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Sun CC, Zhao WJ, Yue WZ, Cheng H, Sun FL, Wang YT, Wu ML, Engel A, Wang YS. Polymeric carbohydrates utilization separates microbiomes into niches: insights into the diversity of microbial carbohydrate-active enzymes in the inner shelf of the Pearl River Estuary, China. Front Microbiol 2023; 14:1180321. [PMID: 37425997 PMCID: PMC10322874 DOI: 10.3389/fmicb.2023.1180321] [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: 03/06/2023] [Accepted: 05/31/2023] [Indexed: 07/11/2023] Open
Abstract
Polymeric carbohydrates are abundant and their recycling by microbes is a key process of the ocean carbon cycle. A deeper analysis of carbohydrate-active enzymes (CAZymes) can offer a window into the mechanisms of microbial communities to degrade carbohydrates in the ocean. In this study, metagenomic genes encoding microbial CAZymes and sugar transporter systems were predicted to assess the microbial glycan niches and functional potentials of glycan utilization in the inner shelf of the Pearl River Estuary (PRE). The CAZymes gene compositions were significantly different between in free-living (0.2-3 μm, FL) and particle-associated (>3 μm, PA) bacteria of the water column and between water and surface sediments, reflecting glycan niche separation on size fraction and selective degradation in depth. Proteobacteria and Bacteroidota had the highest abundance and glycan niche width of CAZymes genes, respectively. At the genus level, Alteromonas (Gammaproteobacteria) exhibited the greatest abundance and glycan niche width of CAZymes genes and were marked by a high abundance of periplasmic transporter protein TonB and members of the major facilitator superfamily (MFS). The increasing contribution of genes encoding CAZymes and transporters for Alteromonas in bottom water contrasted to surface water and their metabolism are tightly related with particulate carbohydrates (pectin, alginate, starch, lignin-cellulose, chitin, and peptidoglycan) rather than on the utilization of ambient-water DOC. Candidatus Pelagibacter (Alphaproteobacteria) had a narrow glycan niche and was primarily preferred for nitrogen-containing carbohydrates, while their abundant sugar ABC (ATP binding cassette) transporter supported the scavenging mode for carbohydrate assimilation. Planctomycetota, Verrucomicrobiota, and Bacteroidota had similar potential glycan niches in the consumption of the main component of transparent exopolymer particles (sulfated fucose and rhamnose containing polysaccharide and sulfated-N-glycan), developing considerable niche overlap among these taxa. The most abundant CAZymes and transporter genes as well as the widest glycan niche in the abundant bacterial taxa implied their potential key roles on the organic carbon utilization, and the high degree of glycan niches separation and polysaccharide composition importantly influenced bacterial communities in the coastal waters of PRE. These findings expand the current understanding of the organic carbon biotransformation, underlying the size-fractionated glycan niche separation near the estuarine system.
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Affiliation(s)
- Cui-Ci Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, China
| | - Wen-Jie Zhao
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei-Zhong Yue
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Hao Cheng
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Fu-Lin Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, China
| | - Yu-Tu Wang
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, China
| | - Mei-Lin Wu
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Anja Engel
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - You-Shao Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, China
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Fei J, Wang YS, Cheng H, Sun FL, Sun CC. Comparative physiological and proteomic analyses of mangrove plant Kandelia obovata under cold stress. Ecotoxicology 2021; 30:1826-1840. [PMID: 34618290 DOI: 10.1007/s10646-021-02483-6] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
Cold events had broadly affected the survival and geographic distribution of mangrove plants. Kandelia obovata, has an excellent cold tolerance as a true halophyte and widespread mangrove species. In this study, physiological characters and comparative proteomics of leaves of K. obovata were performed under cold treatment. The physiological analysis showed that K. obovata could alleviate its cold-stress injuries through increasing the levels of antioxidants, the activities of related enzymes, as well as osmotic regulation substances (proline). It was detected 184 differentially expressed protein spots, and of 129 (70.11%) spots were identified. These proteins have been involved in several pathways such as the stress and defense, photosynthesis and photorespiration, signal transduction, transcription factors, protein biosynthesis and degradation, molecular chaperones, ATP synthesis, the tricarboxylic acid (TCA) cycle and primary metabolisms. The protein post-translational modification may be a common phenomenon and plays a key role in cold-response process in K. obovata. According to our precious work, a schematic diagram was drawn for the resistance or adaptation strategy of mangrove plants under cold stress. This study provided valuable information to understand the mechanism of cold tolerance of K. obovata.
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Affiliation(s)
- Jiao Fei
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering Chinese Academy of Sciences, Guangzhou, 510301, China
| | - You-Shao Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- Innovation Academy of South China Sea Ecology and Environmental Engineering Chinese Academy of Sciences, Guangzhou, 510301, China.
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, 518121, China.
| | - Hao Cheng
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Fu-Lin Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering Chinese Academy of Sciences, Guangzhou, 510301, China
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, 518121, China
| | - Cui-Ci Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering Chinese Academy of Sciences, Guangzhou, 510301, China
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, 518121, China
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Sun FL, Wang YS, Wu ML, Sun CC, Jiang ZY, Cheng H, Fei J. Bacterial community variations in the South China Sea driven by different chemical conditions. Ecotoxicology 2021; 30:1808-1815. [PMID: 34269924 DOI: 10.1007/s10646-021-02455-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/03/2021] [Indexed: 06/13/2023]
Abstract
In this study, Illumina MiSeq sequencing of the 16 S rRNA gene was used to describe the bacterial communities in the South China Sea (SCS) during the southwest monsoon period. We targeted different regions in the SCS and showed that bacterial community was driven by the effects of the river, upwelling, and mesoscale eddy through changing the environmental factors (salinity, temperature, and nutrients). Distinct bacterial communities were observed among different chemical conditions, especially between the estuary and the open sea. The abundance of Burkholderiales, Frankiales, Flavobacteriales, and Rhodobacterales dominated the estuary and its adjacent waters. Bacteria in cyclonic eddy were dominated by Methylophilales and Pseudomonadales, whereas Prochlorococcus, SAR11 clade, and Oceanospirillales had relatively high abundance in the anticyclonic eddy. Overall, the abundance of specific phylotypes significantly varied among samples with different chemical conditions. Chemical conditions probably act as a driver that shapes and controls the diversity of bacteria in the SCS. This study suggests that the interaction between microbial and environmental conditions needs to be further considered to fully understand the diversity and function of marine microbes.
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Affiliation(s)
- Fu-Lin Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Daya Bay Marine Biology Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shenzhen, 518121, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - You-Shao Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- Daya Bay Marine Biology Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shenzhen, 518121, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China.
| | - Mei-Lin Wu
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Cui-Ci Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Daya Bay Marine Biology Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shenzhen, 518121, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Zhao-Yu Jiang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Hao Cheng
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Jiao Fei
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
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Wu ML, Cheng H, Zhao H, Sun FL, Wang YT, Yin JP, Fei J, Sun CC, Wang YS. Distribution patterns and source identification for heavy metals in Mirs Bay of Hong Kong in China. Ecotoxicology 2020; 29:762-770. [PMID: 32342292 DOI: 10.1007/s10646-020-02211-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/31/2020] [Indexed: 05/12/2023]
Abstract
Sediment quality caused by heavy metals was investigated in the Mirs Bay and Tolo Harbor, Hong Kong, China. Samples were collected in January and July, 2010. One-way analysis of variance showed that sediment quality variables (Fe, Zn, Mn, Pb, V, Cu, Cr, Ba, Ni and As) were significantly different (p < 0.05) among the sampling areas, whereas the average concentration of V, Eh and Ba exhibited the significant seasonal variations (p < 0.05) between January and July. The spatial pattern of heavy metals (Pb, Zn and Cu) can probably be attributed to anthropogenic and tidal flushing influence in the harbor. Both geo-accumulation index (Igeo) and enrichment factor (EF) were used to identify the metal pollution level and its related source. Pb, Zn, and Cu are considered as "polluted metal" in Tolo Harbor. Cluster analysis (CA) identified three distinct clusters with the Tolo Habor and Shatou Jiao, the inner bay and the south part of the bay. Principal component analysis (PCA) identified the spatial patterns and their affected parameters in the studying area. Results showed metals distribution in Mirs Bay and its adjacent area is principally affected by human activities such as marineculture, dumping, located mostly in Tolo Harbor and Shatou Jiao, where was closely related with anthropogenic influence. While the monitoring stations including MS13-MS16 and MS8 locating in the south part of the studying area might be corresponded to natural influence.
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Affiliation(s)
- Mei-Lin Wu
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, 510301, Guangzhou, China
| | - Hao Cheng
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, 510301, Guangzhou, China
| | - Hui Zhao
- College of Chemistry and Environmental Science, Guangdong Ocean University, 524088, Zhanjiang, China
| | - Fu-Lin Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, 510301, Guangzhou, China
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, 518121, Shenzhen, China
| | - Yu-Tu Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, 510301, Guangzhou, China
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, 518121, Shenzhen, China
| | - Jian-Ping Yin
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, 510301, Guangzhou, China
| | - Jiao Fei
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, 510301, Guangzhou, China
| | - Cui-Ci Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, 510301, Guangzhou, China
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, 518121, Shenzhen, China
| | - You-Shao Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301, Guangzhou, China.
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, 510301, Guangzhou, China.
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, 518121, Shenzhen, China.
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5
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Wu ML, Wang YT, Cheng H, Sun FL, Fei J, Sun CC, Yin JP, Zhao H, Wang YS. Phytoplankton community, structure and succession delineated by partial least square regression in Daya Bay, South China Sea. Ecotoxicology 2020; 29:751-761. [PMID: 32189146 DOI: 10.1007/s10646-020-02188-2] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/25/2020] [Indexed: 06/10/2023]
Abstract
Daya Bay is facing the influence of human activities and nature changes, which result in phytoplankton adjusting to the changing environment. The data about environmental changes and phytoplankton were obtained from four seasonal cruises in 2013 in the bay. It is helpful to explore seasonal succession of phytoplankton driven by the determining environmental factors in this bay. Temperature is a significant indicator of season change. The limiting factor of phytoplankton growth totally changed from P (PO4-P) limiting during the southwest monsoon to Si (SiO3-Si) limiting during northeast monsoon. The order of diatoms and dinoflagellates was the dominant phytoplankton groups in Daya Bay. The dominant species included chain-forming diatoms (Skeletonema, Pseudo-nitzschia, Thalassionema, Chaetoceros and Rhizosolenia) were found all the year round and filamentous cyanobacteria (Trichodesmium) in spring and autumn. Partial least square regression (PLS) found that salinity, temperature and nutrients were important driving force for phytoplankton seasonal succession.
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Affiliation(s)
- Mei-Lin Wu
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Yu-Tu Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, 518121, China
| | - Hao Cheng
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Fu-Lin Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, 518121, China
| | - Jiao Fei
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Cui-Ci Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, 518121, China
| | - Jian-Ping Yin
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Hui Zhao
- College of Chemistry and Environmental Science, Guangdong Ocean University, Zhanjiang, 524088, China
| | - You-Shao Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China.
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, 518121, China.
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Cheng H, Wu ML, Li CD, Sun FL, Sun CC, Wang YS. Dynamics of radial oxygen loss in mangroves subjected to waterlogging. Ecotoxicology 2020; 29:684-690. [PMID: 32394359 DOI: 10.1007/s10646-020-02221-4] [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] [Accepted: 04/25/2020] [Indexed: 06/11/2023]
Abstract
Tidal flooding can directly result in oxygen (O2) shortage, however the functions of root aeration in flooding tolerance and O2 dynamics within mangroves are still poorly understood. Thus, in this study, the correlations among waterlogging tolerance, root porosity and O2 movement within the plants were investigated using two mangrove species (Aegiceras corniculatum and Bruguiera gymnorrhiza) and a semi-mangrove Heritiera littoralis. Based on the present data, the species A. corniculatum and B. gymnorrhiza, which possessed higher root porosity, exhibited higher waterlogging tolerance, while H. littoralis is intolerant. Increased root porosity, leaf stoma, and total ROL were observed in the roots of A. corniculatum and B. gymnorrhiza growing in stagnant solution when compared to respective aerated controls. As for ROL spatial pattern along roots, external anaerobic condition could promote ROL from apical root regions but reduce ROL from basal roots, leading to a 'tighter barrier'. In summary, the present study indicated that the plants (e.g., A. corniculatum and B. gymnorrhiza) prioritized to ensure O2 diffusion towards root tips under waterlogging by increasing aerenchyma formation and reducing O2 leakage at basal root regions.
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Affiliation(s)
- Hao Cheng
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, 518121, China
| | - Mei-Lin Wu
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, 518121, China
| | - Chang-Da Li
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Fu-Lin Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, 518121, China
- Marine and fisheries Development Research Center, Dongtou District, Wenzhou, 325009, China
| | - Cui-Ci Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, 518121, China
- Marine and fisheries Development Research Center, Dongtou District, Wenzhou, 325009, China
| | - You-Shao Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, 518121, China.
- Marine and fisheries Development Research Center, Dongtou District, Wenzhou, 325009, China.
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Sun FL, Fan LL, Wang YS, Huang LY. Metagenomic analysis of the inhibitory effect of chromium on microbial communities and removal efficiency in A 2O sludge. J Hazard Mater 2019; 368:523-529. [PMID: 30710781 DOI: 10.1016/j.jhazmat.2019.01.076] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 07/16/2018] [Revised: 01/21/2019] [Accepted: 01/22/2019] [Indexed: 06/09/2023]
Abstract
This is the first study exploring the effects of persistent Cr(VI) treatment on microbial communities and function as well as the process efficiency of an A2O system. The inhibitory effect was clearly higher at a high Cr(VI) concentration than a low Cr(VI) concentration, and different Cr(VI) concentrations had distinct effects on the microbial communities as well as on the performance efficiency of the system. Functional annotation analysis indicated that Cr(VI) stress inhibited most of the metabolic pathway and functional genes of the microbial communities, especially those involved in the denitrification pathway. Network analysis was used to investigate the co-occurrence patterns between denitrification genes and microbial taxa; the results indicated that microorganisms with functional genes had high diversity and were adversely affected by Cr(VI) exposure. This study is the first to establish a relationship between Cr(VI) stress and microbial communities and function as well as to determine the underlying mechanisms and roles of Cr(VI) in A2O sludge.
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Affiliation(s)
- Fu-Lin Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen 518000, China.
| | - Lei-Lei Fan
- Department of Resources and Environment, Zunyi Normal College, Zunyi 563002, China
| | - You-Shao Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen 518000, China
| | - Li-Yan Huang
- Hebei Zhengrun Environmental Technology Co. Ltd, Shijiazhuang 050000, China
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Zheng S, Sun FL, Zhang HJ, Shi WZ, Ma JH. [Current applications of artificial intelligence in tumor histopathology]. Zhonghua Zhong Liu Za Zhi 2018; 40:885-889. [PMID: 30605976 DOI: 10.3760/cma.j.issn.0253-3766.2018.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The tasks of artificial intelligence (AI) in tumor histopathology include image segmentation and classification. Currently, the specific contents including lymph node metastasis, pathological classification, grade and prognostic evaluation of malignant diseases, such as breast cancer, lung cancer and prostate cancer, have been studied by AI. Evaluation of sentinel lymph node metastasis of breast cancer has been the most mature application of AI technology, whose level can be analogous to the excellent pathologists. In the future, with the close cooperation of pathologists and engineers, the research of AI will be focus on improving the technology of simple and repetitive clinical diagnosis and differential diagnosis, such as the diagnosis of sentinel lymph node metastasis of breast cancer from biopsy frozen section and the judgment of incisal margin. Ultimately, AI will help us to precisely diagnose the tumor.
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Affiliation(s)
- S Zheng
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - F L Sun
- Digital China Health Technologies Corporation, Beijing 100080, China
| | - H J Zhang
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - W Z Shi
- Digital China Health Technologies Corporation, Beijing 100080, China
| | - J H Ma
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
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Wu ML, Wang YS, Wang YT, Sun FL, Sun CC, Cheng H, Dong JD. Seasonal and spatial variations of water quality and trophic status in Daya Bay, South China Sea. Mar Pollut Bull 2016; 112:341-348. [PMID: 27491363 DOI: 10.1016/j.marpolbul.2016.07.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 04/06/2016] [Revised: 07/11/2016] [Accepted: 07/26/2016] [Indexed: 06/06/2023]
Abstract
Coastal water quality and trophic status are subject to intensive environmental stress induced by human activities and climate change. Quarterly cruises were conducted to identify environmental characteristics in Daya Bay in 2013. Water quality is spatially and temporally dynamic in the bay. Cluster analysis (CA) groups 12 monitoring stations into two clusters. Cluster I consists of stations (S1, S2, S4-S7, S9, and S12) located in the central, eastern, and southern parts of the bay, representing less polluted regions. Cluster II includes stations (S3, S8, S10, and S11) located in the western and northern parts of the bay, indicating the highly polluted regions receiving a high amount of wastewater and freshwater discharge. Principal component analysis (PCA) identified that water quality experience seasonal change (summer, winter, and spring-autumn seasons) because of two monsoons in the study area. Eutrophication in the bay is graded as high by Assessment of Estuarine Trophic Status (ASSETS).
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Affiliation(s)
- Mei-Lin Wu
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, People's Republic of China; Key Laboratory of Marine Bio-resources Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, People's Republic of China.
| | - You-Shao Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, People's Republic of China; Marine Biology Research Station at Daya Bay, Chinese Academy of Sciences, Shenzhen 518121, People's Republic of China; Key Laboratory of Marine Bio-resources Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, People's Republic of China
| | - Yu-Tu Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, People's Republic of China; Marine Biology Research Station at Daya Bay, Chinese Academy of Sciences, Shenzhen 518121, People's Republic of China; Key Laboratory of Marine Bio-resources Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, People's Republic of China
| | - Fu-Lin Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, People's Republic of China; Marine Biology Research Station at Daya Bay, Chinese Academy of Sciences, Shenzhen 518121, People's Republic of China; Key Laboratory of Marine Bio-resources Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, People's Republic of China
| | - Cui-Ci Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, People's Republic of China; Marine Biology Research Station at Daya Bay, Chinese Academy of Sciences, Shenzhen 518121, People's Republic of China; Key Laboratory of Marine Bio-resources Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, People's Republic of China
| | - Hao Cheng
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, People's Republic of China; Key Laboratory of Marine Bio-resources Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, People's Republic of China
| | - Jun-De Dong
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, People's Republic of China; Key Laboratory of Marine Bio-resources Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, People's Republic of China
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10
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Sun FL, Fan LL, Xie GJ. Effect of copper on the performance and bacterial communities of activated sludge using Illumina MiSeq platforms. Chemosphere 2016; 156:212-219. [PMID: 27179238 DOI: 10.1016/j.chemosphere.2016.04.117] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [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: 06/12/2015] [Revised: 04/26/2016] [Accepted: 04/27/2016] [Indexed: 06/05/2023]
Abstract
The anaerobic-anoxic-aerobic (A2O) process is a highly efficient sewage treatment method, which uses complex bacterial communities. However, the effect of copper on this process and the bacterial communities involved remains unknown. In this study, a systematic investigation of the effect of persistent exposure of copper in the A2O wastewater treatment system was performed. An A2O device was designed to examine the effect of copper on the removal efficiency and microbial community compositions of activated sludge that was continuously treated with 10, 20, and 40 mg L(-1) copper, respectively. Surprisingly, a decrease in chemical oxygen demand (COD) and ammonia nitrogen (NH4N) removal efficiency was observed, and the toxicity of high copper concentration was significantly greater at 7d than at 1d. Proteobacteria, Bacteroidetes, Acidobacteria, Chlorobi, and Nitrospirae were the dominant bacterial taxa in the A2O system, and significant changes in microbial community were observed during the exposure period. Most of the dominant bacterial groups were easily susceptible to copper toxicity and diversely changed at different copper concentrations. However, not all the bacterial taxa were inhibited by copper treatment. At high copper concentration, many bacterial species were stimulated and their abundance increased. Cluster analysis and principal coordinate analysis (PCoA) based on operational taxonomic units (OTUs) revealed clear differences in the bacterial communities among the samples. These findings indicated that copper severely affected the performance and key microbial populations in the A2O system as well as disturbed the stability of the bacterial communities in the system, thus decreasing the removal efficiency.
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Affiliation(s)
- Fu-Lin Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Daya Bay Marine Biology Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shenzhen 518121, China.
| | - Lei-Lei Fan
- Department of Resources and Environment, Zunyi Normal College, Zunyi 563002, China
| | - Guang-Jian Xie
- Department of Environmental Engineering, Guangdong Industry Technical College, Guangzhou 510301, China
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11
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Sun FL, Wang YS, Wu ML, Sun CC, Cheng H. Spatial and vertical distribution of bacterial community in the northern South China Sea. Ecotoxicology 2015; 24:1478-1485. [PMID: 25956981 DOI: 10.1007/s10646-015-1472-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/28/2015] [Indexed: 06/04/2023]
Abstract
Microbial communities are highly diverse in coastal oceans and response rapidly with changing environments. Learning about this will help us understand the ecology of microbial populations in marine ecosystems. This study aimed to assess the spatial and vertical distributions of the bacterial community in the northern South China Sea. Multi-dimensional scaling analyses revealed structural differences of the bacterial community among sampling sites and vertical depth. Result also indicated that bacterial community in most sites had higher diversity in 0-75 m depths than those in 100-200 m depths. Bacterial community of samples was positively correlation with salinity and depth, whereas was negatively correlation with temperature. Proteobacteria and Cyanobacteria were the dominant groups, which accounted for the majority of sequences. The α-Proteobacteria was highly diverse, and sequences belonged to Rhodobacterales bacteria were dominant in all characterized sequences. The current data indicate that the Rhodobacterales bacteria, especially Roseobacter clade are the diverse group in the tropical waters.
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Affiliation(s)
- Fu-Lin Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Daya Bay Marine Biology Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shenzhen, 518121, China
| | - You-Shao Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- Daya Bay Marine Biology Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shenzhen, 518121, China.
| | - Mei-Lin Wu
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Cui-Ci Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Daya Bay Marine Biology Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shenzhen, 518121, China
| | - Hao Cheng
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
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12
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Cheng H, Jiang ZY, Liu Y, Ye ZH, Wu ML, Sun CC, Sun FL, Fei J, Wang YS. Metal (Pb, Zn and Cu) uptake and tolerance by mangroves in relation to root anatomy and lignification/suberization. Tree Physiol 2014; 34:646-656. [PMID: 24965807 DOI: 10.1093/treephys/tpu042] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Metal pollution has been widely reported in mangrove wetlands; however, the mechanisms involved in metal detoxification by mangroves are still poorly understood. This study aimed to investigate the possible function of root anatomy and lignification/suberization on metal uptake and tolerance in seedlings of six species of mangroves. The results revealed that the three rhizophoraceous species (Bruguiera gymnorrhiza (L.) Poir, Kandelia obovata Sheue, Liu & Yong and Rhizophora stylosa Griff) consistently exhibited higher metal tolerances than the three pioneer species (Aegiceras corniculatum (Linn.) Blanco, Acanthus ilicifolius L. and Avicennia marina (Forsk.) Viern.). Moreover, metal-tolerant species often exhibited a thick exodermis with high lignification and suberization. The tolerance indices of the mangroves were found to be positively correlated with the amounts of lignin and suberin deposition within the exodermal cell walls. The observed metal uptake by the excised roots further illustrated that a lignified/suberized exodermis directly delayed the entry of metals into the roots, and thereby contributed to a higher tolerance to heavy metals. In summary, the present study proposes a barrier property of the lignified/suberized exodermis in dealing with the stresses of heavy metals, such that the mangroves which possessed more extensive lignification/suberization within the exodermis appeared to exhibit higher metal tolerance.
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Affiliation(s)
- Hao Cheng
- State Key Laboratory of Tropical Oceanography and Daya Bay Marine Biology Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Zhao-Yu Jiang
- State Key Laboratory of Tropical Oceanography and Daya Bay Marine Biology Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Yong Liu
- Key Laboratory for Exploitation & Utilization of Marine Fisheries Resource in South China Sea, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Zhi-Hong Ye
- State Key Laboratory for Bio-control, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Mei-Lin Wu
- State Key Laboratory of Tropical Oceanography and Daya Bay Marine Biology Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Cui-Ci Sun
- State Key Laboratory of Tropical Oceanography and Daya Bay Marine Biology Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Fu-Lin Sun
- State Key Laboratory of Tropical Oceanography and Daya Bay Marine Biology Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Jiao Fei
- State Key Laboratory of Tropical Oceanography and Daya Bay Marine Biology Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - You-Shao Wang
- State Key Laboratory of Tropical Oceanography and Daya Bay Marine Biology Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
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13
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Zhang XZ, Xie JJ, Sun FL. Effects of Three Polycyclic Aromatic Hydrocarbons on Sediment Bacterial Community. Curr Microbiol 2014; 68:756-62. [DOI: 10.1007/s00284-014-0535-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Accepted: 12/17/2013] [Indexed: 10/25/2022]
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14
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Wu P, Wang YS, Sun FL, Wu ML, Peng YL. Bacterial polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenases in the sediments from the Pearl River estuary, China. Appl Microbiol Biotechnol 2013; 98:875-84. [PMID: 23558584 DOI: 10.1007/s00253-013-4854-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 03/10/2013] [Accepted: 03/11/2013] [Indexed: 11/24/2022]
Abstract
Bacterial community compositions were characterized using denaturing gradient gel electrophoresis analysis of bacterial 16S rRNA gene in the sediments of the Pearl River estuary. Sequencing analyses of the excised bands indicated that Gram-negative bacteria, especially Gammaproteobacteria, were dominant in the Pearl River estuary. The diversity of polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase (PAH-RHD) gene in this estuary was then assessed by clone library analysis. The phylogenetic analyses showed that all PAH-RHD gene sequences of Gram-negative bacteria (PAH-RHD[GN]) were closely related to the nagAc gene described for Ralstonia sp. U2 or nahAc gene for Pseudomonas sp. 9816-4, while the PAH-RHD gene sequences of Gram-positive bacteria (PAH-RHD[GP]) at sampling site A1 showed high sequence similarity to the nidA gene from Mycobacterium species. Meanwhile, molecular diversity of the two functional genes was higher at the upstream of this region, while lower at the downstream. Redundancy analysis indicated that environmental factors, such as NH₄--N, ∑PAHs, pH, SiO₃--Si, and water depth, affected the distribution of the PAH-RHD[GN] gene in the Pearl River estuary.
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Affiliation(s)
- Peng Wu
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
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15
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Sun FL, Wang YS, Sun CC, Peng YL, Deng C. Effects of three different PAHs on nitrogen-fixing bacterial diversity in mangrove sediment. Ecotoxicology 2012; 21:1651-1660. [PMID: 22699412 DOI: 10.1007/s10646-012-0946-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/24/2012] [Indexed: 06/01/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are of great environmental and human health concerns due to their widespread occurrence, persistence and carcinogenic properties. There is now compelling evidence that the mangrove sediment microbial structure is susceptible to PAHs contamination. The study aimed to assess the effects of PAHs on the nitrogen-fixing bacterial community of mangrove sediment. Three types of PAHs, naphthalene (NAP), a two-ring PAH; fluorene (FLU), a three-ring PAH; and pyrene (PYR), a four-ring PAH; were applied at three doses. After 7 and 24 days of incubation, the nitrogen-fixing bacterial population and diversity were evidenced in the nifH gene polymerase chain reaction denaturing gradient gel electrophoresis profile. DGGE pattern shows that the nitrogen-fixing bacterial community changed significantly with the types and doses of PAHs, and the incubation time. As far as single PAH is concerned, high concentration of PAH has larger impact on the nitrogen-fixing bacteria than low concentration of PAH. Besides, among the three types of PAHs, NAP has the greatest short term toxicity; PYR has the strongest long-term impact, whereas FLU has relatively higher long-time effect. Multidimensional scaling analysis and correspondence analysis are two reliable multivariate analysis methods for investigating the relationship between the nitrogen-fixing bacterial community and PAHs contamination. Investigating the effect of PAHs on the nitrogen-fixing bacterial diversity could yield useful information for understanding the process of biogeochemical cycling of nitrogen in mangrove sediment. The present study reveals that nitrogen-fixing bacterial community can be used as an important parameter indicating the impact of PAHs on mangrove sediment ecosystem.
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Affiliation(s)
- Fu-Lin Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
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16
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Ling J, Dong JD, Wang YS, Zhang YY, Deng C, Lin L, Wu ML, Sun FL. Spatial variation of bacterial community structure of the Northern South China Sea in relation to water chemistry. Ecotoxicology 2012; 21:1669-1679. [PMID: 22707093 DOI: 10.1007/s10646-012-0941-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/24/2012] [Indexed: 06/01/2023]
Abstract
Spatial distribution, diversity and composition of bacterial communities of the northern South China Sea (SCS) surface water and the relationship with the in situ environmental chemistry were investigated. Polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) was used to investigate the bacterial community structure. The DGGE gel showed that each sample harbored a distinct bacterial community structure and spatial variations of bacterial community composition among all samples were obviously. A total of 17 intensive bands were excised and the sequence analysis of these DGGE bands revealed that Proteobacteria were the dominant bacterial group of surface water in the north part of SCS. Results of the taxonomic analysis showed that the communities consisted of Proteobacteria (α-subdivision, β-subdivision, γ-subdivision), Actinobacteria, Cyanobacteria, Bacteroidetes and Firmicutes. Unweighted pair group method with arithmetic averages clustering of the sampling stations indicated that all stations were classified mainly based on geographical proximity. Canonical correspondence analysis (CCA) was employed to further investigate the relationships between DGGE band pattern and the environmental variables and the first two CCA ordination axes suggested that the structure of the bacterial community was significantly correlated with the variables of nitrate (F = 1.24, P < 0.05).
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Affiliation(s)
- Juan Ling
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
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17
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Hu YS, Li CX, Sun FL, Wu K, Jia XC. [Improved culturability of soil bacteria using proper combination with various culturing medium]. Wei Sheng Wu Xue Bao 2007; 47:882-887. [PMID: 18062267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
To isolate more unique and previously unrecognized bacteria in soil samples, the culture difference under three incubation modes was investigated by using trophic, low-nutrient broth and soil extract as growth medium. Plate count proved that the oligotrophic medium resulted in a slow growth and consecutive colony formation over the course of incubation. On the 5th day, the most number of colony-forming unit was found on trophic LB and low-nutrient R2A, which was approximate 5 times as many as that isolated on 0.1 x LB. Of the 7 media, LB broth harvested the maximum bacterial communities, and novel species could be isolated as the nutrient was diluted to appropriate extent. The DGGE patterns of oligotrophic and rich nutrient culture collection displayed low similarity, however, the bands at various lanes exhibited complementary effect. When cultivated with static flask, LB and R2A media obtained more bacterial species, which concluded most species isolated by the other five media. Under the test tube incubation mode, the most species was also found in LB medium except some appeared only on R2A and TSB. Apparent bacterial communities difference could be detected between R2A, LB and TSB media. The experiment data may contribute much to the special medium design as well as improvement of bacterial culturability by using proper medium.
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Affiliation(s)
- Yuan-Sen Hu
- College of bioengineering, Henan University of Technology, Zhengzhou 450052, China.
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18
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Abstract
We have used line HS-2 of Drosophila melanogaster, carrying a silenced transgene in the pericentric heterochromatin, to investigate in detail the chromatin structure imposed by this environment. Digestion of the chromatin with micrococcal nuclease (MNase) shows a nucleosome array with extensive long-range order, indicating regular spacing, and with well-defined MNase cleavage fragments, indicating a smaller MNase target in the linker region. The repeating unit is ca. 10 bp larger than that observed for bulk Drosophila chromatin. The silenced transgene shows both a loss of DNase I-hypersensitive sites and decreased sensitivity to DNase I digestion within an array of nucleosomes lacking such sites; within such an array, sensitivity to digestion by MNase is unchanged. The ordered nucleosome array extends across the regulatory region of the transgene, a shift that could explain the loss of transgene expression in heterochromatin. Highly regular nucleosome arrays are observed over several endogenous heterochromatic sequences, indicating that this is a general feature of heterochromatin. However, genes normally active within heterochromatin (rolled and light) do not show this pattern, suggesting that the altered chromatin structure observed is associated with regions that are silent, rather than being a property of the domain as a whole. The results indicate that long-range nucleosomal ordering is linked with the heterochromatic packaging that imposes gene silencing.
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Affiliation(s)
- F L Sun
- Department of Biology, Washington University, St. Louis, Missouri 63130, USA
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19
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Sun FL, Cuaycong MH, Craig CA, Wallrath LL, Locke J, Elgin SC. The fourth chromosome of Drosophila melanogaster: interspersed euchromatic and heterochromatic domains. Proc Natl Acad Sci U S A 2000; 97:5340-5. [PMID: 10779561 PMCID: PMC25830 DOI: 10.1073/pnas.090530797] [Citation(s) in RCA: 112] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/1999] [Indexed: 11/18/2022] Open
Abstract
The small fourth chromosome of Drosophila melanogaster (3.5% of the genome) presents a puzzle. Cytological analysis suggests that the bulk of the fourth, including the portion that appears banded in the polytene chromosomes, is heterochromatic; the banded region includes blocks of middle repetitious DNA associated with heterochromatin protein 1 (HP1). However, genetic screens indicate 50-75 genes in this region, a density similar to that in other euchromatic portions of the genome. Using a P element containing an hsp70-white gene and a copy of hsp26 (marked with a fragment of plant DNA designated pt), we have identified domains that allow for full expression of the white marker (R domains), and others that induce a variegating phenotype (V domains). In the former case, the hsp26-pt gene shows an accessibility and heat-shock-inducible activity similar to that seen in euchromatin, whereas in the latter case, accessibility and inducible expression are reduced to levels typical of heterochromatin. Mapping by in situ hybridization and by hybridization of flanking DNA sequences to a collection of cosmid and bacterial artificial chromosome clones shows that the R domains (euchromatin-like) and V domains (heterochromatin-like) are interspersed. Examination of the effect of genetic modifiers on the variegating transgenes shows some differences among these domains. The results suggest that heterochromatic and euchromatic domains are interspersed and closely associated within this 1.2-megabase region of the genome.
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Affiliation(s)
- F L Sun
- Department of Biology, Washington University, St. Louis, MO 63130, USA
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20
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Affiliation(s)
- F L Sun
- Department of Biology, Washington University, St. Louis, Missouri 63130, USA
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21
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Ji QS, Ermini S, Baulida J, Sun FL, Carpenter G. Epidermal growth factor signaling and mitogenesis in Plcg1 null mouse embryonic fibroblasts. Mol Biol Cell 1998; 9:749-57. [PMID: 9529375 PMCID: PMC25303 DOI: 10.1091/mbc.9.4.749] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/1997] [Accepted: 01/14/1998] [Indexed: 02/07/2023] Open
Abstract
Gene targeting techniques and early mouse embryos have been used to produce immortalized fibroblasts genetically deficient in phospholipase C (PLC)-gamma1, a ubiquitous tyrosine kinase substrate. Plcg1(-/-) embryos die at embryonic day 9; however, cells derived from these embryos proliferate as well as cells from Plcg1(+/+) embryos. The null cells do grow to a higher saturation density in serum-containing media, as their capacity to spread out is decreased compared with that of wild-type cells. In terms of epidermal growth factor receptor activation and internalization, or growth factor induction of mitogen-activated protein kinase, c-fos, or DNA synthesis in quiescent cells, PLcg1(-/-) cells respond equivalently to PLcg1(+/+) cells. Also, null cells are able to migrate effectively in a wounded monolayer. Therefore, immortalized fibroblasts do not require PLC-gamma1 for many responses to growth factors.
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Affiliation(s)
- Q S Ji
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
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22
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Abstract
The gene IGF2, which encodes a fetal insulin-like growth factor, is imprinted, so only one of two parental copies of the gene is expressed. The altered expression of IGF2 has been implicated in Beckwith-Wiedemann syndrome, a human fetal overgrowth syndrome, which is characterized by overgrowth of several organs and an increased risk of developing childhood tumours. We have introduced Igf2 transgenes into the mouse genome by using embryonic stem cells, which leads to transactivation of the endogenous Igf2 gene. The consequent overexpression of Igf2 results in most of the symptoms of Beckwith-Wiedemann syndrome, including prenatal overgrowth, polyhydramnios, fetal and neonatal lethality, disproportionate organ overgrowth including tongue enlargement, and skeletal abnormalities. These phenotypes establish Igf2 overexpression as a key determinant of Beckwith-Wiedemann syndrome.
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Affiliation(s)
- F L Sun
- Laboratory of Developmental Genetics and Imprinting, Department of Development and Genetics, The Babraham Institute, Cambridge, UK
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23
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Sun FL, Li DM, Li GY. [Influence of different combination of mental activity and respiratory cycle on heart rate variability]. Zhongguo Zhong Xi Yi Jie He Za Zhi 1996; 16:153-5. [PMID: 9208537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
By means of spectral analysis of P-R interval, different characteristics of heart rate variability in different form of respiratory exercise was observed. The results of observation on 32 volunteers showed that mental activity that affected respiration can influence the function of autonomic nerve system in a different way. When the mind was concentrated at the inspiration, the function of autonomic nerve system was kept in balance, and both the sympathetic and the vagal activities enhanced significantly and while mind concentrated at the expiration could induce a reduction of vagal activity so as to produce marked change in the sympathovagal balance.
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Affiliation(s)
- F L Sun
- Xiyuan Hospital, China Academy of TCM, Beijing
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24
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Reik W, Bowden L, Constancia M, Dean W, Feil R, Forné T, Kelsey G, Maher E, Moore T, Sun FL, Walter J. Regulation of Igf2 imprinting in development and disease. Int J Dev Biol 1996; Suppl 1:53S-54S. [PMID: 9087693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- W Reik
- Laboratory of Developmental Genetics and Imprinting, Babraham Institute, Cambridge
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25
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Chen K, Chen KJ, Sun FL. [Effects of an ever-young pill on decreased intelligence and symptoms associated with aging]. Zhong Xi Yi Jie He Za Zhi 1989; 9:398-401, 387-8. [PMID: 2791157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A test was carried out to evaluate the effect of Ever-Young Pill (EYP) on decreased fluid intelligence and symptoms associated with aging. Nootropil and placebo were used as control drugs. Random, single-blind and self-control observation methods were applied. 90 days were spent for the clinical study. 154 older persons were divided into three groups (EYP 63, nootropil 60, placebo 31). The method of measuring intelligence was talking between man and computer. The computerized program was worked out by our department. The measure included eight parameters. A semi-quantitative method was used to evaluate the symptoms of aging. The main results were as follows: In the group of EYP, there were significant differences (P less than 0.01) in speed of calculation (SC, 5.92 +/- 2.5, 5.1 +/- 2.1), speed of digits and pictures (SDP, 24.2 +/- 6.2, 21.7 +/- 6.7), two digits span (2.8 +/- 1.0, 3.2 +/- 0.8) and other two parameters before and after treatment. In the group of nootropil, SDP and SC were also improved significantly. In the normal control's there was not any evident change. In the early declined health group treated with EYP and nootropil separately, four parameters were improved in each group. The best effect of EYP obtained was on Kidney Yang deficiency and Kidney and Heart Qi Yang deficiency Syndromes. In other syndromes, the results were less satisfactory. By using EYP for treating symptoms of aging the total effective rate was 96.8%, nootropil 71.7% and placebo 44.2%. There were noticeable differences in three groups. Those results suggested that EYP was one of the effective therapies for decreased fluid intelligence with aging.
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Sun FL, Lei SP. [Clinical method of evaluating declined intelligence with aging and its application in traditional Chinese medicine research]. Zhong Xi Yi Jie He Za Zhi 1989; 9:203-6, 195. [PMID: 2758514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A practical program edited by BASIC was used in this test. The test included 7 indexes of fluid intelligence by using the method of talking between man and computer: speed of mental mathematic, digit-symbol, choice reaction time, counting visual number span, tracing reaction and recognition of meaningless figures. Through the principal component analysis and multiple stepwise regression techniques, the authors found out the mathematical model of the intelligence aging from 506 normal subjects and established a measuring system for the declined fluid intelligence and physiological age could be measured with the system. The correlation of the repetition of the test was 0.9528. This method was suitable for mental workers of 46-75 years old. The measured accuracy among the subjects of 50-70 years old was higher. The method was applied practically in clinical evaluation of the effects of traditional herbal medicines and Qigong on fluid intelligence with aging. Through the analysis of validity and reliability, it was proved that this method was suitable for geriatric research.
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Chen YQ, Chen KJ, Sun FL. [Power spectral analysis of heart rate in qi deficiency and both qi and yin deficiency in patients with coronary heart disease]. Zhong Xi Yi Jie He Za Zhi 1989; 9:76-8, 67. [PMID: 2736691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Qi deficiency (QD) and both Qi and Yin deficiency (QYD) are most common in TCM classification of CHD patients with insufficiency syndrome. The authors used the power spectrum of spontaneous heart rate fluctuation (PSHF) to analyze the function of cardiac regulation in 30 QD patients and 27 QYD patients with CHD and compare with the control group of 30 cases for discussing the association between different TCM syndrome patterns and the function of cardiac nerve regulation. The main results were as follows: (1) Low-frequency areas of PSHF in QYD (34.15 +/- 11.60%) were significantly higher than those in QD group (26.24 +/- 11.57%) and the control group (27.80 +/- 11.65%). The L/H ratio in QYD (1.78 +/- 0.96) was significantly higher than those in QD (0.91 +/- 0.64) and the control group (0.98 +/- 0.58). The changes of PSHF in QYD could have some relations with the increasing of the activity of sympathetic nervous system. (2) The change in body posture was used as a load test to study cardiovascular regulation in different TCM patterns of insufficiency syndrome with CHD. In control group the L/H ratio increased with the change of body posture from 0.98 +/- 0.58 to 4.29 +/- 0.89 (P less than 0.001), while in QD group and QYD group increased from 0.91 +/- 0.64 to 1.67 +/- 0.83 (P less than 0.05) and 1.78 +/- 0.96 to 1.85 +/- 0.87 (P greater than 0.2) respectively. The results suggested that cardiovascular baroreceptor reflex was decreased in CHD patients, and QYD group was inferior to DQ group.
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Sun FL, Lin DM. [An animal model for a heart deficiency syndrome induced by sleep deprivation]. Zhong Xi Yi Jie He Za Zhi 1987; 7:35-7, 6. [PMID: 3594711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Sun FL. [A new insect virus of Pieris rapae. III. Nucleic acid properties of the virus]. Wei Sheng Wu Xue Bao 1986; 26:188-90. [PMID: 3751017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Li DM, Sun FL, Ning LL. [Effects of anisodine on EEG power spectrum, frequency distribution and coherence in rats]. Zhongguo Yao Li Xue Bao 1985; 6:225-7. [PMID: 2945358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Wang JZ, Sun FL, Han HW, Zhang BH, Yuan JS, Ma L. [Effect of total flavones of Sophora flavescens root on arrhythmia of cultured rat heart cells]. Zhongguo Yao Li Xue Bao 1983; 4:32-5. [PMID: 6223495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Han HW, Wang JZ, Sun FL. [Effect of dl-demethylcoclaurine on cultured rat heart cells (author's transl)]. Zhongguo Yao Li Xue Bao 1981; 2:111-4. [PMID: 6278830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Sun FL. [A simple method for recording beats of cultured myocardial cell (author's transl)]. Sheng Li Ke Xue Jin Zhan 1981; 12:90-2. [PMID: 7031890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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