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Liu S, Luo S, Yang D, Huang J, Jiang X, Yu S, Fu J, Zhou D, Chen X, He H, Fu H. Alternative polyadenylation profiles of susceptible and resistant rice (Oryza sativa L.) in response to bacterial leaf blight using RNA-seq. BMC PLANT BIOLOGY 2024; 24:145. [PMID: 38413866 PMCID: PMC10900630 DOI: 10.1186/s12870-024-04839-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 02/20/2024] [Indexed: 02/29/2024]
Abstract
BACKGROUND Alternative polyadenylation (APA) is an important pattern of post-transcriptional regulation of genes widely existing in eukaryotes, involving plant physiological and pathological processes. However, there is a dearth of studies investigating the role of APA profile in rice leaf blight. RESULTS In this study, we compared the APA profile of leaf blight-susceptible varieties (CT 9737-613P-M) and resistant varieties (NSIC RC154) following bacterial blight infection. Through gene enrichment analysis, we found that the genes of two varieties typically exhibited distal poly(A) (PA) sites that play different roles in two kinds of rice, indicating differential APA regulatory mechanisms. In this process, many disease-resistance genes displayed multiple transcripts via APA. Moreover, we also found five polyadenylation factors of similar expression patterns of rice, highlighting the critical roles of these five factors in rice response to leaf blight about PA locus diversity. CONCLUSION Notably, the present study provides the first dynamic changes of APA in rice in early response to biotic stresses and proposes a possible functional conjecture of APA in plant immune response, which lays the theoretical foundation for in-depth determination of the role of APA events in plant stress response and other life processes.
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Affiliation(s)
- Shaochun Liu
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Shuqi Luo
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Dewei Yang
- Institute of Rice, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Junying Huang
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xinlei Jiang
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Shangwei Yu
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Junru Fu
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Dahu Zhou
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiaorong Chen
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Haihui Fu
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China.
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Zhang A, Zhang H, Wang R, He H, Song B, Song R. Bactericidal bissulfone B 7 targets bacterial pyruvate kinase to impair bacterial biology and pathogenicity in plants. SCIENCE CHINA. LIFE SCIENCES 2024; 67:391-402. [PMID: 37987940 DOI: 10.1007/s11427-023-2449-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/11/2023] [Indexed: 11/22/2023]
Abstract
The prevention and control of rice bacterial leaf blight (BLB) disease has not yet been achieved due to the lack of effective agrochemicals and available targets. Herein, we develop a series of novel bissulfones and a novel target with a unique mechanism to address this challenge. The developed bissulfones can control Xanthomonas oryzae pv. oryzae (Xoo), and 2-(bis(methylsulfonyl)methylene)-N-(4-chlorophenyl) hydrazine-1-carboxamide (B7) is more effective than the commercial drugs thiodiazole copper (TC) and bismerthiazol (BT). Pyruvate kinase (PYK) in Xoo has been identified for the first time as the target protein of our bissulfone B7. PYK modulates bacterial virulence via a CRP-like protein (Clp)/two-component system regulatory protein (regR) axis. The elucidation of this pathway facilitates the use of B7 to reduce PYK expression at the transcriptional level, block PYK activity at the protein level, and impair the interaction within the PYK-Clp-regR complex via competitive inhibition, thereby attenuating bacterial biology and pathogenicity. This study offers insights into the molecular and mechanistic aspects underlying anti-Xoo strategies that target PYK. We believe that these valuable discoveries will be used for bacterial disease control in the future.
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Affiliation(s)
- Awei Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Haizhen Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Ronghua Wang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Hongfu He
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Baoan Song
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China.
| | - Runjiang Song
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China.
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A X, Yang Y, Chen X, Tang C, Zhang F, Dong C, Wang B, Liu P, Dai L. Complete Genome Resource of a Hypervirulent Xanthomonas oryzae pv. oryzae Strain YNCX Isolated from Yunnan Plateau Japonica Rice. PLANT DISEASE 2023; 107:3623-3626. [PMID: 37189043 DOI: 10.1094/pdis-04-23-0674-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial leaf blight (BLB), is one of the most destructive bacterial pathogens in rice production worldwide. Although several complete genome sequences of Xoo strains have been released in public databases, they are mainly isolated from low-altitude indica rice cultivating areas. Here, a hypervirulent strain, YNCX, isolated from the high-altitude japonica rice-growing region in Yunnan Plateau, was used to extract genomic DNA for PacBio sequencing and Illumina sequencing. After assembly, a high-quality complete genome consisting of a circular chromosome and six plasmids was generated. The genome sequence of YNCX provides a valuable resource for high-altitude races and enables the identification of new virulence TALE effectors, contributing to a better understanding of rice-Xoo interactions.
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Affiliation(s)
- Xinxiang A
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences/Yunnan Provincial Key Lab of Agricultural Biotechnology/Key Laboratory of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture and Rural Affairs/Scientific Observation Station for Rice Germplasm Resources of Yunnan, Kunming 650223, Yunnan, China
| | - Yayun Yang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences/Yunnan Provincial Key Lab of Agricultural Biotechnology/Key Laboratory of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture and Rural Affairs/Scientific Observation Station for Rice Germplasm Resources of Yunnan, Kunming 650223, Yunnan, China
| | - Xifeng Chen
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Cuifeng Tang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences/Yunnan Provincial Key Lab of Agricultural Biotechnology/Key Laboratory of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture and Rural Affairs/Scientific Observation Station for Rice Germplasm Resources of Yunnan, Kunming 650223, Yunnan, China
| | - Feifei Zhang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences/Yunnan Provincial Key Lab of Agricultural Biotechnology/Key Laboratory of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture and Rural Affairs/Scientific Observation Station for Rice Germplasm Resources of Yunnan, Kunming 650223, Yunnan, China
| | - Chao Dong
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences/Yunnan Provincial Key Lab of Agricultural Biotechnology/Key Laboratory of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture and Rural Affairs/Scientific Observation Station for Rice Germplasm Resources of Yunnan, Kunming 650223, Yunnan, China
| | - Bin Wang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences/Yunnan Provincial Key Lab of Agricultural Biotechnology/Key Laboratory of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture and Rural Affairs/Scientific Observation Station for Rice Germplasm Resources of Yunnan, Kunming 650223, Yunnan, China
| | - Pengcheng Liu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Luyuan Dai
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences/Yunnan Provincial Key Lab of Agricultural Biotechnology/Key Laboratory of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture and Rural Affairs/Scientific Observation Station for Rice Germplasm Resources of Yunnan, Kunming 650223, Yunnan, China
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Gu X, Si F, Feng Z, Li S, Liang D, Yang P, Yang C, Yan B, Tang J, Yang Y, Li T, Li L, Zhou J, Li J, Feng L, Liu JY, Yang Y, Deng Y, Wu XN, Zhao Z, Wan J, Cao X, Song X, He Z, Liu J. The OsSGS3-tasiRNA-OsARF3 module orchestrates abiotic-biotic stress response trade-off in rice. Nat Commun 2023; 14:4441. [PMID: 37488129 PMCID: PMC10366173 DOI: 10.1038/s41467-023-40176-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 07/14/2023] [Indexed: 07/26/2023] Open
Abstract
Recurrent heat stress and pathogen invasion seriously threaten crop production, and abiotic stress often antagonizes biotic stress response against pathogens. However, the molecular mechanisms of trade-offs between thermotolerance and defense remain obscure. Here, we identify a rice thermo-sensitive mutant that displays a defect in floret development under high temperature with a mutation in SUPPRESSOR OF GENE SILENCING 3a (OsSGS3a). OsSGS3a interacts with its homolog OsSGS3b and modulates the biogenesis of trans-acting small interfering RNA (tasiRNA) targeting AUXIN RESPONSE FACTORS (ARFs). We find that OsSGS3a/b positively, while OsARF3a/b and OsARF3la/lb negatively modulate thermotolerance. Moreover, OsSGS3a negatively, while OsARF3a/b and OsARF3la/lb positively regulate disease resistance to the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo) and the fungal pathogen Magnaporthe oryzae (M. oryzae). Taken together, our study uncovers a previously unknown trade-off mechanism that regulates distinct immunity and thermotolerance through the OsSGS3-tasiRNA-OsARF3 module, highlighting the regulation of abiotic-biotic stress response trade-off in plants.
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Affiliation(s)
- Xueting Gu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Fuyan Si
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Zhengxiang Feng
- Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500, Kunming, China
| | - Shunjie Li
- Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500, Kunming, China
| | - Di Liang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Pei Yang
- Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500, Kunming, China
| | - Chao Yang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Bin Yan
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Jun Tang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Yu Yang
- Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500, Kunming, China
| | - Tai Li
- Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500, Kunming, China
| | - Lin Li
- Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500, Kunming, China
| | - Jinling Zhou
- Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500, Kunming, China
| | - Ji Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Lili Feng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Ji-Yun Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Yuanzhu Yang
- Department of Rice Breeding, Hunan Yahua Seed Scientific Research Institute, 410119, Changsha, Hunan, China
| | - Yiwen Deng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Xu Na Wu
- Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500, Kunming, China
| | - Zhigang Zhao
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Jianmin Wan
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100039, Beijing, China
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 100101, Beijing, China
| | - Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China.
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China.
| | - Junzhong Liu
- Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500, Kunming, China.
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Zhan C, Lei L, Guo H, Zhou S, Xu C, Liu Z, Wu Z, Deng Y, Miao Y, Han Y, Zhang M, Li H, Huang S, Yang C, Zhang F, Li Y, Liu L, Liu X, Abbas HMK, Fernie AR, Yuan M, Luo J. Disease resistance conferred by components of essential chrysanthemum oil and the epigenetic regulation of OsTPS1. SCIENCE CHINA LIFE SCIENCES 2022; 66:1108-1118. [PMID: 36462108 DOI: 10.1007/s11427-022-2241-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 11/10/2022] [Indexed: 12/04/2022]
Abstract
The sesquiterpene alpha-bisabolol is the predominant active ingredient in essential oils that are highly valued in the cosmetics industry due to its wound healing, anti-inflammatory, and skin-soothing properties. Alpha-bisabolol was thought to be restricted to Compositae plants. Here we reveal that alpha-bisabolol is also synthesized in rice, a non-Compositae plant, where it acts as a novel sesquiterpene phytoalexin. Overexpressing the gene responsible for the biosynthesis of alpha-bisabolol, OsTPS1, conferred bacterial blight resistance in rice. Phylogenomic analyses revealed that alpha-bisabolol-synthesizing enzymes in rice and Compositae evolved independently. Further experiments demonstrated that the natural variation in the disease resistance level was associated with differential transcription of OsTPS1 due to polymorphisms in its promoter. We demonstrated that OsTPS1 was regulated at the epigenetic level by JMJ705 through the methyl jasmonate pathway. These data reveal the cross-family accumulation and regulatory mechanisms of alpha-bisabolol production.
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Yin X, Qian W. Sword in the woods: How plant hosts defend against vascular pathogens. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1465-1468. [PMID: 35766351 DOI: 10.1111/jipb.13321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
This Commentary discusses two recent papers exploring how plants combat infection by vascular pathogens via modulating lignin production and via MAP kinase signaling cascades.
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Affiliation(s)
- Xin Yin
- State Key Laboratory of Plant Genomics, Institution of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Qian
- State Key Laboratory of Plant Genomics, Institution of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
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Chen XL, Sun MC, Chong SL, Si JP, Wu LS. Transcriptomic and Metabolomic Approaches Deepen Our Knowledge of Plant-Endophyte Interactions. FRONTIERS IN PLANT SCIENCE 2021; 12:700200. [PMID: 35154169 PMCID: PMC8828500 DOI: 10.3389/fpls.2021.700200] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 12/22/2021] [Indexed: 05/10/2023]
Abstract
In natural systems, plant-symbiont-pathogen interactions play important roles in mitigating abiotic and biotic stresses in plants. Symbionts have their own special recognition ways, but they may share some similar characteristics with pathogens based on studies of model microbes and plants. Multi-omics technologies could be applied to study plant-microbe interactions, especially plant-endophyte interactions. Endophytes are naturally occurring microbes that inhabit plants, but do not cause apparent symptoms in them, and arise as an advantageous source of novel metabolites, agriculturally important promoters, and stress resisters in their host plants. Although biochemical, physiological, and molecular investigations have demonstrated that endophytes confer benefits to their hosts, especially in terms of promoting plant growth, increasing metabolic capabilities, and enhancing stress resistance, plant-endophyte interactions consist of complex mechanisms between the two symbionts. Further knowledge of these mechanisms may be gained by adopting a multi-omics approach. The involved interaction, which can range from colonization to protection against adverse conditions, has been investigated by transcriptomics and metabolomics. This review aims to provide effective means and ways of applying multi-omics studies to solve the current problems in the characterization of plant-microbe interactions, involving recognition and colonization. The obtained results should be useful for identifying the key determinants in such interactions and would also provide a timely theoretical and material basis for the study of interaction mechanisms and their applications.
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