Many animals can detect the multi-frequency signals from their external surroundings.The understanding for underlying mechanism of signal detection can apply the theory of vibrational resonance,in which the moderate h...Many animals can detect the multi-frequency signals from their external surroundings.The understanding for underlying mechanism of signal detection can apply the theory of vibrational resonance,in which the moderate high frequency driving can maximize the nonlinear system's response to the low frequency subthreshold signal.In this work,we study the roles of chemical autapse on the vibrational resonance in a single neuron for signal detection.We reveal that the vibrational resonance is strengthened significantly by the inhibitory autapse in the neuron,while it is weakened typically by the excitatory autapse.It is generally believed that the inhibitory synapse has a suppressive effect in neuronal dynamics.However,we find that the detection of the neuron to the low frequency subthreshold signal can be improved greatly by the inhibitory autapse.Our finding indicates that the inhibitory synapse may act constructively on the detection of weak signal in the brain and neuronal system.展开更多
Synchronization rhythm and oscillating in biological systems can give clues to understanding the cooperation and competition between cells under appropriate biological and physical conditions. As a result, the network...Synchronization rhythm and oscillating in biological systems can give clues to understanding the cooperation and competition between cells under appropriate biological and physical conditions. As a result, the network setting is appreciated to detect the stability and transition of collective behaviors in a network with different connection types. In this paper, the synchronization performance in time-delayed excitable homogeneous random networks（EHRNs） induced by diversity in system parameters is investigated by calculating the synchronization parameter and plotting the spatiotemporal evolution pattern, and distinct impacts induced by parameter-diversity are detected by setting different time delays. It is found that diversity has no distinct effect on the synchronization performance in EHRNs with small time delay being considered. When time delay is increased greatly, the synchronization performance of EHRN degenerates remarkably as diversity is increased. Surprisingly, by setting a moderate time delay, appropriate parameter-diversity can promote the synchronization performance in EHRNs, and can induce the synchronization transition from the asynchronous state to the weak synchronization. Moreover, the bistability phenomenon, which contains the states of asynchronous state and weak synchronization,is observed. Particularly, it is confirmed that the parameter-diversity promoted synchronization performance in time-delayed EHRN is manifested in the enhancement of the synchronization performance of individual oscillation and the increase of the number of synchronization transitions from the asynchronous state to the weak synchronization. Finally, we have revealed that this kind of parameter-diversity promoted synchronization performance is a robust phenomenon.展开更多
Revealing how a biological network is organized to realize its function is one of the main topics in systems biology. Tile functional backbone network, defined as the primary structure of the biological network, is of...Revealing how a biological network is organized to realize its function is one of the main topics in systems biology. Tile functional backbone network, defined as the primary structure of the biological network, is of great importance in maintaining the main function of the biological network. We propose a new algorithm, the tinker algorithm, to determine this core structure and apply it in the cell-cycle system. With this algorithm, the backbone network of the cell-cycle network can be determined accurately and efficiently in various models such as the Boolean model, stochastic model, and ordinary differential equation model. Results show that our algorithm is more efficient than that used in the previous research. We hope this method can be put into practical use in relevant future studies.展开更多
Inflammasomes are essential complexes of innate immune system, which form the first line of host defense against pathogens. Mounting evidence accumulates that inflammasome signaling is highly correlated with coronavir...Inflammasomes are essential complexes of innate immune system, which form the first line of host defense against pathogens. Mounting evidence accumulates that inflammasome signaling is highly correlated with coronavirus disease 2019 (COVID-19). However, there remains a significant gap in our understanding of the regulatory mechanism of inflammasome signaling. Combining mathematical modeling with experimental analysis of NLRP1b inflammasome signaling, we found that only the expression levels of caspase-1 and GSDMD have the potential to individually switch cell death modes. Reduction of caspase-1 or GSDMD switches cell death from pyroptosis to apoptosis. Caspase-1 and GSDMD present different thresholds and exert distinct pathway choices in switching death modes. Pyroptosis switches to apoptosis with an extremely low threshold level of caspase-1, but with a high threshold of GSDMD. Caspase-1-impaired cells employ ASC-caspase-8-dependent pathway for apoptosis, while GSDMD-impaired cells primarily utilize caspase-1-dependent pathway. Additionally, caspase-1 and GSDMD can severally ignite the cooccurrence of pyroptosis and apoptosis. Landscape topography unravels that the cooccurrence is dramatically different in caspase-1- and GSDMD-impaired cells. Besides pyroptosis state and apoptosis state, a potential new “coexisting” state in single cells is proposed when GSDMD acts as the driving force of the landscape. The “seesaw model” is therefore proposed, which can well describe the death states that are controlled by caspase-1 or GSDMD in single cells. Our study sheds new light on NLRP1b inflammasome signaling and uncovers the switching mechanisms among various death modes, providing potential clues to guide the development of more rational control strategies for diseases.展开更多
基金Project supported partially by the National Natural Science Foundation of China(Grant Nos.11675112,11705116,11675134,and 11874310)the National Natural Science Foundation of China for the 111 Project(Grant No.B16029).
文摘Many animals can detect the multi-frequency signals from their external surroundings.The understanding for underlying mechanism of signal detection can apply the theory of vibrational resonance,in which the moderate high frequency driving can maximize the nonlinear system's response to the low frequency subthreshold signal.In this work,we study the roles of chemical autapse on the vibrational resonance in a single neuron for signal detection.We reveal that the vibrational resonance is strengthened significantly by the inhibitory autapse in the neuron,while it is weakened typically by the excitatory autapse.It is generally believed that the inhibitory synapse has a suppressive effect in neuronal dynamics.However,we find that the detection of the neuron to the low frequency subthreshold signal can be improved greatly by the inhibitory autapse.Our finding indicates that the inhibitory synapse may act constructively on the detection of weak signal in the brain and neuronal system.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.11675001,11675112,11775020,and 11372122)
文摘Synchronization rhythm and oscillating in biological systems can give clues to understanding the cooperation and competition between cells under appropriate biological and physical conditions. As a result, the network setting is appreciated to detect the stability and transition of collective behaviors in a network with different connection types. In this paper, the synchronization performance in time-delayed excitable homogeneous random networks（EHRNs） induced by diversity in system parameters is investigated by calculating the synchronization parameter and plotting the spatiotemporal evolution pattern, and distinct impacts induced by parameter-diversity are detected by setting different time delays. It is found that diversity has no distinct effect on the synchronization performance in EHRNs with small time delay being considered. When time delay is increased greatly, the synchronization performance of EHRN degenerates remarkably as diversity is increased. Surprisingly, by setting a moderate time delay, appropriate parameter-diversity can promote the synchronization performance in EHRNs, and can induce the synchronization transition from the asynchronous state to the weak synchronization. Moreover, the bistability phenomenon, which contains the states of asynchronous state and weak synchronization,is observed. Particularly, it is confirmed that the parameter-diversity promoted synchronization performance in time-delayed EHRN is manifested in the enhancement of the synchronization performance of individual oscillation and the increase of the number of synchronization transitions from the asynchronous state to the weak synchronization. Finally, we have revealed that this kind of parameter-diversity promoted synchronization performance is a robust phenomenon.
基金This study was supported partially by the National Science Foundation of China （Grant Nos. 11475253, 11405263, and 11675112） and the Natural Science Foundation of Zhejiang Province （Grant No. LY16A050001）.
文摘Revealing how a biological network is organized to realize its function is one of the main topics in systems biology. Tile functional backbone network, defined as the primary structure of the biological network, is of great importance in maintaining the main function of the biological network. We propose a new algorithm, the tinker algorithm, to determine this core structure and apply it in the cell-cycle system. With this algorithm, the backbone network of the cell-cycle network can be determined accurately and efficiently in various models such as the Boolean model, stochastic model, and ordinary differential equation model. Results show that our algorithm is more efficient than that used in the previous research. We hope this method can be put into practical use in relevant future studies.
基金This work was supported by the National Natural Science Foundation of China(Grants Nos.12090052 and 11874310)the Ministry of Science and Technology of the People’s Republic of China under grant nos.2021ZD0201900 and 2021ZD0201904the Fujian Province Foundation(Grant No.2020Y4001).
文摘Inflammasomes are essential complexes of innate immune system, which form the first line of host defense against pathogens. Mounting evidence accumulates that inflammasome signaling is highly correlated with coronavirus disease 2019 (COVID-19). However, there remains a significant gap in our understanding of the regulatory mechanism of inflammasome signaling. Combining mathematical modeling with experimental analysis of NLRP1b inflammasome signaling, we found that only the expression levels of caspase-1 and GSDMD have the potential to individually switch cell death modes. Reduction of caspase-1 or GSDMD switches cell death from pyroptosis to apoptosis. Caspase-1 and GSDMD present different thresholds and exert distinct pathway choices in switching death modes. Pyroptosis switches to apoptosis with an extremely low threshold level of caspase-1, but with a high threshold of GSDMD. Caspase-1-impaired cells employ ASC-caspase-8-dependent pathway for apoptosis, while GSDMD-impaired cells primarily utilize caspase-1-dependent pathway. Additionally, caspase-1 and GSDMD can severally ignite the cooccurrence of pyroptosis and apoptosis. Landscape topography unravels that the cooccurrence is dramatically different in caspase-1- and GSDMD-impaired cells. Besides pyroptosis state and apoptosis state, a potential new “coexisting” state in single cells is proposed when GSDMD acts as the driving force of the landscape. The “seesaw model” is therefore proposed, which can well describe the death states that are controlled by caspase-1 or GSDMD in single cells. Our study sheds new light on NLRP1b inflammasome signaling and uncovers the switching mechanisms among various death modes, providing potential clues to guide the development of more rational control strategies for diseases.
