308 results on '"Mingwang Zhang"'
Search Results
102. Extension of a Polynomial Time Mehrotra-Type Predictor-Corrector Safeguarded Algorithm to Monotone Linear Complementarity Problems.
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Mingwang Zhang and Yanli Lv
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- 2008
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- View/download PDF
103. A Wide-Neighborhood Algorithm for Monotone Nonlinear Complementarity Problem.
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Yanli Lv and Mingwang Zhang
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- 2008
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104. Specific microRNA/mRNA expression profiles and novel immune regulation mechanisms are induced in THP‐1 macrophages by in vitro exposure to Trichosporon asahii
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Mingwang Zhang, Xin Yang, Rongya Yang, Zhikuan Xia, and Junhong Ao
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0301 basic medicine ,THP-1 Cells ,030106 microbiology ,Dermatology ,Trichosporon asahii ,Biology ,030207 dermatology & venereal diseases ,03 medical and health sciences ,0302 clinical medicine ,Immune system ,Trichosporonosis ,microRNA ,Humans ,RNA, Messenger ,KEGG ,Gene ,Messenger RNA ,Reporter gene ,Basidiomycota ,Macrophages ,Reproducibility of Results ,General Medicine ,Cell biology ,MicroRNAs ,Infectious Diseases ,Real-time polymerase chain reaction ,Gene Expression Regulation ,Signal Transduction - Abstract
Background Trichosporon asahii is considered the most prominent species associated with invasive trichosporonosis, but little is known about the pathogenesis of T. asahii infection in the host. MicroRNAs (miRNAs) are a class of noncoding endogenous small RNAs that play vital roles by manipulating immune responses against pathogenic microorganisms. Nevertheless, the exact functions of miRNAs in T. asahii infection are still unknown. Objective To investigate the interactions involved in the miRNA immune response in THP-1 macrophages following in vitro exposure to T. asahii. Methods We utilized next-generation sequencing to detect differentially expressed (DE) miRNAs and mRNAs in THP-1 cells after 24 h of in vitro exposure to T. asahii. Real-time quantitative polymerase chain reaction (RT-qPCR) was used to verify the sequencing results. The miRNA-mRNA regulatory network was constructed with the DE miRNAs and DE mRNAs. We performed Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis of the predicted targeting mRNAs in the miRNA-mRNA network. A dual-luciferase reporter assay and enzyme-linked immunosorbent assay (ELISA) were utilized to demonstrate the reliability of the miR-342-3p/Dectin-1 pair. Results A total of 120 DE miRNAs and 588 DE mRNAs were identified after 24 h of in vitro exposure to T. asahii. The miRNA-mRNA regulatory network was constructed with 39 DE miRNAs and 228 DE mRNAs. KEGG pathway analysis revealed that the up-regulated DE mRNAs in the complex interaction network were mainly involved in immune-related pathways. In addition, we verified the target relationship between miR-342-3p and Dectin-1 and found that miR-342-3p could promote the expression of TNF-α and IL-6 by negatively regulating Dectin-1. Conclusions This study evaluated the expression profiles of miRNA/mRNA and revealed the immunological consequences of THP-1 macrophages in response to T. asahii exposure. Moreover, our data suggest that miR-342-3p can indirectly promote inflammatory responses and may be a potential therapeutic target against trichosporonosis.
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- 2021
105. Complete Mitogenomes of
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Lin, Cui, An, Huang, Zhi, He, Lisha, Ao, Fei, Ge, Xiaolan, Fan, Bo, Zeng, Mingyao, Yang, Deying, Yang, Qingyong, Ni, Yan, Li, Yongfang, Yao, Huailiang, Xu, Jiandong, Yang, Zhimin, Wei, Tongqing, Li, Taiming, Yan, and Mingwang, Zhang
- Abstract
New developments in sequencing technology and nucleotide analysis have allowed us to make great advances in reconstructing anuran phylogeny. As a clade of representative amphibians that have radiated from aquatic to arboreal habitats, our understanding of the systematic status and molecular biology of rhacophorid tree frogs is still limited. We determined two new mitogenomes for the genus
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- 2022
106. Genetic Variation in
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Jiayang, He, Zhi, He, Deying, Yang, Zhijun, Ma, Hongjun, Chen, Qian, Zhang, Faqiang, Deng, Lijuan, Ye, Yong, Pu, Mingwang, Zhang, Song, Yang, Shiyong, Yang, and Taiming, Yan
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- 2022
107. A wide neighborhood arc-search interior-point algorithm for convex quadratic programming with box constraints and linear constraints
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Mingwang Zhang, Yanli Lv, and Kun Huang
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021103 operations research ,Control and Optimization ,Mechanical Engineering ,0211 other engineering and technologies ,Aerospace Engineering ,02 engineering and technology ,Ellipse ,Arc (geometry) ,Path (graph theory) ,021108 energy ,Electrical and Electronic Engineering ,Initial point ,Algorithm ,Software ,Convex quadratic programming ,Interior point method ,Civil and Structural Engineering ,Mathematics - Abstract
In this paper, a wide neighborhood arc-search interior-point algorithm for convex quadratic programming with box constrains and linear constraints (BLCQP) is presented. The algorithm searches the optimizers along the ellipses that approximate the entire central path. Assuming a strictly feasible initial point is available, we show that the algorithm has $$O(n^{\frac{3}{4}}\log \frac{{({x^0} - l)^T}{s^0} + {(w - {x^0})^T}{t^0}}{\varepsilon })$$ iteration complexity bound, which is the best known complexity result for such methods. The numerical results show that our algorithm is effective and promising.
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- 2021
108. Dihydromyricetin promotes longevity and activates the transcription factors FOXO and AOP in Drosophila
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Qi Wu, Bo Zeng, Diyan Li, Mingwang Zhang, Mingyao Yang, Yan Li, Qingyong Ni, Yue Gao, Deying Yang, Xiaolan Fan, Yao Zeng, Fan Ziqiang, Wenhao Song, Xueping Mao, Liang Cui, and Tao Wang
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MAPK/ERK pathway ,Aging ,biology ,media_common.quotation_subject ,fungi ,Longevity ,food and beverages ,Cell Biology ,biology.organism_classification ,Cell biology ,Protein kinase B ,Drosophila ,Transcription factor ,media_common - Abstract
Drugs or compounds have been shown to promote longevity in various approaches. We used Drosophila to explore novel natural compounds can be applied to anti-aging. Here we reported that a flavonoid named Dihydromyricetin can increase stress that tolerance and lipid levels, slow down gut dysfunction and extend Drosophila lifespan. Dihydromyricetin can also lessen pERK and pAKT signaling, consequently activating FOXO and AOP to modulate longevity. Our results suggested that DHM could be used as an effective compound for anti-aging intervention, which could likely be applied to both mammals and humans.
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- 2020
109. Epidemiological investigation and genotypes of Enterocytozoon bieneusi in 11 captive Rhesus macaque populations
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Yongfang Yao, Mingwang Zhang, Meng Xie, Mengshi Yu, Diyan Li, Liu Xue, Huailiang Xu, Qingyong Ni, and Jiayun Wu
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0301 basic medicine ,Zoonotic potential ,Enterocytozoon bieneusi ,030231 tropical medicine ,Population ,Microsporidiosis ,03 medical and health sciences ,fluids and secretions ,0302 clinical medicine ,lcsh:Zoology ,parasitic diseases ,Genotype ,medicine ,lcsh:QL1-991 ,Internal transcribed spacer ,education ,Feces ,education.field_of_study ,biology ,fungi ,virus diseases ,030108 mycology & parasitology ,medicine.disease ,biology.organism_classification ,Macaca mulatta ,Virology ,Rhesus macaque ,Infectious Diseases ,Animal Science and Zoology ,Parasitology ,ITS ,Nested polymerase chain reaction - Abstract
Enterocytozoon bieneusi is an obligate intracellular parasite and the most common pathogen of microsporidiosis in humans and animals. In this study, a total of 198 fecal samples were collected from 11 captive populations of Rhesus macaque in Chinese zoos, to investigate the prevalence and analyze the zoonotic potential of E. bieneusi by genotype of the Internal Transcribed Spacer (ITS) gene on the rRNA of E. bieneusi via nested PCR. Results showed that the average infection rate of E. bieneusi in the 11 populations was 13.6%, and the highest infection rate was 56.5% in the population of Xinjiang Tianshan Zoo. Seven genotypes were identified including 2 known genotypes (D and CM1) and 5 novel genotypes (Mul1, Mul2, Mul3, Mul4 and Mul5). Phylogenetic analysis revealed that the novel genotypes Mul2, Mul3, Mul4 and Mul5 belonged to Group 1 showed the zoonotic potential.These findings extend the distribution of E. bieneusi genotypes and provide baseline data for controlling E. bieneusi infection.
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- 2020
110. A second order Mehrotra-type predictor-corrector algorithm for semidefinite optimization.
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Mingwang Zhang
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- 2012
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- View/download PDF
111. Improvac immunocastration affects the development of thigh muscles but not pectoral muscles in male chickens
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Changjun Zeng, Guang-Bin Zhou, Huadong Yin, Qing Zhu, Yao Zhang, Yutian Zeng, Zhicai Zuo, Mingwang Zhang, Chun Wang, Ling Xu, and T.Z. Song
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Male ,Fiber type ,Physiology and Reproduction ,Pectoral muscle ,Thigh muscle ,Physiology ,Skeletal muscle ,General Medicine ,Biology ,fiber type ,Pectoralis Muscles ,broiler chicken ,immunocastration ,medicine.anatomical_structure ,medicine ,Animals ,muscle development ,Animal Science and Zoology ,lcsh:Animal culture ,Muscle fibre ,Muscle, Skeletal ,Chickens ,Orchiectomy ,Improvac ,lcsh:SF1-1100 - Abstract
Improvac has been tentatively used to immune-castrate roosters. The aim of this study was to investigate whether Improvac affected skeletal muscle development in chickens. The muscle fiber type and size and the expression levels of genes related to muscle development in pectoral and thigh muscles were examined at 5, 9, and 14 wk of age in the control, early, late, and early + late Improvac-treated groups. Immunocastration with Improvac affected the development of thigh muscles and the expression of MYH1B, MSTN, and SM. The cross-sectional area in the early group was significantly larger than in the control group at the 14th week (P < 0.01). At the fifth week, the expression levels of MYH1B, MYOD, and MSTN in the early group were significantly higher than those in the control group (P
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- 2020
112. A new primal-dual interior-point method for semidefinite optimization based on a parameterized kernel function
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Zhengwei Huang, Mingwang Zhang, Mengmeng Li, and Kun Huang
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Discrete mathematics ,021103 operations research ,Control and Optimization ,Current (mathematics) ,Generalization ,Mechanical Engineering ,0211 other engineering and technologies ,Center (category theory) ,Aerospace Engineering ,Parameterized complexity ,02 engineering and technology ,Measure (mathematics) ,Primal dual ,Point (geometry) ,021108 energy ,Electrical and Electronic Engineering ,Software ,Interior point method ,Civil and Structural Engineering ,Mathematics - Abstract
As indicated in the recent studies about primal-dual interior-point methods (IPMs) based on kernel functions, a kernel function not only serves to determine the search direction and measure the distance of the current iteration point to the $$\mu $$ -center, but also affects the iteration complexity and the practical computational efficiency of the algorithm. In this paper, we propose a new IPM for semidefinite optimization (SDO) based on a parameterized kernel function which is a generalization of the one presented by Bai et al. (Optim Methods Softw 17(6):985–1008, 2002). By using the good properties of the parameterized kernel function, we deduce that the iteration bound for large-update method is $$O(\sqrt{n}\log {n}\log {\frac{n}{\epsilon }})$$ for $$q=O(n)$$ , which is the best known complexity results for such methods. In our knowledge, this result is the first instance of primal-dual interior point method for SDO which involving the kernel function. Some numerical results have been provided.
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- 2020
113. Variation in Gut Microbiota of Captive Bengal Slow Lorises
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Xin He, Diyan Li, Yongfang Yao, Mingyao Yang, Qingyong Ni, Xiaolan Fan, Meng Xie, Bo Zeng, Deying Yang, Huailiang Xu, Ying Li, Mingwang Zhang, Xiangyun Meng, and Yan Li
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China ,Firmicutes ,Nycticebus bengalensis ,Zoology ,Gut flora ,Applied Microbiology and Biotechnology ,Microbiology ,03 medical and health sciences ,RNA, Ribosomal, 16S ,Proteobacteria ,Prevotella ,Animals ,Humans ,Microbiome ,Feces ,030304 developmental biology ,0303 health sciences ,biology ,030306 microbiology ,Gastrointestinal Microbiome ,Bacteroidetes ,General Medicine ,biology.organism_classification ,Lorisidae - Abstract
Gastrointestinal microbiome plays an important role in animal metabolism, immune system and pathology associated with health and disease. Many wild slow lorises were confiscated from illegal trade into captivities and experienced a range of changes in living environment and diet. Microbiome analysis contributes to improving captive management by identifying the alteration in their gastrointestinal microbial communities and aiding in determining the factors affecting the health of captive slow lorises. The fecal samples of eighteen Bengal slow lorises (Nycticebus bengalensis) were used to compare gut microbiota from four rescue centers located in Dehong, Gejiu, Nanning and Puer cities of China. The results showed a significant site-dependent difference in microbial community diversity. Similar to other Lorisinae species, the Phyla including Bacteroidetes, Firmicutes and Proteobacteria dominated their gut microbiome composition. The Gejiu group exhibited a higher overall diversity and the unique OTUs, which is resulted from long-term isolated husbandry and heavy human disturbances. The scarcity of gums in the captive diet was likely to cause a lower abundance of Prevotella associated with soluble fiber degradation. The variation of intestinal microbiota in different environments highlights the necessity to improve feed preparation and husbandry management for the captive Bengal slow lorises.
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- 2020
114. A new full-Newton step interior-point method for $$P_{*}(\kappa )$$-LCP based on a positive-asymptotic kernel function
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Yanli Lv, Mingwang Zhang, Kun Huang, and Mengmeng Li
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Path (topology) ,021103 operations research ,Linear programming ,Applied Mathematics ,010102 general mathematics ,0211 other engineering and technologies ,02 engineering and technology ,01 natural sciences ,Linear complementarity problem ,Newton's method in optimization ,Combinatorics ,Computational Mathematics ,Theory of computation ,Point (geometry) ,0101 mathematics ,Algebraic number ,Interior point method ,Mathematics - Abstract
In this paper, we propose a new full-Newton step interior-point method (IPM) for $$P_{*}(\kappa )$$ linear complementarity problem (LCP). The search direction is obtained by applying algebraic equivalent transformation on the centering equation of the central path which is introduced by Darvay et al. for linear optimization (Optim Lett 12(5):1099–1116, 2018). They point out that the search direction can also be obtained by using a positive-asymptotic kernel function. This kernel function has not been used in the complexity analysis of IPMs for $$P_{*}(\kappa )$$ -LCP before. Assuming a strictly feasible starting point is available, we show that the algorithm has the iteration complexity bound $$O((1+4\kappa )\sqrt{n}\log {\frac{n}{\epsilon }})$$ , which is the best known complexity result for such methods. Some numerical results have been provided.
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- 2020
115. Differences in the gut microbiota between Cercopithecinae and Colobinae in captivity
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Yongfang Yao, Yu Jianqiu, Qingyong Ni, Zhao Bo, Meng Xie, Meirong Li, Zongjin Huan, Huailiang Xu, Chen Hongwei, Mingwang Zhang, and Chaojun Yang
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Firmicutes ,Cercopithecinae ,Zoology ,Captivity ,Context (language use) ,Gut flora ,digestive system ,Applied Microbiology and Biotechnology ,Microbiology ,03 medical and health sciences ,Animals ,030304 developmental biology ,0303 health sciences ,Colobinae ,Bacteria ,biology ,030306 microbiology ,Bacteroidetes ,Biodiversity ,General Medicine ,biology.organism_classification ,Diet ,Gastrointestinal Microbiome ,Metagenome ,Ruminococcaceae - Abstract
The gut microbiome of captive primates can provide a window into their health and disease status. The diversity and composition of gut microbiota are influenced by not only host phylogeny, but also host diet. Old World monkeys (Cercopithecidae) are divided into two subfamilies: Cercopithecinae and Colobinae. The diet and physiological digestive features differ between these two subfamilies. Accordingly, highthroughput sequencing was used to examine gut microbiota differences between these two subfamilies, using data from 29 Cercopithecinae individuals and 19 Colobinae individuals raised in captivity. Through a comparative analysis of operational taxonomic units (OTUs), significant differences in the diversity and composition of gut microbiota were observed between Cercopithecinae and Colobinae. In particular, the gut microbiota of captive Old World monkeys clustered strongly by the two subfamilies. The Colobinae microbial diversity was higher than that of Cercopithecinae. Additionally, Firmicutes, Lactobacillaceae, Veillonellaceae, and Prevotella abundance were higher in Cercopithecinae, while Bacteroidetes, Ruminococcaceae, Christensenellaceae, Bacteroidaceae, and Acidaminococcaceae abundance were higher in Colobinae. PICRUSt analysis revealed that the predicted metagenomes of metabolic pathways associated with proteins, carbohydrates, and amino acids were significantly higher in Colobinae. In the context of host phylogeny, these differences between Cercopithecinae and Colobinae could reflect adaptations associated with their respective diets. This well-organized dataset is a valuable resource for future related research on primates and gut microbiota. Moreover, this study may provide useful insight into animal management practices and primate conservation.
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- 2020
116. Transplant of microbiota from long-living people to mice reduces aging-related indices and transfers beneficial bacteria
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Ying Li, Mingwang Zhang, Bo Zeng, Yan Li, Mingyao Yang, Jiangchao Zhao, De Wu, Qingyong Ni, Yinfeng Chen, and Siyuan Zhang
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Male ,Aging ,food.ingredient ,Physiology ,Gut flora ,digestive system ,Coprococcus ,law.invention ,Feces ,Probiotic ,food ,longevity ,law ,Lactobacillus ,Animals ,Humans ,Bifidobacterium ,gut microbiota ,biology ,Ruminococcus ,fecal microbiota transplantation ,Cell Biology ,biology.organism_classification ,Gastrointestinal Microbiome ,Mice, Inbred C57BL ,healthy aging ,aging-related index ,Roseburia ,Research Paper - Abstract
A close relationship between age and gut microbiota exists in invertebrates and vertebrates, including humans. Long-living people are a model for studying healthy aging; they also have a distinctive microbiota structure. The relationship between the microbiota of long-living people and aging phenotype remains largely unknown. Herein, the feces of long-living people were transplanted into mice, which were then examined for aging-related indices and beneficial bacteria. Mice transplanted with fecal matter from long-living people (L group) had greater α diversity, more probiotic genera (Lactobacillus and Bifidobacterium), and short-chain fatty acid producing genera (Roseburia, Faecalibacterium, Ruminococcus, Coprococcus) than the control group. L group mice also accumulated less lipofuscin and β-galactosidase and had longer intestinal villi. This study indicates the effects that the gut microbiota from long-living people have on healthy aging.
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- 2020
117. Design and Implementation of Benchmarks for Multimodal Databases
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Man Yang, Mingwang Zhang, Tao Leng, Weize Dong, and Yu Yan
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- 2021
118. Spatial heterogeneity and socioeconomic transformation challenge the prevention of illegal wildlife consumption in China
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Qingyong Ni, Guozhi Yu, Vincent Nijman, K. Anne-Isola Nekaris, Huailiang Xu, Mingwang Zhang, Yongfang Yao, and Meng Xie
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Ecology, Evolution, Behavior and Systematics ,Nature and Landscape Conservation - Published
- 2022
119. Record of New Genotypes of Enterocytozoon Bieneusi in Wild Populations of Rhesus Macaque (Macaca Mulatta) in China
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Qingyong Ni, Huailiang Xu, Meng Xie, Liu Xue, Fazal Karim, Mengshi Yu, Diyan Li, Jiayun Wu, Mingwang Zhang, and Yongfang Yao
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Rhesus macaque ,Genotype ,Enterocytozoon bieneusi ,Biology ,biology.organism_classification ,Virology - Abstract
Background: Enterocytozoon bieneusi is a zoonotic pathogen with a wide range of animal host. In China, there are only a few reports of E. bieneusi infection in wild populations of Rhesus macaque. Here, we determined the prevalence of E. bieneusi in 9 populations of Rhesus macaque and assessed their zoonotic potential.Methods: A total of 324 fecal samples of Rhesus macaque were collected from 9 populations in 5 provinces (Sichuan, Chongqing, Qinghai, Tibet and Hainan) in China, and performed genotype of ITS gene to analyze the zoonotic potential.Results: 38 of the 324 (11.72%) specimens from wild Rhesus macaques were infected with E. bieneusi. 11 genotypes were identified including 3 known genotypes: D (n= 24), EbpC (n= 4) and SCC-2 (n= 1); 8 novel genotypes named Mul6 (n= 1), Mul7 (n= 1), Mul8 (n= 1), Mul9 (n= 1), Mul10 (n= 2), Mul11 (n= 1), Mul12 (n= 1) and Mul13 (n= 1). According to the phylogenetic analysis, Mul6, Mul7, Mul8, Mul9, Mul11 Mul12 and Mul13 were clustered into Group 1, while Mul10 were clustered into Group 5.Conclusions: To the best of our knowledge, this is the first study reporting the prevalence and genotypes of E. bieneusi in several wild populations of Rhesus macaque in China. It is concluded that, population of Rhesus Macaques is likely to prone of E. bieneusi transmission in many regions of China, which found the zoonotic genotypes D and EbpC and the novel genotypes with zoonotic potential, it should be paid more attention to prevent.
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- 2021
120. Association of female reproductive tract microbiota with egg production in layer chickens
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Mengnan He, Bo Zeng, Tao Wang, Qing Zhu, Xiaolan Fan, Yuan Su, Shailendra Kumar Mishra, Deying Yang, Qingyong Ni, Xiaoling Zhao, Huadong Yin, Mingzhou Li, Diyan Li, Wei Zhu, Mingyao Yang, Shilin Tian, Mingwang Zhang, Ranlei Wei, Yan Li, and Zhongxian Xu
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Bacteroides salanitronis ,biology ,Reproductive tract ,Microbiota ,Clostridium leptum ,Zoology ,Health Informatics ,biology.organism_classification ,Computer Science Applications ,Gastrointestinal Tract ,Immune system ,Animals ,Digestive tract ,Female ,Microbiome ,Bacteroides fragilis ,Female Reproductive Tract ,Chickens - Abstract
Background The microbiota of the female reproductive tract is increasingly recognized as playing fundamental roles in animal reproduction. To explore the relative contribution of reproductive tract microbiomes to egg production in chickens, we investigated the microbiota in multiple reproductive and digestive tract sites from 128 female layer (egg-producing) chickens in comparable environments. Results We identified substantial differences between the diversity, composition, and predicted function of site-associated microbiota. Differences in reproductive tract microbiota were more strongly associated with egg production than those in the digestive tract. We identified 4 reproductive tract microbial species, Bacteroides fragilis, Bacteroides salanitronis, Bacteroides barnesiae, and Clostridium leptum, that were related to immune function and potentially contribute to enhanced egg production. Conclusions These findings provide insights into the diverse microbiota characteristics of reproductive and digestive tracts and may help in designing strategies for controlling and manipulating chicken reproductive tract microbiota to improve egg production.
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- 2021
121. The complete mitochondrial genome of Amyda cartilaginea (Testudines: Trionychidae)
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Dingqi Rao, Mingwang Zhang, and Lin Cui
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0106 biological sciences ,0301 basic medicine ,Mitochondrial DNA ,biology ,Trionychidae ,Zoology ,Amyda cartilaginea ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,DNA sequencing ,Nilssonia ,law.invention ,03 medical and health sciences ,030104 developmental biology ,Sister group ,Phylogenetics ,law ,Genetics ,Turtle (robot) ,Molecular Biology - Abstract
The Asiatic softshell turtle, also known as the black-rayed softshell turtle (Amyda cartilaginea; Accession no: MT039230), is found in northeastern India (Mizoram), Brunei Darussalam, Indonesia, Malaysia, Singapore, Myanmar, Laos, Vietnam, Cambodia, and Thailand. This turtle is thought to have been introduced into the Sunda Islands, Sulawesi, and Yunnan, China, through the Malay Peninsula to Sumatra, Java, and Borneo. Herein, we determined the complete mitochondrial genome of A. cartilaginea for the first time using next-generation sequencing (NGS). The assembled mitogenome was 16,763 bp in length and encoded 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes (12S rRNA and 16S rRNA), and one control region (CR). The PCGs based maximum-likelihood phylogeny discriminated A. cartilaginea from other Testudines and clusters within family Trionychidae with the sister taxa of Nilssonia nigricans.
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- 2020
122. A primal-dual interior-point algorithm with arc-search for semidefinite programming
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Zhengwei Huang, Yiyuan Zhou, Mingwang Zhang, Xiaoyu Luo, and Beibei Yuan
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Semidefinite programming ,021103 operations research ,Control and Optimization ,Linear programming ,0211 other engineering and technologies ,010103 numerical & computational mathematics ,02 engineering and technology ,Ellipse ,01 natural sciences ,Ellipsoid ,Arc (geometry) ,TheoryofComputation_ANALYSISOFALGORITHMSANDPROBLEMCOMPLEXITY ,Path (graph theory) ,Point (geometry) ,0101 mathematics ,Algorithm ,Interior point method ,Mathematics - Abstract
We propose a wide neighborhood primal-dual interior-point algorithm with arc-search for semidefinite programming. In every iteration, the algorithm constructs an ellipse and searches an $$\varepsilon $$ -approximate solution of the problem along the ellipsoidal approximation of the central path. Assuming a strictly feasible starting point is available, we show that the algorithm has the iteration complexity bound $$O\left( n^{\frac{3}{4}}\log \frac{{X^{0}}\bullet {S}^{0}}{\varepsilon }\right) $$ for the Nesterov–Todd direction, which is similar to that of the corresponding algorithm for linear programming. The numerical results show that our algorithm is efficient and promising.
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- 2019
123. A wide neighborhood interior-point algorithm with arc-search for P⁎(κ) linear complementarity problem
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Zhengwei Huang, Beibei Yuan, and Mingwang Zhang
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Numerical Analysis ,Applied Mathematics ,010103 numerical & computational mathematics ,01 natural sciences ,Linear complementarity problem ,Ellipsoid ,010101 applied mathematics ,Arc (geometry) ,Computational Mathematics ,Path (graph theory) ,Point (geometry) ,0101 mathematics ,Algorithm ,Interior point method ,Mathematics - Abstract
We propose a wide neighborhood interior-point algorithm with arc-search for P ⁎ ( κ ) linear complementarity problem (LCP). Along the ellipsoidal approximation of the central path, the algorithm searches optimizers in every iteration. Assuming a strictly starting point is available, we show that the algorithm has O ( ( 1 + 2 κ ) ( 1 + 18 κ ) 2 n log ( x 0 ) T s 0 e ) iteration complexity. It matches the currently best known iteration bound for P ⁎ ( κ ) LCP. Some preliminary numerical results show that the proposed algorithm is efficient and reliable.
- Published
- 2019
124. On complexity of a new Mehrotra-type interior point algorithm for P∗(κ) $P_{*}(\kappa )$ linear complementarity problems
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Zhengwei Huang, Yiyuan Zhou, and Mingwang Zhang
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Polynomial complexity ,P ∗ ( κ ) $P_{*}(\kappa )$ linear complementarity problem ,Applied Mathematics ,lcsh:Mathematics ,010102 general mathematics ,Mehrotra-type algorithm ,lcsh:QA1-939 ,01 natural sciences ,Complementarity (physics) ,010101 applied mathematics ,Discrete Mathematics and Combinatorics ,0101 mathematics ,Algorithm ,Analysis ,Kappa ,Interior point method ,Mathematics ,Interior point algorithm - Abstract
In this paper, a variant of Mehrotra-type predictor–corrector algorithm is proposed for $P_{*}(\kappa )$ linear complementarity problems. In this algorithm, a safeguard step is used to avoid small step sizes and a new corrector direction is adopted. The algorithm has polynomial iteration complexity and the iteration bound is $O ((14\kappa +11)\sqrt{(1+4 \kappa )(1+2\kappa )}~n\log \frac{(x^{0})^{T}s^{0}}{\varepsilon } )$ . Some numerical results are reported as well.
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- 2019
125. Corrigendum to 'Transcriptome Profiling across Five Tissues of Giant Panda'
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Feng Li, Chengdong Wang, Zhongxian Xu, Mingzhou Li, Linhua Deng, Ming Wei, Hemin Zhang, Kai Wu, Ruihong Ning, Diyan Li, Mingyao Yang, Mingwang Zhang, Qingyong Ni, Bo Zeng, Desheng Li, and Ying Li
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General Immunology and Microbiology ,General Medicine ,General Biochemistry, Genetics and Molecular Biology - Published
- 2022
126. Age-related ceRNA networks and the mRNA/protein correlation in Drosophila ageing
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Jiamei Li, Taiming Yan, He Zhi, Qingyong Ni, Yan Li, Xiaolan Fan, Yang Mingyao, Pu Zhang, Bo Zeng, Xueping Mao, Siqi Wang, Jianbo Tu, Mingwang Zhang, Diyan Li, Deying Yang, and Ya Yuan
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Correlation ,Genetics ,Messenger RNA ,biology ,Competing endogenous RNA ,Ageing ,Age related ,Drosophila (subgenus) ,biology.organism_classification - Abstract
Background As Drosophila is a classic model organism, understanding of the regulatory networks has great significance in revealing the genetic mechanisms of ageing and human diseases. Competing endogenous RNA (ceRNA)-mediated regulation is an important mechanism of circular RNA (circRNA) and long non-coding RNA (lncRNA) regulation in ageing and age-related disease. However, extensive analyses of the multi-omics (circRNA/miRNA/mRNA, lncRNA/miRNA/mRNA, and mRNA/protein) characteristics of adult Drosophila ageing have not been reported. Our results determine the ceRNA networks and the mRNA/protein correlations of key differentially expressed genes in adult Drosophila aging, and provide a solid foundation for understanding mechanisms of human ageing and ageing-related diseases. Results Here, differentially expressed circRNAs and microRNAs (miRNAs) between 7 and 42 day old Drosophila were screened and identified. Then, the differentially expressed mRNAs, circRNAs, miRNAs, lncRNAs, and proteins between day 7 and day 42 were used to analyse fly age-related circRNA/miRNA/mRNA and lncRNA/miRNA/mRNA networks and the mRNA/protein correlation in Drosophila ageing. Several key ceRNA networks were identified, such as the circ_0006913/miR-985-3p/Abl, circ_0009500/miR-14-5p/SERCA, XLOC_100429/miR-14-5p/SERCA, and XLOC_100429/miR-14-5p/Vha100-4 networks. Subsequently, 16 pairs of differentially expressed interacting mRNAs/proteins were found, including 10 pairs with the same expression trends and 6 pairs with the opposite expression trends. Furthermore, real-time quantitative PCR (qPCR) was used to verify the expression level of those genes. Conclusions The discovery of these ceRNA networks and the mRNA/protein correlations in adult Drosophila ageing will provide new information for research on human ageing and age-related disease.
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- 2021
127. Comprehensive circRNA-microRNA-mRNA network analysis revealed the novel regulatory mechanism of Trichosporon asahii infection
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Xin Yang, Rongya Yang, Wan-Ting Luo, Zhi-Hong Zhu, Mingwang Zhang, Zhikuan Xia, and Junhong Ao
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0301 basic medicine ,Leukocyte migration ,Trichosporon asahii ,03 medical and health sciences ,0302 clinical medicine ,Circular RNA ,Trichosporonosis ,microRNA ,Humans ,Medicine ,RNA, Messenger ,KEGG ,Genetics ,lcsh:R5-920 ,lcsh:Military Science ,Competing endogenous RNA ,business.industry ,Basidiomycota ,lcsh:U ,Research ,RNA ,RNA sequencing ,RNA, Circular ,General Medicine ,Non-coding RNA ,MicroRNAs ,030104 developmental biology ,030220 oncology & carcinogenesis ,lcsh:Medicine (General) ,business ,Signal Transduction - Abstract
Background Invasive Trichosporon asahii (T. asahii) infection frequently occurs with a high mortality in immunodeficient hosts, but the pathogenesis of T. asahii infection remains elusive. Circular RNAs (circRNAs) are a type of endogenous noncoding RNA that participate in various disease processes. However, the mechanism of circRNAs in T. asahii infection remains completely unknown. Methods RNA sequencing (RNA-seq) was performed to analyze the expression profiles of circRNAs, microRNAs (miRNAs), and mRNAs in THP-1 cells infected with T. asahii or uninfected samples. Some of the RNA-seq results were verified by RT-qPCR. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were used to analyze the differentially expressed mRNAs. A circRNA-miRNA-mRNA network was constructed and verified by dual-luciferase reporter assay and overexpression experiments. Results A total of 46 circRNAs, 412 mRNAs and 47 miRNAs were differentially expressed at 12 h after T. asahii infection. GO and KEGG analyses showed that the differentially expressed mRNAs were primarily linked to the leukocyte migration involved in the inflammatory response, the Toll-like receptor signaling pathway, and the TNF signaling pathway. A competing endogenous RNA (ceRNA) network was constructed with 5 differentially expressed circRNAs, 5 differentially expressed miRNAs and 42 differentially expressed mRNAs. Among them, hsa_circ_0065336 was found to indirectly regulate PTPN11 expression by sponging miR-505-3p. Conclusions These data revealed a comprehensive circRNA-associated ceRNA network during T. asahii infection, thus providing new insights into the pathogenesis of the T. asahii-host interactions.
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- 2021
128. Proteomic analysis of serial isolates of Trichosporon asahii identifies host-specific adaptations using the TMT/MRM approach
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Haitao Li, Dequan Zhang, Haihao Zheng, Xin Yang, Rongya Yang, Mingwang Zhang, Yong Liao, Zhikuan Xia, and Junhong Ao
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Proteomics ,Antifungal Agents ,Basidiomycota ,Selected reaction monitoring ,Biophysics ,Virulence ,Paromomycin ,Trichosporon asahii ,Biology ,Tandem mass tag ,Biochemistry ,Microbiology ,Immune system ,Trichosporon ,Tandem Mass Spectrometry ,Proteome ,medicine ,Humans ,medicine.drug ,Chromatography, Liquid - Abstract
The opportunistic fungal pathogen Trichosporon asahii (T. asahii) is an important causal agent of mortality in immunocompromised patients and associated with frequent relapses, even with sufficient antifungal treatment. Investigating the proteomes of initial and recurrent isolates may help to identify within-host adaptive changes. In this study, using tandem mass tag (TMT)-labeling combined with liquid chromatography-mass spectrometry/mass spectrometry (LC–MS/MS) technology, we analyzed the proteomes of two T. asahii strains that were isolated 15 years apart from the same patient who suffered initial and recurrent episodes of systemic disseminated trichosporonosis. A total of 597 differentially expressed proteins were identified. Functional analysis showed that the increased proteins were primarily concentrated on peptide/protein/energy/drug metabolism and translation. Most of the results were determined to be consistent with the findings of phenotypic assays, such as tests for drug susceptibility, temperature growth, biofilm formation, melanization and paromomycin assays. Moreover, we performed multiple reaction monitoring (MRM) mass spectrometry to verify 27 candidate proteins, and the results of this experiment were also highly consistent with the results of the TMT analysis. Therefore, to the best of our knowledge, these data provide the first molecular evidence of how the T. asahii proteome changes related to host-specific adaptation during human infection. Significance Systemic infection with Trichosporon asahii (T. asahii) has recently been recognized as an important causal agent of mortality in immunocompromised patients. Although triazole treatment usually works efficiently in the early phase of infection, many patients relapse. Hence, comparative analyses of the proteomics of initial and recurrent isolates may reveal evidence of adaptive changes within the host. Our study demonstrates that the recurrent strain has undergone proteomic changes using tandem mass tag (TMT)-labeling combined with liquid chromatography-mass spectrometry/mass spectrometry (LC–MS/MS). Moreover, the results of phenotypic assays, including drug susceptibility, temperature growth, biofilm formation, melanization and paromomycin assays, were highly consistent with the proteomic changes, and multiple reaction monitoring (MRM) verification also showed similar trends to the TMT results. In summary, our study is the first to investigate the adaptation of T. asahii under pressure from antifungal chemotherapy and host immune responses.
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- 2021
129. Complete mitochondrial genome and phylogenetic analysis of a Chinese Eurasian lynx (
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Yuhan, Wu, Huailiang, Xu, Diyan, Li, Meng, Xie, Jiayun, Wu, Anxiang, Wen, Qin, Wang, Guangxiang, Zhu, Qingyong, Ni, Mingwang, Zhang, and Yongfang, Yao
- Subjects
mitochondrial genome ,phylogenetic analysis ,Lynx lynx ,Mitogenome Announcement ,Research Article - Abstract
The complete mitochondrial genome of Eurasian lynx (Lynx lynx) from China has been described in this study. It has a circular genome of 16,996 bp with a higher A + T content of 58.65%, and the base composition is A: 32.31%, G: 14.29%, T: 26.35%, C: 27.06%. When compared with the reported individual (KR919624) from China, there are 81 variations and 58 base deletion between the two sequences. The phylogenetic analysis indicated our sequence separated clearly from Eurasian lynx individuals in the previous publications. These results could provide more molecular information for the conservation of Eurasian lynx genetic resources.
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- 2021
130. The complete mitochondrial genome of the blue-crested lizard
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Mo, Wang, Zhuoyun, Jiang, Jishan, Wang, Lin, Cui, and Mingwang, Zhang
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mitogenome ,phylogenetic analysis ,Calotes mystaceus ,Mitogenome Announcement ,Research Article - Abstract
A complete mitogenome sequence of the blue-crested lizard (Calotes mystaceus) was determined in this study. The 16,506 bp genome consists 13 protein-coding genes (PCG), two ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes, and a control region. The phylogenetic tree reveals that the Calotes mystaceus is closely related to the C. versicolor. This report provides the basic data for further studies of Calotes species classification and phylogeny.
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- 2021
131. Seasonal dynamics of gut microbiota in a cohort of wild Tibetan macaques (Macaca thibetana) in western China
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Yongfang Yao, Mengmeng Dong, Huailiang Xu, Cong Wang, Yuhan Wu, Diyan Li, Qingyong Ni, Meng Xie, Mingwang Zhang, and Tianrui Xia
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0106 biological sciences ,Ecology ,biology ,Firmicutes ,010604 marine biology & hydrobiology ,Macaca thibetana ,Beta diversity ,Endangered species ,Zoology ,Bacteroidetes ,Gut microbiota ,Gut flora ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,lcsh:QH540-549.5 ,Labahe nature reserve ,Alpha diversity ,16S rRNA gene ,lcsh:Ecology ,Adaptation ,Ecology, Evolution, Behavior and Systematics ,Feces ,Nature and Landscape Conservation - Abstract
Previous researches have highlighted the finding that the availability of food resources plays an important role in reshaping the gut microbiota of wild animals as they to adapt to the surrounding habitat. The gut microbial characteristics were examined in Tibetan macaques (Macaca thibetana) from eastern China (Huangshan, Anhui), but little is known about other geographical populations. Herein, we collected 40 fecal samples of Tibetan macaques from the Labahe Natural Reserve in western China over four seasons and analyzed the seasonal variation of gut microbiota using 16S rRNA gene V3–V4 sequencing. The analysis showed that gut microbial diversity and composition varied by season. Autumn exhibited the lowest alpha diversity and remarkably separated from the other three seasons for beta diversity. There were statistically significant differences in the composition of gut microbiota during different seasons. Autumn presented the lowest Firmicutes/Bacteroidetes ratio while winter had the highest. The family Ruminococcaceae and Lactobacillaceae within Firmicutes accounted for a high proportion in each season, but the abundance of Lactobacillaceae was significantly lower in winter. During autumn, Preotella, which can utilize carbohydrates increased significantly. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) prediction revealed that metabolism of cofactors of vitamin pathways and glycan biosynthesis pathways were highly enriched in autumn. Our results revealed that the gut microbiota potentially play an important role in the adaptation of wild Tibetan macaques to the seasonal fluctuations of food availability, which may contribute to the conservation of this endangered species.
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- 2021
132. Complete mitochondrial genome of red panda (
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Zuxiang, Jin, Huailiang, Xu, Diyan, Li, Meng, Xie, Mingwang, Zhang, Qingyong, Ni, and Yongfang, Yao
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Mitochondrial genome ,phylogenetic analysis ,red panda ,Mitogenome Announcement ,Research Article - Abstract
In this study, we reported the complete mitochondrial genome sequence of a red panda (Ailurus fulgens). The mitogenome (GenBank accession number MK886830) length is 16,517 bp and exhibits the typical structure of mammalian mitochondrial genomes contains 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and one control region. The tRNASer (AGY) gene failed to form the typical clover-leaf secondary structure as it lacked the dihydrouridine (DHU) arm. phylogenetically, our sequence cluster together with genus Ailurus, which showed a closer genetic relationship. The mitogenome provides new data to further elucidation and understand the phylogeny of red pandas.
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- 2020
133. The complete mitogenome of the granular torrent frog
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An, Huang, Hongdi, Luo, Sangdawa, Luo, Haijun, Li, Qingyong, Ni, Yongfang, Yao, Huailiang, Xu, Bo, Zeng, Ying, Li, Zhimin, Wei, and Mingwang, Zhang
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Mitochondrial genome ,gene arrangement ,Amolops granulosus ,Mitogenome Announcement ,Research Article - Abstract
We obtained the complete mitochondrial genome of Amolops granulosus, which was 17,785 bp in length and it contained the 37 typical mitochondrial genes: 2 ribosomal RNAs, 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), and 1 control region (CR). The hotspot of gene arrangement was ranged as ‘W-gap-OL-gap-A-N-gap-C-Y’ which consisted with most published Amolops mitogenomes. Our phylogenetic results suggested the gene arrangement of ‘WANCY’ region can facilitate to distinguish the Amolops species as an efficient genetic marker.
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- 2020
134. The complete mitochondrial genome sequence and phylogenetic analysis of yellow weasel (
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Mengshi, Yu, Huailiang, Xu, Diyan, Li, Jiayun, Wu, Anxiang, Wen, Meng, Xie, Qin, Wang, Guangxiang, Zhu, Qingyong, Ni, Mingwang, Zhang, and Yongfang, Yao
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Mustela sibirica ,mitochondrial genome ,phylogenetic analysis ,Mitogenome Announcement ,Research Article - Abstract
In this study, we determined the complete mitochondrial genome sequence of the Mustela sibirica. The complete mitogenome of M. sibirica is 16,529 bp in length and consist of 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a D-loop region. The overall base composition of the mitochondrial DNA is 32.88%A, 13.84%G, 27.32%T, and 25.96%C. The phylogenetic tree of the family Mustelidae constructed by using mitogenome sequences from 10 mustelid species of the family Mustelidae. These results provide necessary information for molecular phylogeny and evolutionary analysis of the M. sibirica.
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- 2020
135. Use of RNA Sequencing to Perform Comprehensive Analysis of Long Noncoding RNA Expression Profiles in Macrophages Infected with Trichosporon asahii
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Dequan Zhang, Xin Yang, Rongya Yang, Mingwang Zhang, Zhikuan Xia, and Junhong Ao
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0301 basic medicine ,Genetics ,Gene knockdown ,Sequence Analysis, RNA ,Veterinary (miscellaneous) ,Basidiomycota ,Gene Expression Profiling ,Macrophages ,030106 microbiology ,RNA ,Trichosporon asahii ,Biology ,Applied Microbiology and Biotechnology ,Microbiology ,Long non-coding RNA ,030207 dermatology & venereal diseases ,03 medical and health sciences ,0302 clinical medicine ,Real-time polymerase chain reaction ,Immune system ,RNA, Long Noncoding ,RNA, Messenger ,KEGG ,Agronomy and Crop Science ,Gene - Abstract
Trichosporon asahii (T. asahii) is a clinically important opportunistic pathogenic fungus capable of causing systemic lethal infection in immunosuppressive and immunodeficient hosts. However, the mechanism of the host immune response upon T. asahii infection has not been elucidated. Recent evidence has shown that long noncoding RNAs (lncRNAs) play key roles in regulating the immune response to resist microbial infections. In this study, we analyzed the expression profiles of lncRNAs at 12 and 24 h post-infection (hpi) in THP-1 cells infected with T. asahii using RNA sequencing (RNA-Seq). A total of 64 and 160 lncRNAs displayed significant differentially expressed (DE) at 12 h and 24 hpi, respectively. Among these lncRNAs, 18 lncRNAs were continuous DE at two time points. The DE of eight candidate lncRNAs were verified by real time quantitative polymerase chain reaction (RT-qPCR). Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed to analyze the cis-target genes of 18 DE lncRNAs. The results showed that they were enriched in signaling pathways related to the host immune response, indicating that these lncRNAs might play important roles in fungi–host interactions. Finally, we explored the function of lncRNA NEAT1 and found that the expression of TNF-α and IL-1β declined after NEAT1 knockdown in T. asahii-infected THP-1 cells. To our knowledge, this is the first report of a expression analysis of lncRNAs in macrophages infected with T. asahii. Our study helps to elucidate the role of lncRNAs in the host immune response to early infection by T. asahii.
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- 2020
136. Deubiquitinase USP7 regulates Drosophila aging through ubiquitination and autophagy
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Ting Lian, Yao Zeng, Bo Zeng, Huang Tiantian, Mingyao Yang, Deying Yang, Wenhao Song, Xueping Mao, Yan Li, Mingwang Zhang, Cui Lang, Fan Ziqiang, Xiaolan Fan, Tao Wang, Qingyong Ni, Qi Wu, and Diyan Li
- Subjects
Aging ,Gene knockdown ,biology ,DNA damage ,Autophagy ,Cell Biology ,Protein degradation ,biology.organism_classification ,Cell biology ,Deubiquitinating enzyme ,Ubiquitin ,biology.protein ,Drosophila melanogaster ,Signal transduction - Abstract
Ubiquitination-mediated protein degradation is the selective degradation of diverse forms of damaged proteins that are tagged with ubiquitin, while deubiquitinating enzymes reverse ubiquitination-mediated protein degradation by removing the ubiquitin chain from the target protein. The interactions of ubiquitinating and deubiquitinating enzymes are required to maintain protein homeostasis. The ubiquitin-specific protease USP7 is a deubiquitinating enzyme that indirectly plays a role in repairing DNA damage and development. However, the mechanism of its participation in aging has not been fully explored. Regarding this issue, we found that USP7 was necessary to maintain the normal lifespan of Drosophila melanogaster, and knockdown of dusp7 shortened the lifespan and reduced the ability of Drosophila to cope with starvation, oxidative stress and heat stress. Furthermore, we showed that the ability of USP7 to regulate aging depends on the autophagy and ubiquitin signaling pathways. Furthermore, 2,5-dimethyl-celecoxib (DMC), a derivative of celecoxib, can partially restore the shortened lifespan and aberrant phenotypes caused by dusp7 knockdown. Our results suggest that USP7 is an important factor involved in the regulation of aging, and related components in this regulatory pathway may become new targets for anti-aging treatments.
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- 2020
137. Influence of the digestive/reproductive tract microbiota on chicken egg production beyond host genetics
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Bo Zeng, Tianyuan Ma, Xiaoling Zhao, Dejing Zhang, Xuxu Lin, Yan Wang, Shilin Tian, Xiaolan Fan, Huadong Yin, Ranlei Wei, Mingwang Zhang, Mingzhou Li, Deying Yang, Shailendra Kumar Mishra, Qing Zhu, Qingyong Ni, Mingyao Yang, Zhongxian Xu, Diyan Li, Tao Wang, Yuan Su, Yaodong Hu, Yongfang Yao, Yan Li, Chunyou Ning, Wei Zhu, Shi Lianzhe, and Huailiang Xu
- Subjects
Genetics ,Host (biology) ,Reproductive tract ,Biology - Abstract
Background: The microbiota of the digestive and reproductive systems has a prominent role in animal health and performance, but the extent of its contribution is difficult to determine. In chickens, the effect of host genetics on the reproductive and digestive tract microbiota is unclear, and the means by which digestive/reproductive microbiomes help improve egg production in chicken are unknown.Results: To gain insight into this, we examined genomes from 128 chickens reared under identical conditions and described their digestive (crop, gizzard and small intestine) and reproductive tract (vagina, uterus and isthmus) microbiota. Although the diversity, composition and predicted function of the digestive and reproductive tract microbiota exhibited notable microbiota variation substantially between different parts, host genetics had limited effects on the reproductive and digestive tract microbial community. The digestive and reproductive tract microbiota had a significant effect on egg production (accounting for 52.31% - 98.86% of the variance), after correcting for host genetic effects; in particular, the uterus and isthmus microbiota accounted for an average of 93.59% and 98.86%, respectively, of variance in egg production. We further identified four reproductive tract microbial species which were related to immune system, Bacteroides fragilis, Bacteroides salanitronis, Bacteroides barnesiae and Clostridium leptum, that were significantly positively correlated with egg production. Chickens with a lower abundance of these species had produced significantly fewer eggs at 300 days of age (37.13 vs. 113.75) than those with a higher abundance of these microorganisms. These taxa indicate potential roles play in promoting reproductive performance. Especially uterus and isthmus tract microbiota were major factors in regulating the chicken egg production.Conclusions: Host genetics has limited effect on digestive/reproductive microbiome composition. The distinct site-associated chicken microbiome may be determined by the differences of their physical function. These findings may help design strategies for controlling and altering the digestive/reproductive tract microbiota in chickens to improve egg production.
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- 2020
138. Conprehensive Analysis of circRNA-microRNA-mRNA Network Revealed Novel Regulatory Mechanism in Trichosposon Asahii Infection
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Zhikuan Xia, Junhong Ao, Zhi-Hong Zhu, Mingwang Zhang, Wan-Ting Luo, Xin Yang, and Rongya Yang
- Subjects
Messenger RNA ,Mechanism (biology) ,microRNA ,Biology ,Cell biology - Abstract
Background: Trichosporon asahii (T. asahii) invasive infection frequently occurs in immunodeficient hosts with high mortality, but the pathogenesis of T. asahii infection remains elusive. Circular RNAs (circRNAs) are a type of endogenous noncoding RNAs that participant various disease processes. However, the mechanism of circRNAs in T. asahii infection are still completely unknown.Methods: RNA sequencing (RNA-seq) was performed to analyse the expression profiles of circRNA, microRNA (miRNA), and mRNA in THP-1 cells infected with T. asahii or uninfected samples. Part of the RNA-seq results were verified by RT-qPCR. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were used to analyse the differentially expressed (DE) mRNA. The circRNA-miRNA-mRNA network was constructed and verified with dual-luciferase reporter assay and overexpression experiment.Results: A total of 46 circRNAs , 412 mRNAs and 47 miRNAs were DE after T. asahii infection at 12 h. GO and KEGG analysis showed that the DE mRNAs were primary linked to the leukocyte migration involved in inflammatory response, Toll-like receptor signaling pathway, and TNF signaling pathway. A competing endogenous RNA (ceRNA) network was constructed with five DE circRNAs, five DE miRNAs and 42 DE mRNAs. Among them, we verified that hsa_circ_0065336 indirectly regulate PTPN11 expression by sponging miR-505-3p.Conclusions: These data revealed a comprehensive circRNA-associated ceRNA network during T. asahii infection, thus providing new insights to clarify the pathogenesis between T. asahii-host interation.
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- 2020
139. AFB1 Induced Transcriptional Regulation Related to Apoptosis and Lipid Metabolism in Liver of Chicken
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Xiaoling Zhao, Xiaolan Fan, Mingwang Zhang, Yan Wang, Shailendra Kumar Mishra, Bo Zeng, Huadong Yin, Yan Li, Tao Wang, Zhongxian Xu, Deying Yang, Qing Zhu, Diyan Li, Mingyao Yang, Qingyong Ni, Xueqin Liu, and Feng Chen
- Subjects
Peroxisome proliferator-activated receptor gamma ,Transcription, Genetic ,Health, Toxicology and Mutagenesis ,Roman layer ,lcsh:Medicine ,Apoptosis ,Biology ,Toxicology ,liver ,Article ,differential expression ,Transcriptome ,Andrology ,03 medical and health sciences ,0302 clinical medicine ,microRNA ,Transcriptional regulation ,medicine ,Animals ,Gene Regulatory Networks ,RNA, Messenger ,Gene ,030304 developmental biology ,0303 health sciences ,Liver cell ,Fatty liver ,lcsh:R ,food and beverages ,high-throughput sequencing ,Lipid metabolism ,medicine.disease ,Lipid Metabolism ,MicroRNAs ,Gene Expression Regulation ,030220 oncology & carcinogenesis ,aflatoxin B1 ,Hepatocytes ,fat deposition ,RNA ,Female ,RNA, Long Noncoding ,Chickens - Abstract
Aflatoxin B1 (AFB1) leads to a major risk to poultry and its residues in meat products can also pose serious threat to human health. In this study, after feeding 165-day-old Roman laying hens for 35 days, the toxic effects of aflatoxin B1 at different concentrations were evaluated. The purpose of this study was to explore the mechanism of liver toxicosis responses to AFB1. We found that highly toxic group exposure resulted in liver fat deposition, increased interstitial space, and hepatocyte apoptosis in laying hens. Furthermore, a total of 164 differentially expressed lnRNAs and 186 differentially expressed genes were found to be highly correlated (Pearson Correlation Coefficient >, 0.80, p-value <, 0.05) by sequencing the transcriptome of control (CB) and highly toxic group (TB3) chickens. We also identify 29 differentially expressed genes and 19 miRNAs that have targeted regulatory relationships. Based on the liver cell apoptosis and fatty liver syndrome that this research focused on, we found that the highly toxic AFB1 led to dysregulation of the expression of PPARG and BCL6. They are cis-regulated by TU10057 and TU45776, respectively. PPARG was the target gene of gga-miR-301a-3p, gga-miR-301b-3p, and BCL6 was the target gene of gga-miR-190a-3p. In summary, highly toxic AFB1 affects the expression levels of protein-coding genes and miRNAs in the liver of Roman layer hens, as well as the expression level of long non-coding RNA in the liver, which upregulates the expression of PPARG and downregulates the expression of Bcl-6. Our study provides information on possible genetic regulatory networks in AFB1-induced hepatic fat deposition and hepatocyte apoptosis.
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- 2020
140. Transcriptome analysis reveals differentially expressed genes associated with high rates of egg production in chicken hypothalamic-pituitary-ovarian axis
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Qingyong Ni, Mingyao Yang, Chunyou Ning, Huadong Yin, Shailendra Kumar Mishra, Yan Wang, Qing Zhu, Deying Yang, Binlong Chen, Xiaolan Fan, Xiaoling Zhao, Zhongxian Xu, Diyan Li, Yan Li, and Mingwang Zhang
- Subjects
0301 basic medicine ,Hypothalamo-Hypophyseal System ,Pituitary gland ,Eggs ,Transcriptional regulatory elements ,Hypothalamus ,Gene Expression ,lcsh:Medicine ,Hypothalamic–pituitary–gonadal axis ,Ovary ,02 engineering and technology ,Breeding ,Biology ,Article ,Cellular glucose homeostasis ,Transcriptome ,03 medical and health sciences ,medicine ,Animals ,lcsh:Science ,Animal breeding ,Regulator gene ,Multidisciplinary ,Gene Expression Profiling ,lcsh:R ,Wnt signaling pathway ,021001 nanoscience & nanotechnology ,Cell biology ,030104 developmental biology ,medicine.anatomical_structure ,Pituitary Gland ,embryonic structures ,Female ,lcsh:Q ,0210 nano-technology ,Chickens ,Hormone - Abstract
The hypothalamic-pituitary-ovarian (HPO) axis regulates the breeding process cycle of laying hens. However, the key regulatory genes of the HPO axis and pathways that drive chicken egg laying performance remain elusive. A total of 856 Chinese Luhua chicken was raised and the highest two hundred and the lowest two hundred chicken egg production were considered as high egg production (HEP) and low egg production (LEP) according to the total egg number at 300 days of age, respectively. RNA-seq sequencing (RNA-Seq) was conducted to explore the chicken transcriptome from the hypothalamus, pituitary gland and ovary tissue of 6 Chinese Luhua chicken with 3 high and low-rate egg production. In total, 76.09 Gb RNA-seq sequences were generated from 15 libraries with an average of 5.07 Gb for each library. Further analysis showed that 414, 356 and 10 differentially expressed genes (DEGs) were identified in pituitary gland, ovary and hypothalamus between HEP and LEP chickens, respectively. In pituitary gland, DEGs were involve in regulation of cellular glucose homeostasis, Ras protein signal transduction, negative regulation of hormone secretion. In Ovary DEGs were mainly involved in embryonic organ development, regulation of canonical Wnt signaling, response to peptide hormone. Our study identified DEGs that regulate mTOR signaling pathway, Jak-STAT signaling pathway, Tryptophan metabolism and PI3K-Akt signaling pathways at HPO-axis in laying hens. These important data contribute to improve our understanding of reproductive biology of chicken and isolating effective molecular markers that can be used for genetic selection in Chinese domestic Luhua chicken.
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- 2020
141. Genetic characterization of rhesus macaque populations along the southeastern Qinghai-Tibetan plateau based on a mitochondrial ATP6 gene closely related to energy metabolism
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Kechu Zhang, Mingwang Zhang, Qingyong Ni, Yongfang Yao, Meng Xie, Diyan Li, Pu Zhao, Huailiang Xu, and Zuxiang Jin
- Subjects
Qinghai tibetan plateau ,Rhesus macaque ,Evolutionary biology ,Energy metabolism ,Biology ,biology.organism_classification ,Gene - Abstract
Background Rhesus macaque ( Macaca mulatta ) is widely distributed in China, across different altitudes. The mitochondrial ATP6 gene,an ATPase subunit coding gene with fast evolution rate in the mitochondrial genome, plays an important role in the energy metabolism of animals, which may be a good molecular marker for studying the adaptive evolution of animals. Herein, we detected ATP6 genes of 334 rhesus macaques of 19 populations from multiple regions in China with an elevation span of 5-4000m, and mainly carried out the population genetic and evolutionary analysis in these macaques. Our aim is to explore the molecular mechanism of rhesus macaques in adapting to different environments, especially in high altitude extreme environments. Results A total of 50 haplotypes were identified, and significant differences were found in haplotype sequences of rhesus macaque ATP6 gene at different elevations, especially in the high altitude haplotypes with multiple specific variation sites, leading to some region-specific haplotypes. Population genetic analysis showed that rhesus macaque had high genetic diversity ( Pi =0.02332 ± 0.00226, Hd =0.802 ± 0.022 and K =14.982), and there was obvious genetic differentiation among different geographical populations. Conclusions The results showed that the ATP6 gene had undergone adaptive evolution in the process of rhesus macaque adapting to different elevations, especially the high altitude environments. We also found that geographical isolation was an important factor in the genetic differentiation of rhesus macaque. Phylogenetic analysis showed that there were two subspecies of rhesus macaque in western Sichuan, namely, M. m. lasiotus and M. m. vestita , the former distributed in the western Sichuan region of the Yalong River Basin and the Qinghai-Tibet Plateau, while the latter distributed in the Dadu River Basin and northwest Sichuan. We speculated that the Daxueshan Mountains in western Sichuan was a critical geographical barrier for the differentiation of the two subspecies populations.
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- 2020
142. Characterisation of the gut microbial community of rhesus macaques in high-altitude environments
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Qingyong Ni, Yuhan Wu, Mengmeng Dong, Yongfang Yao, Meng Xie, Qin Wang, Anxiang Wen, Jiayun Wu, Guangxiang Zhu, Tianrui Xia, Diyan Li, Huailiang Xu, and Mingwang Zhang
- Subjects
DNA, Bacterial ,Microbiology (medical) ,Gut microbial community ,Rikenellaceae ,Firmicutes ,Population ,Gene Dosage ,Beta diversity ,lcsh:QR1-502 ,Zoology ,Gut flora ,Prevotellaceae ,DNA, Ribosomal ,Microbiology ,lcsh:Microbiology ,Feces ,03 medical and health sciences ,Bacterial Proteins ,RNA, Ribosomal, 16S ,Rhesus macaque ,Animals ,education ,Phylogeny ,030304 developmental biology ,0303 health sciences ,education.field_of_study ,Bacteria ,biology ,030306 microbiology ,Altitude ,High-Throughput Nucleotide Sequencing ,Bacteroidetes ,Biodiversity ,Sequence Analysis, DNA ,biology.organism_classification ,Macaca mulatta ,Gastrointestinal Microbiome ,Alpha diversity ,16S rRNA gene ,High-altitude environment ,Research Article - Abstract
Background The mammal intestinal microbiota is involved in various physiological processes and plays a key role in host environment adaption. However, for non-human primates (NHPs), little is known about their gut microbial community in high-altitude environments and even less about their adaption to such habitats. We characterised the gut microbial community of rhesus macaques from multiple high-altitude environments and compared it to those of low-altitude populations. Results We collected faecal samples of rhesus macaques from four high-altitude populations (above 3000 m) and three low-altitude populations (below 500 m). By calculating the alpha diversity index, we found that high-altitude populations exhibited a higher diversity. Statistical analysis of beta diversity indicated significant differences between high- and low-altitude populations. Significant differences were also detected at the phylum and family levels. At the phylum level, the high-altitude gut microbial community was dominated by Firmicutes (63.42%), while at low altitudes, it was dominated by Bacteroidetes (47.4%). At the family level, the high-altitude population was dominated by Ruminococcaceae (36.2%), while the low-altitude one was dominated by Prevotellaceae (39.6%). Some families, such as Christensenellaceae and Rikenellaceae, were consistently higher abundant in all high-altitude populations. We analysed the overlap of operational taxonomic units (OTUs) in high-altitude populations and determined their core OTUs (shared by all four high-altitude populations). However, when compared with the low-altitude core OTUs, only 65% were shared, suggesting a divergence in core OTUs. Function prediction indicated a significant difference in gene copy number of 35 level-2 pathways between high- and low-altitude populations; 29 of them were higher in high altitudes, especially in membrane transport and carbohydrate metabolism. Conclusions The gut microbial community of high-altitude rhesus macaques was significantly distinct from that of low-altitude populations in terms of diversity, composition and function. High-altitude populations were dominated by Firmicutes and Ruminococcace, while in low-altitude populations, Bacteroidetes and Prevotellaceae were dominant. The difference in gut microbiota between these two populations may be caused by differences in host diet, environmental temperature and oxygen pressure. These differentiated gut microbial microorganisms may play a critical role in the adaptive evolution of rhesus macaques to high-altitude environments.
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- 2020
143. The carnivorous digestive system and bamboo diet of giant pandas may shape their low gut bacterial diversity
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Chengdong Wang, Jingsi Tang, Bo Zeng, Qingyong Ni, Yinfeng Chen, Caiwu Li, Mingwang Zhang, Yan Li, Wei Guo, Xueqin Ni, Ruihong Ning, Ying Li, Hemin Zhang, Desheng Li, and Jiangchao Zhao
- Subjects
Bamboo ,dietary switch ,Physiology ,carnivorous digestive system ,Zoology ,Management, Monitoring, Policy and Law ,Biology ,Gut flora ,digestive system ,Complementary food ,diversity ,PANDAS ,medicine ,Restricted diet ,Carnivore ,Nature and Landscape Conservation ,Herbivore ,Ecological Modeling ,respiratory system ,bamboo diet ,biology.organism_classification ,medicine.disease ,gut microbiotas ,Digestive tract ,human activities ,Research Article - Abstract
The gut microbiota diversity of eight panda cubs was assessed during a dietary switch. Gut microbiota diversity of panda cubs significantly decreased after bamboo consumption. Carnivorous species living on a plant-based diet possess low microbial diversity. Mice were fed a bamboo diet but did not display low gut microbiota diversity. Giant pandas have an exclusive diet of bamboo; however, their gut microbiotas are more similar to carnivores than herbivores in terms of bacterial composition and their functional potential. This is inconsistent with observations that typical herbivores possess highly diverse gut microbiotas. It is unclear why the gut bacterial diversity of giant pandas is so low. Herein, the dynamic variations in the gut microbiota of eight giant panda cubs were measured using 16S rRNA gene paired-end sequencing during a dietary switch. Similar data from red panda (an herbivorous carnivore) and carnivorous species were compared with that of giant pandas. In addition, mice were fed a high-bamboo diet (80% bamboo and 20% rat feed) to determine whether a bamboo diet could lower the gut bacterial diversity in a non-carnivorous digestive tract. The diversity of giant panda gut microbiotas decreased significantly after switching from milk and complementary food to bamboo diet. Carnivorous species living on a plant-based diet, including giant and red pandas, possess a lower microbial diversity than other carnivore species. Mouse gut microbiota diversity significantly increased after adding high-fibre bamboo to their diet. Findings suggest that a very restricted diet (bamboo) within a carnivorous digestive system might be critical for shaping a low gut bacterial diversity in giant pandas., The gut microbiota diversity of eight panda cubs was assessed during a dietary switch. Gut microbiota diversity of panda cubs significantly decreased after bamboo consumption. Carnivorous species living on a plant-based diet possess low microbial diversity. Mice were fed a bamboo diet but did not display low gut microbiota diversity.
- Published
- 2020
144. Dihydromyricetin promotes longevity and activates the transcription factors FOXO and AOP in
- Author
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Xiaolan, Fan, Yao, Zeng, Ziqiang, Fan, Liang, Cui, Wenhao, Song, Qi, Wu, Yue, Gao, Deying, Yang, Xueping, Mao, Bo, Zeng, Mingwang, Zhang, Qingyong, Ni, Yan, Li, Tao, Wang, Diyan, Li, and Mingyao, Yang
- Subjects
Aging ,Flavonols ,Dihydromyricetin ,AKT ,anti-aging ,fungi ,Longevity ,food and beverages ,Forkhead Transcription Factors ,Repressor Proteins ,ERK ,Drosophila melanogaster ,Animals ,Drosophila Proteins ,FOXO ,Eye Proteins ,Research Paper - Abstract
Drugs or compounds have been shown to promote longevity in various approaches. We used Drosophila to explore novel natural compounds can be applied to anti-aging. Here we reported that a flavonoid named Dihydromyricetin can increase stress that tolerance and lipid levels, slow down gut dysfunction and extend Drosophila lifespan. Dihydromyricetin can also lessen pERK and pAKT signaling, consequently activating FOXO and AOP to modulate longevity. Our results suggested that DHM could be used as an effective compound for anti-aging intervention, which could likely be applied to both mammals and humans.
- Published
- 2020
145. The Roles and Mechanisms of lncRNAs in Liver Fibrosis
- Author
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Yan Li, Mingyao Yang, Xiaobin Gu, Zhi He, Xiaolan Fan, Mingwang Zhang, and Deying Yang
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0301 basic medicine ,Liver Cirrhosis ,mechanism ,Review ,Biology ,Catalysis ,Inorganic Chemistry ,Transcriptome ,lcsh:Chemistry ,03 medical and health sciences ,0302 clinical medicine ,Gene expression ,Animals ,Humans ,Physical and Theoretical Chemistry ,Molecular Biology ,lcsh:QH301-705.5 ,Spectroscopy ,liver fibrosis ,MEG3 ,function ,Competing endogenous RNA ,Organic Chemistry ,HOTAIR ,General Medicine ,Computer Science Applications ,030104 developmental biology ,lncrna ,Gene Expression Regulation ,Liver ,lcsh:Biology (General) ,lcsh:QD1-999 ,030220 oncology & carcinogenesis ,Cancer research ,RNA, Long Noncoding ,GAS5 ,Hepatic fibrosis ,HOX Transcript Antisense RNA ,Biomarkers ,Signal Transduction - Abstract
Many studies have revealed that circulating long noncoding RNAs (lncRNAs) regulate gene and protein expression in the process of hepatic fibrosis. Liver fibrosis is a reversible wound healing response followed by excessive extracellular matrix accumulation. In the development of liver fibrosis, some lncRNAs regulate diverse cellular processes by acting as competing endogenous RNAs (ceRNAs) and binding proteins. Previous investigations demonstrated that overexpression of lncRNAs such as H19, maternally expressed gene 3 (MEG3), growth arrest-specific transcript 5 (GAS5), Gm5091, NR_002155.1, and HIF 1alpha-antisense RNA 1 (HIF1A-AS1) can inhibit the progression of liver fibrosis. Furthermore, the upregulation of several lncRNAs [e.g., nuclear paraspeckle assembly transcript 1 (NEAT1), hox transcript antisense RNA (Hotair), and liver-enriched fibrosis-associated lncRNA1 (lnc-LFAR1)] has been reported to promote liver fibrosis. This review will focus on the functions and mechanisms of lncRNAs, the lncRNA transcriptome profile of liver fibrosis, and the main lncRNAs involved in the signalling pathways that regulate hepatic fibrosis. This review provides insight into the screening of therapeutic and diagnostic markers of liver fibrosis.
- Published
- 2020
146. Transcriptome Profiling across Five Tissues of Giant Panda
- Author
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Ming Wei, Bo Zeng, Ying Li, Zhongxian Xu, Diyan Li, Qingyong Ni, Chengdong Wang, Ruihong Ning, Hemin Zhang, Mingzhou Li, Desheng Li, Mingyao Yang, Wu Kai, Mingwang Zhang, Feng Li, and Deng Linhua
- Subjects
Article Subject ,Sequence analysis ,Computational biology ,General Biochemistry, Genetics and Molecular Biology ,Transcriptome ,biology.animal ,Gene expression ,Animals ,Tissue Distribution ,Protein Interaction Maps ,KEGG ,Gene ,Ailuropoda melanoleuca ,Genome ,General Immunology and Microbiology ,biology ,Sequence Analysis, RNA ,Gene Expression Profiling ,High-Throughput Nucleotide Sequencing ,General Medicine ,CD79B ,Gene expression profiling ,Medicine ,Ursidae ,Research Article - Abstract
Gene differential expression studies can serve to explore and understand the laws and characteristics of animal life activities, and the difference in gene expression between different animal tissues has been well demonstrated and studied. However, for the world-famous rare and protected species giant panda (Ailuropoda melanoleuca), only the transcriptome of the blood and spleen has been reported separately. Here, in order to explore the transcriptome differences between the different tissues of the giant panda, transcriptome profiles of the heart, liver, spleen, lung, and kidney from five captive giant pandas were constructed with Illumina HiSeq 2500 platform. The comparative analysis of the intertissue gene expression patterns was carried out based on the generated RNA sequencing datasets. Analyses of Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and protein-protein interaction (PPI) network were performed according to the identified differentially expressed genes (DEGs). We generated 194.52 GB clean base data from twenty-five sequencing libraries and identified 18,701 genes, including 3492 novel genes. With corrected p value 2FoldChange| >2, we finally obtained 921, 553, 574, 457, and 638 tissue-specific DEGs in the heart, liver, spleen, lung, and kidney, respectively. In addition, we identified TTN, CAV3, LDB3, TRDN, and ACTN2 in the heart; FGA, AHSG, and SERPINC1 in the liver; CD19, CD79B, and IL21R in the spleen; NKX2-4 and SFTPB in the lung; GC and HRG in the kidney as hub genes in the PPI network. The results of the analyses showed a similar gene expression pattern between the spleen and lung. This study provided for the first time the heart, liver, lung, and kidney’s transcriptome resources of the giant panda, and it provided a valuable resource for further genetic research or other potential research.
- Published
- 2020
147. MiRNA Profiling in Pectoral Muscle Throughout Pre- to Post-Natal Stages of Chicken Development
- Author
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Qingyong Ni, Yan Wang, Jian Gao, Deying Yang, Shailendra Kumar Mishra, Min Chen, Xiaoling Zhao, Mingwang Zhang, Diyan Li, Bo Zeng, Mingyao Yang, Xiaolan Fan, Huadong Yin, Qing Zhu, Zhongxian Xu, Shaolan Zhang, and Yan Li
- Subjects
0301 basic medicine ,lcsh:QH426-470 ,chicken ,Pectoral muscle ,Regulator ,Biology ,Muscle hypertrophy ,03 medical and health sciences ,0302 clinical medicine ,microRNA ,medicine ,Genetics ,Myocyte ,Genetics (clinical) ,Original Research ,miRNA ,Skeletal muscle ,differentiation ,Phenotype ,In vitro ,Cell biology ,lcsh:Genetics ,030104 developmental biology ,medicine.anatomical_structure ,030220 oncology & carcinogenesis ,Molecular Medicine ,myoblast ,gga-miRNA-454 - Abstract
MicroRNA (miRNA) is known to be an important regulator of muscle growth and development. The regulation of microRNA on the skeletal muscle phenotype of animals is mainly achieved by regulating the proliferation and differentiation of myoblasts. In this study, we sequenced a total of 60 samples from 15 developing stages of the pectoral muscle and five other tissues at 300 days of Tibetan chicken. We characterized the expression patterns of miRNAs across muscle developmental stages, and found that the chicken growth and development stage was divided into early-embryonic and late-embryonic as well as postnatal stages. We identified 81 and 21 DE-miRNAs by comparing the miRNA profiles of pectoral muscle of three broad periods and different tissues, respectively; and 271 miRNAs showed time-course patterns. Their potential targets were predicted and used for functional enrichment to understand their regulatory functions. Significantly, GgmiRNA-454 is a time-dependent and tissue-differential expression miRNA. In order to elucidate the role of gga-miRNA-454 in the differentiation of myoblasts, we cultured chicken myoblasts in vitro. The results show that although gga-miRNA-454-3p initiates increase and thereafter decrease during the chicken myoblasts differentiation, it had no effect on primary myoblasts proliferation. Furthermore, we confirm that gga-miRNA-454 inhibits myoblast differentiation by targeting the myotube-associated protein SBF2.
- Published
- 2020
148. Evolution by Gene Duplication, Recombination and Selection in MHC Class I Genes of Odorrana margaretae
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Huailiang Xu, Fuyao Han, Yongfang Yao, Xiaorong Tan, Mingwang Zhang, and Hu Chen
- Subjects
0301 basic medicine ,Multidisciplinary ,Lineage (genetic) ,biology ,Phylogenetic tree ,MHC Class I Gene ,Odorrana margaretae ,chemical and pharmacologic phenomena ,biology.organism_classification ,Major histocompatibility complex ,03 medical and health sciences ,030104 developmental biology ,Evolutionary biology ,Gene duplication ,MHC class I ,biology.protein ,Synonymous substitution - Abstract
Amphibians have undergone catastrophic declines worldwide and the major histocompatibility complex (MHC) is an attractive candidate for investigating the link between adaptive variation and individual fitness. Nonetheless, little research has been conducted to study the amphibians MHC genes. Thus, MHC class Ia of Odorrana margaretae, a representative species of the Odorrana, was isolated and used to analyze the adaptive mechanism. We isolated alleles and determined evolution patterns of MHC class Ia in O. margaretae. The phylogenetic tree of MHC class Ia was reconstructed to understand the evolutionary relationship of Anura. In O. margaretae of MHC class Ia: there were more non-synonymous mutations compared to synonymous mutations; there are at least two loci; the recombination alleles took place for a large proportion (55.56%) of the alleles and recombination usually took place between whole exon of Ia genes of MHC class; positive selection sites were detected and most (10 of 19) located at the α1 and α2 domains belonged to the presumed ABS. The diversity of genes of MHC class Ia was led by recombination, gene duplication and positive selection. Trans-species polymorphisms of anuran genes of MHC class Ia were evident in anurans. Therefore, the MHC class Ia present demonstrative candidates for investigating the link between adaptive variation and individual fitness. We argue that knowledge of the MHC of other anuran lineage, especially focusing a genus such as O. margaretae, should provide an overall more complete picture of the organization of MHC in anurans.
- Published
- 2018
149. The MHC Class Ia Genes in Chenfu’s Treefrog (Zhangixalus chenfui) Evolved via Gene Duplication, Recombination, and Selection
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Siqi Huang, Qingyong Ni, Ye Jiang, Mishra Sudhanshu, Hu Chen, Huailiang Xu, Mingwang Zhang, Yongfang Yao, and Fuyao Han
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0106 biological sciences ,0301 basic medicine ,chemical and pharmacologic phenomena ,Major histocompatibility complex ,010603 evolutionary biology ,01 natural sciences ,Article ,polymorphism ,03 medical and health sciences ,Molecular evolution ,MHC class I ,Gene duplication ,lcsh:Zoology ,Coding region ,lcsh:QL1-991 ,Gene ,lcsh:Veterinary medicine ,General Veterinary ,biology ,Phylogenetic tree ,molecular evolution ,MHC Class I Gene ,immunogenetics ,030104 developmental biology ,Evolutionary biology ,biology.protein ,lcsh:SF600-1100 ,Animal Science and Zoology ,amphibian ,paralog - Abstract
The molecular mechanisms underlying the evolution of adaptive immunity-related proteins can be deduced by a thorough examination of the major histocompatibility complex (MHC). Currently, in vertebrates, there is a relatively large amount of research on MHCs in mammals and birds. However, research related to amphibian MHC genes and knowledge about the evolutionary patterns is limited. This study aimed to isolate the MHC class I genes from Chenfu&rsquo, s Treefrog (Zhangixalus chenfui) and reveal the underlying evolutionary processes. A total of 23 alleles spanning the coding region of MHC class Ia genes were identified in 13 individual samples. Multiple approaches were used to test and identify recombination from the 23 alleles. Amphibian MHC class Ia alleles, from NCBI, were used to construct the phylogenetic relationships in MEGA. Additionally, the partition strategy was adopted to construct phylogenetic relationships using MrBayes and MEGA. The sites of positive selection were identified by FEL, PAML, and MEME. In Chenfu&rsquo, s Treefrog, we found that: (1) recombination usually takes place between whole exons of MHC class Ia genes, (2) there are at least 3 loci for MHC class Ia, and (3) the diversity of genes in MHC class Ia can be attributed to recombination, gene duplication, and positive selection. We characterized the evolutionary mechanisms underlying MHC class Ia genes in Chenfu&rsquo, s Treefrog, and in so doing, broadened the knowledge of amphibian MHC systems.
- Published
- 2019
150. Gut microbiota of Tibetans and Tibetan pigs varies between high and low altitude environments
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Qingyong Ni, Ping Wang, Mingwang Zhang, Bo Zeng, Ruihong Ning, Ying Li, Huailiang Xu, Yan Li, Siyuan Zhang, Xianqiong Yu, Xiaolan Fan, Fanli Kong, Deying Yang, Mingyao Yang, Jiangchao Zhao, and Diyan Li
- Subjects
Swine ,Acclimatization ,Zoology ,Gut flora ,Carbohydrate metabolism ,Tibet ,Microbiology ,03 medical and health sciences ,Feces ,Asian People ,Animals ,Humans ,030304 developmental biology ,0303 health sciences ,biology ,Sphingobacterium ,Bacteria ,030306 microbiology ,Altitude ,Ribosomal RNA ,Effects of high altitude on humans ,biology.organism_classification ,Macaca mulatta ,Gastrointestinal Microbiome ,Metagenomics ,Metabolome ,Metagenome ,Host adaptation ,Rabbits ,Energy Metabolism ,Metabolic Networks and Pathways - Abstract
This study set out to investigate the relationship between gut microbiota composition and host adaptation to high altitude conditions. Fecal samples from both high and low altitude humans and pigs were studied using multi-omics methods. 16S ribosomal meta-analysis results showed significant differences in bacterial diversity and composition between high and low altitude members of the same species, as well as between different species. Acinetobacter, Pseudomonas, and Sphingobacterium were the three most abundant bacterial genera found in high altitude fecal samples of both humans and pigs. The alpha diversities of microbiota from Chinese people were found to be relatively lower than those of people in other countries. We found significant convergent trends in microbial metagenome compositions between Tibetans and Tibetan pigs living at high altitudes, and significant differences between these and their low-altitude counterparts. Metabolic pathways related to energy metabolism, amino-acid metabolism, and carbohydrate metabolism were consistently enriched at high altitudes, in both Tibetans and Tibetan pigs. Propanoic acid and octadecanoic acid were significantly elevated in high-altitude Tibetan pigs, and genes related to these two metabolites were also up-regulated. Thus, this study revealed that unique gut bacteriomes and their functions may be closely related to environmental host adaptation in high altitude conditions, such as those in the Tibetan plateau.
- Published
- 2019
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