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Yang S, Deng W, Li G, Jin L, Huang Y, He Y, Wu D, Li D, Zhang A, Liu C, Li C, Zhang H, Xu H, Penttinen P, Zhao K, Zou L. Reference gene catalog and metagenome-assembled genomes from the gut microbiome reveal the microbial composition, antibiotic resistome, and adaptability of a lignocellulose diet in the giant panda. Environ Res 2024; 245:118090. [PMID: 38163545 DOI: 10.1016/j.envres.2023.118090] [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] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/29/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
The giant panda, a strict herbivore that feeds on bamboo, still retains a typical carnivorous digestive system. Reference catalogs of microbial genes and genomes are lacking, largely limiting the antibiotic resistome and functional exploration of the giant panda gut microbiome. Here, we integrated 177 fecal metagenomes of captive and wild giant pandas to construct a giant panda integrated gene catalog (GPIGC) comprised of approximately 4.5 million non-redundant genes and reconstruct 393 metagenome-assembled genomes (MAGs). Taxonomic and functional characterization of genes revealed that the captivity of the giant panda significantly changed the core microbial composition and the distribution of microbial genes. Higher abundance and prevalence of antibiotic resistance genes (ARGs) were detected in the guts of captive giant pandas, and ARG distribution was influenced by geography, for both captive and wild individuals. Escherichia, as the prevalent genus in the guts of captive giant pandas, was the main carrier of ARGs, meaning there is a high risk of ARG transmission by Escherichia. We also found that multiple mcr gene variants, conferring plasmid-mediated mobile colistin resistance, were widespread in the guts of captive and wild giant pandas. There were low proportions of carbohydrate-active enzyme (CAZyme) genes in GPIGC and MAGs compared with several omnivorous and herbivorous mammals. Many members of Clostridium MAGs were significantly enriched in the guts of adult, old and wild giant pandas. The genomes of isolates and MAGs of Clostridiaceae harbored key genes or enzymes in complete pathways for degrading lignocellulose and producing short-chain fatty acids (SCFAs), indicating the potential of these bacteria to utilize the low-nutrient bamboo diet. Overall, our data presented an exhaustive reference gene catalog and MAGs in giant panda gut and provided a comprehensive understanding of the antibiotic resistome and microbial adaptability for a high-lignocellulose diet.
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Affiliation(s)
- Shengzhi Yang
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Wenwen Deng
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China; Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, 610051, Sichuan, China
| | - Guo Li
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China; Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, 610051, Sichuan, China
| | - Lei Jin
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yan Huang
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, 610051, Sichuan, China
| | - Yongguo He
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, 610051, Sichuan, China
| | - Daifu Wu
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, 610051, Sichuan, China
| | - Desheng Li
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, 610051, Sichuan, China
| | - Anyun Zhang
- College of Life Science, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Chengxi Liu
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Caiwu Li
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, 610051, Sichuan, China
| | - Hemin Zhang
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, 610051, Sichuan, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Petri Penttinen
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Ke Zhao
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Likou Zou
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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Li Y, Xu W, Wang J, Liu H, Liu J, Zhang L, Hou R, Shen F, Liu Y, Cai K. Giant pandas in captivity undergo short-term adaptation in nerve-related pathways. BMC ZOOL 2024; 9:4. [PMID: 38383502 PMCID: PMC10880213 DOI: 10.1186/s40850-024-00195-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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 02/07/2024] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND Behaviors in captive animals, including changes in appetite, activity level, and social interaction, are often seen as adaptive responses. However, these behaviors may become progressively maladaptive, leading to stress, anxiety, depression, and other negative reactions in animals. RESULTS In this study, we investigated the whole-genome sequencing data of 39 giant panda individuals, including 11 in captivity and 28 in the wild. To eliminate the mountain range effect and focus on the factor of captivity only, we first performed a principal component analysis. We then enumerated the 21,474,180 combinations of wild giant pandas (11 chosen from 28) and calculated their distances from the 11 captive individuals. The 11 wild individuals with the closest distances were used for the subsequent analysis. The linkage disequilibrium (LD) patterns demonstrated that the population was almost eliminated. We identified 505 robust selected genomic regions harboring at least one SNP, and the absolute frequency difference was greater than 0.6 between the two populations. GO analysis revealed that genes in these regions were mainly involved in nerve-related pathways. Furthermore, we identified 22 GO terms for which the selection strength significantly differed between the two populations, and there were 10 nerve-related pathways among them. Genes in the differentially abundant regions were involved in nerve-related pathways, indicating that giant pandas in captivity underwent minor genomic selection. Additionally, we investigated the relationship between genetic variation and chromatin conformation structures. We found that nucleotide diversity (θπ) in the captive population was correlated with chromatin conformation structures, which included A/B compartments, topologically associated domains (TADs) and TAD-cliques. For each GO term, we then compared the expression level of genes regulated by the above four factors (AB index, TAD intactness, TAD clique and PEI) with the corresponding genomic background. The retained 10 GO terms were all coordinately regulated by the four factors, and three of them were associated with nerve-related pathways. CONCLUSIONS This study revealed that giant pandas in captivity undergo short-term adaptation in nerve-related pathways. Furthermore, it provides new insights into the molecular mechanism of gene expression regulation under short-term adaptation to environmental change.
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Affiliation(s)
- Yan Li
- Chengdu Research Base of Giant Panda Breeding, Panda Avenue, Northern Suburb, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, Panda Avenue, Northern Suburb, Chengdu, China
| | - Wei Xu
- Chengdu Research Base of Giant Panda Breeding, Panda Avenue, Northern Suburb, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, Panda Avenue, Northern Suburb, Chengdu, China
| | - Juan Wang
- Chengdu Research Base of Giant Panda Breeding, Panda Avenue, Northern Suburb, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, Panda Avenue, Northern Suburb, Chengdu, China
| | - Hong Liu
- Chengdu Research Base of Giant Panda Breeding, Panda Avenue, Northern Suburb, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, Panda Avenue, Northern Suburb, Chengdu, China
| | - Jiawen Liu
- Chengdu Research Base of Giant Panda Breeding, Panda Avenue, Northern Suburb, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, Panda Avenue, Northern Suburb, Chengdu, China
| | - Liang Zhang
- Chengdu Research Base of Giant Panda Breeding, Panda Avenue, Northern Suburb, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, Panda Avenue, Northern Suburb, Chengdu, China
| | - Rong Hou
- Chengdu Research Base of Giant Panda Breeding, Panda Avenue, Northern Suburb, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, Panda Avenue, Northern Suburb, Chengdu, China
| | - Fujun Shen
- Chengdu Research Base of Giant Panda Breeding, Panda Avenue, Northern Suburb, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, Panda Avenue, Northern Suburb, Chengdu, China
| | - Yuliang Liu
- Chengdu Research Base of Giant Panda Breeding, Panda Avenue, Northern Suburb, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, Panda Avenue, Northern Suburb, Chengdu, China
| | - Kailai Cai
- Chengdu Research Base of Giant Panda Breeding, Panda Avenue, Northern Suburb, Chengdu, China.
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, Panda Avenue, Northern Suburb, Chengdu, China.
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Yue Y, Yang Z, Wei W, Yang B, Qi D, Gu X, Yang X, Lu S, Zhang W, Dai Q, Zhang Z. The effectiveness of using giant panda as a surrogate for protecting sympatric species. J Environ Manage 2024; 351:119803. [PMID: 38134503 DOI: 10.1016/j.jenvman.2023.119803] [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] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/13/2023] [Accepted: 12/03/2023] [Indexed: 12/24/2023]
Abstract
The use of umbrella species to promote biodiversity conservation is practiced worldwide. The giant panda (Ailuropoda melanoleuca) an iconic species for world wildlife conservation, that inhabits regions with significant biodiversity. Given that the functions at wildlife of different trophic levels and in different body size groups are different within the ecosystem, it is unknown whether those groups of wildlife co-occurring with giant pandas are each likewise protected. To examine the umbrella effect of giant pandas on sympatric species, we used an extensive dataset of wildlife from more than 78% of giant panda habitats. We analysed the changes in distribution for four wildlife categories (large carnivores, large herbivores, medium carnivores and medium herbivores) using a generalized linear mixed model, and the underlying driving factors using binomial logistic regression models. Changes in forests in giant panda habitats were evaluated using Fragstats. The results have shown that the counts of herbivores and medium carnivores increased significantly during the decade. However, those of large carnivores significantly declined. Forest cover and nature reserves showed significant and positive effects on wildlife in 2001 and 2011, while the human population had significant and negative impacts on the herbivores and carnivores. Our results have also suggested that there has been a slight alleviation in forest fragmentation in areas unaffected by earthquakes. We concluded that the umbrella strategy of using the giant panda as an umbrella species achieved partial success by promoting the recovery of herbivores and medium carnivores. Meanwhile, this has indicated that the strategy was not sufficient for large carnivores, and therefore not enough for local ecosystems, given the critical role of large carnivores. We have suggested integrating habitat patches, controlling human disturbance, and preparing for potential human-wildlife conflict management in the Giant Panda National Park to restore large carnivore populations and maintain ecosystem functioning.
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Affiliation(s)
- Ying Yue
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China; University of Chinese Academy of Sciences, 100101, Beijing, China
| | - Zhisong Yang
- Sichuan Academy of Giant Panda, Chengdu, 610081, China
| | - Wei Wei
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, 637002, China
| | - Biao Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, 637002, China
| | - Dunwu Qi
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
| | - Xiaodong Gu
- Sichuan Provincial Administration of Giant Panda National Park, 610081, Chengdu, China
| | - Xuyu Yang
- Sichuan Provincial Nature Protected Area Administration Station, 610081, Chengdu, China
| | - Song Lu
- College of Life Science, Sichuan University, 610064, Chengdu, China
| | - Wen Zhang
- Sichuan Forestry and Grassland Survey and Planning Institute, 610081, Chengdu, China
| | - Qiang Dai
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China; University of Chinese Academy of Sciences, 100101, Beijing, China.
| | - Zejun Zhang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, 637002, China; College of Chemistry and Life Sciences, Chengdu Normal University, 611130, Chengdu, China.
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Yang S, Lan T, Wei R, Zhang L, Lin L, Du H, Huang Y, Zhang G, Huang S, Shi M, Wang C, Wang Q, Li R, Han L, Tang D, Li H, Zhang H, Cui J, Lu H, Huang J, Luo Y, Li D, Wan QH, Liu H, Fang SG. Single-nucleus transcriptome inventory of giant panda reveals cellular basis for fitness optimization under low metabolism. BMC Biol 2023; 21:222. [PMID: 37858133 PMCID: PMC10588165 DOI: 10.1186/s12915-023-01691-2] [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: 02/19/2023] [Accepted: 08/25/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Energy homeostasis is essential for the adaptation of animals to their environment and some wild animals keep low metabolism adaptive to their low-nutrient dietary supply. Giant panda is such a typical low-metabolic mammal exhibiting species specialization of extremely low daily energy expenditure. It has low levels of basal metabolic rate, thyroid hormone, and physical activities, whereas the cellular bases of its low metabolic adaptation remain rarely explored. RESULTS In this study, we generate a single-nucleus transcriptome atlas of 21 organs/tissues from a female giant panda. We focused on the central metabolic organ (liver) and dissected cellular metabolic status by cross-species comparison. Adaptive expression mode (i.e., AMPK related) was prominently displayed in the hepatocyte of giant panda. In the highest energy-consuming organ, the heart, we found a possibly optimized utilization of fatty acid. Detailed cell subtype annotation of endothelial cells showed the uterine-specific deficiency of blood vascular subclasses, indicating a potential adaptation for a low reproductive energy expenditure. CONCLUSIONS Our findings shed light on the possible cellular basis and transcriptomic regulatory clues for the low metabolism in giant pandas and helped to understand physiological adaptation response to nutrient stress.
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Affiliation(s)
- Shangchen Yang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Tianming Lan
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150040, China
| | - Rongping Wei
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Ling Zhang
- China Wildlife Conservation Association, Beijing, 100714, China
| | - Lin Lin
- Department of Biomedicine, Aarhus University, 8000, Aarhus, Denmark
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, 266555, China
- Steno Diabetes Center Aarhus, Aarhus University Hospital, 8000, Aarhus, Denmark
| | - Hanyu Du
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yunting Huang
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Guiquan Zhang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Shan Huang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Minhui Shi
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chengdong Wang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Qing Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rengui Li
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Lei Han
- College of Wildlife Resources, Northeast Forestry University, Harbin, 150040, China
| | - Dan Tang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Haimeng Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hemin Zhang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Jie Cui
- The Genome Synthesis and Editing Platform, BGI-Shenzhen, Shenzhen, 518120, China
| | - Haorong Lu
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China
| | - Jinrong Huang
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, 8000, Aarhus, Denmark
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, 266555, China
- Steno Diabetes Center Aarhus, Aarhus University Hospital, 8000, Aarhus, Denmark
| | - Desheng Li
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China.
| | - Qiu-Hong Wan
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150040, China.
| | - Sheng-Guo Fang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
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Yan M, Xu C, Li C, Feng Y, Duan J, Zhao K, Wu D, Li G, Yang S, Han X, Xie Y, Huang Y, Yu X, Wu J, Zou L. Effects of environmental disinfection on microbial population and resistance genes: A case study of the microecology within a panda enclosure. Environ Res 2023; 235:116662. [PMID: 37453509 DOI: 10.1016/j.envres.2023.116662] [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] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/02/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Widespread use of disinfectants raises concerns over their involvement in altering microbial communities and promoting antimicrobial resistance. This study explores the influence of disinfection protocols on microbial populations and resistance genes within an isolated enclosure environment and in the gut of giant pandas (GPs) held within. Samples of panda feces, air conditioning ducts, soil and bamboo were collected before and after disinfection. High-throughput sequencing characterized the microbial flora of GP gut and environmental microbes inside the artificial habitat. Microbial cultures showed that Escherichia coli (34.6%), Enterococcus (15.4%) and other pathogenic bacteria deposited in feces and the enclosure. Isolates exhibit a consistent resistance to disinfectant, with the greatest resistance shown to cyanuric acid, and the lowest to glutaraldehyde-dodecyl dimethyl ammonium bromide (GD-DDAB) and dodecyl dimethyl ammonium bromide (DDAB). The total number of the culturable bacteria in soil and bamboo were significantly diminished after disinfection but increased in the gut. After disinfection, the richness (Chao1 index) of environment samples increased significantly (P < 0.05), while the richness in gut decreased significantly (P < 0.05). Ten genera showed significant change in feces after disinfection. Metagenome sequencing showed that 126 types of virulence genes were present in feces before disinfection and 37 in soil. After disinfection, 110 virulence genes localized in feces and 53 in soil. Eleven virulence genes including ECP and T2SS increased in feces. A total of 182 antibiotic resistance genes (ARGs) subtypes, potentially conferring resistance to 20 classes of drugs, were detected in the soils and feces, with most belonging to efflux pump protein pathways. After disinfection, the number of resistance genes increased both in gut and soil, which suggests disinfection protocols increase the number of resistance pathways. Our study shows that the use of disinfectants helps to shape the microbial community of GPs and their habitat, and increases populations of resistant strain bacteria.
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Affiliation(s)
- Min Yan
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Chunzhong Xu
- Shanghai Wild Animal Park, Shanghai, 201399, China
| | - Caiwu Li
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Dujiangyan, 611830, China
| | - Yongqi Feng
- Shanghai Wild Animal Park, Shanghai, 201399, China
| | - Juntang Duan
- Shanghai Wild Animal Park, Shanghai, 201399, China
| | - Ke Zhao
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Daifu Wu
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Dujiangyan, 611830, China
| | - Guo Li
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Dujiangyan, 611830, China
| | - Shengzhi Yang
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Xinfeng Han
- College of Veterinary Science, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yue Xie
- College of Veterinary Science, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yan Huang
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Dujiangyan, 611830, China
| | - Xiumei Yu
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jiawei Wu
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Likou Zou
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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Huang G, Shi W, Wang L, Qu Q, Zuo Z, Wang J, Zhao F, Wei F. PandaGUT provides new insights into bacterial diversity, function, and resistome landscapes with implications for conservation. Microbiome 2023; 11:221. [PMID: 37805557 PMCID: PMC10559513 DOI: 10.1186/s40168-023-01657-0] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 08/23/2023] [Indexed: 10/09/2023]
Abstract
BACKGROUND The gut microbiota play important roles in host adaptation and evolution, but are understudied in natural population of wild mammals. To address host adaptive evolution and improve conservation efforts of threatened mammals from a metagenomic perspective, we established a high-quality gut microbiome catalog of the giant panda (pandaGUT) to resolve the microbiome diversity, functional, and resistome landscapes using approximately 7 Tbp of long- and short-read sequencing data from 439 stool samples. RESULTS The pandaGUT catalog comprises 820 metagenome-assembled genomes, including 40 complete closed genomes, and 64.5% of which belong to species that have not been previously reported, greatly expanding the coverage of most prokaryotic lineages. The catalog contains 2.37 million unique genes, with 74.8% possessing complete open read frames, facilitating future mining of microbial functional potential. We identified three microbial enterotypes across wild and captive panda populations characterized by Clostridium, Pseudomonas, and Escherichia, respectively. We found that wild pandas exhibited host genetic-specific microbial structures and functions, suggesting host-gut microbiota phylosymbiosis, while the captive cohorts encoded more multi-drug resistance genes. CONCLUSIONS Our study provides largely untapped resources for biochemical and biotechnological applications as well as potential intervention avenues via the rational manipulation of microbial diversity and reducing antibiotic usage for future conservation management of wildlife. Video Abstract.
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Affiliation(s)
- Guangping Huang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenyu Shi
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Le Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qingyue Qu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhenqiang Zuo
- Laboratory for Computational Genomics, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinfeng Wang
- Laboratory for Computational Genomics, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fangqing Zhao
- Laboratory for Computational Genomics, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Fuwen Wei
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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7
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Ma YJ, Wang M, Hu XY, Gu XD, Li YM, Wei FW, Nie YG. Identifying priority protection areas of key food resources of the giant panda. Zool Res 2023; 44:860-866. [PMID: 37537140 PMCID: PMC10559099 DOI: 10.24272/j.issn.2095-8137.2022.526] [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: 04/06/2023] [Accepted: 07/31/2023] [Indexed: 08/05/2023] Open
Abstract
Animals that live in seasonal environments adjust their reproduction cycle to optimize seasonal forage quality. Giant pandas ( Ailuropoda melanoleuca) are seasonal altitudinal migrants that feed on bamboo shoots and leaves with different nutritional quality. However, the importance of bamboo shoots to giant pandas, especially small and isolated populations, is not fully appreciated. Here, we explored whether mating time of giant pandas is shaped by bamboo shoot phenology. We also assessed the intensity of ongoing bamboo shoot harvesting by local communities in 42 giant panda reserves based on questionnaire surveys. Varying intensity and protection levels of bamboo shoot harvesting were found. From these data, we developed a priority ranking scheme of protection areas for this key food resource. Our study showed that pandas time their mating behavior to coincide with bamboo shoot phenology due to the high nutritional demands associated with mating and pregnancy. We also found that bamboo shoots were not well protected in many places. Liangshan, Daxiangling, and Xiaoxiangling, containing the most isolated panda populations, were identified as the areas with the most urgent need of protection. Furthermore, equal attention should be paid to the QiongL-B population, as this region holds considerable potential to serve as a corridor between the Minshan and Qionglai populations. To address the challenges posed by bamboo shoot harvesting, we recommend establishing more practical bamboo shoot management policies, increasing public awareness of bamboo shoot protection, and providing alternative sources of income for local communities.
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Affiliation(s)
- Ying-Jie Ma
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang 830017, China
| | - Meng Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Yu Hu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Dong Gu
- Sichuan Giant Panda National Park Administration, Chengdu, Sichuan 610081, China
| | - Yu-Mei Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fu-Wen Wei
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China
| | - Yong-Gang Nie
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China. E-mail:
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Wang X, Chen X, Song X, Cao L, Yang S, Shen Q, Ji L, Lu X, Zhang W. Identification of novel anelloviruses in the blood of giant panda (Ailuropoda melanoleuca). Comp Immunol Microbiol Infect Dis 2023; 100:102038. [PMID: 37572592 DOI: 10.1016/j.cimid.2023.102038] [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: 06/07/2023] [Revised: 07/15/2023] [Accepted: 08/02/2023] [Indexed: 08/14/2023]
Abstract
In recent years, the continuous development of metagenomics has revealed that in addition to the digestive tract, some viruses are also common in mammalian blood. To explore and monitor potential novel viruses, in April 2015, a blood sample was collected from a healthy captive giant panda at the Chengdu Research Base of Giant Panda Breeding in Sichuan Province, China. The genomes of 25 different anelloviruses containing the complete ORF1 region have been identified. The BLASTp results showed that the amino acid sequence identity of these viruses with the best match in GenBank ranged from 27.15% to 41.29%. Based on phylogenetic analysis and SDT (Species Demarcation Tool) analysis of the complete ORF1 regions of these 25 viruses, these sequences were deduced to represent one or several novel virus genera or species. This virological study has increased our understanding of the diversity of anelloviruses in the blood of giant pandas, but further laboratory analysis is needed to verify its possible pathogenicity.
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Affiliation(s)
- Xiaochun Wang
- Department of laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xurong Chen
- Department of laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xulai Song
- Department of laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ling Cao
- Department of laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Shixing Yang
- Department of laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Quan Shen
- Department of laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Likai Ji
- Department of laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xiang Lu
- Department of laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China.
| | - Wen Zhang
- Department of laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China.
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Chang L, Wang XL, Yu C, Liu CH, Zhang Q, Wu Y, Jia R, Ma Q, Pan G, Tong D, Wang X. Chronic kidney disease in a giant panda (Ailuropoda melanoleuca): a case report. BMC Vet Res 2023; 19:131. [PMID: 37612662 PMCID: PMC10464369 DOI: 10.1186/s12917-023-03663-8] [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: 12/02/2022] [Accepted: 07/18/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND Chronic kidney disease (CKD) is a common cause of morbidity and mortality in captive wildlife species. However, CKD has been rarely documented in giant pandas. CASE PRESENTATION The following report describes a case of an eight-year-old female giant panda showing clinical signs of epistaxis, bloody diarrhea, polyuria, azotemia and anemia. The animal died despite of supportive treatments. Necropsy was performed. Grossly, both kidneys were shrunken and scarred with pallor. Subcutis edema and petechia on the epicardium of the heart were observed. The tissue samples were made into paraffin sections and stained by H.E and special staining including Periodic Acid-Schiff (PAS), von Kossa, Masson's trichrome, Phosphotungstic acid-hematoxylin (PTAH), and Congo red. Histopathology examination revealed severe chronic tubulointerstitial nephritis with marked interstitial fibrosis, glomerulosclerosis, tubular atrophy and calcification in kidneys, and acute necrotizing hemorrhagic myocarditis with calcification in heart. Other lesions included intestinal hemorrhage, hepatic fatty degeneration and necrosis with hemosiderin, and splenic hemosiderin. CONCLUSIONS In summary, chronic kidney disease was finally diagnosed based on the association of clinical, gross, and histopathological findings. Heart failure secondary to CKD is the leading cause of death in this giant panda. The potential cause of CKD in this animal is possibly due to long term and uncontrolled hypertension. Blood pressure monitoring is essential in establishing the diagnosis and management of hypertension in giant panda.
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Affiliation(s)
- Lingling Chang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Xiangyang L Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Chenfei Yu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Chen-Hsuan Liu
- Graduate Institute of Molecular and Comparative Pathobiology, School of Veterinary Medicine, National Taiwan University, Taipei, Taiwan
| | - Qiang Zhang
- Qinling Giant Panda Research Center, Xi'an, China
| | - Yaping Wu
- Qinling Giant Panda Research Center, Xi'an, China
| | - Ruoyi Jia
- Qinling Giant Panda Research Center, Xi'an, China
| | - Qingyi Ma
- Qinling Giant Panda Research Center, Xi'an, China
| | - Guanglin Pan
- Qinling Giant Panda Research Center, Xi'an, China.
| | - Dewen Tong
- College of Veterinary Medicine, Northwest A&F University, Yangling, China.
| | - Xinglong Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China.
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Liu YL, Chen JS, An JH, Cai ZG, Lan JC, Li Y, Kong XW, Zhang MY, Hou R, Wang DH. Characteristics of mesenchymal stem cells and their exosomes derived from giant panda (Ailuropoda melanoleuca) endometrium. In Vitro Cell Dev Biol Anim 2023; 59:550-563. [PMID: 37639049 DOI: 10.1007/s11626-023-00802-1] [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: 05/26/2023] [Accepted: 07/27/2023] [Indexed: 08/29/2023]
Abstract
Conservation of genetic resources is an important way to protect endangered species. At present, mesenchymal stem cells (MSCs) have been isolated from the bone marrow and umbilical cords of giant pandas. However, the types and quantities of preserved cell resources were rare and limited, and none of MSCs was derived from female reproductive organs. Here, we first isolated MSCs from the endometrium of giant panda. These cells showed fibroblast morphology and expressed Sox2, Klf4, Thy1, CD73, CD105, CD44, CD49f, and CD105. Endometrium mesenchymal stem cells (eMSCs) of giant panda could induce differentiation into three germ layers in vitro. RNA-seq analysis showed that 833 genes were upregulated and 716 genes were downregulated in eMSCs compared with skin fibroblast cells. The results of GO and the KEGG analysis of differentially expressed genes (DEGs) were mainly focused on transporter activity, signal transducer activity, pathways regulating pluripotency of stem cells, MAPK signaling pathway, and PI3K-Akt signaling pathway. The genes PLCG2, FRK, JAK3, LYN, PIK3CB, JAK2, CBLB, and MET were identified as hub genes by PPI network analysis. In addition, the exosomes of eMSCs were also isolated and identified. The average diameter of exosomes was 74.26 ± 13.75 nm and highly expressed TSG101 and CD9 but did not express CALNEXIN. A total of 277 miRNAs were detected in the exosomes; the highest expression of miRNA was the has-miR-21-5p. A total of 14461 target genes of the whole miRNAs were predicted and proceeded with functional analysis. In conclusion, we successfully isolated and characterized the giant panda eMSCs and their exosomes, and analyzed their functions through bioinformatics techniques. It not only enriched the conservation types of giant panda cell resources and promoted the protection of genetic diversity, but also laid a foundation for the application of eMSCs and exosomes in the disease treatment of giant pandas.
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Affiliation(s)
- Yu-Liang Liu
- Chengdu Research Base of Giant Panda Breeding, Sichuan Province, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Sichuan Province, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Sichuan Province, Chengdu, 610081, China
| | - Jia-Song Chen
- Chengdu Research Base of Giant Panda Breeding, Sichuan Province, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Sichuan Province, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Sichuan Province, Chengdu, 610081, China
| | - Jun-Hui An
- Chengdu Research Base of Giant Panda Breeding, Sichuan Province, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Sichuan Province, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Sichuan Province, Chengdu, 610081, China
| | - Zhi-Gang Cai
- Chengdu Research Base of Giant Panda Breeding, Sichuan Province, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Sichuan Province, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Sichuan Province, Chengdu, 610081, China
| | - Jing-Chao Lan
- Chengdu Research Base of Giant Panda Breeding, Sichuan Province, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Sichuan Province, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Sichuan Province, Chengdu, 610081, China
| | - Yuan Li
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Sichuan Province, Chengdu, 610081, China
| | - Xiang-Wei Kong
- Chengdu Research Base of Giant Panda Breeding, Sichuan Province, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Sichuan Province, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Sichuan Province, Chengdu, 610081, China
| | - Ming-Yue Zhang
- Chengdu Research Base of Giant Panda Breeding, Sichuan Province, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Sichuan Province, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Sichuan Province, Chengdu, 610081, China
| | - Rong Hou
- Chengdu Research Base of Giant Panda Breeding, Sichuan Province, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Sichuan Province, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Sichuan Province, Chengdu, 610081, China
| | - Dong-Hui Wang
- Chengdu Research Base of Giant Panda Breeding, Sichuan Province, Chengdu, 610081, China.
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Sichuan Province, Chengdu, 610081, China.
- Sichuan Academy of Giant Panda, Sichuan Province, Chengdu, 610081, China.
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Xiong L, Chen L, Chen Y, Shen N, Hua R, Yang G. Evaluation of the immunoprotective effects of eight recombinant proteins from Baylisascaris schroederi in mice model. Parasit Vectors 2023; 16:254. [PMID: 37501169 PMCID: PMC10375773 DOI: 10.1186/s13071-023-05886-y] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/17/2023] [Indexed: 07/29/2023] Open
Abstract
BACKGROUND Baylisascaris schroederi is the most common and harmful intestinal parasitic nematode of giant pandas, causing ascariasis. Although drug deworming is the main measure to control ascariasis in captive giant pandas, prolonged and repeated use of deworming drugs might induce resistance in nematodes and drug residues in giant pandas. Therefore, developing a safe and effective vaccine might provide a novel strategy to prevent ascariasis in captive giant pandas. METHODS Four highly expressed secretome genes encoding excretory and secretory proteins of B. schroederi, including transthyretin-like protein 46 (BsTLP), uncharacterized protein (BsUP), hypothetical protein 1 (BsHP1), and hypothetical protein 2 (BsHP2) and four functional genes [(encoding Galectin (BsGAL), glutathione S-transferase (BsGST), fatty acid-binding protein (BsFABP), and thioredoxin peroxidase (BsTPX)] were identified based on genome and transcriptome databases of B. schroederi and used to construct recombinant proteins via prokaryotic expression. Kunming mice were vaccinated subcutaneously twice with the recombinant proteins (50 μg/mouse) mixed with Quil A adjuvant with a 2-week interval and then orally challenged with 3000 infective eggs. The immunoprotective effects of the eight recombinant proteins on mice were assessed comprehensively using surface lesion histology scores of the mouse liver and lung, larval worm reduction, serum antibody levels (IgG, IgE, IgA, IgG1, and IgG2a), and cytokine production [interferon gamma (IFN-γ), interleukin (IL)-2, IL-4, IL-5, and IL-10]. RESULTS Mice vaccinated with recombinant (r)BsUP (76.5%), rBsGAL (74.7%), and rBsHP2 (71.5%) showed a significant (P < 0.001) reduction in the larval worm rate compared with that in the adjuvant control. Besides, the surface lesions in the liver and lung of the vaccinated mice were alleviated. Serum levels of total IgG, IgE, IgA, IgG1, IgG2a, and cytokines, including IL-10, IL-5, and IFN-γ, were significantly higher (P < 0.001) than those in the control group. CONCLUSIONS The results showed that candidate three vaccines (rBsUP, rBsGAL, and rBsHP2) could provide effective protection against egg infection in mice associated with a mixed Th1/2-type immune response.
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Affiliation(s)
- Lang Xiong
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ling Chen
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yanxin Chen
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Nengxing Shen
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ruiqi Hua
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guangyou Yang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China.
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Tang J, Swaisgood RR, Owen MA, Zhao X, Wei W, Hong M, Zhou H, Zhang Z. Assessing the effectiveness of protected areas for panda conservation under future climate and land use change scenarios. J Environ Manage 2023; 342:118319. [PMID: 37290306 DOI: 10.1016/j.jenvman.2023.118319] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 05/09/2023] [Accepted: 06/02/2023] [Indexed: 06/10/2023]
Abstract
While the relatively stable land use and land cover (LULC) patterns is an important feature of protected areas (PAs), the influence of this feature on future species distribution and the effectiveness of the PAs has rarely been explored. Here, we assessed the role of land use patterns within PAs on the projected range of the giant panda (Ailuropoda melanoleuca) by comparing projections inside and outside of PAs for four model configurations: (1) only climate covariates, (2) climate and dynamic land use covariates, (3) climate and static land use covariates and (4) climate and hybrid dynamic-static land use covariates. Our objectives were twofold: to understand the role of protected status on projected panda habitat suitability and evaluate the relative efficacy of different climate modeling approaches. The climate and land use change scenarios used in the models include two shared socio-economic pathways (SSPs) scenarios: SSP126 [an optimistic scenario] and SSP585 [a pessimistic scenario]. We found that models including land-use covariates performed significantly better than climate-only models and that these projected more suitable habitat than climate-only models. Static land-use models projected more suitable habitat than both the dynamic and hybrid models under SSP126, while these models did not differ under SSP585. China's panda reserve system was projected to effectively maintain suitable habitat inside PAs. Panda dispersal ability also significantly impacted outcomes, with most models assuming unlimited dispersal forecasting range expansion and models assuming zero dispersal consistently forecasting range contraction. Our findings highlight that policies targeting improved land-use practices should be an effective means for offsetting some of the negative effects of climate change on pandas. As the effectiveness of PAs is projected to be maintained, we recommend the judicious management and expansion of the PA system to ensure the resilience of panda populations into the future.
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Affiliation(s)
- Junfeng Tang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China; Institute of Ecology, China West Normal University, Nanchong, China; Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan Province, China.
| | - Ronald R Swaisgood
- Conservation Science and Wildlife Health, San Diego Zoo Wildlife Alliance, Escondido, CA, USA.
| | - Megan A Owen
- Conservation Science and Wildlife Health, San Diego Zoo Wildlife Alliance, Escondido, CA, USA.
| | - Xuzhe Zhao
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China; Institute of Ecology, China West Normal University, Nanchong, China; Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan Province, China.
| | - Wei Wei
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China; Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan Province, China.
| | - Mingsheng Hong
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China; Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan Province, China.
| | - Hong Zhou
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China; Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan Province, China.
| | - Zejun Zhang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China; Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan Province, China.
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Zhang T, Zhong G, Tang Z, Dong G. Diagnosis and surgical management of testicular seminoma in captive giant panda (Ailuropoda melanoleuca). Vet Anim Sci 2023; 20:100295. [PMID: 37207038 PMCID: PMC10189470 DOI: 10.1016/j.vas.2023.100295] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023] Open
Abstract
A captive adult male giant panda (Guangzhou Chimelong Safari Park, CHINA) presented with azoospermia and enlarged left testicle. A tentative diagnosis of testicular neoplasia was made, and confirmed as testicular seminoma cases by testicular ultrasound, computed tomography (CT), testicular biopsy, and tumor marker examination findings. Based on the diagnostic results, the treatment of choice was surgical resection of the testicular tumor under general anesthesia. And the histopathological findings of the excised neoplasm were consistent with those of testicular seminoma. In addition, no tumor recurrence was observed after surgery, which indicates that our surgical and post-operative treatments were effective. The surgical treatment adopted in this case report is safe for patients and provides the best solution for the diagnosis and treatment of giant panda testicular seminoma. To our knowledge this is the first detailed report of surgical resection of testicular seminoma in the giant panda.
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Affiliation(s)
- Tianyou Zhang
- Guangzhou Chimelong Safari Park, Guangzhou, 511430, China
| | - Gaolong Zhong
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Zhaoxin Tang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
- Corresponding author at: College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
| | - Guixin Dong
- Guangdong Chimelong group, Co. Ltd, Guangzhou, 511400, China
- Guangdong South China Rare Wild Animal Species Conservation Center, Zhuhai, 519000, China
- Corresponding author at: Guangdong South China Rare Wild Animal Species Conservation Center, Zhuhai, 519000, China.
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Zeng Y, Han H, Gong Y, Qubi S, Chen M, Qiu L, Huang Y, Zhou H, Wei W. Feeding habits and foraging patch selection strategy of the giant panda in the Meigu Dafengding National Nature Reserve, Sichuan Province, China. Environ Sci Pollut Res Int 2023; 30:49125-49135. [PMID: 36773257 DOI: 10.1007/s11356-023-25769-0] [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] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 02/02/2023] [Indexed: 04/16/2023]
Abstract
Despite retaining a digestive system with carnivorous characteristics, the giant panda has now specialized to eat bamboo. Therefore, research on its feeding habits and foraging strategies has always been an important field in the study of giant panda population ecology. Located in the core distribution area of the giant panda population in the Liangshan mountains, the Meigu Dafengding Nature Reserve acts as the link between the major panda reserves in the Liangshan mountains and the key corridor zone connecting the giant panda populations in the east and west. This study was performed in 2017 and aimed to determine the feeding habits of giant pandas in this region, the heterogeneity of food resources in different seasons, and the selection strategy for foraging patches. To achieve this, we used the line transect method to investigate the giant panda population, collected fresh feces, analyzed the nutritional composition of bamboo samples, and set up a sampling grid of foraging patches in different seasonal distribution areas. It was found that wild giant pandas in the region spend most of the year at lower elevations(1939-3296 m) foraging for Yushania maculata and Yushania ailuropodina, and only move to higher elevations(2844-3770 m) in summer for Bashania fangiana. Their preferred foraging patches(n = 65) had certain topographical features, such as gentle slopes(< 25°) and closer proximity to water sources(< 500 m), and the nutritional quality of bamboo resources in foraging patches was significantly better than in those they avoided or rarely used. The food habits and foraging patch selection strategies of giant pandas in the Liangshan and Qinling mountains are relatively similar, and the results of this study can help provide a scientific basis for the conservation and management of wild giant panda habitats in different mountain regions.
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Affiliation(s)
- Ying Zeng
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Han Han
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
- Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan Province, Science and Technology Department of Sichuan Province, Nanchong, China
| | - Yihua Gong
- Sichuan Meigu Dafengding National Nature Reserve Administration, Meigu, China
| | - Shibu Qubi
- Sichuan Meigu Dafengding National Nature Reserve Administration, Meigu, China
| | - Minghua Chen
- Sichuan Meigu Dafengding National Nature Reserve Administration, Meigu, China
| | - Lan Qiu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Youyou Huang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Hong Zhou
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
- Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan Province, Science and Technology Department of Sichuan Province, Nanchong, China
| | - Wei Wei
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China.
- Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan Province, Science and Technology Department of Sichuan Province, Nanchong, China.
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15
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Wang M, Nie YG, Swaisgood RR, Wei W, Zhou WL, Zhang ZJ, Wang GM, Wei FW, Wang GM, Wei FW. Stable seasonal migration patterns in giant pandas. Zool Res 2023; 44:341-348. [PMID: 36849789 PMCID: PMC10083218 DOI: 10.24272/j.issn.2095-8137.2022.421] [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] [Indexed: 02/22/2023] Open
Abstract
A critical function of animal movement is to maximize access to essential resources in temporally fluctuating and spatially heterogeneous environments. Seasonally mediated resource fluctuations may influence animal movements, enabling them to track changing resource distributions, resulting in annual migration patterns. The conservation-dependent giant panda ( Ailuropoda melanoleuca) displays seasonal movement patterns; however, the key factor driving these seasonal migration patterns remains poorly understood. Here, we used GPS tracking collars to monitor the movements of six giant pandas over a 12-year period across different elevations, and performed statistical analysis of seasonal migration directions, routes, habitat revisitation, home range overlap, first arrival events, and stability. Our results revealed a compelling pattern of seasonal migrations that facilitated the ability of the pandas to forage at the appropriate time and place to maximize nutritional intake. Our results indicated that pandas utilize spatial memory to locate reliable food resources, as evidenced by their annual return to the same or similar winter and summer home ranges and the consistently maintained percentage of home range overlap. These novel insights into giant panda foraging and movement ecology not only enhance our understanding of its ability to adapt to nutritionally poor dietary resources but also provide important information for the development of resource utilization-based protection and management strategies.
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Affiliation(s)
- Meng Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong-Gang Nie
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ronald R Swaisgood
- Giant Panda Research, San Diego Zoo Institute for Conservation Research, Escondido, California 92027, USA
| | - Wei Wei
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wen-Liang Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ze-Jun Zhang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Gui-Ming Wang
- Department of Wildlife, Fisheries and Aquaculture, Mississippi State University, Mississippi 39762, USA
| | - Fu-Wen Wei
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China. E-mail:
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Ji X, Jiang B, Feng N, Zhu L, Liang B, Liu J, Guo X, Sun Y. Complete genome sequence of a bla NDM-5-producing Escherichia coli DC71 assigned as ST410-O8:H9 and recovered from a captive giant panda (Ailuropoda melanoleuca) in China. J Glob Antimicrob Resist 2023; 32:155-157. [PMID: 36396042 DOI: 10.1016/j.jgar.2022.11.004] [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: 07/26/2022] [Revised: 10/10/2022] [Accepted: 11/06/2022] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVES In this study, we report the complete genome sequence of a multidrug-resistant Escherichia coli strain recovered from a fecal sample from a captive giant panda in China. METHODS Antimicrobial susceptibility testing was performed. Genomic DNA from E. coli DC71 was sequenced using a Nanopore PromethION sequencer instrument (Oxford Nanopore Technologies, UK) and MGI High-throughput Sequencing MGISEQ-2000 platforms. The clean reads were de novo assembled using SPAdes v3.11. The complete genome was annotated and analyzed using multilocus sequence typing, serotyping, plasmid replicons, fimH typing, chromosomal point mutations, acquired antimicrobial resistance, and virulence genes with web tools available at the Center for Genomic Epidemiology. RESULTS The complete genome, 4 991 906 bp in length and comprising 4677 protein-coding sequences, was generated. In silico analysis revealed that E. coli DC71 belonged to the ST410-O8:H9 subclone. A carbapenem resistance gene, blaNDM-5, was located on the pDC71-2 plasmid, coproducing blaTEM-1. Many other resistance determinants encoded by chromosomes and pDC71-3 were found. The virulence related genes carried by chromosomes were mostly related to enterohemorrhagic E. coli (EHEC) O157:H7. CONCLUSIONS To our knowledge, this is the first complete genome of an E. coli ST410-O8:H9 strain recovered from captive giant panda in China. This multidrug-resistant E. coli subclone may pose potential risks to human and animal health. The genome sequence will be helpful to understand the genomic structure, its diversity, and the molecular mechanism allowing bacteria to disseminate the resistance gene.
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Affiliation(s)
- Xue Ji
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, China; Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, China
| | - Bowen Jiang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, China; Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, China
| | - Na Feng
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, China; Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, China
| | - Lingwei Zhu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, China; Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, China
| | - Bing Liang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, China; Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, China
| | - Jun Liu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, China; Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, China
| | - Xuejun Guo
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, China; Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, China
| | - Yang Sun
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, China; Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, China.
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Liu HF, Huang XY, Li ZM, Zhou ZY, Zhong ZJ, Peng GN. Virulence gene detection and antimicrobial resistance analysis of Enterococcus faecium in captive giant pandas (Ailuropoda melanoleuca) in China. Acta Vet Scand 2023; 65:4. [PMID: 36737784 PMCID: PMC9898886 DOI: 10.1186/s13028-023-00668-z] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The emergence of multidrug resistance among enterococci makes effective treatment of enterococcal infections more challenging. Giant pandas (Ailuropoda melanoleuca) are vulnerable to oral trauma and lesions as they feast on bamboo. Enterococci may contaminate such oral lesions and cause infection necessitating treatment with antibiotics. However, few studies have focused on the virulence and drug resistance of oral-derived enterococci, including Enterococcus faecium, in giant pandas. In this study, we analyzed the prevalence of 8 virulence genes and 14 drug resistance genes in E. faecium isolates isolated from saliva samples of giant pandas held in captivity in China and examined the antimicrobial drug susceptibility patterns of the E. faecium isolates. RESULTS Twenty-eight isolates of E. faecium were successfully isolated from the saliva samples. Four virulence genes were detected, with the acm gene showing the highest prevalence (89%). The cylA, cpd, esp, and hyl genes were not detected. The isolated E. faecium isolates possessed strong resistance to a variety of drugs; however, they were sensitive to high concentrations of aminoglycosides. The resistance rates to vancomycin, linezolid, and nitrofurantoin were higher than those previously revealed by similar studies in China and other countries. CONCLUSIONS The findings of the present study indicate the drugs of choice for treatment of oral E. faecium infection in the giant panda.
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Affiliation(s)
- Hai-Feng Liu
- grid.80510.3c0000 0001 0185 3134Department of Veterinary Surgery, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130 People’s Republic of China
| | - Xiao-Yao Huang
- grid.80510.3c0000 0001 0185 3134Department of Veterinary Surgery, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130 People’s Republic of China
| | - Zhe-Meng Li
- grid.80510.3c0000 0001 0185 3134Department of Veterinary Surgery, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130 People’s Republic of China
| | - Zi-Yao Zhou
- grid.80510.3c0000 0001 0185 3134Department of Veterinary Surgery, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130 People’s Republic of China
| | - Zhi-Jun Zhong
- grid.80510.3c0000 0001 0185 3134Department of Veterinary Surgery, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130 People’s Republic of China
| | - Guang-Neng Peng
- grid.80510.3c0000 0001 0185 3134Department of Veterinary Surgery, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130 People’s Republic of China
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Ma J, Zhang L, Shen F, Geng Y, Huang Y, Wu H, Fan Z, Hou R, Song Z, Yue B, Zhang X. Gene expressions between obligate bamboo-eating pandas and non-herbivorous mammals reveal converged specialized bamboo diet adaptation. BMC Genomics 2023; 24:23. [PMID: 36647013 PMCID: PMC9843897 DOI: 10.1186/s12864-023-09111-z] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND It is inevitable to change the function or expression of genes during the environmental adaption of species. Both the giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens) belong to Carnivora and have developed similar adaptations to the same dietary switch to bamboos at the morphological and genomic levels. However, the genetic adaptation at the gene expression level is unclear. Therefore, we aimed to examine the gene expression patterns of giant and red panda convergent specialized bamboo-diets. We examined differences in liver and pancreas transcriptomes between the two panda species and other non-herbivorous species. RESULTS The clustering and PCA plots suggested that the specialized bamboo diet may drive similar expression shifts in these two species of pandas. Therefore, we focused on shared liver and pancreas DEGs (differentially expressed genes) in the giant and red panda relative to other non-herbivorous species. Genetic convergence occurred at multiple levels spanning carbohydrate metabolism, lipid metabolism, and lysine degradation. The shared adaptive convergence DEGs in both organs probably be an evolutionary response to the high carbohydrate, low lipid and lysine bamboo diet. Convergent expression of those nutrient metabolism-related genes in both pandas was an intricate process and subjected to multi-level regulation, including DNA methylation and transcription factor. A large number of lysine degradation and lipid metabolism related genes were hypermethylated in promoter regions in the red panda. Most genes related to carbohydrate metabolism had reduced DNA methylation with increased mRNA expression in giant pandas. Unlike the red panda, the core gene of the lysine degradation pathway (AASS) doesn't exhibit hypermethylation modification in the giant panda, and dual-luciferase reporter assay showed that transcription factor, NR3C1, functions as a transcriptional activator in AASS transcription through the binding to AASS promoter region. CONCLUSIONS Our results revealed the adaptive expressions and regulations of the metabolism-related genes responding to the unique nutrients in bamboo food and provided data accumulation and research hints for the future revelation of complex mechanism of two pandas underlying convergent adaptation to a specialized bamboo diet.
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Affiliation(s)
- Jinnan Ma
- grid.13291.380000 0001 0807 1581Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065 China ,grid.410739.80000 0001 0723 6903College of Continuing Education, Yunnan Normal University, Kunming, 650092 China
| | - Liang Zhang
- grid.452857.9The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081 China
| | - Fujun Shen
- grid.452857.9The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081 China
| | - Yang Geng
- grid.13291.380000 0001 0807 1581Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065 China
| | - Yan Huang
- China Conservation and Research Center for the Giant Panda, Wolong, 623006 Sichuan China
| | - Honglin Wu
- China Conservation and Research Center for the Giant Panda, Wolong, 623006 Sichuan China
| | - Zhenxin Fan
- grid.13291.380000 0001 0807 1581Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065 China ,grid.13291.380000 0001 0807 1581Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065 China
| | - Rong Hou
- grid.452857.9The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081 China
| | - Zhaobin Song
- grid.13291.380000 0001 0807 1581Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065 China ,grid.13291.380000 0001 0807 1581Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065 China
| | - Bisong Yue
- grid.13291.380000 0001 0807 1581Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065 China ,grid.13291.380000 0001 0807 1581Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065 China
| | - Xiuyue Zhang
- grid.13291.380000 0001 0807 1581Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065 China ,grid.13291.380000 0001 0807 1581Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065 China
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Zhou W, Wang M, Ma Y, Wang L, Hu Y, Wei F, Nie Y. Community structure of the solitary giant pandas is maintained by indirect social connections. Mov Ecol 2022; 10:53. [PMID: 36457062 PMCID: PMC9716724 DOI: 10.1186/s40462-022-00354-1] [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] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Indirect interactions between individual solitary mammals, such as the giant panda, are often overlooked because of their nature, yet are important for maintaining the necessary sociality in solitary species. METHODS AND RESULTS Here, we determined the genetic identity of all giant panda individuals in a local population and matched these identities with their associations to determine social network of this solitary animal. Total thirty-five giant panda individuals were found in our field survey, and we constructed genetic and social networks for thirty-three individuals who successfully obtained genetic, age and sex information. The results showed that sex had great impact on both social network and genetic network, and age may have the potential to influence the social network of the giant pandas. Adult males, mostly in the central of the social network, which appeared significantly larger network connections than adult females. Due to the female-biased dispersal pattern of wild giant pandas, male-male pairs showed higher relatedness than female-female ones and multi-generational patrilinear assemblages are expected in the study area. CONCLUSIONS The relatedness of individuals has an influence on the formation of community social structure of giant pandas, and indirect interactions among solitary giant pandas potentially function to reduce competition for resources and inbreeding.
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Affiliation(s)
- Wenliang Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1-5 Beichen Xilu, Chaoyang District, Beijing, China
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Meng Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1-5 Beichen Xilu, Chaoyang District, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yingjie Ma
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1-5 Beichen Xilu, Chaoyang District, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Le Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1-5 Beichen Xilu, Chaoyang District, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yibo Hu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1-5 Beichen Xilu, Chaoyang District, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Fuwen Wei
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1-5 Beichen Xilu, Chaoyang District, Beijing, China
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Yonggang Nie
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1-5 Beichen Xilu, Chaoyang District, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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Li Y, Xu W, Wang Y, Kou J, Zhang J, Hu S, Zhang L, Wang J, Liu J, Liu H, Luo L, Wang C, Lan J, Hou R, Shen F. An improved, chromosome-level genome of the giant panda (Ailuropoda melanoleuca). Genomics 2022; 114:110501. [PMID: 36270383 DOI: 10.1016/j.ygeno.2022.110501] [Citation(s) in RCA: 2] [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: 05/13/2022] [Revised: 09/21/2022] [Accepted: 10/04/2022] [Indexed: 01/14/2023]
Abstract
BACKGROUND The iconic giant panda (Ailuropoda melanoleuca), as both a flagship and umbrella species endemic to China, is a world famous symbol for wildlife conservation. The giant panda has several specific biological traits and holds a relatively small place in evolution. A high-quality genome of the giant panda is key to understanding the biology of this vulnerable species. FINDINGS We generated a 2.48-Gb chromosome-level genome (GPv1) of the giant panda named "Jing Jing" with a contig N50 of 28.56 Mb and scaffold N50 of 134.17 Mb, respectively. The total length of chromosomes (n = 21) was 2.39-Gb, accounting for 96.4% of the whole genome. Compared with the previously published four genomes of the giant panda, our genome is characterized by the highest completeness and the correct sequence orientation. A gap-free and 850 kb length of immunoglobulin heavy-chain gene cluster was manually annotated in close proximity to the telomere of chromosome 14. Additionally, we developed an algorithm to predict the centromere position of each chromosome. We also constructed a complete chromatin structure for "Jing Jing", which includes inter-chromosome interaction pattern, A/B compartment, topologically associated domain (TAD), TAD-clique and promoter-enhancer interaction (PEI). CONCLUSIONS We presented an improved chromosome-level genome and complete chromatin structure for the giant panda. This is a valuable resource for the future genetic and genomic studies on giant panda.
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Affiliation(s)
- Yan Li
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Wei Xu
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Ye Wang
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Jie Kou
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Jiaman Zhang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, China
| | - Silu Hu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, China
| | - Liang Zhang
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Juan Wang
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Jiawen Liu
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Hong Liu
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Li Luo
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Chengdong Wang
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Jingchao Lan
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Rong Hou
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China.
| | - Fujun Shen
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China.
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Su X, Yan X, Li Y, Zhang D, Li L, Geng Y, Su F, Yue C, Hou R, Liu S. Identification of extended-spectrum beta-lactamase (CTX-M)-producing Klebsiella pneumoniae belonging to ST37, ST290, and ST2640 in captive giant pandas. BMC Vet Res 2022; 18:186. [PMID: 35581595 DOI: 10.1186/s12917-022-03276-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 01/11/2021] [Accepted: 04/28/2022] [Indexed: 11/10/2022] Open
Abstract
Background Extended-spectrum β-lactamases (ESBL)-producing strains of Klebsiella pneumoniae remain a worldwide, critical clinical concern. However, limited information was available concerning ESBL-producing Klebsiella pneumoniae in giant pandas. The objective of this study was to characterize ESBL-producing Klebsiella pneumoniae isolates from captive giant pandas. A total of 211 Klebsiella pneumoniae isolates were collected from 108 giant pandas housed at the Chengdu Research Base of Giant Panda Breeding (CRBGP), China. Samples were screened for the ESBL-producing phenotype via the double-disk synergy test. Result A total of three (1.42%, n = 3/211) ESBL-producing Klebsiella pneumoniae strains were identified, and characterization of ESBL-producing Klebsiella pneumoniae isolates were studied by the detection of ESBL genes and mobile genetic elements (MGEs), evaluation of antimicrobial susceptibility and detection of associated resistance genes. Clonal analysis was performed by multi-locus sequencing type (MLST). Among the three ESBL-producing isolates, different ESBL-encoding genes, including blaCTX-M, and blaTEM, were detected. These three isolates were found to carry MGEs genes (i.e., IS903 and tnpU) and antimicrobial resistance genes (i.e., aac(6')-Ib, aac(6')-I, qnrA, and qnrB). Furthermore, it was found that the three isolates were not hypermucoviscosity, resistant to at least 13 antibiotics and belonged to different ST types (ST37, ST290, and ST2640). Conclusion Effective surveillance and strict infection control strategies should be implemented to prevent outbreaks of ESBL-producing Klebsiella pneumoniae in giant pandas.
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Zhao M, Yue C, Yang Z, Li Y, Zhang D, Zhang J, Yang S, Shen Q, Su X, Qi D, Ma R, Xiao Y, Hou R, Yan X, Li L, Zhou Y, Liu J, Wang X, Wu W, Zhang W, Shan T, Liu S. Viral metagenomics unveiled extensive communications of viruses within giant pandas and their associated organisms in the same ecosystem. Sci Total Environ 2022; 820:153317. [PMID: 35066043 DOI: 10.1016/j.scitotenv.2022.153317] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/17/2022] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Cross-species transmission events were commonplace, with numerous cases of host-switching during the viral evolutionary history, but relatively little evidence for onward transmission in different species living in the same ecosystem. For understanding the communications of viruses in giant pandas (Ailuropoda melanoleuca) and their associated organisms, based on a large size of samples (N = 2305) collected between 2015 and 2020 from giant panda (N = 776) and other four giant panda-associated organisms in the same ecosystem, red pandas (N = 700), stray cats (N = 32), wild rats (N = 42), and mosquitoes (N = 755), viromics was used for the virus identification and subsequent virus traceability. The results showed that a feline panleukopenia virus (FPV) was found in giant pandas with clinical signs of vomiting and mild diarrhea. Meanwhile, the same FPV strain was also prevalent in the healthy red panda (Ailurus fulgens) population. From the viromes of the five different organisms, 250 virus genomes were determined. Our data revealed that besides FPV, other putative pathogenic viruses, such as red panda amdoparvoviruses (RPAVs) and Getah viruses (GETVs) were responsible for previous disease or death of some red pandas. We also demonstrated that a number of viruses were involved in potential interspecies jumping events between giant pandas and their associated species. Collectively, our results shed light on the genetic diversity and relationship of diverse viral pathogens in 'Giant pandas-Associated animals-Arthropods' and report some cases of possible viral host-switching among these host species living in the same ecosystem.
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Affiliation(s)
- Min Zhao
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Chanjuan Yue
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Zijun Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Yunli Li
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Dongsheng Zhang
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Ju Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Shixing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Quan Shen
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Xiaoyan Su
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Dunwu Qi
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Rui Ma
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Yuqing Xiao
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Rong Hou
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Xia Yan
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Lin Li
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Yanshan Zhou
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Jiabin Liu
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Xiaochun Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Wei Wu
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China.
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
| | - Songrui Liu
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China.
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Zhu Y, Deng T, Qiao M, Tang D, Huang X, Deng W, Liu H, Li R, Lan T. Comparison of genetic characteristics between captive and wild giant pandas based on 13 mitochondrial coding genes. Mol Biol Rep 2022; 49:4901-4908. [PMID: 35534585 DOI: 10.1007/s11033-022-07350-z] [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: 01/04/2022] [Accepted: 03/09/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUND Research on genetic diversity based on mitochondrial DNA of giant pandas mainly focused on a single marker or a few genes. OBJECTIVE To provide a more comprehensive assessment of the genetic diversity on giant pandas based on 13 mitochondrial protein coding genes. METHODS We assembled 13 protein coding genes in the mitochondrial genome of the giant panda based on the whole genome sequencing data, including ND1, ND2, COX1, COX2, ATP8, ATP6, COX3, ND3, ND4L, ND4, ND5, ND6 and Cyt b. RESULTS We successfully obtained long sequence of 11,416 base pairs with all 13 genes for 110 giant panda individual, accounting for 67.93% in length of the mitochondrial reference genome. Haplotype diversity was 0.9518 ± 0.009 and nucleotide diversity (π) was 0.00157 ± 0.00014. We detected three new haplotypes, including GPC10 and GPC21 for the CR sequence and GPB12 for the Cyt b gene. CONCLUSION These multi-gene sequences provided more genetic variable information to compare captive and wild giant panda population.
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Affiliation(s)
- Yixin Zhu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tao Deng
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
- China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Maiju Qiao
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
- China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Dan Tang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
- China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Xiaoyu Huang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
- China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Wenwen Deng
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
- China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China
| | - Rengui Li
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China.
- China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China.
| | - Tianming Lan
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
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Ma J, Zhang L, Huang Y, Shen F, Wu H, Yang Z, Hou R, Song Z, Yue B, Zhang X. Epigenomic profiling indicates a role for DNA methylation in the postnatal liver and pancreas development of giant pandas. Genomics 2022; 114:110342. [PMID: 35306168 DOI: 10.1016/j.ygeno.2022.110342] [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: 05/27/2021] [Revised: 02/14/2022] [Accepted: 03/13/2022] [Indexed: 01/14/2023]
Abstract
Giant pandas are unique within Carnivora with a strict bamboo diet. Here, the epigenomic profiles of giant panda liver and pancreas tissues collected from three important feeding stages were investigated using BS-seq. Few differences in DNA methylation profiles were exhibited between no feeding and suckling groups in both tissues. However, we observed a tendency toward a global loss of DNA methylation in the gene-body and promoter region of metabolism-related genes from newborn to adult. Correlation analysis revealed a significant negative correlation between the changes in methylation levels within gene promoters and gene expression. The majority of genes related to nutrition metabolism had lost DNA methylation with increased mRNA expression in adult giant pandas. The few galactose metabolism and unsaturated fatty acid metabolism related genes that were hypomethylated and highly-expressed at early stages of giant panda development may meet the nutritional requirement of this species' highly altricial neonates.
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Affiliation(s)
- Jinnan Ma
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, Sichuan 610065, China
| | - Liang Zhang
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, 1375 Panda Road, Northern Suburb, Chengdu, Sichuan 610081, China
| | - Yan Huang
- China Conservation and Research Center for the Giant Panda, 98 Tongjiang Road, Dujiangyan, Chengdu, Sichuan 611800, China
| | - Fujun Shen
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, 1375 Panda Road, Northern Suburb, Chengdu, Sichuan 610081, China
| | - Honglin Wu
- China Conservation and Research Center for the Giant Panda, 98 Tongjiang Road, Dujiangyan, Chengdu, Sichuan 611800, China
| | - Zhisong Yang
- Sichuan Academy of Giant Panda, 1375 Panda Road, Northern Suburb, Chengdu, Sichuan 610081, China
| | - Rong Hou
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, 1375 Panda Road, Northern Suburb, Chengdu, Sichuan 610081, China
| | - Zhaobin Song
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, Sichuan 610065, China
| | - Bisong Yue
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, Sichuan 610065, China
| | - Xiuyue Zhang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, Sichuan 610065, China.
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25
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Shen H, Li C, He M, Huang Y, Wang J, Luo J, Wang M, Yue B, Zhang X. Whole blood transcriptome profiling identifies candidate genes associated with alopecia in male giant pandas (Ailuropoda melanoleuca). BMC Genomics 2022; 23:297. [PMID: 35413801 PMCID: PMC9004003 DOI: 10.1186/s12864-022-08501-z] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 03/22/2022] [Indexed: 11/16/2022] Open
Abstract
Background The giant panda (Ailuropoda melanoleuca) is a threatened species endemic to China. Alopecia, characterized by thinning and broken hair, mostly occurs in breeding males. Alopecia significantly affects the health and public image of the giant panda and the cause of alopecia is unclear. Results Here, we researched gene expression profiles of four alopecia giant pandas and seven healthy giant pandas. All pandas were approximately ten years old and their blood samples collected during the breeding season. A total of 458 up-regulated DEGs and 211 down-regulated DEGs were identified. KEGG pathway enrichment identified that upregulated genes were enriched in the Notch signaling pathway and downregulated genes were enriched in ribosome, oxidative phosphorylation, and thermogenesis pathways. We obtained 28 hair growth-related DEGs, and identified three hub genes NOTCH1, SMAD3, and TGFB1 in PPI analysis. Five hair growth-related signaling pathways were identified with abnormal expression, these were Notch, Wnt, TGF-β, Mapk, and PI3K-Akt. The overexpression of NOTCH1 delays inner root sheath differentiation and results in hair shaft abnormalities. The delayed hair regression was associated with a significant decrease in the expression levels of TGFB1. Conclusions Our data confirmed the abnormal expression of several hair-related genes and pathways and identified alopecia candidate genes in the giant panda. Results of this study provide theoretical basis for the establishment of prevention and treatment strategies for giant pandas with alopecia. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08501-z.
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Affiliation(s)
- Haibo Shen
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610064, PR China
| | - Caiwu Li
- Key Laboratory of State Forestry and Grassland Administration On Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, Sichuan, PR China
| | - Ming He
- Key Laboratory of State Forestry and Grassland Administration On Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, Sichuan, PR China
| | - Yan Huang
- Key Laboratory of State Forestry and Grassland Administration On Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, Sichuan, PR China
| | - Jing Wang
- Key Laboratory of State Forestry and Grassland Administration On Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, Sichuan, PR China
| | - Jing Luo
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610064, PR China
| | - Minglei Wang
- Key Laboratory of State Forestry and Grassland Administration On Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, Sichuan, PR China
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064, PR China
| | - Xiuyue Zhang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610064, PR China. .,No. 24 South Section 1, Yihuan Road, Chengdu, 610065, Sichuan, China.
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Xie Y, Wang S, Wu S, Gao S, Meng Q, Wang C, Lan J, Luo L, Zhou X, Xu J, Gu X, He R, Yang Z, Peng X, Hu S, Yang G. Genome of the Giant Panda Roundworm Illuminates Its Host Shift and Parasitic Adaptation. Genomics Proteomics Bioinformatics 2022; 20:366-381. [PMID: 34487863 PMCID: PMC9684166 DOI: 10.1016/j.gpb.2021.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 08/17/2021] [Accepted: 08/25/2021] [Indexed: 01/05/2023]
Abstract
Baylisascaris schroederi, a roundworm (ascaridoid) parasite specific to the bamboo-feeding giant panda (Ailuropoda melanoleuca), represents a leading cause of mortality in wild giant panda populations. Here, we present a 293-megabase chromosome-level genome assembly of B. schroederi to infer its biology, including host adaptations. Comparative genomics revealed an evolutionary trajectory accompanied by host-shift events in ascaridoid parasite lineages after host separations, suggesting their potential for transmission and rapid adaptation to new hosts. Genomic and anatomical lines of evidence, including expansion and positive selection of genes related to the cuticle and basal metabolisms, indicate that B. schroederi undergoes specific adaptations to survive in the sharp-edged bamboo-enriched gut of giant pandas by structurally increasing its cuticle thickness and efficiently utilizing host nutrients through gut parasitism. Additionally, we characterized the secretome of B. schroederi and predicted potential drug and vaccine targets for new control strategies. Overall, this genome resource provides new insights into the host adaptation of B. schroederi to the giant panda as well as the host-shift events in ascaridoid parasite lineages. Our findings on the unique biology of B. schroederi will also aid in the development of prevention and treatment measures to protect giant panda populations from roundworm parasitism.
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Affiliation(s)
- Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Sen Wang
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Shuangyang Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Department of Oncology and Pathology, Karolinska Institutet, Stockholm 17164, Sweden
| | - Shenghan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qingshu Meng
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Chengdong Wang
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Jingchao Lan
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Li Luo
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Xuan Zhou
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jing Xu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaobin Gu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Ran He
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Zijiang Yang
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD 20740, USA
| | - Xuerong Peng
- Department of Chemistry, College of Life and Basic Science, Sichuan Agricultural University, Chengdu 611130, China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Guangyou Yang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China.
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Wang J, Pu Y, Zeng Y, Chen Y, Zhao W, Niu L, Chen B, Yang Z, Wu L, Pan K, Jing B, Zeng D, Ni X. Multi-functional Potential of Five Lactic Acid Bacteria Strains Derived from Giant Panda (Ailuropoda melanoleuca). Probiotics Antimicrob Proteins 2022; 15:668-681. [PMID: 35000110 DOI: 10.1007/s12602-021-09881-6] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2021] [Indexed: 10/19/2022]
Abstract
The multi-functional properties of lactic acid bacteria (LAB) on host health have been a popular research topic. The aim of present study was to assess the multi-functional potential of five LAB strains isolated from giant panda. In this study, we analyzed five giant panda LAB strains (Weissella confuse WJ202003 (W3), WJ202009 (W9), WJ202021 (W21), BSP201703 (X3); Lactiplantibacillus plantarum BSGP201683 (G83)) and found that they exhibited rapid growth as well as strong acid production capacity. The five LAB strains possessed high cell surface hydrophobicity to the four tested solvents (xylene, hexadecane, chloroform, ethyl acetate; except strain W9), auto-aggregation ability, co-aggregation ability with three pathogens (Escherichia coli, Enterotoxigenic Escherichia coli, Salmonella), adhesion ability to Caco-2 cell line, and strongly biofilm formation ability, suggesting an adhesion property. As investigated for their antioxidative potential, all the strains showed good tolerance to H2O2, high scavenging ability against 1, 1-diphenyl-2-picrylhydrazyl (DPPH), and hydroxyl (OH-), and reduction ability. Furthermore, the five LAB strains could produce multiple probiotic substances, including exopolysaccharide (EPS), gamma-aminobutyric acid (GABA), bile salt hydrolase (BSH), cellulase (only strain G83), and protease (except strain X3), which was the first to report the production of EPS, GABA, BSH, cellulase, and protease in giant panda-derived LAB strain. These results demonstrated that strains W3, W9, W21, X3, and G83 had multi-functional potential and could be utilized as potential probiotics for giant panda.
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Affiliation(s)
- Jie Wang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yang Pu
- Chengdu Wildlife Institute, Chengdu Zoo, Chengdu, 610081, Sichuan, China
| | - Yan Zeng
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yingyi Chen
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Wei Zhao
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Lili Niu
- Chengdu Wildlife Institute, Chengdu Zoo, Chengdu, 610081, Sichuan, China
| | - Benhao Chen
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zihan Yang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Liqian Wu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Kangcheng Pan
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Bo Jing
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Dong Zeng
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Xueqin Ni
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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Yang M, Huang Y, Wu H, Li C, Ling S, Sun J, Shen H, Yue B, Zhang X. Blood transcriptome analysis revealed the immune changes and immunological adaptation of wildness training giant pandas. Mol Genet Genomics 2022; 297:227-239. [PMID: 34985592 DOI: 10.1007/s00438-021-01841-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 08/01/2020] [Accepted: 11/23/2021] [Indexed: 01/06/2023]
Abstract
The giant panda (Ailuropoda melanoleuca) is a global flagship species for biodiversity conservation. As the time for captive giant pandas to be released into the wild matures, wildness training is provided to allow adaptation to their natural environment. It is assumed that changes in the immune system would be integral in this adaptation from captive to wild, where many more pathogens would be encountered in their natural habitats. Therefore, this study aims to determine the expression changes of immune-related genes and their potential as immunoassay markers for adaptation monitoring in wildness training giant pandas, and then to understand the adaptation strategy of wildness training giant pandas to the wild environment, thereby improving the success rate of panda reintroduction. We obtained 300 differentially expressed genes (DEGs) by RNA-seq, with 239 up-regulated and 61 down-regulated DEGs in wildness training giant pandas compared to captive pandas. Functional enrichment analysis indicated that up-regulated DEGs were enriched in several immune-related terms and pathways. There were 21 immune-related DEGs, in which most of them were up-regulated in wildness training giant pandas, including several critical innate and cellular immune genes. IL1R2 was the most significantly up-regulated gene and is a signature of homeostasis within the immune system. In the protein-protein interaction (PPI) analysis, CXCL8, CXCL10, and CCL5 were identified as the hub immune genes. Our results suggested that wildness training giant pandas have stronger innate and cellular immunity than captive giant pandas, and we proposed that a gene set of CXCL8, CXCL10, CCL5, CD3D, NFKBIA, TBX21, IL12RB2, and IL1R2 may serve as potential immunoassay markers to monitor and assess the immune status of wildness training giant pandas. Our study offers the first insight into immune alterations of wildness training giant pandas, paving the way for monitoring and evaluating the immune status of giant pandas when reintroducing them into the wild.
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Affiliation(s)
- Miao Yang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Yan Huang
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 623006, Sichuan, People's Republic of China
| | - Honglin Wu
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 623006, Sichuan, People's Republic of China
| | - Caiwu Li
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 623006, Sichuan, People's Republic of China
| | - Shanshan Ling
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 623006, Sichuan, People's Republic of China
| | - Jie Sun
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Haibo Shen
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Xiuyue Zhang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610064, People's Republic of China.
- Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, Sichuan, China.
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Chen Z, Tian Z, Liu X, Sun W. The potential risks and exposure of Qinling giant pandas to polycyclic aromatic hydrocarbon (PAH) pollution. Environ Pollut 2022; 292:118294. [PMID: 34626712 DOI: 10.1016/j.envpol.2021.118294] [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] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 09/28/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
Rapid industrialization and urbanization have created a substantial urban-rural gradient for various pollutants. The Qinling Mountains are highly important in terms of biodiversity, providing habitat for giant pandas, which are endemic to China and are a widely recognized symbol for conservation. Whether polycyclic aromatic hydrocarbon (PAH) exposure risks regarding in situ animal conservation zones are affected by environmental pollution or even enhanced by the mountain-trapping effect requires further research. Our group carried out a large-scale investigation on the area ranging from Xi'an to Hanzhong across the giant panda habitat in the Qinling Mountains by collecting atmosphere, soil, bamboo, and fecal samples from different sites over a two-year period. The total toxicity of atmospheric PAHs and the frequencies of soil PAHs above effect range low (ERL) values showed a decreasing trend from urban areas to the central mountains, suggesting a distance effect from the city. The proportions of total 5- and 6-ring PAHs in the atmosphere were higher in the central mountainous areas than in the urban areas, while this difference was reversed in the soil. Health risk assessments showed that the incremental lifetime carcinogenic risks (ILCR) of PAH exposure by bamboo ingestion ranged from 2.16 × 10-4 to 3.11 × 10-4, above the critical level of 10-4. Bamboo ingestion was the main driver of the PAH exposure risks. The concentration difference between bamboo and fecal samples provided a reference for the level of PAHs absorbed by the panda digestive system. Since the Qinling Mountains possess the highest density of giant pandas and provide habitats to many other endangered animal and plant species, we should not ignore the probability of health risks posed by PAHs. Monitoring the pollution level and reducing the atmospheric emissions of toxic pollutants are recommended actions. Further detailed research should also be implemented on pandas' health effects of contaminant exposure.
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Affiliation(s)
- Zhigang Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, And School of Environment, Tsinghua University, Beijing, 100084, China
| | - Zhaoxue Tian
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, And School of Environment, Tsinghua University, Beijing, 100084, China
| | - Xuehua Liu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, And School of Environment, Tsinghua University, Beijing, 100084, China.
| | - Wanlong Sun
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, And School of Environment, Tsinghua University, Beijing, 100084, China
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Dong J, Chen Y, Shi L, Shen B, Sun X, Ruan K, Xia X, Feng H, Feng N. Nanoparticles of conformation-stabilized canine distemper virus hemagglutinin are highly immunogenic and induce robust immunity. Virol J 2021; 18:229. [PMID: 34809642 PMCID: PMC8607554 DOI: 10.1186/s12985-021-01702-0] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/04/2021] [Indexed: 11/13/2022] Open
Abstract
Background Canine distemper virus (CDV) infection of ferrets, dogs, and giant pandas causes an acute systemic disease involving multiple organ systems, including the respiratory tract, lymphoid system, and central nervous system. In this study, we tested a new candidate CDV vaccine-CDV nanoparticles-based on hemagglutinin protein. Methods The nanoparticles were generated from conformation-stabilized CDV hemagglutinin tetramers. Immune responses against CDV were evaluated in mice. Immunization was initiated 6 weeks after birth and boosted two times with 4-week intervals. The blood and mucosal samples were collected 2 weeks after each immunization. Results Vaccination with CDV nanoparticles elicited high levels of IgG antibody titers in mice (approximately sevenfold to eightfold higher than that obtained with soluble CDV H protein) and mucosal immune responses and developed increased CDV-specific neutralizing antibody. The mice that received nanoparticles showed significantly higher IFN-γ- and IL-4-secreting cell population in the spleen and lymph node compared with mice immunized with soluble H protein. The co-stimulatory molecular expression of CD80 and CD86 on the surface of DCs was also upregulated. Conclusion The results demonstrate that self-assembly into nanoparticles can increase the immunogenicity of vaccine antigens, and nanoparticles assembled from conformation-stabilized CDV H protein can serve as a new CDV vaccine.
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Affiliation(s)
- Jingjian Dong
- Medical School of Jiaxing University, Jiahang Road 118#, Nanhu District, Jiaxing City, Zhejiang Province, 314001, People's Republic of China
| | - Yan Chen
- Medical School of Jiaxing University, Jiahang Road 118#, Nanhu District, Jiaxing City, Zhejiang Province, 314001, People's Republic of China
| | - Lili Shi
- Medical School of Jiaxing University, Jiahang Road 118#, Nanhu District, Jiaxing City, Zhejiang Province, 314001, People's Republic of China
| | - Bing Shen
- Medical School of Jiaxing University, Jiahang Road 118#, Nanhu District, Jiaxing City, Zhejiang Province, 314001, People's Republic of China
| | - Xianliang Sun
- Medical School of Jiaxing University, Jiahang Road 118#, Nanhu District, Jiaxing City, Zhejiang Province, 314001, People's Republic of China
| | - Kaiyi Ruan
- Medical School of Jiaxing University, Jiahang Road 118#, Nanhu District, Jiaxing City, Zhejiang Province, 314001, People's Republic of China
| | - Xianzhu Xia
- Military Veterinary Research Institute of Academy of Military Medical Sciences, Changchun, 130122, People's Republic of China
| | - Hao Feng
- Medical School of Jiaxing University, Jiahang Road 118#, Nanhu District, Jiaxing City, Zhejiang Province, 314001, People's Republic of China.
| | - Na Feng
- Military Veterinary Research Institute of Academy of Military Medical Sciences, Changchun, 130122, People's Republic of China.
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Guang X, Lan T, Wan QH, Huang Y, Li H, Zhang M, Li R, Zhang Z, Lei Y, Zhang L, Zhang H, Li D, Li X, Li H, Xu Y, Qiao M, Wu D, Tang K, Zhao P, Lin JQ, Kumar Sahu S, Liang Q, Jiang W, Zhang D, Xu X, Liu X, Lisby M, Yang H, Kristiansen K, Liu H, Fang SG. Chromosome-scale genomes provide new insights into subspecies divergence and evolutionary characteristics of the giant panda. Sci Bull (Beijing) 2021; 66:2002-2013. [PMID: 36654170 DOI: 10.1016/j.scib.2021.02.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 06/06/2020] [Revised: 09/27/2020] [Accepted: 12/25/2020] [Indexed: 02/03/2023]
Abstract
Extant giant pandas are divided into Sichuan and Qinling subspecies. The giant panda has many species-specific characteristics, including comparatively small organs for body size, small genitalia of male individuals, and low reproduction. Here, we report the most contiguous, high-quality chromosome-level genomes of two extant giant panda subspecies to date, with the first genome assembly of the Qinling subspecies. Compared with the previously assembled giant panda genomes based on short reads, our two assembled genomes increased contiguity over 200-fold at the contig level. Additional sequencing of 25 individuals dated the divergence of the Sichuan and Qinling subspecies into two distinct clusters from 10,000 to 12,000 years ago. Comparative genomic analyses identified the loss of regulatory elements in the dachshund family transcription factor 2 (DACH2) gene and specific changes in the synaptotagmin 6 (SYT6) gene, which may be responsible for the reduced fertility of the giant panda. Positive selection analysis between the two subspecies indicated that the reproduction-associated IQ motif containing D (IQCD) gene may at least partly explain the different reproduction rates of the two subspecies. Furthermore, several genes in the Hippo pathway exhibited signs of rapid evolution with giant panda-specific variants and divergent regulatory elements, which may contribute to the reduced inner organ sizes of the giant panda.
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Affiliation(s)
- Xuanmin Guang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Tianming Lan
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China; Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Qiu-Hong Wan
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yan Huang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, China
| | - Hong Li
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Mingchun Zhang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, China
| | - Rengui Li
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, China
| | - Zhizhong Zhang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, China
| | - Yinghu Lei
- Qinling Research Center of Giant Panda Breeding, Shaanxi Academy of Forestry, Xi'an 710082, China
| | - Ling Zhang
- China Wildlife Conservation Association, Beijing 100714, China
| | - Heming Zhang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, China
| | - Desheng Li
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, China
| | - Xiaoping Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China; Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Haimeng Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Yan Xu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Maiju Qiao
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, China
| | - Daifu Wu
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, China
| | - Keyi Tang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Pengpeng Zhao
- Qinling Research Center of Giant Panda Breeding, Shaanxi Academy of Forestry, Xi'an 710082, China
| | - Jian-Qing Lin
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Qiqi Liang
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Wenkai Jiang
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Danhui Zhang
- Qinling Research Center of Giant Panda Breeding, Shaanxi Academy of Forestry, Xi'an 710082, China
| | - Xun Xu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | - Xin Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Michael Lisby
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Huanming Yang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China; Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen 518120, China
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark; Qingdao-Europe Advanced Institute for Life Sciences, Qingdao 266555, China.
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China; Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark.
| | - Sheng-Guo Fang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
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Dai Z, Wang H, Feng Z, Ma L, Yang S, Shen Q, Wang X, Zhou T, Zhang W. Identification of a novel circovirus in blood sample of giant pandas (Ailuropoda melanoleuca). Infect Genet Evol 2021; 95:105077. [PMID: 34506957 DOI: 10.1016/j.meegid.2021.105077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/31/2021] [Accepted: 09/04/2021] [Indexed: 11/20/2022]
Abstract
The members of the family Circoviridae are considered to be one of the smallest autonomously replicating viruses that are classified into two genera, Circovirus and Cyclovirus. Circoviruses have been found in a variety of vertebrates, but whether they infect endangered protected animals has not been studied in much detail. Here, viral metagenomics and PCR methods were used to detect and verify viral nucleic acid in the blood sample from giant pandas. According to these methods, the complete genome sequence of a novel circovirus, the giant panda associated circovirus (GPCV) from the blood sample of three giant pandas was identified. The GPCV genome is 2090 bp in size and reveals two putative ambisense open-reading frames, encoding the major structural capsid protein and the replication associated protein, respectively, the latter having two predicted introns. Pairwise sequence comparison and phylogenetic analyses indicated GPCV was a putative new species within genus Circovirus based on the species demarcation criteria of the International Committee on the Taxonomy of Viruses. It is the first time that circovirus has been identified from blood sample of giant pandas. These efforts will contribute to future analyses to illuminate the evolutionary relationships between classified and newly identified members of the family Circoviridae.
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Yao Y, Xu Q, He X, Wang H, Yan H, Gao J, Hou R, Li X, Wang H. Preliminary investigation on iodine nutrition in captive giant pandas. J Trace Elem Med Biol 2021; 67:126780. [PMID: 34023729 DOI: 10.1016/j.jtemb.2021.126780] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 04/12/2021] [Accepted: 05/10/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND/OBJECTIVE The giant panda belongs to the family Ursidae and, as a species of bear, still retains the simple digestive system of a Carnivoran. However, under the pressure of a specific habitat they had to adapt to a plant mono-diet consisting of bamboo with different species and growth stages around the year. A plant-based diet has relatively low iodine content with risk of iodine deficiency. Furthermore, bamboo contains cyanogenic glycosides releasing cyanide whose detoxification metabolite the thiocyanate acts as antagonist against iodine uptake and storage in the thyroid. To date very little is known about the iodine nutritional status of the giant panda, thus this study was conducted to receive the first information about the iodine nutrition of captive giant panda. SUBJECTS/METHODS Here we investigated the iodine content of bamboo with different plant parts/vegetation stage and species and further compounds of the captive giant panda diet. Next, the urinary iodine (UI) and urinary thiocyanate (UT) levels of infant, sub-adult, adult and geriatric captive giant pandas was measured during the periods when the pandas consume both bamboo leaves- and culm (bamboo leaf-culm stage). Afterwards, the UI of 19 adult giant pandas was measured again for the different iodine intake during bamboo shoot stage. Finally, in this study part also the fecal iodine concentration was analyzed for calculation of total iodine excretion in relation to the iodine intake. RESULTS Bamboo leaves had the highest iodine content (453 μg/kg dry matter (DM)), followed by the shoots (84 μg/kg DM, p < 0.05), while bamboo culm had the lowest value (12 μg/kg DM, p < 0.05). During bamboo leaf-culm stage, giant pandas of different age groups had different UI and UT levels (p < 0.05). Furthermore, UI and UT were positively correlated among sub-adult, adult and geriatric giant pandas (p < 0.05). In adult giant pandas during bamboo shoot stage, the iodine excretion in feces was not different from that in urine while their total iodine excretion was less than their iodine intake (p < 0.05). Moreover, during bamboo shoot stage, the UI level of adult giant pandas was much lower than noted during bamboo leaf-culm stage (p < 0.05). CONCLUSIONS Our results indicate that UI of captive giant pandas was related to their age as well as to the vegetation stage/part of bamboo they consumed reflecting a different periodic iodine supply. Thiocyanate and fecal excretion should be emphasized when considering the iodine nutrition of giant pandas.
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Affiliation(s)
- Ying Yao
- Chengdu Research Base of Giant Panda Breeding, 610081, Chengdu, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, 610081, Chengdu, China; Sichuan Academy of Giant Panda, 610081, Chengdu, China
| | - Qin Xu
- Chengdu Research Base of Giant Panda Breeding, 610081, Chengdu, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, 610081, Chengdu, China; Sichuan Academy of Giant Panda, 610081, Chengdu, China
| | - Xin He
- Chengdu Research Base of Giant Panda Breeding, 610081, Chengdu, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, 610081, Chengdu, China; Sichuan Academy of Giant Panda, 610081, Chengdu, China
| | - Haiyan Wang
- Key Laboratory of Trace Element Nutrition of National Health Commission of the People's Republic of China, Department of Trace Element Nutrition, National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, 100050, Beijing, China
| | - Honglin Yan
- School of Life Science and Engineering, Southwest University of Science and Technology, 621010, Mianyang, China
| | - Jie Gao
- Chengdu Research Base of Giant Panda Breeding, 610081, Chengdu, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, 610081, Chengdu, China; Sichuan Academy of Giant Panda, 610081, Chengdu, China
| | - Rong Hou
- Chengdu Research Base of Giant Panda Breeding, 610081, Chengdu, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, 610081, Chengdu, China; Sichuan Academy of Giant Panda, 610081, Chengdu, China
| | - Xiuwei Li
- Key Laboratory of Trace Element Nutrition of National Health Commission of the People's Republic of China, Department of Trace Element Nutrition, National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, 100050, Beijing, China.
| | - Hairui Wang
- Chengdu Research Base of Giant Panda Breeding, 610081, Chengdu, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, 610081, Chengdu, China; Sichuan Academy of Giant Panda, 610081, Chengdu, China.
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34
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Jin L, Huang Y, Yang S, Wu D, Li C, Deng W, Zhao K, He Y, Li B, Zhang G, Xiong Y, Wei R, Li G, Wu H, Zhang H, Zou L. Diet, habitat environment and lifestyle conversion affect the gut microbiomes of giant pandas. Sci Total Environ 2021; 770:145316. [PMID: 33517011 DOI: 10.1016/j.scitotenv.2021.145316] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/02/2021] [Accepted: 01/16/2021] [Indexed: 06/12/2023]
Abstract
Gut microbiota (GM) are important for the health of giant pandas (GPs), in addition to the utilization of bamboo in their diets. However, it is not fully understood how diet, habitat environment and lifestyle contribute to the composition of GM in GP. Consequently, we evaluated how dietary changes, habitat environment conversions and lifestyle shifts influence the GM of GPs using high-throughput sequencing and genome-resolved metagenomics. The GM of GPs were more similar when their hosts exhibited the same diet. High fiber diets significantly increased the diversity and decreased the richness of gut bacterial communities alone or interacted with the age factor (p < 0.05). The abundances of Streptococcus, Pseudomonas, Enterococcus, Lactococcus, Acinetobacter, and Clostridium significantly increased during diet conversion process (Non-parametric factorial Kruskal-Wallis sum-rank test, LDA > 4). Reconstruction of 60 metagenome-assembled-genomes (MAGs) indicated that these bacteria were likely responsible for bamboo digestion via gene complements involved in cellulose, hemicellulose, and lignin degradation. While habitat environment may play a more important role in shaping the GM of GP, lifestyle can also greatly affect bacterial communities. The GM structure in reintroduced GPs notably converged to that of wild pandas. Importantly, the main bacterial genera of wild GPs could aid in lignin degradation, while those of reintroduced GPs were related to cellulose and hemicellulose digestion. Streptococcus, Pseudomonas, Enterococcus, Lactococcus, Acinetobacter, and Clostridium may contribute to lignocellulose digestion in GP. The results revealed that diet conversion, habitat environment and lifestyle could remarkably influence the GM of GP. In addition, results suggested that increasing the ability of lignin degradation with GM may aid to change the GM of reintroduced pandas to resemble those of wild pandas.
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Affiliation(s)
- Lei Jin
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yan Huang
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, the China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, China
| | - Shengzhi Yang
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Daifu Wu
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, the China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, China
| | - Caiwu Li
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, the China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, China
| | - Wenwen Deng
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, the China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, China
| | - Ke Zhao
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yongguo He
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, the China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, China
| | - Bei Li
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Guiquan Zhang
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, the China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, China
| | - Yaowu Xiong
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, the China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, China
| | - Rongping Wei
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, the China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, China
| | - Guo Li
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, the China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, China
| | - Hongning Wu
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, the China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, China
| | - Hemin Zhang
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, the China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, China
| | - Likou Zou
- College of Resources, Sichuan Agricultural University, Chengdu, China.
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Qin Z, Liu S, Bai M, Geng Y, Miller DL, Zhao R, Hou R, Huang W, Zhang D, Su X. First report of fatal baylisascariasis-induced acute pancreatitis in a giant panda. Parasitol Int 2021; 84:102380. [PMID: 33984514 DOI: 10.1016/j.parint.2021.102380] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 08/24/2020] [Revised: 05/02/2021] [Accepted: 05/07/2021] [Indexed: 10/21/2022]
Abstract
A wild adult male giant panda that was rescued from a nature reserve in Sichuan Province, China, has died. The panda had been in poor physical condition: it was wheezing and had increased serum amylase. A pathological examination was performed in order to determine the cause of death. Gross examination revealed 1380 mL of yellowish fluid in the abdominal cavity, 356 nematodes in the digestive tract and one filling the pancreatic duct, contractions and variably-sized dark purple areas in the spleen, a collapsed right lung and consolidation of the left lung. Acute pancreatitis was confirmed histopathologically via edema, focal necrosis and hemorrhage with inflammatory cell infiltration. Other major histopathological changes included serous-hemorrhagic pneumonia, lymphocytic necrosis and depletion in the spleen, and degeneration and necrosis of renal tubular epithelial cells. The nematodes were identified as Baylisascaris schroederi via molecular assays. In conclusion, the cause of death of the giant panda was determined to be multiple organ dysfunction syndrome caused by baylisascariasis-induced acute pancreatitis. To our knowledge, this is the first report of fatal baylisascariasis-induced acute pancreatitis in the giant panda.
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Affiliation(s)
- Zhenyang Qin
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Sichuan, China
| | - Songrui Liu
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, Chengdu, Sichuan, China
| | - Minghuan Bai
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Sichuan, China
| | - Yi Geng
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Sichuan, China.
| | - D L Miller
- Center for Wildlife Health, University of Tennessee Institute of Agriculture, Knoxville, TN, USA
| | - Ruoxuan Zhao
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Sichuan, China
| | - Rong Hou
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, Chengdu, Sichuan, China
| | - Wenjun Huang
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, Chengdu, Sichuan, China
| | - Dongsheng Zhang
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, Chengdu, Sichuan, China
| | - Xiaoyan Su
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, Chengdu, Sichuan, China
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Huang P, Yu Y, Meng X, Wang T, Yan F, Li E, Shi Z, He H, Yang S, Xia X, Wang J, Feng N. Development of recombinase polymerase amplification assays for rapid and visual detection of canine distemper virus infecting giant panda. BMC Vet Res 2021; 17:172. [PMID: 33892731 PMCID: PMC8063184 DOI: 10.1186/s12917-021-02880-3] [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: 09/29/2020] [Accepted: 04/14/2021] [Indexed: 12/29/2022] Open
Abstract
Background Canine distemper virus (CDV) is an enveloped negative-strand RNA virus that exhibits a high mutation rate and continuously expands the range of hosts. Notably, CDV has infected giant panda with spill over from viral reservoirs in canines. Giant pandas (Ailuropoda melanoleuca), especially captive pandas, are known to be susceptible to natural infection with CDV. The high fatality rate of CDV poses a serious threat to the safety of the giant panda population. However, vaccines or drugs for canine distemper in giant pandas have not been developed to date. Therefore, a rapid test that can achieve accurate onsite detection of CDV is important to enable the timely implementation of control measures. In this study, we established a nucleic acid visualization assay for targeting the CDV N gene by using combines reverse transcription recombinase polymerase amplification with a closed vertical flow visualization strip (RT-RPA-VF). Results The RT-RPA-VF assay does not require sophisticated equipment, and it was determined to provide rapid detection at 35 °C for 30 min, while the limit of detection was 5 × 101 copies/μl RNA transcripts and 100.5 TCID50 ml− 1 viruses. The results showed that the assay was high specific to CDV and had no cross-reactivity with other viruses infecting the giant panda. Compared with RT-qPCR, RT-RPA-VF assay had a sensitivity of 100% and a specificity of 100% in 29 clinical samples. The coincidence rate between RT-RPA-VF and RT-qPCR was 100% (kappa = 1), indicating that the RT-RPA-VF assay possessed good diagnostic performance on clinical samples. Conclusions The RT-RPA-VF provides a novel alternative for the simple, sensitive, and specific identification of CDV and showed great potential for point of care diagnostics for captive and wild giant panda.
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Affiliation(s)
- Pei Huang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China.,Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Yue Yu
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
| | - Xianyong Meng
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China.,Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Tiecheng Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,College of Life Sciences, Shandong Normal University, Jinan, China
| | - Feihu Yan
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Entao Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Zhikang Shi
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China.,Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Hongbin He
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Songtao Yang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China.,Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Xianzhu Xia
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Jianzhong Wang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China.
| | - Na Feng
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China. .,College of Life Sciences, Shandong Normal University, Jinan, China.
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37
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Cserhati M. A tail of two pandas- whole genome k-mer signature analysis of the red panda (Ailurus fulgens) and the Giant panda (Ailuropoda melanoleuca). BMC Genomics 2021; 22:228. [PMID: 33794768 PMCID: PMC8015091 DOI: 10.1186/s12864-021-07531-3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 03/14/2021] [Indexed: 11/29/2022] Open
Abstract
Background The red panda (Ailurus fulgens) is a riddle of morphology, making it hard to tell whether it is an ursid, a procyonid, a mustelid, or a member of its own family. Previous genetic studies have given quite contradictory results as to its phylogenetic placement. Results A recently developed whole genome-based algorithm, the Whole Genome K-mer Signature algorithm was used to analyze the genomes of 28 species of Carnivora, including A. fulgens and several felid, ursid, mustelid, one mephitid species. This algorithm has the advantage of holistically using all the information in the genomes of these species. Being a genomics-based algorithm, it also reduces stochastic error to a minimum. Besides the whole genome, the mitochondrial DNA from 52 mustelids, mephitids, ursids, procyonids and A. fulgens were aligned to draw further phylogenetic inferences. The results from the whole genome study suggested that A. fulgens is a member of the mustelid clade (p = 9·10− 97). A. fulgens also separates from the mephitid Spilogala gracilis. The giant panda, Ailuropoda melanoleuca also clusters away from A. fulgens, together with other ursids (p = 1.2·10− 62). This could be due to the geographic isolation of A. fulgens from other mustelid species. However, results from the mitochondrial study as well as neighbor-joining methods based on the sequence identity matrix suggests that A. fulgens forms a monophyletic group. A Maximum Likelihood tree suggests that A. fulgens and Ursidae form a monophyletic group, although the bootstrap value is weak. Conclusions The main conclusion that we can draw from this study is that on a whole genome level A. fulgens possibly belongs to the mustelid clade, and not an ursid or a mephitid. This despite the fact that previously some researchers classified A. fulgens and A. melanoleuca as relatives. Since the genotype determines the phenotype, molecular-based classification takes precedence over morphological classifications. This affirms the results of some previous studies, which studied smaller portions of the genome. However, mitochondrial analyses based on neighbor-joining and maximum likelihood methods suggest otherwise. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07531-3.
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Affiliation(s)
- Matyas Cserhati
- Independent Scholar, 2615C Muscatel Avenue, Rosemead, CA, 91770, USA.
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Liu Y, Li F, Cai Z, Wang D, Hou R, Zhang H, Zhang M, Yie S, Wu K, Zeng C, An J. Isolation and characterization of mesenchymal stem cells from umbilical cord of giant panda. Tissue Cell 2021; 71:101518. [PMID: 33676235 DOI: 10.1016/j.tice.2021.101518] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/05/2021] [Accepted: 02/22/2021] [Indexed: 10/22/2022]
Abstract
Umbilical cord-derived mesenchymal stem cells (UC-MSCs) constitute a class of cells with significant self-renewal and multilineage differentiation properties and have great potential for therapeutic applications and the genetic conservation of endangered animals. In this study, we successfully isolated and cultured UC-MSCs from the blood vessels of giant panda umbilical cord (UC). The cells were arranged in a vortex or cluster pattern and exhibited a normal karyotype, showing the morphological characteristics of fibroblasts. In addition, we found that basic fibroblast growth factor (bFGF) and epidermal growth factor (EGF) promoted cell proliferation, whereas stem cell factor (SCF) did not promote cell proliferation. Cultured UC-MSCs were negative for CD34 (hematopoietic stem cell marker) and CD31 (endothelial cell marker), but positive for MSC markers (CD44, CD49f, CD105, and CD73) and stem cell markers (KLF4, SOX2, and THY1). Similar to other MSCs, giant panda UC-MSCs have multiple differentiation ability and can differentiate into adipocytes, osteoblasts and chondrocytes. Giant panda UC-MSCs are new resources for basic research as cell models following their differentiation into different cell types and for future clinical treatments of giant panda diseases.
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Affiliation(s)
- Yuliang Liu
- College of Animal Sciences and Technology, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, 611130, China; Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan Province, 610000, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, Sichuan Province, 610000, China
| | - Feiping Li
- Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan Province, 610000, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, Sichuan Province, 610000, China
| | - Zhigang Cai
- Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan Province, 610000, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, Sichuan Province, 610000, China
| | - Donghui Wang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan Province, 610000, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, Sichuan Province, 610000, China
| | - Rong Hou
- Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan Province, 610000, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, Sichuan Province, 610000, China
| | - Hao Zhang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan Province, 610000, China
| | - Ming Zhang
- College of Animal Sciences and Technology, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, 611130, China
| | - Shangmian Yie
- Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan Province, 610000, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, Sichuan Province, 610000, China
| | - Kongju Wu
- Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan Province, 610000, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, Sichuan Province, 610000, China
| | - Changjun Zeng
- College of Animal Sciences and Technology, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, 611130, China.
| | - Junhui An
- Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan Province, 610000, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, Sichuan Province, 610000, China.
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Bai C, You Y, Liu X, Xia M, Wang W, Jia T, Pu T, Lu Y, Zhang C, Li X, Yin Y, Wang L, Zhou J, Niu L. A novel missense mutation in the gene encoding major intrinsic protein (MIP) in a Giant panda with unilateral cataract formation. BMC Genomics 2021; 22:100. [PMID: 33530927 PMCID: PMC7856726 DOI: 10.1186/s12864-021-07386-8] [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: 01/04/2021] [Accepted: 01/13/2021] [Indexed: 11/20/2022] Open
Abstract
Background Cataracts are defects of the lens that cause progressive visual impairment and ultimately blindness in many vertebrate species. Most cataracts are age-related, but up to one third have an underlying genetic cause. Cataracts are common in captive zoo animals, but it is often unclear whether these are congenital or acquired (age-related) lesions. Results Here we used a functional candidate gene screening approach to identify mutations associated with cataracts in a captive giant panda (Ailuropoda melanoleuca). We screened 11 genes often associated with human cataracts and identified a novel missense mutation (c.686G > A) in the MIP gene encoding major intrinsic protein. This is expressed in the lens and normally accumulates in the plasma membrane of lens fiber cells, where it plays an important role in fluid transport and cell adhesion. The mutation causes the replacement of serine with asparagine (p.S229N) in the C-terminal tail of the protein, and modeling predicts that the mutation induces conformational changes that may interfere with lens permeability and cell–cell interactions. Conclusion The c.686G > A mutation was found in a captive giant panda with a unilateral cataract but not in 18 controls from diverse regions in China, suggesting it is most likely a genuine disease-associated mutation rather than a single-nucleotide polymorphism. The mutation could therefore serve as a new genetic marker to predict the risk of congenital cataracts in captive giant pandas. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07386-8.
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Affiliation(s)
- Chao Bai
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Yuyan You
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China.
| | - Xuefeng Liu
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | | | - Wei Wang
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Ting Jia
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | | | - Yan Lu
- Beijing Zoo, Beijing, China
| | - Chenglin Zhang
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | | | | | | | - Jun Zhou
- , Chongqing Zoo, Chongqing, China
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Mustafa GR, Li C, Zhao S, Jin L, He X, Shabbir MZ, He Y, Li T, Deng W, Xu L, Xiong Y, Zhang G, Zhang H, Huang Y, Zou L. Metagenomic analysis revealed a wide distribution of antibiotic resistance genes and biosynthesis of antibiotics in the gut of giant pandas. BMC Microbiol 2021; 21:15. [PMID: 33413128 PMCID: PMC7792088 DOI: 10.1186/s12866-020-02078-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 12/20/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The gut microbiome is essential for the host's health and serves as an essential reservoir of antibiotic resistance genes (ARGs). We investigated the effects of different factors, including the dietary shifts and age, on the functional characteristics of the giant panda's gut microbiome (GPs) through shotgun metagenome sequencing. We explored the association between gut bacterial genera and ARGs within the gut based on network analysis. RESULTS Fecal samples (n=60) from captive juvenile, adult, and geriatric GPs were processed, and variations were identified in the gut microbiome according to different ages, the abundance of novel ARGs and the biosynthesis of antibiotics. Among 667 ARGs identified, nine from the top ten ARGs had a higher abundance in juveniles. For 102 ARGs against bacteria, a co-occurrence pattern revealed a positive association for predominant ARGs with Streptococcus. A comparative KEGG pathways analysis revealed an abundant biosynthesis of antibiotics among three different groups of GPs, where it was more significantly observed in the juvenile group. A co-occurrence pattern further revealed a positive association for the top ten ARGs, biosynthesis of antibiotics, and metabolic pathways. CONCLUSION Gut of GPs serve as a reservoir for novel ARGs and biosynthesis of antibiotics. Dietary changes and age may influence the gut microbiome's functional characteristics; however, it needs further studies to ascertain the study outcomes.
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Affiliation(s)
- Ghulam Raza Mustafa
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Caiwu Li
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Dujiangyan, 611830, China
| | - Siyue Zhao
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lei Jin
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xueping He
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Muhammad Zubair Shabbir
- Institute of Microbiology, The University of Veterinary and Animal Sciences, Lahore, 54600, Pakistan
| | - Yongguo He
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Dujiangyan, 611830, China
| | - Ti Li
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Dujiangyan, 611830, China
| | - Wenwen Deng
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Dujiangyan, 611830, China
| | - Lin Xu
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Dujiangyan, 611830, China
| | - Yaowu Xiong
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Dujiangyan, 611830, China
| | - Guiquan Zhang
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Dujiangyan, 611830, China
| | - Hemin Zhang
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Dujiangyan, 611830, China
| | - Yan Huang
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Dujiangyan, 611830, China.
| | - Likou Zou
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, China.
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Zhou Y, Ni X, Duan L, Niu L, Liu Q, Zeng Y, Wang Q, Wang J, Khalique A, Pan K, Jing B, Zeng D. Lactobacillus plantarum BSGP201683 Improves the Intestinal Barrier of Giant Panda Microbiota-Associated Mouse Infected by Enterotoxigenic Escherichia coli K88. Probiotics Antimicrob Proteins 2020; 13:664-676. [PMID: 33190214 DOI: 10.1007/s12602-020-09722-y] [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] [Accepted: 10/21/2020] [Indexed: 01/10/2023]
Abstract
Giant pandas often suffered from gastrointestinal disease, especially the captive sub-adult one. Our study aims to investigate whether L. plantarum G83, a good panda-derived probiotic, can improve the intestinal barrier against the enterotoxigenic Escherichia coli K88 (E. coli K88) infection in giant panda microbiota-associated mice (GPAM). We treated SPF mice with antibiotics cocktail and transplanted the giant panda intestinal microbiota to set up a GPAM. Our results demonstrated that the microbiota of GPAM changed over time and was relatively stable in the short-term experiment (2-4 weeks). Whereafter, the GPAM pretreated with L. plantarum G83 for 15 days and infected with enterotoxigenic E. coli K88. The result indicated that the number of Bifidobacteria spp. increased in GPAM-G and GPAM-GE groups; the Lactobacillus spp. only increased in the GPAM-G group. Although the abundance of Enterobacteriaceae spp. only decreased in the GPAM-G group, the copy number of Escherichia coli in the GPAM-E group was significantly lower than that in the other groups. Meanwhile, the L. plantarum G83-induced alteration of microbiota could increase the mRNA expression of Claudin-1, Zo-1, and Occludin-1 in the GPAM-G group in the ileum; only Occludin-1 was increased in the GPAM-GE group. The sIgA in the ileum showed a positive response, also the result of body weight and histology in both the GPAM-G and GPAM-GE group. These results indicated that the L. plantarum G83 could improve the intestinal barrier to defense the enterotoxigenic E. coli K88 invasion.
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Affiliation(s)
- Yi Zhou
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xueqin Ni
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Ling Duan
- Qu Country Extension Station for Animal Husbandry Technology, Dazhou, 635299, Sichuan, China
| | - Lili Niu
- Chengdu Wildlife Institute, Chengdu Zoo, Chengdu, 610081, Sichuan, China
| | - Qian Liu
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yan Zeng
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qiang Wang
- Chengdu Wildlife Institute, Chengdu Zoo, Chengdu, 610081, Sichuan, China
| | - Jie Wang
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Abdul Khalique
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Kangcheng Pan
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Bo Jing
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Dong Zeng
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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Yue C, Deng Z, Qi D, Li Y, Bi W, Ma R, Yang G, Luo X, Hou R, Liu S. First detection and molecular identification of Babesia sp. from the giant panda, Ailuropoda melanoleuca, in China. Parasit Vectors 2020; 13:537. [PMID: 33121531 PMCID: PMC7597363 DOI: 10.1186/s13071-020-04412-8] [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: 06/08/2020] [Accepted: 10/21/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Parasitic infections are among the important causes of death of giant pandas (Ailuropoda melanoleuca) that hamper their survival in the wild. There are about 35 species of parasites which have been identified in giant pandas, but no information is currently available regarding the infection of Babesia in giant pandas. Babesia spp. are common intraerythrocytic parasite in wildlife, transmitted by ixodid ticks, which cause babesiosis. Clinical signs of babesiosis include fever, hemolysis, anemia, jaundice and death. METHODS A species of Babesia was detected in the blood of a giant panda based on morphology and PCR amplification of the 18S rRNA gene. The phylogenetic relationship of Babesia sp. infecting giant panda was assessed by gene sequence alignment and phylogenetic analysis. RESULTS Our analysis revealed that the Babesia isolate detected was most similar to an unidentified species of Babesia identified in black bears (Ursus thibetanus japonicus) from Japan (Babesia sp. Iwate, AB586027.1) with a 99.56% sequence similarity, followed by Babesia sp. EBB (AB566229.1, 99.50%) and Babesia sp. Akita (AB566229.1, 99.07%). CONCLUSIONS To our knowledge, this is the first report of Babesia detected in the giant panda. The results indicate that this Babesia sp. may be a novel species, currently named Babesia sp. strain EBP01.
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Affiliation(s)
- Chanjuan Yue
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, 1375 Panda Road, Chenghua District, 610081, Sichuan, China
| | - Zeshuai Deng
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, 1375 Panda Road, Chenghua District, 610081, Sichuan, China
| | - Dunwu Qi
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, 1375 Panda Road, Chenghua District, 610081, Sichuan, China
| | - Yunli Li
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, 1375 Panda Road, Chenghua District, 610081, Sichuan, China
| | - Wenlei Bi
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, 1375 Panda Road, Chenghua District, 610081, Sichuan, China
| | - Rui Ma
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, 1375 Panda Road, Chenghua District, 610081, Sichuan, China
| | - Guangyou Yang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xue Luo
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Rong Hou
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, 1375 Panda Road, Chenghua District, 610081, Sichuan, China.
| | - Songrui Liu
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, 1375 Panda Road, Chenghua District, 610081, Sichuan, China.
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Wang C, Li F, Deng L, Li M, Wei M, Zeng B, Wu K, Xu Z, Wei R, Wei L, Liu W, Zhang S, Xu L, Huang Y, Li D, Li Y, Zhang H. Identification and characterization of miRNA expression profiles across five tissues in giant panda. Gene 2021; 769:145206. [PMID: 33059030 DOI: 10.1016/j.gene.2020.145206] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 09/15/2020] [Accepted: 09/29/2020] [Indexed: 12/29/2022]
Abstract
microRNA (miRNA) is a small endogenous noncoding RNA molecule that plays multiple roles in regulating most biological processes. However, for China's national treasure giant panda, a world-famous rare and protected species, reports of its miRNA have been found only in blood and breast milk. To explore the miRNA expression differences between different giant panda tissues, here, we generated the miRNA profiles of five tissues (heart, liver, spleen, lung, and kidney) from four giant pandas with Illumina Hiseq 2500 platform, and filtered the differentially expressed miRNAs (DEmiRs) in each tissue, predicted the target genes of miRNA from each tissue based on the DEmiRs. Then, the GO and KEGG enrichment analysis were conducted using the target genes predicted from DEmiRs in each tissue. The RNA-seq generated an average of 0.718 GB base per sample. A total of 1,256 known miRNAs and 12 novel miRNAs were identified, and there were 215, 131, 185, 83, and 126 tissue-specific DEmiRs filtered in the heart, liver, spleen, lung, and kidney, respectively, including miR-1b-5p, miR-122-5p, miR-143, miR-126-5p, and miR-10b-5p, respectively. The predicted target genes, including MYL2, LRP5, MIF, CFD, and PEBP1 in the heart, liver, spleen, lung, and kidney, respectively, were closely associated with tissue-specific biological functions. The enrichment analysis results of target genes showed tissue-specific characteristics, such as the significantly enriched GO terms extracellular matrix in the heart and insulin-like growth factor binding in the liver. The miRNA profiles of the heart, liver, spleen, lung, and kidney of giant panda have been reported in this study, it reveals the miRNA expression differences between different tissues of the giant panda, and provides valuable genetic resources for the further related molecular genetic research of the rare and protected species giant panda and other mammals.
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Guo M, Liu G, Chen J, Ma J, Lin J, Fu Y, Fan G, Lee SMY, Zhang L. Dynamics of bacteriophages in gut of giant pandas reveal a potential regulation of dietary intake on bacteriophage composition. Sci Total Environ 2020; 734:139424. [PMID: 32464399 DOI: 10.1016/j.scitotenv.2020.139424] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 05/09/2020] [Accepted: 05/12/2020] [Indexed: 06/11/2023]
Abstract
Fecal samples of cubs and adults of giant pandas were examined to determine the effects of diets on the diversity and dynamics of gut bacteriophages. Enterobacteria phage, Salmonella phage, Escherichia phage, Shigella phage, Klebsiella phage, and Lactococcus phage were found to be dominant in both cub and adult samples. Citrobacter phage, Cronobacter phage, Pectobacterium phage, Erwinia phage, Dickeya phage, Erwinia phage, Enterococcus phage, and Pseudomonas phage were more abundant in adults, while Lactococcus phage, Streptococcus phage, Lactobacillus phage, and Leuconostoc phage were more abundant in cubs. The abundance and diversity of the majority of phage species were increased in pandas with age. There was an increase in the abundance of Pectobacterium phage and a decrease in the abundance of Lactobacillus phage, Leuconostoc phage, Bacillus phage, and Streptococcus phage in adults. As cubs and adults of giant pandas have different dietary habits, these observations suggest a significant effect of diets on the composition and abundance of gut bacteriophages in giant pandas.
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Affiliation(s)
- Min Guo
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangdong Academy of Science, Guangzhou, China; State Key Laboratory of Quality Research of Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Guilin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Jianwei Chen
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China; Synthetic Biology Technology Innovation Center of Shandong Province, Qingdao, China
| | | | | | - Ying Fu
- Faculty of Science and Technology, University of Macau, Macao, China
| | - Guangyi Fan
- State Key Laboratory of Quality Research of Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macao, China; BGI-Qingdao, BGI-Shenzhen, Qingdao, China; BGI-Shenzhen, Shenzhen, China
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research of Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Libiao Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangdong Academy of Science, Guangzhou, China.
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Li J, Karim MR, Li J, Zhang L, Zhang L. Review on parasites of wild and captive giant pandas ( Ailuropoda melanoleuca): Diversity, disease and conservation impact. Int J Parasitol Parasites Wildl 2020; 13:38-45. [PMID: 32793415 PMCID: PMC7415634 DOI: 10.1016/j.ijppaw.2020.07.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/18/2020] [Accepted: 07/19/2020] [Indexed: 11/28/2022]
Abstract
The giant panda (Ailuropoda melanoleuca) is a rare species with a small global population size, and lives in the wild in only a few fragmented mountain ranges of Southwest China. Parasitic infections are among the important causes of death of giant pandas that hamper their group development. We reviewed the parasitic infections prevailing in giant pandas, and the parasitic diversity, diseases and their impact on conservation of this animal. A total of 35 parasitic species were documented in giant pandas, belonging to nematode (n = 6), trematode (n = 1), cestode (n = 2), protozoa (n = 9), and ectozoa (n = 17 (tick = 13, mite = 2, and flea = 2)). Among them, Baylisascaris schroederi had the highest prevalence and was the leading cause of death for giant pandas. Some parasites caused asymptomatic infections in giant pandas, and their health implications for the pandas remain unknown. As a whole, parasites are reported to be an important threat to the conservation of the giant pandas. Regular deworming and environmental disinfection appear to be effective ways to prevent captive giant pandas from parasitoses. In wild panda populations, parasitic control measures are suggested to include detailed examination of the ecology of the host-parasite assembly, with particular attention to density-dependent transmission. The parasitic pathogenesis and detection methods together with their biology, epidemiology, treatment, prevention and control need to be further studied for better protection of giant pandas from parasitoses.
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Affiliation(s)
- Junqiang Li
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, 450046, China.,College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Md Robiul Karim
- Department of Medicine, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Jun Li
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, 450046, China
| | - Liping Zhang
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, 450046, China
| | - Longxian Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
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46
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Abstract
Modifying the affinity of odorant-binding proteins (OBPs) to small ligands by replacement of specific residues in the binding pocket may lead to several technological applications. Thanks to their compact and stable structures, OBPs are currently regarded as the best candidates to be used in biosensing elements for odorants and volatiles detection. The wide and rich information on the structure of these proteins both in their apo-forms and in complexes with specific ligands provides guidelines to design reliable mutants to monitor specific targets. The same engineered proteins may also find applications in the slow release of pheromones and other chemicals in the environment, as well as in the fine purification of drugs, including the resolution of racemates. Apart from such useful applications, site-directed mutagenesis represents an interesting approach to dissect the specific interactions between small chemicals and amino acid residues in the binding pocket. These studies can lead to design of better ligands, such as pheromone analogues with desired physico-chemical characteristics. In this chapter we examine the different uses of mutagenesis applied to OBPs and report a couple of protocols that have been successful in our hands.
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Affiliation(s)
- Jiao Zhu
- AIT Austrian Institute of Technology GmbH, Biosensor Technologies, Tulln, Austria; Faculty of Biology, Institute of Molecular Physiology, Johannes Gutenberg-Universität, Mainz, Germany
| | - Valeriia Zaremska
- AIT Austrian Institute of Technology GmbH, Biosensor Technologies, Tulln, Austria; Department of Nanobiotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Chiara D'Onofrio
- AIT Austrian Institute of Technology GmbH, Biosensor Technologies, Tulln, Austria; Department of Nanobiotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Wolfgang Knoll
- AIT Austrian Institute of Technology GmbH, Biosensor Technologies, Tulln, Austria; CEST Competence Center for Electrochemical Surface Technology, Tulln, Austria
| | - Paolo Pelosi
- AIT Austrian Institute of Technology GmbH, Biosensor Technologies, Tulln, Austria.
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47
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Wang DH, Liu YL, Cai ZG, An JH, Lan JC, Chen JS, Li Y, He L, Zhang Y, He P, Zhang ZH, Yie SM, Hou R. Effects of extender type on the quality of post-thaw giant panda (Ailuropoda melanoleuca) semen. Cryobiology 2020; 94:95-99. [PMID: 32304703 DOI: 10.1016/j.cryobiol.2020.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/10/2020] [Accepted: 04/10/2020] [Indexed: 10/24/2022]
Abstract
Sperm cryopreservation is an essential approach for assisted reproduction and genetic resources conservation in captive giant pandas. Cryopreservation, however, leads to a significant decrease in sperm quality and, consequently, a low fertilization rate. Therefore, it is mandatory to disclose more suitable and efficient freezing strategies for sperm cryopreservation. In the present study, we compared for the first time the performance of two commercial freeze extender (INRA96 versus TEST) freezing methods on post-thawed semen quality. Semen cryopreserved with the INRA96 showed better total motility (73.00 ± 4.84% vs 57.56 ± 3.60%, P < 0.001), membrane integrity (60.92 ± 2.27% vs 40.53 ± 2.97%, P < 0.001) and acrosome integrity (90.39 ± 2.74% vs 84.26 ± 4.27%, P < 0.05) than stored with TEST. There was no significant difference in DNA integrity after thawing between the two extenders (95.69 ± 3.60% vs 94.26 ± 4.84%). In conclusion, the INRA96 method showed to be better for giant panda sperm cryopreservation and should therefore be recommended for use in order to increase success of artificial insemination.
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Affiliation(s)
- Dong-Hui Wang
- Chengdu Research Base of Giant Panda Breeding, 610000, Chengdu, Sichuan Province, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, 610000, Chengdu, Sichuan Province, China; Sichuan Academy of Giant Panda, 610000, Chengdu, Sichuan Province, China
| | - Yu-Liang Liu
- Chengdu Research Base of Giant Panda Breeding, 610000, Chengdu, Sichuan Province, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, 610000, Chengdu, Sichuan Province, China; Sichuan Academy of Giant Panda, 610000, Chengdu, Sichuan Province, China.
| | - Zhi-Gang Cai
- Chengdu Research Base of Giant Panda Breeding, 610000, Chengdu, Sichuan Province, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, 610000, Chengdu, Sichuan Province, China; Sichuan Academy of Giant Panda, 610000, Chengdu, Sichuan Province, China
| | - Jun-Hui An
- Chengdu Research Base of Giant Panda Breeding, 610000, Chengdu, Sichuan Province, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, 610000, Chengdu, Sichuan Province, China; Sichuan Academy of Giant Panda, 610000, Chengdu, Sichuan Province, China
| | - Jing-Chao Lan
- Chengdu Research Base of Giant Panda Breeding, 610000, Chengdu, Sichuan Province, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, 610000, Chengdu, Sichuan Province, China; Sichuan Academy of Giant Panda, 610000, Chengdu, Sichuan Province, China
| | - Jia-Song Chen
- Chengdu Research Base of Giant Panda Breeding, 610000, Chengdu, Sichuan Province, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, 610000, Chengdu, Sichuan Province, China; Sichuan Academy of Giant Panda, 610000, Chengdu, Sichuan Province, China
| | - Yuan Li
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, 610000, Chengdu, Sichuan Province, China
| | - Ling He
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, 610000, Chengdu, Sichuan Province, China
| | - Ying Zhang
- Chengdu Research Base of Giant Panda Breeding, 610000, Chengdu, Sichuan Province, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, 610000, Chengdu, Sichuan Province, China; Sichuan Academy of Giant Panda, 610000, Chengdu, Sichuan Province, China
| | - Ping He
- Chengdu Research Base of Giant Panda Breeding, 610000, Chengdu, Sichuan Province, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, 610000, Chengdu, Sichuan Province, China; Sichuan Academy of Giant Panda, 610000, Chengdu, Sichuan Province, China
| | - Zhi-He Zhang
- Chengdu Research Base of Giant Panda Breeding, 610000, Chengdu, Sichuan Province, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, 610000, Chengdu, Sichuan Province, China; Sichuan Academy of Giant Panda, 610000, Chengdu, Sichuan Province, China
| | - Shang-Mian Yie
- Chengdu Research Base of Giant Panda Breeding, 610000, Chengdu, Sichuan Province, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, 610000, Chengdu, Sichuan Province, China; Sichuan Academy of Giant Panda, 610000, Chengdu, Sichuan Province, China
| | - Rong Hou
- Chengdu Research Base of Giant Panda Breeding, 610000, Chengdu, Sichuan Province, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, 610000, Chengdu, Sichuan Province, China; Sichuan Academy of Giant Panda, 610000, Chengdu, Sichuan Province, China.
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Xiong L, Ni X, Niu L, Zhou Y, Wang Q, Khalique A, Liu Q, Zeng Y, Shu G, Pan K, Jing B, Zeng D. Isolation and Preliminary Screening of a Weissella confusa Strain from Giant Panda (Ailuropoda melanoleuca). Probiotics Antimicrob Proteins 2020; 11:535-544. [PMID: 29654473 DOI: 10.1007/s12602-018-9402-2] [Citation(s) in RCA: 16] [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] [Indexed: 12/27/2022]
Abstract
Weissella confusa has recently received attention for its probiotic potential. Some W. confusa and Weissella cibaria strains isolated from fermented foods show favorable probiotic effects. However, the probiotic properties of W. confusa isolated from giant panda remain unreported to date. Thus, this study isolated a W. confusa strain from giant panda feces and then investigated its characteristics and probiotic properties. A lactic acid bacteria strain was isolated from giant panda fecal samples. The isolated strain was screened by in vitro probiotic property tests, including in vitro antimicrobial test, antioxidant test, surface hydrophobicity, and stress resistance. On the basis of biochemical identification and 16S rDNA sequencing, the W. confusa strain was identified as BSP201703. This Weissella confusa strain can survive at pH 2 and 0.3% (w/v) concentration of bile salt environment and inhibit common intestinal pathogens. It also possesses an in vitro antioxidant capacity, a high auto-aggregation ability, and a high surface hydrophobicity. BSP201703 might serve as a probiotic to giant pandas.
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Affiliation(s)
- Lvchen Xiong
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xueqin Ni
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Lili Niu
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Chengdu Wildlife Institute, Chengdu Zoo, Chengdu, China
| | - Yi Zhou
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qiang Wang
- Chengdu Wildlife Institute, Chengdu Zoo, Chengdu, China
| | - Abdul Khalique
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qian Liu
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yan Zeng
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Gang Shu
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Kangcheng Pan
- Key laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Bo Jing
- Key laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Dong Zeng
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.
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49
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Yung DTC, Jani R, Azizi R, Ramli MN, Haidi Y, Zainudin AN, Samsuddin AH, Hashim NH, Afiq Ramlee MN, Zahidin MA, Mohd Raffi MA, Lola MS, Abdullah MT. Data on diet and growth by giant panda in zoo Negara, Malaysia. Data Brief 2020; 29:105082. [PMID: 31993462 PMCID: PMC6971374 DOI: 10.1016/j.dib.2019.105082] [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: 10/09/2019] [Revised: 12/09/2019] [Accepted: 12/23/2019] [Indexed: 11/17/2022] Open
Abstract
In this data article we present the determinations of the diet preference and growth of a pair of the giant panda, Ailuropoda melanoleuca (David, 1869) from Zoo Negara Malaysia. Once considered as endangered, the captive giant pandas were given with nine species of local bamboo in separate indoor enclosures. We recorded data between May 25, 2014 and December 31, 2016 and analysed it based on food preference, the pattern toward food consumption and body weights using SPSS v25.0 (IBM, USA). Data on the bamboo preference, daily average bamboo provided and consumed, and factors predicting of body weight per individual are reported in this article. The data highlight correlation between panda growth (kg) to the part of bamboo consumed (kg) and exhibit the pattern of preferred part of food (i.e.: either the leaf, culm or shoots of bamboo variety) for panda consumptions. The food consumption toward the body weight was modelled using logistic regression analysis to help determine the pattern of food consumption and body weight of giant panda in the future and based on regression model 1, only consumed variable is significance to the model.
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Affiliation(s)
- Dennis Ten Choon Yung
- Department of Wildlife and National Park Peninsular Malaysia, KM10, Jalan Cheras, 56100, Kuala Lumpur, Malaysia
- Institute for Advanced Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia
- Corresponding author. Department of Wildlife and National Park Peninsular Malaysia, KM10, Jalan Cheras, 56100, Kuala Lumpur, Malaysia.
| | - Rohana Jani
- Department of Applied Statistics, Faculty of Economics and Administration, University of Malaya, 50603, Kuala Lumpur, Malaysia
- Corresponding author. Department of Applied Statistics, Faculty of Economics and Administration, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Ridza Azizi
- Department of Applied Statistics, Faculty of Economics and Administration, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Mat Naim Ramli
- Veterinary Department, Zoo Negara Malaysia, Hulu Kelang, 68000, Ampang, Selangor, Malaysia
| | - Yang Haidi
- China Conservation and Research Center for the Giant Panda, Dujiangyen, China
| | - Ahmad Nizam Zainudin
- Veterinary Department, Zoo Negara Malaysia, Hulu Kelang, 68000, Ampang, Selangor, Malaysia
| | - Akmal Hadi Samsuddin
- Veterinary Department, Zoo Negara Malaysia, Hulu Kelang, 68000, Ampang, Selangor, Malaysia
| | - Noor Hashida Hashim
- Center of Matriculation Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Mohd Noor Afiq Ramlee
- Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Malaysia
| | - Muhamad Aidil Zahidin
- Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Malaysia
- Faculty of Earth Science, Universiti Malaysia Kelantan, Jeli Campus, 17600, Jeli, Kelantan, Malaysia
| | - Mohd Akmal Mohd Raffi
- Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Malaysia
| | - Muhamad Safiih Lola
- Faculty of Ocean Engineering Technology and Informatics, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
| | - Mohd Tajuddin Abdullah
- Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Malaysia
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
- Corresponding author. Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Malaysia.
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50
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Geng Y, Shen F, Wu W, Zhang L, Luo L, Fan Z, Hou R, Yue B, Zhang X. First demonstration of giant panda's immune response to canine distemper vaccine. Dev Comp Immunol 2020; 102:103489. [PMID: 31473266 DOI: 10.1016/j.dci.2019.103489] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 08/28/2019] [Accepted: 08/28/2019] [Indexed: 06/10/2023]
Abstract
The Canine Distemper Virus (CDV) is a high fatal virus to the giant panda (Ailuropoda melanoleuca), where CDV vaccination is a key preventative measure in captive giant pandas. However, the immune response of giant pandas to CDV vaccination has been little studied. In this study, we investigated the blood transcriptome expression profiles of five giant panda cubs after three inoculations, 21 days apart. Blood samples were collected before vaccination (0 Day), and 24 h after each of the three inoculations; defined here as 1 Day, 21 Day, and 42 Day. Compared to 0 Day, we obtained 1262 differentially expressed genes (DEGs) during inoculations. GO and KEGG pathways enrichment analysis of these DEGs found 222 GO terms and 40 pathways. The maximum immune-related terms were enriched by DEGs from comparisons of 21 Day and 0 Day. In the PPI analysis, we identified RSAD2, IL18, ISG15 immune-related hub genes from 1 Day and 21 Day comparison. Compared to 0 Day, innate immune-related genes, TLR4 and TLR8, were up-regulated at 1 Day, and the expressions of IRF1, RSAD2, MX1, and OAS2 were highest at 21 Day. Of the adaptive immune-related genes, IL15, promoting T cell differentiation into CD8+T cells, was up-regulated after the first two inoculations, IL12β, promoting T cell differentiation into memory cells, and IL10, promoting B cell proliferation and differentiation, were down-regulated during three inoculations. Our results indicated that the immune response of five giant panda cubs was strongest after the second inoculation, most likely protected against CDV infection through innate immunity and T cells, but did not produce enough memory cells to maintain long-term immunity after CDV vaccination.
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Affiliation(s)
- Yang Geng
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610064, China.
| | - Fujun Shen
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China.
| | - Wei Wu
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610064, China.
| | - Liang Zhang
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China.
| | - Li Luo
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China.
| | - Zhenxin Fan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064, PR China.
| | - Rong Hou
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China.
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064, PR China.
| | - Xiuyue Zhang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610064, China.
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