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Li L, Quan J, Liu H, Yu H, Chen H, Xia C, Zhao S, Gao C. Identification of the genetic characteristics of copy number variations in experimental specific pathogen-free ducks using whole-genome resequencing. BMC Genomics 2024; 25:17. [PMID: 38166615 PMCID: PMC10759622 DOI: 10.1186/s12864-023-09928-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Specific pathogen-free ducks are a valuable laboratory resource for waterfowl disease research and poultry vaccine development. High throughput sequencing allows the systematic identification of structural variants in genomes. Copy number variation (CNV) can explain the variation of important duck genetic traits. Herein, the genome-wide CNVs of the three experimental duck species in China (Jinding ducks (JD), Shaoxing ducks (SX), and Fujian Shanma ducks (SM)) were characterized using resequencing to determine their genetic characteristics and selection signatures. RESULTS We obtained 4,810 CNV regions (CNVRs) by merging 73,012 CNVs, covering 4.2% of the duck genome. Functional analysis revealed that the shared CNVR-harbored genes were significantly enriched for 31 gene ontology terms and 16 Kyoto Encyclopedia of Genes and Genomes pathways (e.g., olfactory transduction and immune system). Based on the genome-wide fixation index for each CNVR, growth (SPAG17 and PTH1R), disease resistance (CATHL3 and DMBT1), and thermoregulation (TRPC4 and SLIT3) candidate genes were identified in strongly selected signatures specific to JD, SM, and SX, respectively. CONCLUSIONS In conclusion, we investigated the genome-wide distribution of experimental duck CNVs, providing a reference to establish the genetic basis of different phenotypic traits, thus contributing to the management of experimental animal genetic resources.
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Affiliation(s)
- Lanlan Li
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, 730070, P.R. China
- College of Animal Science & Technology, Ningxia University, Yinchuan, 750021, P.R. China
| | - Jinqiang Quan
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, 730070, P.R. China.
| | - Hongyi Liu
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, P.R. China
| | - Haibo Yu
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, P.R. China
| | - Hongyan Chen
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, P.R. China
| | - Changyou Xia
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, P.R. China
| | - Shengguo Zhao
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, 730070, P.R. China
| | - Caixia Gao
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, P.R. China.
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Effects of Dietary Supplementation with Vitamin A on Antioxidant and Intestinal Barrier Function of Broilers Co-Infected with Coccidia and Clostridium perfringens. Animals (Basel) 2022; 12:ani12233431. [PMID: 36496951 PMCID: PMC9740507 DOI: 10.3390/ani12233431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/24/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022] Open
Abstract
Necrotic enteritis (NE) impairs poultry production and causes great economic loss. The nutritional regulation of diets has the potential to alleviate NE. The present study was conducted to investigate the effects of dietary supplementation with vitamin A (VA) on the antioxidant and intestinal barrier function of broilers co-infected with coccidia and C. perfringens (CCP). In a 2 × 2 factorial arrangement, 336 one-day-old Ross 308 broilers were divided into four treatments with two levels of VA (0 or 12,000 IU/kg) and challenged with or without CCP. The animal trial lasted for 42 days. The results showed that dietary supplemental VA improved body weight gain (BWG) and the feed intake (FI), and the FI was negatively affected by CCP. Additionally, the levels of catalase (CAT) in the serum, total superoxide dismutase (T-SOD), and CAT in the jejunum and glutathione peroxidase (GSH-Px) in the liver decreased with the CCP challenge (p < 0.05). The mRNA levels of SOD, CAT, GSH-Px1, and GSH-Px3 in the liver and jejunum were upregulated by the CCP challenge (p < 0.05). In addition, the level of serum diamine oxidase (DAO), and the mRNA level of ZO-1 were also upregulated with the CCP challenge. Dietary supplementation with VA contributed to the intestinal villi height and the mRNA level of Mucin-2 in the jejunum (p < 0.05). Additionally, dietary VA had the ability to alleviate the upregulation of SOD in the liver and SOD, CAT, GSH-Px1, GSH-Px3, ZO-1, and claudin-1 in the jejunum with the CCP challenge (p < 0.05). However, the mRNA level of GSH-Px3 and the levels of SOD in the liver and jejunum were downregulated with the VA supplementation in the diet. In conclusion, dietary VA improved the growth performance and the intestinal barrier function; nonetheless, it failed to alleviate the negative effects of CCP on the antioxidant function in broilers.
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Gao F, Guo Z, Gao Y, Wang C, Wang H, Yao X, Shi B. Maternal oxidized soybean oil exposure in rats during lactation damages offspring kidneys via Nrf2/HO-1 and NF-κB signaling pathway. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:3119-3129. [PMID: 34791653 DOI: 10.1002/jsfa.11653] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 08/11/2021] [Accepted: 11/18/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Cooking oil is an indispensable component of the human diet. However, oils usually undergo thermal oxidation. Oxidized soybean oil (OSO) has been shown to have detrimental effects on humans and has emerged as a root cause of many chronic diseases. The objective of this work was to evaluate the effects of puerpera exposure to OSO on kidney damage in the mother and offspring using lactating rats as an experimental model. RESULTS Pathological sections and ultrastructure showed that OSO exposure resulted in various levels of damage to lactating rats and their offspring. OSO induced oxidative stress in the kidneys of lactating rats, as evidenced by increased levels of hydrogen peroxide, interleukin (IL)-1β, and IL-8. OSO increased the activities of glutathione peroxidase and superoxide dismutase. OSO upregulated the expression of apoptosis-related genes, nuclear factor-erythroid 2-related factor 2 (Nrf2), and nuclear factor κB-related inflammatory factor genes. In the offspring of the OSO-exposed mothers, hydrogen peroxide, malondialdehyde, IL-6, and tumor necrosis factor-alpha contents were increased. Furthermore, OSO enhanced the levels of Nrf2, NAD(P)H quinone oxidoreductase 1, heme oxygenase 1, and p65 and decreased B-cell lymphoma 2. CONCLUSION These findings indicated that the kidneys of two generations of rats were compromised by oxidative damage when fed OSO during lactation. This study provides evidence for increasing the genes expression of the Nrf2/heme oxygenase 1 pathway to alleviate the kidney damage caused by OSO in the mother and offspring. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Feng Gao
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Zhiqiang Guo
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Yanan Gao
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Chuanqi Wang
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Huiting Wang
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Xinxin Yao
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Baoming Shi
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
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Luo M, Xu L, Qian Z, Sun X. Infection-Associated Thymic Atrophy. Front Immunol 2021; 12:652538. [PMID: 34113341 PMCID: PMC8186317 DOI: 10.3389/fimmu.2021.652538] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 05/07/2021] [Indexed: 12/17/2022] Open
Abstract
The thymus is a vital organ of the immune system that plays an essential role in thymocyte development and maturation. Thymic atrophy occurs with age (physiological thymic atrophy) or as a result of viral, bacterial, parasitic or fungal infection (pathological thymic atrophy). Thymic atrophy directly results in loss of thymocytes and/or destruction of the thymic architecture, and indirectly leads to a decrease in naïve T cells and limited T cell receptor diversity. Thus, it is important to recognize the causes and mechanisms that induce thymic atrophy. In this review, we highlight current progress in infection-associated pathogenic thymic atrophy and discuss its possible mechanisms. In addition, we discuss whether extracellular vesicles/exosomes could be potential carriers of pathogenic substances to the thymus, and potential drugs for the treatment of thymic atrophy. Having acknowledged that most current research is limited to serological aspects, we look forward to the possibility of extending future work regarding the impact of neural modulation on thymic atrophy.
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Affiliation(s)
- Mingli Luo
- Department of Parasitology of Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China.,Provincial Engineering Technology Research Center for Biological Vector Control, Guangzhou, China
| | - Lingxin Xu
- Department of Parasitology of Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China.,Provincial Engineering Technology Research Center for Biological Vector Control, Guangzhou, China
| | - Zhengyu Qian
- Department of Parasitology of Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China.,Provincial Engineering Technology Research Center for Biological Vector Control, Guangzhou, China
| | - Xi Sun
- Department of Parasitology of Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China.,Provincial Engineering Technology Research Center for Biological Vector Control, Guangzhou, China
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Yang D, Lv X, Zhang S, Zheng S. Tandem Mass Tag-Based Quantitative Proteomic Analysis of Chicken Bursa of Fabricius Infected With Reticuloendotheliosis Virus. Front Vet Sci 2021; 8:666512. [PMID: 34113672 PMCID: PMC8186552 DOI: 10.3389/fvets.2021.666512] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/24/2021] [Indexed: 12/03/2022] Open
Abstract
Reticuloendotheliosis virus (REV) is a type C avian retrovirus that causes immunosuppression, dwarf syndrome, and lymphoma in infected hosts. In this study, we used tandem mass tag (TMT) labeling and liquid chromatography–tandem mass spectrometry (LC-MS/MS) to characterize protein alterations in chicken bursa of Fabricius, before and after REV infection at 7, 14, 21, and 28 days. Our data showed that 1,127, 999, 910, and 1,138 differentially expressed proteins were significantly altered at 7, 14, 21, and 28 days after REV infection, respectively. Morphological analysis showed that REV infection reduced in cortical lymphocytes, bursal follicle atrophy, and nuclear damage. Bioinformatics analysis indicated these proteins were mainly involved with immune responses, energy metabolism, cellular processes, biological regulation, metabolic processes, response to stimuli, and multicellular organismal process. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway cluster analysis showed that post-infection, proteins were enriched in the cell cycle, Wnt signaling, antigen processing and presentation, cytokine receptor interaction, adenosine 3′,5′-cyclic monophosphate signaling pathway, and NF-κB signaling. In addition, we observed that peroxiredoxin 4 (PRDX4), peroxiredoxin 6 (PRDX6), glutathione peroxidase 3 (GPX3), catalase (CAT), and peroxidasin (PXDN) were involved in oxidative stress. Some heat shock protein (HSP) family members such as HSPH1, DNAJA4, HSPA8, and HSPA4L also changed significantly after REV infection. These findings help clarify interactions between REV and the host and provides mechanistic insights on REV-induced host immunosuppression.
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Affiliation(s)
- Dahan Yang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory of Laboratory Animals and Comparative Medicine, Harbin, China
| | - Xiaoping Lv
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory of Laboratory Animals and Comparative Medicine, Harbin, China
| | - Shujun Zhang
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Shimin Zheng
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory of Laboratory Animals and Comparative Medicine, Harbin, China
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