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Kotsuka T, Hori Y. Stability Analysis for Large-Scale Multi-Agent Molecular Communication Systems. IEEE Trans Nanobioscience 2024; 23:507-517. [PMID: 38781070 DOI: 10.1109/tnb.2024.3404592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Molecular communication (MC) is recently featured as a novel communication tool to connect individual biological nanorobots. It is expected that a large number of nanorobots can form large multi-agent MC systems through MC to accomplish complex and large-scale tasks that cannot be achieved by a single nanorobot. However, most previous models for MC systems assume a unidirectional diffusion communication channel and cannot capture the feedback between each nanorobot, which is important for multi-agent MC systems. In this paper, we introduce a system theoretic model for large-scale multi-agent MC systems using transfer functions, and then propose a method to analyze the stability for multi-agent MC systems. The proposed method decomposes the multi-agent MC system into multiple single-input and single-output (SISO) systems, which facilitates the application of simple analysis technique for SISO systems to the large-scale multi-agent MC system. Finally, we demonstrate the proposed method by analyzing the stability of a specific large-scale multi-agent MC system and clarify a parameter region to synchronize the states of nanorobots, which is important to make cooperative behaviors at a population level.
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Tang M, Zhao D, Zhang Y, Qian C, Chen H, Chen L, Ye J, Zhou T. Impact of LuxS on virulence and pathogenicity in Klebsiella pneumoniae exhibiting varied mucoid phenotypes. Infect Immun 2024; 92:e0001224. [PMID: 38358274 PMCID: PMC10929404 DOI: 10.1128/iai.00012-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 01/17/2024] [Indexed: 02/16/2024] Open
Abstract
How the LuxS/AI-2 quorum sensing (QS) system influences the pathogenicity of K. pneumoniae is complicated by the heterogeneity of the bacterial mucoid phenotypes. This study aims to explore the LuxS-mediated regulation of the pathogenicity of K. pneumoniae with diverse mucoid phenotypes, including hypermucoid, regular-mucoid, and nonmucoid. The wild-type, luxS knockout, and complemented strains of three K. pneumoniae clinical isolates with distinct mucoid phenotypes were constructed. The results revealed the downregulation of virulence genes of regular-mucoid, and nonmucoid but not hypermucoid strains. The deletion of luxS reduced the pathogenicity of the regular-mucoid, and nonmucoid strains in mice; while in hypermucoid strain, luxS knockout reduced virulence in late growth but enhanced virulence in the early growth phase. Furthermore, the absence of luxS led the regular-mucoid and nonmucoid strains to be more sensitive to the host cell defense, and less biofilm-productive than the wild-type at both the low and high-density growth state. Nevertheless, luxS knockout enhanced the resistances to adhesion and phagocytosis by macrophage as well as serum-killing, of hypermucoid K. pneumoniae at its early low-density growth state, while it was opposite to those in its late high-density growth phase. Collectively, our results suggested that LuxS plays a crucial role in the pathogenicity of K. pneumoniae, and it is highly relevant to the mucoid phenotypes and growth phases of the strains. LuxS probably depresses the capsule in the early low-density phase and promotes the capsule, biofilm, and pathogenicity during the late high-density phase, but inhibits lipopolysaccharide throughout the growth phase, in K. pneumoniae.IMPORTANCECharacterizing the regulation of physiological functions by the LuxS/AI-2 quorum sensing (QS) system in Klebsiella pneumoniae strains will improve our understanding of this important pathogen. The genetic heterogeneity of K. pneumoniae isolates complicates our understanding of its pathogenicity, and the association of LuxS with bacterial pathogenicity has remained poorly addressed in K. pneumoniae. Our results demonstrated strain and growth phase-dependent variation in the contributions of LuxS to the virulence and pathogenicity of K. pneumoniae. Our findings provide new insights into the important contribution of the LuxS/AI-2 QS system to the networks that regulate the pathogenicity of K. pneumoniae. Our study will facilitate our understanding of the regulatory mechanisms of LuxS/AI-2 QS on the pathogenicity of K. pneumoniae under the background of their genetic heterogeneity and help develop new strategies for diminished bacterial virulence within the clinical K. pneumoniae population.
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Affiliation(s)
- Miran Tang
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Deyi Zhao
- Department of Medical Lab Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Ying Zhang
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Changrui Qian
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Huale Chen
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Lijiang Chen
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jianzhong Ye
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Tieli Zhou
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
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3
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Zhao W, Hu T, Ma H, Li D, Zhao Q, Jiang J, Wei L. A review of microbial responses to biochar addition in anaerobic digestion system: Community, cellular and genetic level findings. BIORESOURCE TECHNOLOGY 2024; 391:129929. [PMID: 37923231 DOI: 10.1016/j.biortech.2023.129929] [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: 08/22/2023] [Revised: 10/11/2023] [Accepted: 10/26/2023] [Indexed: 11/07/2023]
Abstract
The biochar is a well-developed porous material with various excellent properties, that has been proven with excellent ability in anaerobic digestion (AD) efficiency promotion. Current research is usually focused on the macro effects of biochar on AD, while the systematic review about the mechanisms of biochar on microbial behavior are still lacking. This review summarizes the effects and potential mechanisms of biochar on microorganisms in AD systems, and found that biochar addition can provide habitats for microbial colonization, alleviate toxins stress, supply essential nutrients, and accelerate interspecies electron transferring. Moreover, it also improves microbial community diversity, facilitates EPS secretion, enhances functional enzyme activity, promotes functional genes expression, and inhibits the antibiotic resistance genes transformation. Future research directions including biochar targeted design, in-depth microbial mechanisms revelation, and modified model development were suggested, which could promote the widely practical application of of biochar-amended AD technology.
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Affiliation(s)
- Weixin Zhao
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Tianyi Hu
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Hao Ma
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Dan Li
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Qingliang Zhao
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Junqiu Jiang
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Liangliang Wei
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin 150090, China.
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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: 17] [Impact Index Per Article: 17.0] [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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Dixon B, Sui C, Briley A, Hsu PC, Howell C. Continuous, Nondestructive Detection of Microorganism Growth at Buried Interfaces with Vascularized Polymers. ACS APPLIED BIO MATERIALS 2023; 6:519-528. [PMID: 36633595 DOI: 10.1021/acsabm.2c00837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Evaluating surface bacterial growth at buried interfaces can be problematic due to the difficulties associated with obtaining samples. In this work, we present a new method to detect signals from microorganisms at buried interfaces that is nondestructive and can be conducted continuously. Inspired by vascular systems in nature that permit chemical communication between the surface and underlying tissues of an organism, we created a system in which an inert carrier fluid could be introduced into an empty vascular network embedded in a polymer matrix. When a microorganism layer was grown on top, small molecules produced by the growth process would diffuse down into the carrier fluid, which could then be collected and analyzed. We used this system to nondestructively detect signals from a surface layer of Escherichia coli using conductivity, ultraviolet-visible (UV-vis) absorbance spectroscopy, and high-performance liquid chromatography (HPLC) for organic acids, methods that ranged in sensitivity, time-to-result, and cost. Carrier fluid from sample vascularized polymers with surface bacterial growth recorded significantly higher values in both conductivity and absorbance at 350 nm compared to controls with no bacteria after 24 h. HPLC analysis showed three clear peaks that varied between the samples with bacteria and the controls without. Tests tracking the change in signals over 48 h showed clear trends that matched the bacterial growth curves, demonstrating the system's ability to monitor changes over time. A 2D finite element model of the system closely matched the experimental results, confirming the predictability of the system. Finally, tests using clinically relevant Staphylococcus aureus and Pseudomonas aeruginosa yielded differences in conductivity, absorbance, and HPLC peak areas unique to each species. This work lays the foundation for the use of vascularized polymers as an adaptive system for the continuous, nondestructive detection of surface microorganisms at buried interfaces in both industry and medicine.
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Affiliation(s)
- Brandon Dixon
- Department of Chemical and Biomedical Engineering, University of Maine, Orono, Maine04469, United States
| | - Chenxi Sui
- Thomas Lord Department of Mechanical Engineering and Material Science, Duke University, Durham, North Carolina27708, United States
| | - Anna Briley
- Department of Chemical and Biomedical Engineering, University of Maine, Orono, Maine04469, United States
| | - Po-Chun Hsu
- Thomas Lord Department of Mechanical Engineering and Material Science, Duke University, Durham, North Carolina27708, United States.,Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois60637, United States
| | - Caitlin Howell
- Department of Chemical and Biomedical Engineering, University of Maine, Orono, Maine04469, United States.,Graduate School of Biomedical Science and Engineering, University of Maine, Orono, Maine04469, United States
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Shevate SN, Shinde SS, Bankar AV, Patil NP. Identification of Quorum Quenching N-Acyl Homoserine Lactonases from Priestia aryabhattai J1D and Bacillus cereus G Isolated from the Rhizosphere. Curr Microbiol 2023; 80:86. [PMID: 36717410 DOI: 10.1007/s00284-023-03186-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 01/07/2023] [Indexed: 02/01/2023]
Abstract
Several pathogenic bacteria communicate using N-acyl homoserine lactone (AHL) as a quorum sensing (QS) molecule. The process of interfering with the QS system is known as quorum quenching (QQ), it is an effective tool to control QS-dependent virulence in pathogens. In the present study, rhizosphere bacterial isolates were screened for their ability to produce AHL lactonase enzyme as QQ molecules, which hydrolyses AHL signalling molecules and consequently blocks the QS system. Potent N-hexanoyl-l-homoserine lactone (C6HSL) hydrolytic QQ activity was detected in rhizosphere isolates namely Bacillus cereus G and Priestia aryabhattai J1D. The cell-free supernatant of the bacterial isolates indicated a reduction in biofilm formation in the human pathogens Vibrio cholerae, Pseudomonas aeruginosa, and Staphylococcus aureus without inhibiting cells, signifying their biocontrol property. Furthermore, liquid chromatography high resolution mass spectrometry analysis confirmed C6HSL hydrolytic activity by AHL lactonase produced by these rhizosphere isolates. Also, the aiiA homologous gene from the bacterial isolates showed similarity with the aiiA lactonase gene from Bacillus species, which was further confirmed by homology modelling. In silico structure analysis by comparing with the structure of Bacillus revealed the similarity in the active site, indicating the same degradation pattern. Based on available reported data, the present study indicates the first report of the presence of the aiiA lactonase gene in P. aryabhattai.
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Affiliation(s)
- Shital Nitin Shevate
- Department of Microbiology, MES Abasaheb Garware College Affiliated to Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Sonali Sudhakar Shinde
- Annasaheb Kulkarni Department of Biodiversity MES Abasaheb Garware College Affiliated to Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Ashok Vanaji Bankar
- Department of Microbiology, MES Abasaheb Garware College Affiliated to Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Niranjan Prakashrao Patil
- Department of Microbiology, MES Abasaheb Garware College Affiliated to Savitribai Phule Pune University, Pune, Maharashtra, India.
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7
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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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Li X, Zhang P, Yin Z, Xu F, Yang ZH, Jin J, Qu J, Liu Z, Qi H, Yao C, Shuai J. Caspase-1 and Gasdermin D Afford the Optimal Targets with Distinct Switching Strategies in NLRP1b Inflammasome-Induced Cell Death. Research (Wash D C) 2022; 2022:9838341. [PMID: 35958114 PMCID: PMC9343085 DOI: 10.34133/2022/9838341] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/17/2022] [Indexed: 12/12/2022] Open
Abstract
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.
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Affiliation(s)
- Xiang Li
- Department of Physics and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen 361005, China
- National Institute for Data Science in Health and Medicine and State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Peipei Zhang
- National Institute for Data Science in Health and Medicine and State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Zhiyong Yin
- Department of Physics and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen 361005, China
| | - Fei Xu
- Department of Physics and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen 361005, China
| | - Zhang-Hua Yang
- National Institute for Data Science in Health and Medicine and State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jun Jin
- Department of Physics and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen 361005, China
| | - Jing Qu
- Department of Physics and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen 361005, China
| | - Zhilong Liu
- Department of Physics and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen 361005, China
| | - Hong Qi
- Complex Systems Research Center, Shanxi University, Shanxi, Taiyuan 030006, China
| | - Chenggui Yao
- College of Data Science, Jiaxing University, Jiaxing 314000, China
| | - Jianwei Shuai
- Department of Physics and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen 361005, China
- National Institute for Data Science in Health and Medicine and State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen 361102, 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
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9
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Gangan MS, Vasconcelos MM, Mitra U, Câmara O, Boedicker JQ. Intertemporal trade-off between population growth rate and carrying capacity during public good production. iScience 2022; 25:104117. [PMID: 35391831 PMCID: PMC8980746 DOI: 10.1016/j.isci.2022.104117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/14/2022] [Accepted: 03/16/2022] [Indexed: 11/19/2022] Open
Abstract
Public goods are biomolecules that benefit cellular populations, such as by providing access to previously unutilized resources. Public good production is energetically costly. To reduce this cost, populations control public good biosynthesis, for example using density-dependent regulation accomplished by quorum sensing. Fitness costs and benefits of public good production must be balanced, similar to optimal investment decisions used in economics. We explore the regulation of a public good that increases the carrying capacity, through experimental measurements of growth in Escherichia coli and analysis using a modified logistic growth model. The timing of public good production showed a sharply peaked optimum in population fitness. The cell density associated with maximum public good benefits was determined by the trade-off between the cost of public good production, in terms of reduced growth rate, and benefits received from public goods, in the form of increased carrying capacity. Public good production creates trade-off between growth rate and carrying capacity Cell density-dependent regulation times the production to optimize this trade-off At this time, benefits of public good are maximum and received instantaneously
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Affiliation(s)
- Manasi S. Gangan
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA, USA
| | - Marcos M. Vasconcelos
- Commonweath Cyber-Initiative and Bradley Department of Electrical Engineering, Virginia Polytechnic Institute and State University, Arlington, VA, USA
| | - Urbashi Mitra
- Ming Hsieh Department of Electrical & Computer Engineering, Department of Computer Science, University of Southern California, Los Angeles, CA, USA
| | - Odilon Câmara
- USC Marshall School of Business, University of Southern California, Los Angeles, CA, USA
| | - James Q. Boedicker
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
- Corresponding author
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10
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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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Tripathi S, Chandra R, Purchase D, Bilal M, Mythili R, Yadav S. Quorum sensing - a promising tool for degradation of industrial waste containing persistent organic pollutants. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 292:118342. [PMID: 34653589 DOI: 10.1016/j.envpol.2021.118342] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/28/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Restoring an environment contaminated with persistent organic pollutants (POPs) is highly challenging. Biodegradation by biofilm-forming bacteria through quorum sensing (QS) is a promising treatment process to remove these pollutants and promotes eco-restoration. QS plays an important role in biofilm formation, solubilization, and biotransformation of pollutants. QS is a density-based communication between microbial cells via signalling molecules, which coordinates specific characters and helps bacteria to acclimatize against stress conditions. Genetic diversification of a biofilm offers excellent opportunities for horizontal gene transfer, improves resistance against stress, and provides a suitable environment for the metabolism of POPs. To develop this technology in industrial scale, it is important to understand the fundamentals and ubiquitous nature of QS bacteria and appreciate the role of QS in the degradation of POPs. Currently, there are knowledge gaps regarding the environmental niche, abundance, and population of QS bacteria in wastewater treatment systems. This review aims to present up-to-date and state-of-the-art information on the roles of QS and QS-mediated strategies in industrial waste treatment including biological treatments (such as activated sludge), highlighting their potentials using examples from the pulp and paper mill industry, hydrocarbon remediation and phytoremediation. The information will help to provide a throughout understanding of the potential of QS to degrade POPs and advance the use of this technology. Current knowledge of QS strategies is limited to laboratory studies, full-scale applications remain challenging and more research is need to explore QS gene expression and test in full-scale reactors for wastewater treatment.
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Affiliation(s)
- Sonam Tripathi
- Department of Environmental Microbiology, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar University (A Central University), VidyaVihar, Raebareli Road, Lucknow, 226025, U.P., India
| | - Ram Chandra
- Department of Environmental Microbiology, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar University (A Central University), VidyaVihar, Raebareli Road, Lucknow, 226025, U.P., India.
| | - Diane Purchase
- Department of Natural Sciences, Facultyof Science and Technology, Middlesex University, The Burroughs, Hendon, London, England NW4 4BT, UK
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Raja Mythili
- PG & Research Department of Biotechnology, Mahendra Arts & Science College, Kalppatti, Namakkal, 637503, Tamil Nadu, India
| | - Sangeeta Yadav
- Department of Environmental Microbiology, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar University (A Central University), VidyaVihar, Raebareli Road, Lucknow, 226025, U.P., India.
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