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The Annotation of Zebrafish Enhancer Trap Lines Generated with PB Transposon. Curr Issues Mol Biol 2022; 44:2614-2621. [PMID: 35735619 PMCID: PMC9221761 DOI: 10.3390/cimb44060178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 11/16/2022] Open
Abstract
An enhancer trap (ET) mediated by a transposon is an effective method for functional gene research. Here, an ET system based on a PB transposon that carries a mini Krt4 promoter (the keratin4 minimal promoter from zebrafish) and the green fluorescent protein gene (GFP) has been used to produce zebrafish ET lines. One enhancer trap line with eye-specific expression GFP named EYE was used to identify the trapped enhancers and genes. Firstly, GFP showed a temporal and spatial expression pattern with whole-embryo expression at 6, 12, and 24 hpf stages and eye-specific expression from 2 to 7 dpf. Then, the genome insertion sites were detected by splinkerette PCR (spPCR). The Krt4-GFP was inserted into the fourth intron of the gene itgav (integrin, alpha V) in chromosome 9 of the zebrafish genome, with the GFP direction the same as that of the itgav gene. By the alignment of homologous gene sequences in different species, three predicted endogenous enhancers were obtained. The trapped endogenous gene itgav, whose overexpression is related to hepatocellular carcinoma, showed a similar expression pattern as GFP detected by in situ hybridization, which suggested that GFP and itgav were possibly regulated by the same enhancers. In short, the zebrafish enhancer trap lines generated by the PB transposon-mediated enhancer trap technology in this study were valuable resources as visual markers to study the regulators and genes. This work provides an efficient method to identify and isolate tissue-specific enhancer sequences.
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Li F, Long Y, Xie J, Ren J, Zhou T, Song G, Li Q, Cui Z. Generation of GCaMP6s-Expressing Zebrafish to Monitor Spatiotemporal Dynamics of Calcium Signaling Elicited by Heat Stress. Int J Mol Sci 2021; 22:ijms22115551. [PMID: 34074030 PMCID: PMC8197303 DOI: 10.3390/ijms22115551] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 01/09/2023] Open
Abstract
The ability of organisms to quickly sense and transduce signals of environmental stresses is critical for their survival. Ca2+ is a versatile intracellular messenger involved in sensing a wide variety of stresses and regulating the subsequent cellular responses. So far, our understanding for calcium signaling was mostly obtained from ex vivo tissues and cultured cell lines, and the in vivo spatiotemporal dynamics of stress-triggered calcium signaling in a vertebrate remains to be characterized. Here, we describe the generation and characterization of a transgenic zebrafish line with ubiquitous expression of GCaMP6s, a genetically encoded calcium indicator (GECI). We developed a method to investigate the spatiotemporal patterns of Ca2+ events induced by heat stress. Exposure to heat stress elicited immediate and transient calcium signaling in developing zebrafish. Cells extensively distributed in the integument of the head and body trunk were the first batch of responders and different cell populations demonstrated distinct response patterns upon heat stress. Activity of the heat stress-induced calcium signaling peaked at 30 s and swiftly decreased to near the basal level at 120 s after the beginning of exposure. Inhibition of the heat-induced calcium signaling by LaCl3 and capsazepine and treatment with the inhibitors for CaMKII (Ca²2/calmodulin-dependent protein kinase II) and HSF1 (Heat shock factor 1) all significantly depressed the enhanced heat shock response (HSR). Together, we delineated the spatiotemporal dynamics of heat-induced calcium signaling and confirmed functions of the Ca2+-CaMKII-HSF1 pathway in regulating the HSR in zebrafish.
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Affiliation(s)
- Fengyang Li
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China;
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (J.X.); (T.Z.); (G.S.); (Q.L.)
| | - Yong Long
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (J.X.); (T.Z.); (G.S.); (Q.L.)
- Correspondence: , (Y.L.); (Z.C.); Tel.: +86-27-68780100 (Y.L.); +86-27-68780090 (Z.C.)
| | - Juhong Xie
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (J.X.); (T.Z.); (G.S.); (Q.L.)
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Ren
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China;
| | - Tong Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (J.X.); (T.Z.); (G.S.); (Q.L.)
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guili Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (J.X.); (T.Z.); (G.S.); (Q.L.)
| | - Qing Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (J.X.); (T.Z.); (G.S.); (Q.L.)
| | - Zongbin Cui
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China;
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence: , (Y.L.); (Z.C.); Tel.: +86-27-68780100 (Y.L.); +86-27-68780090 (Z.C.)
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Chen K, Li X, Song G, Zhou T, Long Y, Li Q, Zhong S, Cui Z. Deficiency in the membrane protein Tmbim3a/Grinaa initiates cold-induced ER stress and cell death by activating an intrinsic apoptotic pathway in zebrafish. J Biol Chem 2019; 294:11445-11457. [PMID: 31171717 DOI: 10.1074/jbc.ra119.007813] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/31/2019] [Indexed: 12/27/2022] Open
Abstract
Most members of the family of proteins containing a transmembrane BAX inhibitor motif (TMBIM) have anti-apoptotic activity, but their in vivo functions and intracellular mechanisms remain obscure. Here, we report that zebrafish Tmbim3a/Grinaa functions in the prevention of cold-induced endoplasmic reticulum (ER) stress and apoptosis. Using a gene-trapping approach, we obtained a mutant zebrafish line in which the expression of the tmbim3a/grinaa gene is disrupted by a Tol2 transposon insertion. Homozygous tmbim3a/grinaa mutant larvae exhibited time-dependently increased mortality and apoptosis under cold exposure (at 16 °C). Mechanistically, using immunofluorescence, fluorescence-based assessments of intracellular/mitochondrial Ca2+ levels, mitochondrial membrane potential measurements, and Ca2+-ATPase assays, we found that cold exposure suppresses sarcoplasmic/ER Ca2+-ATPase (SERCA) activity and induces the unfolded protein response (UPR) and ER stress. We also found that the cold-induced ER stress is increased in homozygous tmbim3a/grinaa mutant embryos. The cold-stress hypersensitivity of the tmbim3a/grinaa mutants was tightly associated with disrupted intracellular Ca2+ homeostasis, followed by mitochondrial Ca2+ overload and cytochrome c release, leading to the activation of caspase 9- and caspase-3-mediated intrinsic apoptotic pathways. Treatment of zebrafish larvae with the intracellular Ca2+ chelator 1,2-bis(2-aminophenoxy)ethane-N,N,N',N'-tetraacetate-acetoxymethyl ester (BAPTA-AM) or with 2-aminoethoxydiphenyl borate (2-APB), an inhibitor of the calcium-releasing protein inositol 1,4,5-trisphosphate receptor (IP3R), alleviated cold-induced cell death. Together, these findings unveil a key role of Tmbim3a/Grinaa in relieving cold-induced ER stress and in protecting cells against caspase 9- and caspase 3-mediated apoptosis during zebrafish development.
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Affiliation(s)
- Kai Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Hubei, Wuhan 430072, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xixi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Hubei, Wuhan 430072, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guili Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Hubei, Wuhan 430072, China
| | - Tong Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Hubei, Wuhan 430072, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong Long
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Hubei, Wuhan 430072, China
| | - Qing Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Hubei, Wuhan 430072, China
| | - Shan Zhong
- Department of Genetics, Wuhan University, Wuhan, Hubei 430071, China
| | - Zongbin Cui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Hubei, Wuhan 430072, China .,Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
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Chan S, Shen D, Sang Y, Wang S, Wang Y, Chen C, Gao B, Song C. Development of enhancer-trapping and -detection vectors mediated by the Tol2 transposon in zebrafish. PeerJ 2019; 7:e6862. [PMID: 31106068 PMCID: PMC6499061 DOI: 10.7717/peerj.6862] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 03/28/2019] [Indexed: 01/02/2023] Open
Abstract
Enhancers are key transcriptional drivers of gene expression. The identification of enhancers in the genome is central for understanding gene-expression programs. Although transposon-mediated enhancer trapping (ET) is a powerful approach to the identification of enhancers in zebrafish, its efficiency varies considerably. To improve the ET efficiency, we constructed Tol2-mediated ET vectors with a reporter gene (mCherry) expression box driven by four minimal promoters (Gata, Myc, Krt4 and Oct4), respectively. The ET efficiency and expression background were compared among the four promoters by zebrafish embryo injection at the one-cell stage. The results showed that the Gata minimal promoter yielded the lowest basic expression and the second-highest trapping efficiency (44.6% at 12 hpf (hour post-fertilization) and 23.1% at 72 hpf, n = 305 and n = 307). The Krt4 promoter had the highest trapping efficiency (64% at 12 hpf and 67.1% at 72 hpf, n = 302 and n = 301) and the strongest basic expression. To detect enhancer activity, chicken 5′HS4 double insulators were cloned into the two ET vectors with the Gata or Krt4 minimal promoter, flanking the mCherry expression box. The resulting detection vectors were injected into zebrafish embryos. mCherry expression driven by the Gata promoter (about 5%, n = 301) was decreased significantly compared with that observed for embryos injected with the ET vectors (23% at 72 hpf, n = 308). These results suggest that the insulators block the genome-position effects and that this vector is fit for enhancer-activity evaluation. To assess the compatibility between the enhancers and the minimal promoters, four enhancers (CNS1, Z48, Hand2 and Hs769) were cloned upstream of the Gata or Beta-globin minimal promoter in the enhancer-activity-detection vectors. The resulting recombinant vectors were assayed by zebrafish embryo injection. We found that Z48 and CNS1 responded to the Gata minimal promoter, and that Hand2 only responded to the Beta-globin minimal promoter. In contrast, Hs769 did not respond to either the Gata or Beta-globin minimal promoters. These results suggest the existence of compatibility between enhancers and minimal promoters. This study represents a systematic approach to the discovery of optional ET and enhancer-detection vectors. We are eager to provide a superior tool for understanding functional genomics.
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Affiliation(s)
- Shuheng Chan
- Yangzhou University, Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou, Jiangsu, China
| | - Dan Shen
- Yangzhou University, Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou, Jiangsu, China
| | - Yatong Sang
- Yangzhou University, Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou, Jiangsu, China
| | - Saisai Wang
- Yangzhou University, Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou, Jiangsu, China
| | - Yali Wang
- Yangzhou University, Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou, Jiangsu, China
| | - Cai Chen
- Yangzhou University, Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou, Jiangsu, China
| | - Bo Gao
- Yangzhou University, Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou, Jiangsu, China
| | - Chengyi Song
- Yangzhou University, Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou, Jiangsu, China
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Enhancer Trapping and Annotation in Zebrafish Mediated with Sleeping Beauty, piggyBac and Tol2 Transposons. Genes (Basel) 2018; 9:genes9120630. [PMID: 30551672 PMCID: PMC6316676 DOI: 10.3390/genes9120630] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/07/2018] [Accepted: 12/10/2018] [Indexed: 12/18/2022] Open
Abstract
Although transposon-mediated enhancer trapping (ET) is successfully applied in diverse models, the efficiency of various transposon systems varies significantly, and little information is available regarding efficiency of enhancer trapping by various transposons in zebrafish. Most potential enhancers (Ens) still lack evidence of actual En activity. Here, we compared the differences in ET efficiency between sleeping beauty (SB), piggyBac (PB) and Tol2 transposons. Tol2 represented the highest germline transfer efficiencies at 55.56% (NF0 = 165), followed by SB (38.36%, NF0 = 151) and PB (32.65%, NF0 = 149). ET lines generated by the Tol2 transposon tended to produce offspring with a single expression pattern per line, while PB and SB tended to generate embryos with multiple expression patterns. In our tests, 10 putative Ens (En1–10) were identified by splinkerette PCR and comparative genomic analysis. Combining the GFP expression profiles and mRNA expression patterns revealed that En1 and En2 may be involved in regulation of the expression of dlx1a and dlx2a, while En6 may be involved in regulation of the expression of line TK4 transgene and rps26, and En7 may be involved in the regulation of the expression of wnt1 and wnt10b. Most identified Ens were found to be transcribed in zebrafish embryos, and their regulatory function may involve eRNAs.
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Zhao Y, Song G, Ren J, Li Q, Zhong S, Cui Z. Sleeping beauty transposon-mediated poly(A)-trapping and insertion mutagenesis in mouse embryonic stem cells. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2018; 59:687-697. [PMID: 30280432 DOI: 10.1002/em.22234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/03/2018] [Accepted: 07/12/2018] [Indexed: 06/08/2023]
Abstract
Saturation mutagenesis of all endogenous genes within the mouse genome remains a challenging task, although a plenty of gene-editing approaches are available for this purpose. Here, a poly(A)-trap vector was generated for insertion mutagenesis in mouse embryonic stem (mES) cells. This vector contains an expression cassette of neomycin (Neo)-resistant gene lacking a poly(A) signal and flanked by two inverted terminal repeats of the Sleeping Beauty (SB) transposon. The whole poly(A)-trap cassette can transpose into target TA dinucleotides, properly splice with endogenous genes and effectively interrupt the transcription of trapped genes in mES cells after transient induction of SB expression by doxycycline (DOX)-treatment at 1 μg/ml, leading to the formation of multiple geneticin (G418)-resistant cell clones. In the first round of mutation screening, we identified six transposition events from 23 cell clones, including four inserted into an endogenous gene and two landed between endogenous genes. The abilities of self-renewal, totipotency, genetic stability and differentiation of syngap1+/- cells were not affected by DOX-treatment and G418-selection. These findings suggest that this SB transposon-mediated poly(A)-trap vector can be used as an alternative tool for a large-scale screening of mES cells with a gene mutation and for further generation of mutant mouse strains. Environ. Mol. Mutagen. 59:687-697, 2018. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Yi Zhao
- Department of Genetics, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Guili Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jing Ren
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Qing Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Shan Zhong
- Department of Genetics, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, Hubei, China
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan, Hubei, China
| | - Zongbin Cui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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Li X, Song G, Zhao Y, Zhao F, Liu C, Liu D, Li Q, Cui Z. Claudin7b is required for the formation and function of inner ear in zebrafish. J Cell Physiol 2017; 233:3195-3206. [DOI: 10.1002/jcp.26162] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 08/21/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Xiaohui Li
- State Key Laboratory of Freshwater Ecology and Biotechnology; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
- University of Chinese Academy of Sciences; Beijing China
| | - Guili Song
- State Key Laboratory of Freshwater Ecology and Biotechnology; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
| | - Yasong Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
- University of Chinese Academy of Sciences; Beijing China
| | - Feng Zhao
- Department of Biology; Southern University of Science and Technology; Shenzhen China
| | - Chunyan Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
| | - Dong Liu
- Department of Biology; Southern University of Science and Technology; Shenzhen China
| | - Qing Li
- State Key Laboratory of Freshwater Ecology and Biotechnology; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
| | - Zongbin Cui
- State Key Laboratory of Freshwater Ecology and Biotechnology; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
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Ma D, Xue Y, Zhang Y, Sun Y, Meng A, Liu F. The rising zebrafish research in China: Meeting report of the 3rd Chinese Zebrafish Principal Investigator Meeting & the Inaugural Meeting of China Zebrafish Society. J Genet Genomics 2016; 43:617-620. [PMID: 27769691 DOI: 10.1016/j.jgg.2016.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 10/03/2016] [Indexed: 10/20/2022]
Affiliation(s)
- Dongyuan Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuanyuan Xue
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yifan Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yonghua Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, China Zebrafish Resource Center, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Anming Meng
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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