ZX, Donvito G, Droz D, Duan JL, Duan KK, D'Urso D, Fan RR, Fan YZ, Fang K, Fang F, Feng CQ, Feng L, Fusco P, Gao M, Gargano F, Gong K, Gong YZ, Guo DY, Guo JH, Guo XL, Han SX, Hu YM, Huang GS, Huang XY, Huang YY, Ionica M, Jiang W, Kong J, Kotenko A, Kyratzis D, Lei SJ, Li S, Li WL, Li X, Li XQ, Liang YM, Liu CM, Liu H, Liu J, Liu SB, Liu WQ, Liu Y, Loparco F, Luo CN, Ma M, Ma PX, Ma T, Ma XY, Marsella G, Mazziotta MN, Mo D, Niu XY, Pan X, Parenti A, Peng WX, Peng XY, Perrina C, Qiao R, Rao JN, Ruina A, Salinas MM, Shang GZ, Shen WH, Shen ZQ, Shen ZT, Silveri L, Song JX, Stolpovskiy M, Su H, Su M, Sun ZY, Surdo A, Teng XJ, Tykhonov A, Wang H, Wang JZ, Wang LG, Wang S, Wang XL, Wang Y, Wang YF, Wang YZ, Wang ZM, Wei DM, Wei JJ, Wei YF, Wen SC, Wu D, Wu J, Wu LB, Wu SS, Wu X, Xia ZQ, Xu HT, Xu ZH, Xu ZL, Xu ZZ, Xue GF, Yang HB, Yang P, Yang YQ, Yao HJ, Yu YH, Yuan GW, Yuan Q, Yue C, Zang JJ, Zhang F, Zhang SX, Zhang WZ, Zhang Y, Zhang YJ, Zhang YL, Zhang YP, Zhang YQ, Zhang Z, Zhang ZY, Zhao C, Zhao HY, Zhao XF, Zhou CY, Zhu Y. Measurement of the Cosmic Ray Helium Energy Spectrum from 70 GeV to 80 TeV with the DAMPE Space Mission. Phys Rev Lett 2021; 126:201102. [PMID: 34110215 DOI: 10.1103/physrevlett.126.201102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/25/2021] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
The measurement of the energy spectrum of cosmic ray helium nuclei from 70 GeV to 80 TeV using 4.5 years of data recorded by the Dark Matter Particle Explorer (DAMPE) is reported in this work. A hardening of the spectrum is observed at an energy of about 1.3 TeV, similar to previous observations. In addition, a spectral softening at about 34 TeV is revealed for the first time with large statistics and well controlled systematic uncertainties, with an overall significance of 4.3σ. The DAMPE spectral measurements of both cosmic protons and helium nuclei suggest a particle charge dependent softening energy, although with current uncertainties a dependence on the number of nucleons cannot be ruled out.
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Affiliation(s)
- F Alemanno
- Gran Sasso Science Institute (GSSI), Via Iacobucci 2, I-67100 L'Aquila, Italy
- Istituto Nazionale di Fisica Nucleare (INFN)-Laboratori Nazionali del Gran Sasso, I-67100 Assergi, L'Aquila, Italy
| | - Q An
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - P Azzarello
- Department of Nuclear and Particle Physics, University of Geneva, CH-1211 Geneva, Switzerland
| | - F C T Barbato
- Gran Sasso Science Institute (GSSI), Via Iacobucci 2, I-67100 L'Aquila, Italy
- Istituto Nazionale di Fisica Nucleare (INFN)-Laboratori Nazionali del Gran Sasso, I-67100 Assergi, L'Aquila, Italy
| | - P Bernardini
- Dipartimento di Matematica e Fisica E. De Giorgi, Università del Salento, I-73100 Lecce, Italy
- Istituto Nazionale di Fisica Nucleare (INFN)-Sezione di Lecce, I-73100 Lecce, Italy
| | - X J Bi
- Institute of High Energy Physics, Chinese Academy of Sciences, Yuquan Road 19B, Beijing 100049, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
| | - M S Cai
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - E Catanzani
- Istituto Nazionale di Fisica Nucleare (INFN)-Sezione di Perugia, I-06123 Perugia, Italy
| | - J Chang
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - D Y Chen
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
| | - J L Chen
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - Z F Chen
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - M Y Cui
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
| | - T S Cui
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian district, Beijing 100190, China
| | - Y X Cui
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - H T Dai
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - A D'Amone
- Dipartimento di Matematica e Fisica E. De Giorgi, Università del Salento, I-73100 Lecce, Italy
- Istituto Nazionale di Fisica Nucleare (INFN)-Sezione di Lecce, I-73100 Lecce, Italy
| | - A De Benedittis
- Dipartimento di Matematica e Fisica E. De Giorgi, Università del Salento, I-73100 Lecce, Italy
- Istituto Nazionale di Fisica Nucleare (INFN)-Sezione di Lecce, I-73100 Lecce, Italy
| | - I De Mitri
- Gran Sasso Science Institute (GSSI), Via Iacobucci 2, I-67100 L'Aquila, Italy
- Istituto Nazionale di Fisica Nucleare (INFN)-Laboratori Nazionali del Gran Sasso, I-67100 Assergi, L'Aquila, Italy
| | - F de Palma
- Dipartimento di Matematica e Fisica E. De Giorgi, Università del Salento, I-73100 Lecce, Italy
- Istituto Nazionale di Fisica Nucleare (INFN)-Sezione di Lecce, I-73100 Lecce, Italy
| | - M Deliyergiyev
- Department of Nuclear and Particle Physics, University of Geneva, CH-1211 Geneva, Switzerland
| | - M Di Santo
- Dipartimento di Matematica e Fisica E. De Giorgi, Università del Salento, I-73100 Lecce, Italy
- Istituto Nazionale di Fisica Nucleare (INFN)-Sezione di Lecce, I-73100 Lecce, Italy
| | - T K Dong
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
| | - Z X Dong
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian district, Beijing 100190, China
| | - G Donvito
- Istituto Nazionale di Fisica Nucleare (INFN)-Sezione di Bari, I-70125 Bari, Italy
| | - D Droz
- Department of Nuclear and Particle Physics, University of Geneva, CH-1211 Geneva, Switzerland
| | - J L Duan
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - K K Duan
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
| | - D D'Urso
- Istituto Nazionale di Fisica Nucleare (INFN)-Sezione di Perugia, I-06123 Perugia, Italy
| | - R R Fan
- Institute of High Energy Physics, Chinese Academy of Sciences, Yuquan Road 19B, Beijing 100049, China
| | - Y Z Fan
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - K Fang
- Institute of High Energy Physics, Chinese Academy of Sciences, Yuquan Road 19B, Beijing 100049, China
| | - F Fang
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - C Q Feng
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - L Feng
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
| | - P Fusco
- Istituto Nazionale di Fisica Nucleare (INFN)-Sezione di Bari, I-70125 Bari, Italy
- Dipartimento di Fisica "M. Merlin" dell'Università e del Politecnico di Bari, I-70126 Bari, Italy
| | - M Gao
- Institute of High Energy Physics, Chinese Academy of Sciences, Yuquan Road 19B, Beijing 100049, China
| | - F Gargano
- Istituto Nazionale di Fisica Nucleare (INFN)-Sezione di Bari, I-70125 Bari, Italy
| | - K Gong
- Institute of High Energy Physics, Chinese Academy of Sciences, Yuquan Road 19B, Beijing 100049, China
| | - Y Z Gong
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
| | - D Y Guo
- Institute of High Energy Physics, Chinese Academy of Sciences, Yuquan Road 19B, Beijing 100049, China
| | - J H Guo
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - X L Guo
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - S X Han
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian district, Beijing 100190, China
| | - Y M Hu
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
| | - G S Huang
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - X Y Huang
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - Y Y Huang
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
| | - M Ionica
- Istituto Nazionale di Fisica Nucleare (INFN)-Sezione di Perugia, I-06123 Perugia, Italy
| | - W Jiang
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - J Kong
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - A Kotenko
- Department of Nuclear and Particle Physics, University of Geneva, CH-1211 Geneva, Switzerland
| | - D Kyratzis
- Gran Sasso Science Institute (GSSI), Via Iacobucci 2, I-67100 L'Aquila, Italy
- Istituto Nazionale di Fisica Nucleare (INFN)-Laboratori Nazionali del Gran Sasso, I-67100 Assergi, L'Aquila, Italy
| | - S J Lei
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
| | - S Li
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
| | - W L Li
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian district, Beijing 100190, China
| | - X Li
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
| | - X Q Li
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian district, Beijing 100190, China
| | - Y M Liang
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian district, Beijing 100190, China
| | - C M Liu
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - H Liu
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
| | - J Liu
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - S B Liu
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - W Q Liu
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - Y Liu
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
| | - F Loparco
- Istituto Nazionale di Fisica Nucleare (INFN)-Sezione di Bari, I-70125 Bari, Italy
- Dipartimento di Fisica "M. Merlin" dell'Università e del Politecnico di Bari, I-70126 Bari, Italy
| | - C N Luo
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - M Ma
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian district, Beijing 100190, China
| | - P X Ma
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
| | - T Ma
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
| | - X Y Ma
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian district, Beijing 100190, China
| | - G Marsella
- Dipartimento di Matematica e Fisica E. De Giorgi, Università del Salento, I-73100 Lecce, Italy
- Istituto Nazionale di Fisica Nucleare (INFN)-Sezione di Lecce, I-73100 Lecce, Italy
| | - M N Mazziotta
- Istituto Nazionale di Fisica Nucleare (INFN)-Sezione di Bari, I-70125 Bari, Italy
| | - D Mo
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - X Y Niu
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - X Pan
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - A Parenti
- Gran Sasso Science Institute (GSSI), Via Iacobucci 2, I-67100 L'Aquila, Italy
- Istituto Nazionale di Fisica Nucleare (INFN)-Laboratori Nazionali del Gran Sasso, I-67100 Assergi, L'Aquila, Italy
| | - W X Peng
- Institute of High Energy Physics, Chinese Academy of Sciences, Yuquan Road 19B, Beijing 100049, China
| | - X Y Peng
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
| | - C Perrina
- Department of Nuclear and Particle Physics, University of Geneva, CH-1211 Geneva, Switzerland
| | - R Qiao
- Institute of High Energy Physics, Chinese Academy of Sciences, Yuquan Road 19B, Beijing 100049, China
| | - J N Rao
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian district, Beijing 100190, China
| | - A Ruina
- Department of Nuclear and Particle Physics, University of Geneva, CH-1211 Geneva, Switzerland
| | - M M Salinas
- Department of Nuclear and Particle Physics, University of Geneva, CH-1211 Geneva, Switzerland
| | - G Z Shang
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian district, Beijing 100190, China
| | - W H Shen
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian district, Beijing 100190, China
| | - Z Q Shen
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
| | - Z T Shen
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - L Silveri
- Gran Sasso Science Institute (GSSI), Via Iacobucci 2, I-67100 L'Aquila, Italy
- Istituto Nazionale di Fisica Nucleare (INFN)-Laboratori Nazionali del Gran Sasso, I-67100 Assergi, L'Aquila, Italy
| | - J X Song
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian district, Beijing 100190, China
| | - M Stolpovskiy
- Department of Nuclear and Particle Physics, University of Geneva, CH-1211 Geneva, Switzerland
| | - H Su
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - M Su
- Department of Physics and Laboratory for Space Research, the University of Hong Kong, Pok Fu Lam, Hong Kong SAR 999077, China
| | - Z Y Sun
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - A Surdo
- Istituto Nazionale di Fisica Nucleare (INFN)-Sezione di Lecce, I-73100 Lecce, Italy
| | - X J Teng
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian district, Beijing 100190, China
| | - A Tykhonov
- Department of Nuclear and Particle Physics, University of Geneva, CH-1211 Geneva, Switzerland
| | - H Wang
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian district, Beijing 100190, China
| | - J Z Wang
- Institute of High Energy Physics, Chinese Academy of Sciences, Yuquan Road 19B, Beijing 100049, China
| | - L G Wang
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian district, Beijing 100190, China
| | - S Wang
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - X L Wang
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - Y Wang
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - Y F Wang
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - Y Z Wang
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
| | - Z M Wang
- Gran Sasso Science Institute (GSSI), Via Iacobucci 2, I-67100 L'Aquila, Italy
- Istituto Nazionale di Fisica Nucleare (INFN)-Laboratori Nazionali del Gran Sasso, I-67100 Assergi, L'Aquila, Italy
| | - D M Wei
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - J J Wei
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
| | - Y F Wei
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - S C Wen
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - D Wu
- Institute of High Energy Physics, Chinese Academy of Sciences, Yuquan Road 19B, Beijing 100049, China
| | - J Wu
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - L B Wu
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - S S Wu
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian district, Beijing 100190, China
| | - X Wu
- Department of Nuclear and Particle Physics, University of Geneva, CH-1211 Geneva, Switzerland
| | - Z Q Xia
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
| | - H T Xu
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian district, Beijing 100190, China
| | - Z H Xu
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - Z L Xu
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
| | - Z Z Xu
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - G F Xue
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian district, Beijing 100190, China
| | - H B Yang
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - P Yang
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - Y Q Yang
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - H J Yao
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - Y H Yu
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - G W Yuan
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - Q Yuan
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - C Yue
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
| | - J J Zang
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
| | - F Zhang
- Institute of High Energy Physics, Chinese Academy of Sciences, Yuquan Road 19B, Beijing 100049, China
| | - S X Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - W Z Zhang
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian district, Beijing 100190, China
| | - Y Zhang
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
| | - Y J Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - Y L Zhang
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - Y P Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - Y Q Zhang
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
| | - Z Zhang
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210023, China
| | - Z Y Zhang
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - C Zhao
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - H Y Zhao
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - X F Zhao
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian district, Beijing 100190, China
| | - C Y Zhou
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian district, Beijing 100190, China
| | - Y Zhu
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian district, Beijing 100190, China
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Yu L, Xu J, Qiao R, Zhong H, Han B, Zhong R. 59P Patterns of recurrence and survival after complete resection of pathological stage N2 small cell lung cancer. J Thorac Oncol 2021. [DOI: 10.1016/s1556-0864(21)01901-8] [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: 11/26/2022]
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Li XJ, Wang M, Xue Y, Duan D, Li C, Ye J, Han X, Qiao R, Wang K, Li XL. Characterization and comparison of the bacterial community between complete intensive and extensive feeding patterns in pigs. AMB Express 2021; 11:32. [PMID: 33630191 PMCID: PMC7907295 DOI: 10.1186/s13568-021-01191-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 02/09/2021] [Indexed: 12/26/2022] Open
Abstract
To investigate and compare the gut microbiota structures in complete intensive feeding pattern (CP) and extensive feeding pattern (EP) groups, a total of 20 pigs were divided into two groups and fed the same diet. The fecal microbial composition was profiled using 16S rRNA gene sequencing. Our results showed that seventeen predominant genera were present in each pig sample and constituted the phylogenetic core of the microbiota at the class level. The abundance of most of the core microbial flora were significantly higher in the CP group than in the EP group (P < 0.05), while the abundance of Gammaproteobacteria was significantly lower in the CP group than in the EP group (P < 0.05). The CP group had significantly greater community diversity, richness, and evenness than the EP group (P < 0.05). Functional prediction analysis indicated that intestinal microbial species potentially led to faster growth and an increased fat accumulation capacity in the CP group; however, disease resistance was weaker in the CP group than in the EP group. In conclusion, EP pigs have a wider range of activity and better animal welfare than CP pigs, which helps reduce the occurrence of diseases and neurological symptoms. To explore the effect of intestinal flora on disease resistance in pigs at the molecular level, Coprococcus, which is a key gut bacterium in the intestine, was selected for isolation and purification and cocultured with intestinal epithelial cells. qPCR was performed to determine the effect of Coprococcus on SLA-DRB gene expression in intestinal epithelial cells. The results showed that Coprococcus enhanced SLA-DRB gene expression in intestinal epithelial cells. The results provide useful reference data for further study on the relationship between intestinal flora and pig disease resistance.
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Xiao Y, Jia S, Zhao W, Zhang Y, Qiao R, Xia X, Hou L, Dong B. The Combined Effect of Hearing Impairment and Cognitive Impairment with Health-Related Outcomes in Chinese Older People. J Nutr Health Aging 2021; 25:783-789. [PMID: 34179934 DOI: 10.1007/s12603-021-1623-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
OBJECTIVES To determine the risk of poor health-related outcomes in older adults with cooccurring hearing impairment and cognitive impairment, and to compare the risk of hearing impairment only, cognitive impairment only, and multiple morbidities. DESIGN Cross-sectional study. SETTING Community-dwelling older adults aged 60 years and older were included. PARTICIPANTS The data of missing hearing and cognitive status were excluded, and 3770 older people participated in the study. MEASUREMENTS The hearing function evaluation was conducted by questionnaire survey. Assessment of cognitive function was completed using the SPMSQ scale. The subjects were divided into hearing impairment and cognitive impairment group, hearing impairment only group, cognitive impairment only group and neither group. Multiple logistic regression was used to analyze the risks of hearing and cognitive impairment and health-related condition. RESULTS The prevalence of hearing impairment and cognitive impairment, hearing impairment only, cognitive impairment only, and neither were 9.4%, 8.3%, 29.9% and 52.4%, respectively. Compared with the control group, the individuals with hearing impairment and cognitive impairment were associated with depression (OR=3.48, 95% CI=2.66, 4.56), anxiety (OR=2.35, 95% CI=1.92, 3.33), frailty (OR=4.30, 95% CI=2.89, 6.40), and ADL impairment (OR=2.77, 95% CI=2.03, 3.77). CONCLUSION The studies shows that hearing impairment combined with cognitive impairment is significantly associated with anxiety, depression, frailty, and ADL impairment. Comprehensive management and intervention should be provided for older people to reduce the occurrence of adverse health consequences.
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Affiliation(s)
- Y Xiao
- Professor Birong Dong, West China Hospital, Sichuan University, No. 37, Guo Xue Xiang Renmin Nan Lu, Chengdu, Sichuan, 610041, China, fax: +86-028-85422321, Telephone: +86-18980601332, E-mail address:
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Xue Y, Li C, Duan D, Wang M, Han X, Wang K, Qiao R, Li XJ, Li XL. Genome-wide association studies for growth-related traits in a crossbreed pig population. Anim Genet 2020; 52:217-222. [PMID: 33372713 DOI: 10.1111/age.13032] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2020] [Indexed: 12/24/2022]
Abstract
Growth-related traits are important economic traits in the pig industry that directly influence pork production efficiency. To detect quantitative trait loci and candidate genes affecting growth traits, genome-wide association studies were performed for backfat thickness (BF) and loin muscle depth (LMD) in 370 Chuying-black pigs using Illumina PorcineSNP50 BeadChip array. We totally identified 14 BF-associated SNPs, which included 11 genome-wide SNPs (P < 1.39E-06) and 3 chromosome-wide suggestive SNPs (P < 2.79E-05) and for LMD, 9 SNPs surpassed the genome-wide significant threshold (P < 1.39E-06). These SNPs explained 30.33 and 27.51% phenotypic variance for BF and LMD respectively. Furthermore, 14 and 9 genes nearest to the significant SNPs were selected to be candidate genes, including MAGED1, GPHN, CCSER1, and GUCY2D for BF and PARM1, COL18A1, HSF5, and SCML2 genes for LMD. One significant SNP, which explained 6.07% of phenotypic variance for BF, mapped to a pleiotropic quantitative trait locus with a 494-kb interval. Together, the SNPs and candidate genes identified in this study will advance our understanding of the complex genetic architecture of BF and LMD traits, and they will also provide important clues for future implementation of a genomic selection program in Chuying-black pigs.
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Affiliation(s)
- Y Xue
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, Henan, 450046, China
| | - C Li
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, Henan, 450046, China
| | - D Duan
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, Henan, 450046, China
| | - M Wang
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, Henan, 450046, China
| | - X Han
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, Henan, 450046, China
| | - K Wang
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, Henan, 450046, China
| | - R Qiao
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, Henan, 450046, China
| | - X-J Li
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, Henan, 450046, China
| | - X-L Li
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, Henan, 450046, China
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Li Q, Qiao R, Mehta A, Lü W, Zhou T, Arenholz E, Wang C, Chen Y, Li L, Tian Y, Bai L, Hussain Z, Zheng R, Yang W, Yan S. Amorphous nonstoichiometric oxides with tunable room-temperature ferromagnetism and electrical transport. Sci Bull (Beijing) 2020; 65:1718-1725. [PMID: 36659244 DOI: 10.1016/j.scib.2020.06.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/20/2020] [Accepted: 06/18/2020] [Indexed: 01/21/2023]
Abstract
Material functionalities strongly depend on the stoichiometry, crystal structure, and homogeneity. Here we demonstrate an approach of amorphous nonstoichiometric inhomogeneous oxides to realize tunable ferromagnetism and electrical transport at room temperature. In order to verify the origin of the ferromagnetism, we employed a series of structural, chemical, and electronic state characterizations. Combined with electron microscopy and transport measurements, synchrotron-based grazing incident wide angle X-ray scattering, soft X-ray absorption and circular dichroism clearly reveal that the room-temperature ferromagnetism originates from the In0.23Co0.77O1-v amorphous phase with a large tunable range of oxygen vacancies. The room-temperature ferromagnetism is tunable from a high saturation magnetization of 500 emu cm-3 to below 25 emu cm-3, with the evolving electrical resistivity from 5 × 103 μΩ cm to above 2.5 × 105 μΩ cm. Inhomogeneous nano-crystallization emerges with decreasing oxygen vacancies, driving the system towards non-ferromagnetism and insulating regime. Our work unfolds the novel functionalities of amorphous nonstoichiometric inhomogeneous oxides, which opens up new opportunities for developing spintronic materials with superior magnetic and transport properties.
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Affiliation(s)
- Qinghao Li
- Spintronics Institute, University of Jinan, Jinan 250022, China; Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ruimin Qiao
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Apurva Mehta
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Weiming Lü
- Spintronics Institute, University of Jinan, Jinan 250022, China
| | - Tie Zhou
- School of Physics, State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
| | - Elke Arenholz
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY 14853, USA
| | - Cheng Wang
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yanxue Chen
- School of Physics, State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
| | - Li Li
- School of Physics, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Yufeng Tian
- School of Physics, State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
| | - Lihui Bai
- School of Physics, State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
| | - Zahid Hussain
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Rongkun Zheng
- School of Physics, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Wanli Yang
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Shishen Yan
- Spintronics Institute, University of Jinan, Jinan 250022, China.
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Li XJ, Wang M, Xue Y, Duan D, Li C, Han X, Wang K, Qiao R, Li XL. Identification of microflora related to growth performance in pigs based on 16S rRNA sequence analyses. AMB Express 2020; 10:192. [PMID: 33123840 PMCID: PMC7596147 DOI: 10.1186/s13568-020-01130-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 10/18/2020] [Indexed: 12/13/2022] Open
Abstract
Intestinal microorganisms have been shown to be important factors affecting the growth performance of pigs. Therefore, to investigate the effect of the intestinal microflora structure on the growth performance of pigs, samples from Duroc (n = 10), Landrace (n = 9) and Yorkshire (n = 21) pigs under the same diet and feeding conditions were collected. The fecal microbial composition was profiled via 16S ribosomal RNA (rRNA) gene sequencing. We also analyzed their growth performance. We found that Duroc and Landrace pigs had significant differences in average daily gain (ADG), feed efficiency ratio (FER), growth index (GI), and number of days taken to reach 100 kg (P < 0.05). Moreover, through analysis of the intestinal flora, we also identified 18 species of intestinal flora with significant differences between Duroc and Landrace pigs (P < 0.05). To eliminate the influence of genetic background, the differential intestinal flora of 21 Yorkshire pigs with differences in growth performance was analyzed. The results showed that there were significant correlations between Barnesiella, Dorea, Clostridium and Lactobacillus and pig growth performance. To explore the effect of the intestinal flora on the growth performance of pigs at the molecular level, Lactobacillus, which is the most abundant in the intestine, was selected for isolation and purification and cocultured with intestinal epithelial cells. qPCR was used to determine the effect of Lactobacillus on MC4R gene expression in intestinal epithelial cells. The results showed that Lactobacillus inhibited MC4R gene expression in these cells. The results provide a useful reference for further study of the relationship between the intestinal flora and pig growth performance.
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Feng X, Sallis S, Shao YC, Qiao R, Liu YS, Kao LC, Tremsin AS, Hussain Z, Yang W, Guo J, Chuang YD. Disparate Exciton-Phonon Couplings for Zone-Center and Boundary Phonons in Solid-State Graphite. Phys Rev Lett 2020; 125:116401. [PMID: 32975957 DOI: 10.1103/physrevlett.125.116401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/26/2020] [Accepted: 07/28/2020] [Indexed: 06/11/2023]
Abstract
The exciton-phonon coupling in highly oriented pyrolytic graphite is studied using resonant inelastic x-ray scattering (RIXS) spectroscopy. With ∼70 meV energy resolution, multiple low energy excitations associated with coupling to phonons can be clearly resolved in the RIXS spectra. Using resonance dependence and the closed form for RIXS cross section without considering the intermediate state mixing of phonon modes, the dimensionless coupling constant g is determined to be 5 and 0.35, corresponding to the coupling strength of 0.42 eV+/-20 meV and 0.20 eV+/-20 meV, for zone center and boundary phonons, respectively. The reduced g value for the zone-boundary phonon may be related to its double resonance nature.
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Affiliation(s)
- Xuefei Feng
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Shawn Sallis
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Yu-Cheng Shao
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Department of Physics, University of Houston, Houston, Texas 77204, USA
| | - Ruimin Qiao
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Yi-Sheng Liu
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Li Cheng Kao
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Anton S Tremsin
- Space Science Laboratory, University of California, Berkeley, California 94720, USA
| | - Zahid Hussain
- Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Wanli Yang
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jinghua Guo
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Yi-De Chuang
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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Chen D, Chu T, Chang Q, Zhang Y, Xiong L, Qiao R, Teng J, Han B, Zhong R. EP1.01-65 The Relationship Between Preliminary Efficacy and Prognosis After First-Line EGFR-TKI Treatment of Advanced NSCLC. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.08.2038] [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: 10/25/2022]
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An Q, Asfandiyarov R, Azzarello P, Bernardini P, Bi XJ, Cai MS, Chang J, Chen DY, Chen HF, Chen JL, Chen W, Cui MY, Cui TS, Dai HT, D’Amone A, De Benedittis A, De Mitri I, Di Santo M, Ding M, Dong TK, Dong YF, Dong ZX, Donvito G, Droz D, Duan JL, Duan KK, D’Urso D, Fan RR, Fan YZ, Fang F, Feng CQ, Feng L, Fusco P, Gallo V, Gan FJ, Gao M, Gargano F, Gong K, Gong YZ, Guo DY, Guo JH, Guo XL, Han SX, Hu YM, Huang GS, Huang XY, Huang YY, Ionica M, Jiang W, Jin X, Kong J, Lei SJ, Li S, Li WL, Li X, Li XQ, Li Y, Liang YF, Liang YM, Liao NH, Liu CM, Liu H, Liu J, Liu SB, Liu WQ, Liu Y, Loparco F, Luo CN, Ma M, Ma PX, Ma SY, Ma T, Ma XY, Marsella G, Mazziotta MN, Mo D, Niu XY, Pan X, Peng WX, Peng XY, Qiao R, Rao JN, Salinas MM, Shang GZ, Shen WH, Shen ZQ, Shen ZT, Song JX, Su H, Su M, Sun ZY, Surdo A, Teng XJ, Tykhonov A, Vitillo S, Wang C, Wang H, Wang HY, Wang JZ, Wang LG, Wang Q, Wang S, Wang XH, Wang XL, Wang YF, Wang YP, Wang YZ, Wang ZM, Wei DM, Wei JJ, Wei YF, Wen SC, Wu D, Wu J, Wu LB, Wu SS, Wu X, Xi K, Xia ZQ, Xu HT, Xu ZH, Xu ZL, Xu ZZ, Xue GF, Yang HB, Yang P, Yang YQ, Yang ZL, Yao HJ, Yu YH, Yuan Q, Yue C, Zang JJ, Zhang F, Zhang JY, Zhang JZ, Zhang PF, Zhang SX, Zhang WZ, Zhang Y, Zhang YJ, Zhang YL, Zhang YP, Zhang YQ, Zhang Z, Zhang ZY, Zhao H, Zhao HY, Zhao XF, Zhou CY, Zhou Y, Zhu X, Zhu Y, Zimmer S. Measurement of the cosmic ray proton spectrum from 40 GeV to 100 TeV with the DAMPE satellite. Sci Adv 2019; 5:eaax3793. [PMID: 31799401 PMCID: PMC6868675 DOI: 10.1126/sciadv.aax3793] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 09/03/2019] [Indexed: 05/23/2023]
Abstract
The precise measurement of the spectrum of protons, the most abundant component of the cosmic radiation, is necessary to understand the source and acceleration of cosmic rays in the Milky Way. This work reports the measurement of the cosmic ray proton fluxes with kinetic energies from 40 GeV to 100 TeV, with 2 1/2 years of data recorded by the DArk Matter Particle Explorer (DAMPE). This is the first time that an experiment directly measures the cosmic ray protons up to ~100 TeV with high statistics. The measured spectrum confirms the spectral hardening at ~300 GeV found by previous experiments and reveals a softening at ~13.6 TeV, with the spectral index changing from ~2.60 to ~2.85. Our result suggests the existence of a new spectral feature of cosmic rays at energies lower than the so-called knee and sheds new light on the origin of Galactic cosmic rays.
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Affiliation(s)
| | - Q. An
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - R. Asfandiyarov
- Department of Nuclear and Particle Physics, University of Geneva, Geneva CH-1211, Switzerland
| | - P. Azzarello
- Department of Nuclear and Particle Physics, University of Geneva, Geneva CH-1211, Switzerland
| | - P. Bernardini
- Dipartimento di Matematica e Fisica E. De Giorgi, Università del Salento, I-73100 Lecce, Italy
- Istituto Nazionale di Fisica Nucleare (INFN)–Sezione di Lecce, I-73100 Lecce, Italy
| | - X. J. Bi
- Institute of High Energy Physics, Chinese Academy of Sciences, Yuquan Road 19B, Beijing 100049, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
| | - M. S. Cai
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - J. Chang
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - D. Y. Chen
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - H. F. Chen
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - J. L. Chen
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - W. Chen
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - M. Y. Cui
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - T. S. Cui
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian District, Beijing 100190, China
| | - H. T. Dai
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - A. D’Amone
- Dipartimento di Matematica e Fisica E. De Giorgi, Università del Salento, I-73100 Lecce, Italy
- Istituto Nazionale di Fisica Nucleare (INFN)–Sezione di Lecce, I-73100 Lecce, Italy
| | - A. De Benedittis
- Dipartimento di Matematica e Fisica E. De Giorgi, Università del Salento, I-73100 Lecce, Italy
- Istituto Nazionale di Fisica Nucleare (INFN)–Sezione di Lecce, I-73100 Lecce, Italy
| | - I. De Mitri
- Gran Sasso Science Institute (GSSI), Via Iacobucci 2, I-67100 L’Aquila, Italy
- Istituto Nazionale di Fisica Nucleare (INFN)–Laboratori Nazionali del Gran Sasso, Assergi, I-67100 L’Aquila, Italy
| | - M. Di Santo
- Dipartimento di Matematica e Fisica E. De Giorgi, Università del Salento, I-73100 Lecce, Italy
- Istituto Nazionale di Fisica Nucleare (INFN)–Sezione di Lecce, I-73100 Lecce, Italy
| | - M. Ding
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - T. K. Dong
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - Y. F. Dong
- Institute of High Energy Physics, Chinese Academy of Sciences, Yuquan Road 19B, Beijing 100049, China
| | - Z. X. Dong
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian District, Beijing 100190, China
| | - G. Donvito
- Istituto Nazionale di Fisica Nucleare (INFN)–Sezione di Bari, I-70125, Bari, Italy
| | - D. Droz
- Department of Nuclear and Particle Physics, University of Geneva, Geneva CH-1211, Switzerland
| | - J. L. Duan
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - K. K. Duan
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - D. D’Urso
- Istituto Nazionale di Fisica Nucleare (INFN)–Sezione di Perugia, I-06123 Perugia, Italy
| | - R. R. Fan
- Institute of High Energy Physics, Chinese Academy of Sciences, Yuquan Road 19B, Beijing 100049, China
| | - Y. Z. Fan
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - F. Fang
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - C. Q. Feng
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - L. Feng
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - P. Fusco
- Istituto Nazionale di Fisica Nucleare (INFN)–Sezione di Bari, I-70125, Bari, Italy
- Dipartimento di Fisica “M. Merlin” dell’Università e del Politecnico di Bari, I-70126 Bari, Italy
| | - V. Gallo
- Department of Nuclear and Particle Physics, University of Geneva, Geneva CH-1211, Switzerland
| | - F. J. Gan
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - M. Gao
- Institute of High Energy Physics, Chinese Academy of Sciences, Yuquan Road 19B, Beijing 100049, China
| | - F. Gargano
- Istituto Nazionale di Fisica Nucleare (INFN)–Sezione di Bari, I-70125, Bari, Italy
| | - K. Gong
- Institute of High Energy Physics, Chinese Academy of Sciences, Yuquan Road 19B, Beijing 100049, China
| | - Y. Z. Gong
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - D. Y. Guo
- Institute of High Energy Physics, Chinese Academy of Sciences, Yuquan Road 19B, Beijing 100049, China
| | - J. H. Guo
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - X. L. Guo
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - S. X. Han
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian District, Beijing 100190, China
| | - Y. M. Hu
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - G. S. Huang
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - X. Y. Huang
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - Y. Y. Huang
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - M. Ionica
- Istituto Nazionale di Fisica Nucleare (INFN)–Sezione di Perugia, I-06123 Perugia, Italy
| | - W. Jiang
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - X. Jin
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - J. Kong
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - S. J. Lei
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - S. Li
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - W. L. Li
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian District, Beijing 100190, China
| | - X. Li
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - X. Q. Li
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian District, Beijing 100190, China
| | - Y. Li
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - Y. F. Liang
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - Y. M. Liang
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian District, Beijing 100190, China
| | - N. H. Liao
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - C. M. Liu
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - H. Liu
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - J. Liu
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - S. B. Liu
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - W. Q. Liu
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - Y. Liu
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - F. Loparco
- Istituto Nazionale di Fisica Nucleare (INFN)–Sezione di Bari, I-70125, Bari, Italy
- Dipartimento di Fisica “M. Merlin” dell’Università e del Politecnico di Bari, I-70126 Bari, Italy
| | - C. N. Luo
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - M. Ma
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian District, Beijing 100190, China
| | - P. X. Ma
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - S. Y. Ma
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - T. Ma
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - X. Y. Ma
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian District, Beijing 100190, China
| | - G. Marsella
- Dipartimento di Matematica e Fisica E. De Giorgi, Università del Salento, I-73100 Lecce, Italy
- Istituto Nazionale di Fisica Nucleare (INFN)–Sezione di Lecce, I-73100 Lecce, Italy
| | - M. N. Mazziotta
- Istituto Nazionale di Fisica Nucleare (INFN)–Sezione di Bari, I-70125, Bari, Italy
| | - D. Mo
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - X. Y. Niu
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - X. Pan
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - W. X. Peng
- Institute of High Energy Physics, Chinese Academy of Sciences, Yuquan Road 19B, Beijing 100049, China
| | - X. Y. Peng
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - R. Qiao
- Institute of High Energy Physics, Chinese Academy of Sciences, Yuquan Road 19B, Beijing 100049, China
| | - J. N. Rao
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian District, Beijing 100190, China
| | - M. M. Salinas
- Department of Nuclear and Particle Physics, University of Geneva, Geneva CH-1211, Switzerland
| | - G. Z. Shang
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian District, Beijing 100190, China
| | - W. H. Shen
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian District, Beijing 100190, China
| | - Z. Q. Shen
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - Z. T. Shen
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - J. X. Song
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian District, Beijing 100190, China
| | - H. Su
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - M. Su
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
- Department of Physics and Laboratory for Space Research, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Z. Y. Sun
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - A. Surdo
- Istituto Nazionale di Fisica Nucleare (INFN)–Sezione di Lecce, I-73100 Lecce, Italy
| | - X. J. Teng
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian District, Beijing 100190, China
| | - A. Tykhonov
- Department of Nuclear and Particle Physics, University of Geneva, Geneva CH-1211, Switzerland
| | - S. Vitillo
- Department of Nuclear and Particle Physics, University of Geneva, Geneva CH-1211, Switzerland
| | - C. Wang
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - H. Wang
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian District, Beijing 100190, China
| | - H. Y. Wang
- Institute of High Energy Physics, Chinese Academy of Sciences, Yuquan Road 19B, Beijing 100049, China
| | - J. Z. Wang
- Institute of High Energy Physics, Chinese Academy of Sciences, Yuquan Road 19B, Beijing 100049, China
| | - L. G. Wang
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian District, Beijing 100190, China
| | - Q. Wang
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - S. Wang
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - X. H. Wang
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - X. L. Wang
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - Y. F. Wang
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - Y. P. Wang
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - Y. Z. Wang
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - Z. M. Wang
- Gran Sasso Science Institute (GSSI), Via Iacobucci 2, I-67100 L’Aquila, Italy
- Istituto Nazionale di Fisica Nucleare (INFN)–Laboratori Nazionali del Gran Sasso, Assergi, I-67100 L’Aquila, Italy
| | - D. M. Wei
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - J. J. Wei
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - Y. F. Wei
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - S. C. Wen
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - D. Wu
- Institute of High Energy Physics, Chinese Academy of Sciences, Yuquan Road 19B, Beijing 100049, China
| | - J. Wu
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - L. B. Wu
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - S. S. Wu
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian District, Beijing 100190, China
| | - X. Wu
- Department of Nuclear and Particle Physics, University of Geneva, Geneva CH-1211, Switzerland
| | - K. Xi
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - Z. Q. Xia
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - H. T. Xu
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian District, Beijing 100190, China
| | - Z. H. Xu
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - Z. L. Xu
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - Z. Z. Xu
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - G. F. Xue
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian District, Beijing 100190, China
| | - H. B. Yang
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - P. Yang
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - Y. Q. Yang
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - Z. L. Yang
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - H. J. Yao
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - Y. H. Yu
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - Q. Yuan
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
- School of Astronomy and Space Science, University of Science and Technology of China, Hefei 230026, China
| | - C. Yue
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - J. J. Zang
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - F. Zhang
- Institute of High Energy Physics, Chinese Academy of Sciences, Yuquan Road 19B, Beijing 100049, China
| | - J. Y. Zhang
- Institute of High Energy Physics, Chinese Academy of Sciences, Yuquan Road 19B, Beijing 100049, China
| | - J. Z. Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - P. F. Zhang
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - S. X. Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - W. Z. Zhang
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian District, Beijing 100190, China
| | - Y. Zhang
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - Y. J. Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - Y. L. Zhang
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - Y. P. Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - Y. Q. Zhang
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - Z. Zhang
- Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210033, China
| | - Z. Y. Zhang
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - H. Zhao
- Institute of High Energy Physics, Chinese Academy of Sciences, Yuquan Road 19B, Beijing 100049, China
| | - H. Y. Zhao
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - X. F. Zhao
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian District, Beijing 100190, China
| | - C. Y. Zhou
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian District, Beijing 100190, China
| | - Y. Zhou
- Institute of Modern Physics, Chinese Academy of Sciences, Nanchang Road 509, Lanzhou 730000, China
| | - X. Zhu
- State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026, China
- Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - Y. Zhu
- National Space Science Center, Chinese Academy of Sciences, Nanertiao 1, Zhongguancun, Haidian District, Beijing 100190, China
| | - S. Zimmer
- Department of Nuclear and Particle Physics, University of Geneva, Geneva CH-1211, Switzerland
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42
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Zhang B, Wang S, Xu J, Zhang Y, Zhang X, Qian J, Lu J, Qiao R, Nie W, Zhang L, Zhao Y, Hu M, Zhang W, Han BH. Clinical management of advanced lung adenocarcinoma with ALK rearrangement: Real-world treatment outcomes and long-term survival. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz063.040] [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: 11/14/2022] Open
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43
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Qiao R, Li X, Han X, Wang K, Lv G, Ren G, Li X. Population structure and genetic diversity of four Henan pig populations. Anim Genet 2019; 50:262-265. [PMID: 30883844 DOI: 10.1111/age.12775] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2019] [Indexed: 12/22/2022]
Abstract
To investigate the population structure and genetic diversity of Henan indigenous pig breeds, samples from a total of 78 pigs of 11 breeds were collected, including four pig populations from Henan Province, three Western commercial breeds, three Chinese native pig breeds from other provinces and one Asian wild boar. The genotyping datasets were obtained by genotyping-by-sequencing technology. We found a high degree of polymorphism and rapid linkage disequilibrium decay in Henan pigs. A neighbor-joining tree, principal component analysis and structure analysis revealed that the Huainan and Erhualian pigs were clustered together and that the Queshan black pigs were clearly grouped together but that the Nanyang and Yuxi pigs were extensively admixed with Western pigs. In addition, heterozygosity values might indicate that Henan indigenous pigs, especially the Queshan black and Huainan pigs, were subjected to little selection during domestication. The results presented here indicate that Henan pig breeds were admixed from Western breeds, especially Nanyang and Yuxi pigs. Therefore, establishment of purification and rejuvenation systems to implement conservation strategies is urgent. In addition, it is also necessary to accelerate genetic resources improvement and utilization using modern breeding technologies, such as genomic selection and genome-wide association studies.
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Affiliation(s)
- R Qiao
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - X Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - X Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - K Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - G Lv
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - G Ren
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - X Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
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44
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Li X, Xu P, Zhang C, Sun C, Li X, Han X, Li M, Qiao R. Genome-wide association study identifies variants in the CAPN9 gene associated with umbilical hernia in pigs. Anim Genet 2019; 50:162-165. [PMID: 30746724 DOI: 10.1111/age.12760] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2018] [Indexed: 11/30/2022]
Abstract
Pig umbilical hernia (UH) affects pig welfare and brings considerable economic loss to the pig industry. To date, the molecular mechanisms underlying pig UH are still poorly understood. To identify potential loci for susceptibility to this disease, we performed a genome-wide association study in an Erhualian × Shaziling F2 intercross population. A total of 45 animals were genotyped using Illumina Porcine SNP60 BeadChips. We observed a SNP (rs80993347) located in the calpain-9 (CAPN9) gene on Sus scrofa chromosome 14 that was significantly associated with UH (P = 1.97 × 10-10 ). Then, we identified a synonymous mutation rs321865883 (g.20164T>C) in exon 10 of the CAPN9 gene that distinguished two affected individuals (CC) from their normal full-sibs (TC). Finally, quantitative polymerase chain reaction was explored to investigate the mRNA expression profile of the CAPN9 gene in 12 tissues in Yorkshire pigs at different developmental stages (3, 90 and 180 days). CAPN9 showed high expression levels in the gastrointestinal tract at these three growth stages. The results of this study indicate that the CAPN9 gene might be implicated in UH. Further studies are required to establish a role of CAPN9 in pig UH.
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Affiliation(s)
- X Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
| | - P Xu
- Jiangsu Agri-animal Husbandry Vocational College, Taizhou, 225300, China
| | - C Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
| | - C Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
| | - X Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
| | - X Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
| | - M Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
| | - R Qiao
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
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45
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Li X, Ye J, Han X, Qiao R, Li X, Lv G, Wang K. Whole-genome sequencing identifies potential candidate genes for reproductive traits in pigs. Genomics 2019; 112:199-206. [PMID: 30707936 DOI: 10.1016/j.ygeno.2019.01.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 01/05/2019] [Accepted: 01/22/2019] [Indexed: 11/24/2022]
Abstract
Reproductive performance is a complex quantitative trait, that is determined by multiple genes, regulatory pathways and environmental factors. A list of major genes with large effect have been detected, although multiple QTLs are identified. To identify candidate genes for pig prolificacy, whole genome variants from five high- and five low-prolificacy Yorkshire sows were collected using whole-genome resequencing. A total of 13,955,609 SNPs and 2,666,366 indels were detected across the genome. Common differential SNPs and indels were identified between the two groups of sows. Genes encoding components of the TGF-beta signaling pathway were enriched with the variations, including BMP5, BMP6, BMP7, ACVR1, INHBA, ZFYVE9, TGFBR2, DCN, ID4, BAMBI, and ACVR2A. Several differential variants within these genes related to reproductive traits were identified to be associated with litter size. A comparison of selective regions and published QTL data suggests that NEDD9, SLC39A11, SNCA, and UNC5D are candidate genes for reproduction traits.
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Affiliation(s)
- Xinjian Li
- College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, People's Republic of China
| | - Jianwei Ye
- College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, People's Republic of China
| | - Xuelei Han
- College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, People's Republic of China
| | - Ruimin Qiao
- College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, People's Republic of China
| | - Xiuling Li
- College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, People's Republic of China
| | - Gang Lv
- College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, People's Republic of China
| | - Kejun Wang
- College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, People's Republic of China.
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46
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Li X, Qiao R, Ye J, Wang M, Zhang C, Lv G, Wang K, Li X, Han X. Integrated miRNA and mRNA transcriptomes of spleen profiles between Yorkshire and Queshan black pigs. Gene 2018; 688:204-214. [PMID: 30529098 DOI: 10.1016/j.gene.2018.11.077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 10/31/2018] [Accepted: 11/22/2018] [Indexed: 12/13/2022]
Abstract
Disease causes large economic losses to the pig industry worldwidely, immunity plays an important role in the process of resistance to disease. In the present study, to elucidate the molecular mechanisms underlying different levels of disease resistance, we obtained the miRNA and mRNA expression profiles from the spleens of three groups of sows, including 180-day-old Queshan Black (Q-F), 3-day-old Yorkshire (Y-N) and 180-day-old Yorkshire (Y-F) pigs. The results showed that 85 miRNAs and 5093 genes were differentially expressed in Y-F vs Y-N, and 20 miRNAs and 1283 genes were differentially expressed in Q-F vs Y-F. Gene ontology analysis of these differentially expressed genes revealed their critical roles in response to immune response-related signaling pathways. To investigate the molecular mechanisms underlying immune diversity based on differentially expressed miRNAs and genes, the regulatory network between the node miRNAs and genes were established using Cytoscape. The results showed that the identified candidate miRNAs and genes were associated with immune response, and also indicated their potential roles in disease resistance variance between different pig breeds and stages. From the above, this research detected the key factors that were involved in disease resistance, and provide useful information for disease resistance breeding.
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Affiliation(s)
- Xinjian Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002), China
| | - Ruimin Qiao
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002), China
| | - Jianwei Ye
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002), China
| | - Mingyu Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002), China
| | - Chen Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002), China
| | - Gang Lv
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002), China
| | - Kejun Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002), China
| | - Xiuling Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002), China
| | - Xuelei Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002), China.
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47
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Zhang B, Xu J, Wang S, Zhang Y, Qian J, Qiao R, Lu J, Zhang L, Zhao Y, Han B. Characteristics and outcome of small cell lung cancer patients (SCLC) transformed from adenocarcinoma after tyrosine kinase inhibitor treatment. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy425.021] [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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48
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Han B, Zhang B, Xu J, Zhang Y, Zhang X, Chu T, Wang S, Qiao R, Qian J, Lu J, Zhang L. P1.01-29 Crizotinib in Advanced Lung Adenocarcinoma Patients with ALK or ROS-1 Rearrangement: Is it the Same? J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.585] [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: 10/28/2022]
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49
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Han B, Zhang B, Zhang Y, Xu J, Zhang X, Chu T, Wang S, Qian J, Qiao R, Lu J, Zhang L. P1.01-30 Crizotinib in Advanced Non-Adenocarcinoma, NSCLC (NA-NSCLC) Patients with ALK Rearrangement: A Retrospective Study and Literature Review. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.586] [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: 10/28/2022]
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50
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Neppl S, Mahl J, Tremsin AS, Rude B, Qiao R, Yang W, Guo J, Gessner O. Towards efficient time-resolved X-ray absorption studies of electron dynamics at photocatalytic interfaces. Faraday Discuss 2018; 194:659-682. [PMID: 27711854 DOI: 10.1039/c6fd00125d] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We present a picosecond time-resolved X-ray absorption spectroscopy (tr-XAS) setup designed for synchrotron-based studies of interfacial photochemical dynamics. The apparatus combines a high power, variable repetition rate picosecond laser system with a time-resolved X-ray fluorescence yield detection technique. Time-tagging of the detected fluorescence signals enables the parallel acquisition of X-ray absorption spectra at a variety of pump-probe delays employing the well-defined time structure of the X-ray pulse trains. The viability of the setup is demonstrated by resolving dynamic changes in the fine structure near the O1s X-ray absorption edge of cuprous oxide (Cu2O) after photo-excitation with a 355 nm laser pulse. Two distinct responses are detected. A pronounced, quasi-static, reversible change of the Cu2O O1s X-ray absorption spectrum by up to ∼30% compared to its static line shape corresponds to a redshift of the absorption edge by ∼1 eV. This value is small compared to the 2.2 eV band gap of Cu2O but in agreement with previously published results. The lifetime of this effect exceeds the laser pulse-to-pulse period of 8 μs, resulting in a quasi-static spectral change that persists as long as the sample is exposed to the laser light, and completely vanishes once the laser is blocked. Additionally, a short-lived response corresponding to a laser-induced shift of the main absorption line by ∼2 eV to lower energies appears within <200 ps and decays with a characteristic timescale of 43 ± 5 ns. Both the picosecond rise and nanosecond decay of this X-ray response are simultaneously captured by making use of a time-tagging approach - highlighting the prospects of the experimental setup for efficient probing of the electronic and structural dynamics in photocatalytic systems on multiple timescales.
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Affiliation(s)
- Stefan Neppl
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
| | - Johannes Mahl
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
| | - Anton S Tremsin
- Space Sciences Laboratory, University of California, Berkeley, California, USA
| | - Bruce Rude
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Ruimin Qiao
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Wanli Yang
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jinghua Guo
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Oliver Gessner
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
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