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Jin J, Xu F, Liu Z, Qi H, Yao C, Shuai J, Li X. Biphasic amplitude oscillator characterized by distinct dynamics of trough and crest. Phys Rev E 2023; 108:064412. [PMID: 38243441 DOI: 10.1103/physreve.108.064412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/28/2023] [Indexed: 01/21/2024]
Abstract
Biphasic amplitude dynamics (BAD) of oscillation have been observed in many biological systems. However, the specific topology structure and regulatory mechanisms underlying these biphasic amplitude dynamics remain elusive. Here, we searched all possible two-node circuit topologies and identified the core oscillator that enables robust oscillation. This core oscillator consists of a negative feedback loop between two nodes and a self-positive feedback loop of the input node, which result in the fast and slow dynamics of the two nodes, thereby achieving relaxation oscillation. Landscape theory was employed to study the stochastic dynamics and global stability of the system, allowing us to quantitatively describe the diverse positions and sizes of the Mexican hat. With increasing input strength, the size of the Mexican hat exhibits a gradual increase followed by a subsequent decrease. The self-activation of input node and the negative feedback on input node, which dominate the fast dynamics of the input node, were observed to regulate BAD in a bell-shaped manner. Both deterministic and statistical analysis results reveal that BAD is characterized by the linear and nonlinear dependence of the oscillation trough and crest on the input strength. In addition, combining with computational and theoretical analysis, we addressed that the linear response of trough to input is predominantly governed by the negative feedback, while the nonlinear response of crest is jointly regulated by the negative feedback loop and the self-positive feedback loop within the oscillator. Overall, this study provides a natural and physical basis for comprehending the occurrence of BAD in oscillatory systems, yielding guidance for the design of BAD in synthetic biology applications.
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Affiliation(s)
- Jun Jin
- Department of Physics, Xiamen University, Xiamen, Fujian 361005, China
| | - Fei Xu
- Department of Physics, Anhui Normal University, Wuhu, Anhui 241002, China
| | - Zhilong Liu
- Department of Physics, Xiamen University, Xiamen, Fujian 361005, China
| | - Hong Qi
- Complex Systems Research Center, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Chenggui Yao
- College of Data Science, Jiaxing University, Jiaxing, Zhejiang 314000, China
| | - Jianwei Shuai
- Department of Physics, Xiamen University, Xiamen, Fujian 361005, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health) and Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
| | - Xiang Li
- Department of Physics, Xiamen University, Xiamen, Fujian 361005, China
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Qu J, Shao C, Ying Y, Wu Y, Liu W, Tian Y, Yin Z, Li X, Yu Z, Shuai J. The spring-like effect of microRNA-31 in balancing inflammatory and regenerative responses in colitis. Front Microbiol 2022; 13:1089729. [PMID: 36590397 PMCID: PMC9800619 DOI: 10.3389/fmicb.2022.1089729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Inflammatory bowel diseases (IBDs) are chronic inflammatory disorders caused by the disruption of immune tolerance to the gut microbiota. MicroRNA-31 (MIR31) has been proven to be up-regulated in intestinal tissues from patients with IBDs and colitis-associated neoplasias. While the functional role of MIR31 in colitis and related diseases remain elusive. Combining mathematical modeling and experimental analysis, we systematically explored the regulatory mechanism of MIR31 in inflammatory and epithelial regeneration responses in colitis. Level of MIR31 presents an "adaptation" behavior in dextran sulfate sodium (DSS)-induced colitis, and the similar behavior is also observed for the key cytokines of p65 and STAT3. Simulation analysis predicts MIR31 suppresses the activation of p65 and STAT3 but accelerates the recovery of epithelia in colitis, which are validated by our experimental observations. Further analysis reveals that the number of proliferative epithelial cells, which characterizes the inflammatory process and the recovery of epithelia in colitis, is mainly determined by the inhibition of MIR31 on IL17RA. MIR31 promotes epithelial regeneration in low levels of DSS-induced colitis but inhibits inflammation with high DSS levels, which is dominated by the competition for MIR31 to either inhibit inflammation or promote epithelial regeneration by binding to different targets. The binding probability determines the functional transformation of MIR31, but the functional strength is determined by MIR31 levels. Thus, the role of MIR31 in the inflammatory response can be described as the "spring-like effect," where DSS, MIR31 action strength, and proliferative epithelial cell number are regarded as external force, intrinsic spring force, and spring length, respectively. Overall, our study uncovers the vital roles of MIR31 in balancing inflammation and the recovery of epithelia in colitis, providing potential clues for the development of therapeutic targets in drug design.
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Affiliation(s)
- Jing Qu
- Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen, China
| | - Chunlei Shao
- State Key Laboratories for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yongfa Ying
- Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen, China
| | - Yuning Wu
- Department of Mathematics and Physics, Fujian Jiangxia University, Fuzhou, China
| | - Wen Liu
- Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen, China
| | - Yuhua Tian
- State Key Laboratories for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhiyong Yin
- Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen, China
| | - Xiang Li
- Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen, China
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Zhengquan Yu
- State Key Laboratories for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jianwei Shuai
- Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen, China
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), University of Chinese Academy of Sciences, Wenzhou, China
- Wenzhou Institute, Wenzhou Key Laboratory of Biophysics, University of Chinese Academy of Sciences, Wenzhou, China
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Zhu L, Li X, Xu F, Yin Z, Jin J, Liu Z, Qi H, Shuai J. Network modeling-based identification of the switching targets between pyroptosis and secondary pyroptosis. CHAOS, SOLITONS, AND FRACTALS 2022; 155:111724. [PMID: 36570873 PMCID: PMC9759288 DOI: 10.1016/j.chaos.2021.111724] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 12/09/2021] [Indexed: 06/17/2023]
Abstract
The newly identified cell death type, pyroptosis plays crucial roles in various diseases. Most recently, mounting evidence accumulates that pyroptotic signaling is highly correlated with coronavirus disease 2019 (COVID-19). Thus, understanding the induction of the pyroptotic signaling and dissecting the detail molecular control mechanisms are urgently needed. Based on recent experimental studies, a core regulatory model of the pyroptotic signaling is constructed to investigate the intricate crosstalk dynamics between the two cell death types, i.e., pyroptosis and secondary pyroptosis. The model well reproduces the experimental observations under different conditions. Sensitivity analysis determines that only the expression level of caspase-1 or GSDMD has the potential to individually change death modes. The decrease of caspase-1 or GSDMD level switches cell death from pyroptosis to secondary pyroptosis. Besides, eight biochemical reactions are identified that can efficiently switch death modes. While from the viewpoint of bifurcation analysis, the expression level of caspase-3 is further identified and twelve biochemical reactions are obtained. The coexistence of pyroptosis and secondary pyroptosis is predicted to be observed not only within the bistable range, but also within proper monostable range, presenting two potential different control mechanisms. Combined with the landscape theory, we further explore the stochastic dynamic and global stability of the pyroptotic system, accurately quantifying how each component mediates the individual occurrence probability of pyroptosis and secondary pyroptosis. Overall, this study sheds new light on the intricate crosstalk of the pyroptotic signaling and uncovers the regulatory mechanisms of various stable state transitions, providing potential clues to guide the development for prevention and treatment of pyroptosis-related diseases.
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Affiliation(s)
- Ligang Zhu
- Department of Physics, and Fujian Provincial Key Lab for Soft Functional Materials Research, Xiamen University, Xiamen 361005, China
| | - Xiang Li
- Department of Physics, and Fujian Provincial Key Lab for Soft Functional Materials Research, Xiamen University, Xiamen 361005, China
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen 361102, China
| | - Fei Xu
- Department of Physics, and Fujian Provincial Key Lab for Soft Functional Materials Research, Xiamen University, Xiamen 361005, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
| | - Zhiyong Yin
- Department of Physics, and Fujian Provincial Key Lab for Soft Functional Materials Research, Xiamen University, Xiamen 361005, China
| | - Jun Jin
- Department of Physics, and Fujian Provincial Key Lab for Soft Functional Materials Research, Xiamen University, Xiamen 361005, China
| | - Zhilong Liu
- Department of Physics, and Fujian Provincial Key Lab for Soft Functional Materials Research, Xiamen University, Xiamen 361005, China
| | - Hong Qi
- Complex Systems Research Center, Shanxi University, Taiyuan 030006, China
| | - Jianwei Shuai
- Department of Physics, and Fujian Provincial Key Lab for Soft Functional Materials Research, Xiamen University, Xiamen 361005, China
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen 361102, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen 361102, China
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Mu R, Lyu X, Ji R, Liu J, Zhao T, Li H, Liu B. GmBICs Modulate Low Blue Light-Induced Stem Elongation in Soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:803122. [PMID: 35185980 PMCID: PMC8850649 DOI: 10.3389/fpls.2022.803122] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/14/2022] [Indexed: 05/19/2023]
Abstract
Blue-light inhibitors of cryptochromes (BICs) promote hypocotyl elongation by suppressing the activity of cryptochromes in Arabidopsis. Nevertheless, the roles of BICs in other plant species are still unclear. Here we investigate their functions by genetic overexpression and CRISPR/Cas9 engineered mutations targeting the six GmBIC genes in soybean. We showed that the GmBICs overexpression (GmBICs-OX) lines strongly promoted stem elongation, while the single, double, and quadruple mutations in the GmBIC genes resulted in incremental dwarfing phenotypes. Furthermore, overexpression of GmBIC2a abolished the low blue light (LBL)-induced stem elongation, demonstrating the involvement of GmBICs in regulating cryptochrome-mediated LBL-induced shade avoidance syndrome (SAS). The Gmbic1a1b2a2b quadruple mutant displayed reduced stem elongation under LBL conditions, which was reminiscent of the GmCRY1b-OX lines. Taken together, this study provided essential genetic resources for elucidating GmBICs functional mechanisms and breeding of shade-tolerant soybean cultivars in future.
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