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Mizohata T, Kobayashi TJ, Bouchard LS, Miyahara H. Information geometric bound on general chemical reaction networks. Phys Rev E 2024; 109:044308. [PMID: 38755923 DOI: 10.1103/physreve.109.044308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 03/21/2024] [Indexed: 05/18/2024]
Abstract
We investigate the convergence of chemical reaction networks (CRNs), aiming to establish an upper bound on their reaction rates. The nonlinear characteristics and discrete composition of CRNs pose significant challenges in this endeavor. To circumvent these complexities, we adopt an information geometric perspective, utilizing the natural gradient to formulate a nonlinear system. This system effectively determines an upper bound for the dynamics of CRNs. We corroborate our methodology through numerical simulations, which reveal that our constructed system converges more rapidly than CRNs within a particular class of reactions. This class is defined by the count of chemicals, the highest stoichiometric coefficients in the reactions, and the total number of reactions involved. Further, we juxtapose our approach with traditional methods, illustrating that the latter falls short in providing an upper bound for CRN reaction rates. Although our investigation centers on CRNs, the widespread presence of hypergraphs across various disciplines, ranging from natural sciences to engineering, indicates potential wider applications of our method, including in the realm of information science.
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Affiliation(s)
- Tsuyoshi Mizohata
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Hokkaido 060-0814, Japan
| | - Tetsuya J Kobayashi
- Institute of Industrial Science, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8505 Japan
| | - Louis-S Bouchard
- Center for Quantum Science and Engineering, University of California, Los Angeles, California 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, California 90095, USA
| | - Hideyuki Miyahara
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Hokkaido 060-0814, Japan
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Takakura Y, Machida M, Terada N, Katsumi Y, Kawamura S, Horie K, Miyauchi M, Ishikawa T, Akiyama N, Seki T, Miyao T, Hayama M, Endo R, Ishii H, Maruyama Y, Hagiwara N, Kobayashi TJ, Yamaguchi N, Takano H, Akiyama T, Yamaguchi N. Mitochondrial protein C15ORF48 is a stress-independent inducer of autophagy that regulates oxidative stress and autoimmunity. Nat Commun 2024; 15:953. [PMID: 38296961 PMCID: PMC10831050 DOI: 10.1038/s41467-024-45206-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 01/18/2024] [Indexed: 02/02/2024] Open
Abstract
Autophagy is primarily activated by cellular stress, such as starvation or mitochondrial damage. However, stress-independent autophagy is activated by unclear mechanisms in several cell types, such as thymic epithelial cells (TECs). Here we report that the mitochondrial protein, C15ORF48, is a critical inducer of stress-independent autophagy. Mechanistically, C15ORF48 reduces the mitochondrial membrane potential and lowers intracellular ATP levels, thereby activating AMP-activated protein kinase and its downstream Unc-51-like kinase 1. Interestingly, C15ORF48-dependent induction of autophagy upregulates intracellular glutathione levels, promoting cell survival by reducing oxidative stress. Mice deficient in C15orf48 show a reduction in stress-independent autophagy in TECs, but not in typical starvation-induced autophagy in skeletal muscles. Moreover, C15orf48-/- mice develop autoimmunity, which is consistent with the fact that the stress-independent autophagy in TECs is crucial for the thymic self-tolerance. These results suggest that C15ORF48 induces stress-independent autophagy, thereby regulating oxidative stress and self-tolerance.
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Affiliation(s)
- Yuki Takakura
- Department of Molecular Cardiovascular Pharmacology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan
- Laboratory of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Moeka Machida
- Department of Molecular Cardiovascular Pharmacology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan
- Laboratory of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan
| | - Natsumi Terada
- Department of Molecular Cardiovascular Pharmacology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan
- Laboratory of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan
| | - Yuka Katsumi
- Department of Molecular Cardiovascular Pharmacology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan
| | - Seika Kawamura
- Department of Molecular Cardiovascular Pharmacology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan
| | - Kenta Horie
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Maki Miyauchi
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230-0045, Japan
| | - Tatsuya Ishikawa
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230-0045, Japan
| | - Nobuko Akiyama
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Takao Seki
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Takahisa Miyao
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230-0045, Japan
| | - Mio Hayama
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230-0045, Japan
| | - Rin Endo
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230-0045, Japan
| | - Hiroto Ishii
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230-0045, Japan
| | - Yuya Maruyama
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230-0045, Japan
| | - Naho Hagiwara
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Tetsuya J Kobayashi
- Institute of Industrial Science, The University of Tokyo, Tokyo, 153-8505, Japan
| | - Naoto Yamaguchi
- Laboratory of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan
| | - Hiroyuki Takano
- Department of Molecular Cardiovascular Pharmacology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan
| | - Taishin Akiyama
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan.
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230-0045, Japan.
| | - Noritaka Yamaguchi
- Department of Molecular Cardiovascular Pharmacology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan.
- Laboratory of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan.
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan.
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Ishikawa T, Horie K, Takakura Y, Ohki H, Maruyama Y, Hayama M, Miyauchi M, Miyao T, Hagiwara N, Kobayashi TJ, Akiyama N, Akiyama T. T-cell receptor repertoire analysis of CD4-positive T cells from blood and an affected organ in an autoimmune mouse model. Genes Cells 2023; 28:929-941. [PMID: 37909727 DOI: 10.1111/gtc.13079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/15/2023] [Accepted: 10/22/2023] [Indexed: 11/03/2023]
Abstract
One hallmark of some autoimmune diseases is the variability of symptoms among individuals. Organs affected by the disease differ between patients, posing a challenge in diagnosing the affected organs. Although numerous studies have investigated the correlation between T cell antigen receptor (TCR) repertoires and the development of infectious and immune diseases, the correlation between TCR repertoires and variations in disease symptoms among individuals remains unclear. This study aimed to investigate the correlation of TCRα and β repertoires in blood T cells with the extent of autoimmune signs that varies among individuals. We sequenced TCRα and β of CD4+ CD44high CD62Llow T cells in the blood and stomachs of mice deficient in autoimmune regulator (Aire) (AIRE KO), a mouse model of human autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy. Data analysis revealed that the degree of similarity in TCR sequences between the blood and stomach varied among individual AIRE KO mice and reflected the extent of T cell infiltration in the stomach. We identified a set of TCR sequences whose frequencies in blood might correlate with extent of the stomach manifestations. Our results propose a potential of using TCR repertoires not only for diagnosing disease development but also for diagnosing affected organs in autoimmune diseases.
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Affiliation(s)
- Tatsuya Ishikawa
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Kenta Horie
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yuki Takakura
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Houko Ohki
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Yuya Maruyama
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Mio Hayama
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Maki Miyauchi
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Takahisa Miyao
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Naho Hagiwara
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Nobuko Akiyama
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Taishin Akiyama
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
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Horie K, Namiki K, Kinoshita K, Miyauchi M, Ishikawa T, Hayama M, Maruyama Y, Hagiwara N, Miyao T, Murata S, Kobayashi TJ, Akiyama N, Akiyama T. Acute irradiation causes a long-term disturbance in the heterogeneity and gene expression profile of medullary thymic epithelial cells. Front Immunol 2023; 14:1186154. [PMID: 38022666 PMCID: PMC10652284 DOI: 10.3389/fimmu.2023.1186154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
The thymus has the ability to regenerate from acute injury caused by radiation, infection, and stressors. In addition to thymocytes, thymic epithelial cells in the medulla (mTECs), which are crucial for T cell self-tolerance by ectopically expressing and presenting thousands of tissue-specific antigens (TSAs), are damaged by these insults and recover thereafter. However, given recent discoveries on the high heterogeneity of mTECs, it remains to be determined whether the frequency and properties of mTEC subsets are restored during thymic recovery from radiation damage. Here we demonstrate that acute total body irradiation with a sublethal dose induces aftereffects on heterogeneity and gene expression of mTECs. Single-cell RNA-sequencing (scRNA-seq) analysis showed that irradiation reduces the frequency of mTECs expressing AIRE, which is a critical regulator of TSA expression, 15 days after irradiation. In contrast, transit-amplifying mTECs (TA-mTECs), which are progenitors of AIRE-expressing mTECs, and Ccl21a-expressing mTECs, were less affected. Interestingly, a detailed analysis of scRNA-seq data suggested that the proportion of a unique mTEC cluster expressing Ccl25 and a high level of TSAs was severely decreased by irradiation. In sum, we propose that the effects of acute irradiation disrupt the heterogeneity and properties of mTECs over an extended period, which potentially leads to an impairment of thymic T cell selection.
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Affiliation(s)
- Kenta Horie
- Laboratory for Immune Homeostasis, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Kano Namiki
- Laboratory for Immune Homeostasis, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Kyouhei Kinoshita
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Maki Miyauchi
- Laboratory for Immune Homeostasis, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
| | - Tatsuya Ishikawa
- Laboratory for Immune Homeostasis, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Mio Hayama
- Laboratory for Immune Homeostasis, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Yuya Maruyama
- Laboratory for Immune Homeostasis, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Naho Hagiwara
- Laboratory for Immune Homeostasis, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
| | - Takahisa Miyao
- YCI Laboratory for Immunological Transcriptomics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Shigeo Murata
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Nobuko Akiyama
- Laboratory for Immune Homeostasis, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Taishin Akiyama
- Laboratory for Immune Homeostasis, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
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Nakashima S, J. Kobayashi T. Population dynamics models for various forms of adaptation. Biophys Physicobiol 2023; 20:e200034. [PMID: 38124797 PMCID: PMC10728623 DOI: 10.2142/biophysico.bppb-v20.0034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/31/2023] [Indexed: 12/23/2023] Open
Abstract
Adaptability to changing environments is one of the universal characteristics of living organisms. Because individual modes of adaptation are diverse, a unified understanding of these diverse modes is essential to comprehend adaptation. Adaptations can be categorized from at least two perspectives with respect to information. One is the passivity and activity of adaptation and the other is the type of information transmission. In Darwinian natural selection, organisms are selected among randomly generated traits under which individual organisms are passive in the sense that they do not process any environmental information. On the other hand, organisms can also adapt by sensing their environment and changing their traits. This is an active adaptation in that it makes use of environmental information. In terms of information transfer, adaptation through phenotypic heterogeneity, such as bacterial bet-hedging, is intragenerational in which traits are not passed on to the next generation. In contrast, adaptation through genetic diversity is intergenerational. The theory of population dynamics enables us to unify these various modes of adaptations and their properties can be analyzed qualitatively and quantitatively using techniques from quantitative genetics and information thermodynamics. In addition, such methods can be applied to situations where organisms can learn from past experiences and pass them on from generation to generation. In this work, we introduce the unified theory of biological adaptation based on population dynamics and show its potential applications to evaluate the fitness value of information and to analyze experimental lineage tree data. Finally, we discuss future perspectives for its development. This review article is an extended version of the Japanese article in SEIBUTSU BUTSURI Vol. 57, p. 287-290 (2017).
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Affiliation(s)
- So Nakashima
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo 153-8505, Japan
| | - Tetsuya J. Kobayashi
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo 153-8505, Japan
- Universal Biology Institute, The University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan
- Department of Mathematical Informatics, Graduate School of Information Science and Technology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan
- Department of Electrical Engineering and Information Systems, Graduate School of Information Science and Technology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan
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Tottori T, Kobayashi TJ. Decentralized Stochastic Control with Finite-Dimensional Memories: A Memory Limitation Approach. Entropy (Basel) 2023; 25:e25050791. [PMID: 37238546 DOI: 10.3390/e25050791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/04/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023]
Abstract
Decentralized stochastic control (DSC) is a stochastic optimal control problem consisting of multiple controllers. DSC assumes that each controller is unable to accurately observe the target system and the other controllers. This setup results in two difficulties in DSC; one is that each controller has to memorize the infinite-dimensional observation history, which is not practical, because the memory of the actual controllers is limited. The other is that the reduction of infinite-dimensional sequential Bayesian estimation to finite-dimensional Kalman filter is impossible in general DSC, even for linear-quadratic-Gaussian (LQG) problems. In order to address these issues, we propose an alternative theoretical framework to DSC-memory-limited DSC (ML-DSC). ML-DSC explicitly formulates the finite-dimensional memories of the controllers. Each controller is jointly optimized to compress the infinite-dimensional observation history into the prescribed finite-dimensional memory and to determine the control based on it. Therefore, ML-DSC can be a practical formulation for actual memory-limited controllers. We demonstrate how ML-DSC works in the LQG problem. The conventional DSC cannot be solved except in the special LQG problems where the information the controllers have is independent or partially nested. We show that ML-DSC can be solved in more general LQG problems where the interaction among the controllers is not restricted.
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Affiliation(s)
- Takehiro Tottori
- Department of Mathematical Informatics, Graduate School of Information Science and Technology, The University of Tokyo, Tokyo 113-8654, Japan
| | - Tetsuya J Kobayashi
- Department of Mathematical Informatics, Graduate School of Information Science and Technology, The University of Tokyo, Tokyo 113-8654, Japan
- Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan
- Department of Electrical Engineering and Information Systems, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8654, Japan
- Universal Biology Institute, The University of Tokyo, Tokyo 113-8654, Japan
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7
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Tottori T, Kobayashi TJ. Forward-Backward Sweep Method for the System of HJB-FP Equations in Memory-Limited Partially Observable Stochastic Control. Entropy (Basel) 2023; 25:e25020208. [PMID: 36832575 PMCID: PMC9955073 DOI: 10.3390/e25020208] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 01/09/2023] [Accepted: 01/16/2023] [Indexed: 06/01/2023]
Abstract
Memory-limited partially observable stochastic control (ML-POSC) is the stochastic optimal control problem under incomplete information and memory limitation. To obtain the optimal control function of ML-POSC, a system of the forward Fokker-Planck (FP) equation and the backward Hamilton-Jacobi-Bellman (HJB) equation needs to be solved. In this work, we first show that the system of HJB-FP equations can be interpreted via Pontryagin's minimum principle on the probability density function space. Based on this interpretation, we then propose the forward-backward sweep method (FBSM) for ML-POSC. FBSM is one of the most basic algorithms for Pontryagin's minimum principle, which alternately computes the forward FP equation and the backward HJB equation in ML-POSC. Although the convergence of FBSM is generally not guaranteed in deterministic control and mean-field stochastic control, it is guaranteed in ML-POSC because the coupling of the HJB-FP equations is limited to the optimal control function in ML-POSC.
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Affiliation(s)
- Takehiro Tottori
- Department of Mathematical Informatics, Graduate School of Information Science and Technology, The University of Tokyo, Tokyo 113-8654, Japan
| | - Tetsuya J. Kobayashi
- Department of Mathematical Informatics, Graduate School of Information Science and Technology, The University of Tokyo, Tokyo 113-8654, Japan
- Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan
- Department of Electrical Engineering and Information Systems, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8654, Japan
- Universal Biology Institute, The University of Tokyo, Tokyo 113-8654, Japan
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Tokuoka Y, Yamada TG, Mashiko D, Ikeda Z, Kobayashi TJ, Yamagata K, Funahashi A. An explainable deep learning-based algorithm with an attention mechanism for predicting the live birth potential of mouse embryos. Artif Intell Med 2022; 134:102432. [PMID: 36462898 DOI: 10.1016/j.artmed.2022.102432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 08/13/2022] [Accepted: 10/19/2022] [Indexed: 11/09/2022]
Abstract
In assisted reproductive technology (ART), embryos produced by in vitro fertilization (IVF) are graded according to their live birth potential, and high-grade embryos are preferentially transplanted. However, rates of live birth following clinical ART remain low worldwide. Grading is based on the embryo shape at a limited number of stages and does not consider the shape of embryos and intracellular structures, e.g., nuclei, at various stages important for normal embryogenesis. Here, we developed a Normalized Multi-View Attention Network (NVAN) that directly predicts live birth potential from the nuclear structure in live-cell fluorescence images of mouse embryos from zygote to across a wide range of stages. The input is morphological features of cell nuclei, which were extracted as multivariate time-series data by using the segmentation algorithm for mouse embryos. The classification accuracy of our method (83.87%) greatly exceeded that of existing machine-learning methods and that of visual inspection by embryo culture specialists. Our method also has a new attention mechanism that allows us to determine which values of multivariate time-series data, used to describe nuclear morphology, were the basis for the prediction. By visualizing the features that contributed most to the prediction of live birth potential, we found that the size and shape of the nucleus at the morula stage and at the time of cell division were important for live birth prediction. We anticipate that our method will help ART and developmental engineering as a new basic technology for IVF embryo selection.
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Affiliation(s)
- Yuta Tokuoka
- Center for Biosciences and Informatics, Graduate School of Fundamental Science and Technology, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama, 223-8522, Japan
| | - Takahiro G Yamada
- Center for Biosciences and Informatics, Graduate School of Fundamental Science and Technology, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama, 223-8522, Japan; Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama, 223-8522, Japan
| | - Daisuke Mashiko
- Faculty of Biology-Oriented Science and Technology, Kindai University, 930 Nishimitani, Kinokawa, Wakayama, 649-6493, Japan
| | - Zenki Ikeda
- Faculty of Biology-Oriented Science and Technology, Kindai University, 930 Nishimitani, Kinokawa, Wakayama, 649-6493, Japan
| | - Tetsuya J Kobayashi
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
| | - Kazuo Yamagata
- Faculty of Biology-Oriented Science and Technology, Kindai University, 930 Nishimitani, Kinokawa, Wakayama, 649-6493, Japan
| | - Akira Funahashi
- Center for Biosciences and Informatics, Graduate School of Fundamental Science and Technology, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama, 223-8522, Japan; Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama, 223-8522, Japan.
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9
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Tottori T, Kobayashi TJ. Memory-Limited Partially Observable Stochastic Control and Its Mean-Field Control Approach. Entropy (Basel) 2022; 24:e24111599. [PMID: 36359688 PMCID: PMC9689590 DOI: 10.3390/e24111599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/28/2022] [Accepted: 10/28/2022] [Indexed: 06/01/2023]
Abstract
Control problems with incomplete information and memory limitation appear in many practical situations. Although partially observable stochastic control (POSC) is a conventional theoretical framework that considers the optimal control problem with incomplete information, it cannot consider memory limitation. Furthermore, POSC cannot be solved in practice except in special cases. In order to address these issues, we propose an alternative theoretical framework, memory-limited POSC (ML-POSC). ML-POSC directly considers memory limitation as well as incomplete information, and it can be solved in practice by employing the technique of mean-field control theory. ML-POSC can generalize the linear-quadratic-Gaussian (LQG) problem to include memory limitation. Because estimation and control are not clearly separated in the LQG problem with memory limitation, the Riccati equation is modified to the partially observable Riccati equation, which improves estimation as well as control. Furthermore, we demonstrate the effectiveness of ML-POSC for a non-LQG problem by comparing it with the local LQG approximation.
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Affiliation(s)
- Takehiro Tottori
- Department of Mathematical Informatics, Graduate School of Information Science and Technology, The University of Tokyo, Tokyo 113-8654, Japan
| | - Tetsuya J. Kobayashi
- Department of Mathematical Informatics, Graduate School of Information Science and Technology, The University of Tokyo, Tokyo 113-8654, Japan
- Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan
- Department of Electrical Engineering and Information Systems, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8654, Japan
- Universal Biology Institute, The University of Tokyo, Tokyo 113-8654, Japan
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10
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Katayama Y, Kobayashi TJ. Comparative Study of Repertoire Classification Methods Reveals Data Efficiency of k-mer Feature Extraction. Front Immunol 2022; 13:797640. [PMID: 35936014 PMCID: PMC9346074 DOI: 10.3389/fimmu.2022.797640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 06/20/2022] [Indexed: 01/18/2023] Open
Abstract
The repertoire of T cell receptors encodes various types of immunological information. Machine learning is indispensable for decoding such information from repertoire datasets measured by next-generation sequencing (NGS). In particular, the classification of repertoires is the most basic task, which is relevant for a variety of scientific and clinical problems. Supported by the recent appearance of large datasets, efficient but data-expensive methods have been proposed. However, it is unclear whether they can work efficiently when the available sample size is severely restricted as in practical situations. In this study, we demonstrate that their performances can be impaired substantially below critical sample sizes. To complement this drawback, we propose MotifBoost, which exploits the information of short k-mer motifs of TCRs. MotifBoost can perform the classification as efficiently as a deep learning method on large datasets while providing more stable and reliable results on small datasets. We tested MotifBoost on the four small datasets which consist of various conditions such as Cytomegalovirus (CMV), HIV, α-chain, β-chain and it consistently preserved the stability. We also clarify that the robustness of MotifBoost can be attributed to the efficiency of k-mer motifs as representation features of repertoires. Finally, by comparing the predictions of these methods, we show that the whole sequence identity and sequence motifs encode partially different information and that a combination of such complementary information is necessary for further development of repertoire analysis.
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Affiliation(s)
- Yotaro Katayama
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
- *Correspondence: Yotaro Katayama,
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11
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Katayama Y, Yokota R, Akiyama T, Kobayashi TJ. Machine Learning Approaches to TCR Repertoire Analysis. Front Immunol 2022; 13:858057. [PMID: 35911778 PMCID: PMC9334875 DOI: 10.3389/fimmu.2022.858057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Sparked by the development of genome sequencing technology, the quantity and quality of data handled in immunological research have been changing dramatically. Various data and database platforms are now driving the rapid progress of machine learning for immunological data analysis. Of various topics in immunology, T cell receptor repertoire analysis is one of the most important targets of machine learning for assessing the state and abnormalities of immune systems. In this paper, we review recent repertoire analysis methods based on machine learning and deep learning and discuss their prospects.
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Affiliation(s)
- Yotaro Katayama
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
- *Correspondence: Yotaro Katayama,
| | - Ryo Yokota
- National Research Institute of Police Science, Kashiwa, Chiba, Japan
| | - Taishin Akiyama
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Tetsuya J. Kobayashi
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
- Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
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12
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Mashiko D, Ikeda Z, Tokoro M, Hatano Y, Yao T, Kobayashi TJ, Fukunaga N, Asada Y, Yamagata K. Asynchronous division at 4–8-cell stage of preimplantation embryos affects live birth through ICM/TE differentiation. Sci Rep 2022; 12:9411. [PMID: 35672442 PMCID: PMC9174281 DOI: 10.1038/s41598-022-13646-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/18/2022] [Indexed: 11/30/2022] Open
Abstract
To improve the performance of assisted reproductive technology, it is necessary to find an indicator that can identify and select embryos that will be born or be aborted. We searched for indicators of embryo selection by comparing born/abort mouse embryos. We found that asynchronous embryos during the 4–8-cell stage were predisposed to be aborted. In asynchronous mouse embryos, the nuclear translocation of YAP1 in some blastomeres and compaction were delayed, and the number of ICMs was reduced. Hence, it is possible that asynchronous embryos have abnormal differentiation. When the synchrony of human embryos was observed, it was confirmed that embryos that did not reach clinical pregnancy had asynchrony as in mice. This could make synchrony a universal indicator common to all animal species.
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13
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Nakamura K, Kobayashi TJ. Connection between the Bacterial Chemotactic Network and Optimal Filtering. Phys Rev Lett 2021; 126:128102. [PMID: 33834835 DOI: 10.1103/physrevlett.126.128102] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 02/12/2021] [Indexed: 06/12/2023]
Abstract
The chemotactic network of Escherichia coli has been studied extensively both biophysically and information theoretically. Nevertheless, connection between these two aspects is still elusive. In this work, we report such a connection. We derive an optimal filtering dynamics under the assumption that E. coli's sensory system optimally infers the binary information whether it is swimming up or down along an exponential ligand gradient from noisy sensory signals. Then we show that a standard biochemical model of the chemotactic network is mathematically equivalent to this information-theoretically optimal dynamics. Moreover, we demonstrate that an experimentally observed nonlinear response relation can be reproduced from the optimal dynamics. These results suggest that the biochemical network of E. coli chemotaxis is designed to optimally extract the binary information along an exponential gradient in a noisy condition.
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Affiliation(s)
- Kento Nakamura
- Department of Mathematical Informatics, Graduate School of Information Science and Technology, The University of Tokyo, Tokyo 113-8654, Japan
| | - Tetsuya J Kobayashi
- Department of Mathematical Informatics, Graduate School of Information Science and Technology, The University of Tokyo, Tokyo 113-8654, Japan
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14
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Tokuoka Y, Yamada TG, Mashiko D, Ikeda Z, Hiroi NF, Kobayashi TJ, Yamagata K, Funahashi A. 3D convolutional neural networks-based segmentation to acquire quantitative criteria of the nucleus during mouse embryogenesis. NPJ Syst Biol Appl 2020; 6:32. [PMID: 33082352 PMCID: PMC7575569 DOI: 10.1038/s41540-020-00152-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 09/11/2020] [Indexed: 12/13/2022] Open
Abstract
During embryogenesis, cells repeatedly divide and dynamically change their positions in three-dimensional (3D) space. A robust and accurate algorithm to acquire the 3D positions of the cells would help to reveal the mechanisms of embryogenesis. To acquire quantitative criteria of embryogenesis from time-series 3D microscopic images, image processing algorithms such as segmentation have been applied. Because the cells in embryos are considerably crowded, an algorithm to segment individual cells in detail and accurately is needed. To quantify the nuclear region of every cell from a time-series 3D fluorescence microscopic image of living cells, we developed QCANet, a convolutional neural network-based segmentation algorithm for 3D fluorescence bioimages. We demonstrated that QCANet outperformed 3D Mask R-CNN, which is currently considered as the best algorithm of instance segmentation. We showed that QCANet can be applied not only to developing mouse embryos but also to developing embryos of two other model species. Using QCANet, we were able to extract several quantitative criteria of embryogenesis from 11 early mouse embryos. We showed that the extracted criteria could be used to evaluate the differences between individual embryos. This study contributes to the development of fundamental approaches for assessing embryogenesis on the basis of extracted quantitative criteria.
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Affiliation(s)
- Yuta Tokuoka
- Department of Biosciences and Informatics, Keio University, Kanagawa, 223-8522, Japan
| | - Takahiro G Yamada
- Department of Biosciences and Informatics, Keio University, Kanagawa, 223-8522, Japan
| | - Daisuke Mashiko
- Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama, 649-6493, Japan
| | - Zenki Ikeda
- Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama, 649-6493, Japan
| | - Noriko F Hiroi
- Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University, Yamaguchi, 756-0884, Japan
| | - Tetsuya J Kobayashi
- Institute of Industrial Science, The University of Tokyo, Tokyo, 153-8505, Japan
| | - Kazuo Yamagata
- Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama, 649-6493, Japan
| | - Akira Funahashi
- Department of Biosciences and Informatics, Keio University, Kanagawa, 223-8522, Japan.
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15
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Nakashima S, Sughiyama Y, Kobayashi TJ. Lineage EM algorithm for inferring latent states from cellular lineage trees. Bioinformatics 2020; 36:2829-2838. [PMID: 31971568 DOI: 10.1093/bioinformatics/btaa040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 11/28/2019] [Accepted: 01/16/2020] [Indexed: 11/14/2022] Open
Abstract
SUMMARY Phenotypic variability in a population of cells can work as the bet-hedging of the cells under an unpredictably changing environment, the typical example of which is the bacterial persistence. To understand the strategy to control such phenomena, it is indispensable to identify the phenotype of each cell and its inheritance. Although recent advancements in microfluidic technology offer us useful lineage data, they are insufficient to directly identify the phenotypes of the cells. An alternative approach is to infer the phenotype from the lineage data by latent-variable estimation. To this end, however, we must resolve the bias problem in the inference from lineage called survivorship bias. In this work, we clarify how the survivorship bias distorts statistical estimations. We then propose a latent-variable estimation algorithm without the survivorship bias from lineage trees based on an expectation-maximization (EM) algorithm, which we call lineage EM algorithm (LEM). LEM provides a statistical method to identify the traits of the cells applicable to various kinds of lineage data. AVAILABILITY AND IMPLEMENTATION An implementation of LEM is available at https://github.com/so-nakashima/Lineage-EM-algorithm. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- So Nakashima
- Department of Mathematical Informatics, Graduate School of Information Science and Technology
| | - Yuki Sughiyama
- Institute of Industrial Science, The University of Tokyo, Tokyo 113-8654, Japan
| | - Tetsuya J Kobayashi
- Department of Mathematical Informatics, Graduate School of Information Science and Technology.,Institute of Industrial Science, The University of Tokyo, Tokyo 113-8654, Japan.,PRESTO, Japan Science and Technology Agency (JST), Saitama 332-0012, Japan
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16
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Kobayashi TJ. Bayesian gates for reliable logical operations under noisy conditions. Phys Rev E 2020; 101:042205. [PMID: 32422804 DOI: 10.1103/physreve.101.042205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/13/2020] [Indexed: 11/07/2022]
Abstract
The reliability of logical operations is indispensable for the reliable operation of computational systems. Since the downsizing of microfabrication generates nonnegligible noise in these systems, a new approach for designing noise-immune gates is required. In this paper, we demonstrate that noise-immune gates can be designed by combining Bayesian inference theory with the idea of computation over noisy channels. To reveal their practical advantages, the performance of these gates is evaluated in comparison with a stochastic resonance-based gate proposed previously. We also demonstrate that, in a high noise-level situation, this approach for computation can be better than a conventional one that conducts information transmission and computation separately.
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Affiliation(s)
- Tetsuya J Kobayashi
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba Meguro-ku, Tokyo 153-8505, Japan
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17
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Kajita MK, Aihara K, Kobayashi TJ. Reliable target ligand detection by noise-induced receptor cluster formation. Chaos 2020; 30:011104. [PMID: 32013460 DOI: 10.1063/1.5140714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 12/27/2019] [Indexed: 06/10/2023]
Abstract
Intracellular reactions are intrinsically stochastic. Nonetheless, cells can reliably respond to the changing environment by sensing their target molecules sensitively and specifically, even with the existence of abundant structurally-similar non-target molecules. The mechanism of how the cells can balance and achieve such different characteristics is not yet fully understood. In this work, we demonstrate that these characteristics can be attained by a ligand-induced stochastic cluster formation of receptors via the noise-induced symmetry breaking, in which the intrinsic stochasticity works to enhance sensitivity and specificity. We also show that the noise-induced cluster formation enables cells to detect the target ligand reliably by compensating the abundant non-target ligands in the environment. The proposed mechanism may lead to a deeper understanding of a biological function of the receptor clustering and provide an alternative candidate for the reliable ligand detection to the kinetic proofreading.
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Affiliation(s)
- Masashi K Kajita
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Kazuyuki Aihara
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Tetsuya J Kobayashi
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
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18
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Kaneko KB, Tateishi R, Miyao T, Takakura Y, Akiyama N, Yokota R, Akiyama T, Kobayashi TJ. Quantitative analysis reveals reciprocal regulations underlying recovery dynamics of thymocytes and thymic environment in mice. Commun Biol 2019; 2:444. [PMID: 31815199 PMCID: PMC6884561 DOI: 10.1038/s42003-019-0688-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 11/10/2019] [Indexed: 01/17/2023] Open
Abstract
Thymic crosstalk, a set of reciprocal regulations between thymocytes and the thymic environment, is relevant for orchestrating appropriate thymocyte development as well as thymic recovery from various exogenous insults. In this work, interactions shaping thymic crosstalk and the resultant dynamics of thymocytes and thymic epithelial cells are inferred based on quantitative analysis and modeling of the recovery dynamics induced by irradiation. The analysis identifies regulatory interactions consistent with known molecular evidence and reveals their dynamic roles in the recovery process. Moreover, the analysis also predicts, and a subsequent experiment verifies, a previously unrecognized regulation of CD4+CD8+ double positive thymocytes which temporarily increases their proliferation rate upon the decrease in their population size. Our model establishes a pivotal step towards the dynamic understanding of thymic crosstalk as a regulatory network system.
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Affiliation(s)
- Kazumasa B. Kaneko
- Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku Tokyo, 113-8656 Japan
| | - Ryosuke Tateishi
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Takahisa Miyao
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Yuki Takakura
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Nobuko Akiyama
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Ryo Yokota
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo, 153-8505 Japan
| | - Taishin Akiyama
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Tetsuya J. Kobayashi
- Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku Tokyo, 113-8656 Japan
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo, 153-8505 Japan
- PREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama, 332-0012 Japan
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19
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Abstract
We construct a pathwise formulation for a multitype age-structured population dynamics, which involves an age-dependent cell replication and transition of gene- or phenotypes. By employing the formulation, we derive a variational representation of the stationary population growth rate; the representation comprises a tradeoff relation between growth effects and a single-cell intrinsic dynamics described by a semi-Markov process. This variational representation leads to a response relation of the stationary population growth rate, in which statistics on a retrospective history work as the response coefficients. These results contribute to predicting and controlling growing populations based on experimentally observed cell-lineage information.
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Affiliation(s)
- Yuki Sughiyama
- Institute of Industrial Science, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8505 Japan
| | - So Nakashima
- Graduate School of Information and Technology, Department of Mathematical Informatics, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8654 Japan
| | - Tetsuya J Kobayashi
- Institute of Industrial Science, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8505 Japan
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8, Honcho, Kawaguchi, Saitama 332-0012 Japan
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20
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Horie K, Kudo T, Yoshinaga R, Akiyama N, Sasanuma H, Kobayashi TJ, Shimbo M, Jeon H, Miyao T, Miyauchi M, Shirakawa M, Shiba D, Yoshida N, Muratani M, Takahashi S, Akiyama T. Long-term hindlimb unloading causes a preferential reduction of medullary thymic epithelial cells expressing autoimmune regulator (Aire). Biochem Biophys Res Commun 2018; 501:745-750. [PMID: 29753741 DOI: 10.1016/j.bbrc.2018.05.060] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 05/10/2018] [Indexed: 11/16/2022]
Abstract
Hindlimb unloading (HU) of rodents has been used as a ground-based model of spaceflight. In this study, we investigated the detailed impact of 14-day HU on the murine thymus. Thymic mass and cell number were significantly reduced after 14 days of hindlimb unloading, which was accompanied by an increment of plasma corticosterone. Although corticosterone reportedly causes selective apoptosis of CD4+CD8+ thymocytes (CD4+CD8+DPs) in mice treated with short-term HU, the reduction of thymocyte cellularity after the 14-day HU was not selective for CD4+CD8+DPs. In addition to the thymocyte reduction, the cellularity of thymic epithelial cells (TECs) was also reduced by the 14-day HU. Flow cytometric and RNA-sequencing analysis suggested that medullary TECs (mTECs) were preferentially reduced after HU. Moreover, immunohistochemical staining suggested that the 14-day HU caused a reduction of the mTECs expressing autoimmune regulator (Aire). Our data suggested that HU impacts both thymocytes and TECs. Consequently, these data imply that thymic T cell repertoire formation could be disturbed during spaceflight-like stress.
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Affiliation(s)
- Kenta Horie
- Center for Integrative Medical Science, RIKEN, Yokohama 230-0045, Japan; Mouse Epigenetics Project, ISS/Kibo experiment, Japan Aerospace Exploration Agency (JAXA), Tsukuba, Japan
| | - Takashi Kudo
- Mouse Epigenetics Project, ISS/Kibo experiment, Japan Aerospace Exploration Agency (JAXA), Tsukuba, Japan; Laboratory Animal Resource Center and Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Ibaraki 305-8575, Japan
| | - Riko Yoshinaga
- Center for Integrative Medical Science, RIKEN, Yokohama 230-0045, Japan; Mouse Epigenetics Project, ISS/Kibo experiment, Japan Aerospace Exploration Agency (JAXA), Tsukuba, Japan
| | - Nobuko Akiyama
- Center for Integrative Medical Science, RIKEN, Yokohama 230-0045, Japan; Mouse Epigenetics Project, ISS/Kibo experiment, Japan Aerospace Exploration Agency (JAXA), Tsukuba, Japan
| | - Hiroki Sasanuma
- Mouse Epigenetics Project, ISS/Kibo experiment, Japan Aerospace Exploration Agency (JAXA), Tsukuba, Japan; Laboratory of Developmental Genetics, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Tetsuya J Kobayashi
- Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan
| | - Miki Shimbo
- Mouse Epigenetics Project, ISS/Kibo experiment, Japan Aerospace Exploration Agency (JAXA), Tsukuba, Japan; Laboratory Animal Resource Center and Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Ibaraki 305-8575, Japan
| | - Hyojung Jeon
- Mouse Epigenetics Project, ISS/Kibo experiment, Japan Aerospace Exploration Agency (JAXA), Tsukuba, Japan; Laboratory Animal Resource Center and Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Ibaraki 305-8575, Japan
| | - Takahisa Miyao
- Center for Integrative Medical Science, RIKEN, Yokohama 230-0045, Japan
| | - Maki Miyauchi
- Center for Integrative Medical Science, RIKEN, Yokohama 230-0045, Japan
| | - Masaki Shirakawa
- Mouse Epigenetics Project, ISS/Kibo experiment, Japan Aerospace Exploration Agency (JAXA), Tsukuba, Japan; JEM Utilization Center, Human Spaceflight Technology Directorate, JAXA, Ibaraki 305-8505, Japan
| | - Dai Shiba
- Mouse Epigenetics Project, ISS/Kibo experiment, Japan Aerospace Exploration Agency (JAXA), Tsukuba, Japan; JEM Utilization Center, Human Spaceflight Technology Directorate, JAXA, Ibaraki 305-8505, Japan
| | - Nobuaki Yoshida
- Mouse Epigenetics Project, ISS/Kibo experiment, Japan Aerospace Exploration Agency (JAXA), Tsukuba, Japan; Laboratory of Developmental Genetics, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Masafumi Muratani
- Mouse Epigenetics Project, ISS/Kibo experiment, Japan Aerospace Exploration Agency (JAXA), Tsukuba, Japan; Department of Genome Biology, Faculty of Medicine, University of Tsukuba, Ibaraki 305-8575, Japan
| | - Satoru Takahashi
- Mouse Epigenetics Project, ISS/Kibo experiment, Japan Aerospace Exploration Agency (JAXA), Tsukuba, Japan; Laboratory Animal Resource Center and Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Ibaraki 305-8575, Japan
| | - Taishin Akiyama
- Center for Integrative Medical Science, RIKEN, Yokohama 230-0045, Japan; Mouse Epigenetics Project, ISS/Kibo experiment, Japan Aerospace Exploration Agency (JAXA), Tsukuba, Japan.
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21
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Yokota R, Kaminaga Y, Kobayashi TJ. Quantification of Inter-Sample Differences in T-Cell Receptor Repertoires Using Sequence-Based Information. Front Immunol 2017; 8:1500. [PMID: 29187849 PMCID: PMC5694755 DOI: 10.3389/fimmu.2017.01500] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 10/24/2017] [Indexed: 11/13/2022] Open
Abstract
Inter-sample comparisons of T-cell receptor (TCR) repertoires are crucial for gaining a better understanding of the immunological states determined by different collections of T cells from different donor sites, cell types, and genetic and pathological backgrounds. For quantitative comparison, most previous studies utilized conventional methods in ecology, which focus on TCR sequences that overlap between pairwise samples. Some recent studies attempted another approach that is categorized into Poisson abundance models using the abundance distribution of observed TCR sequences. However, these methods ignore the details of the measured sequences and are consequently unable to identify sub-repertoires that might have important contributions to the observed inter-sample differences. Moreover, the sparsity of sequence data due to the huge diversity of repertoires hampers the performance of these methods, especially when few overlapping sequences exist. In this paper, we propose a new approach for REpertoire COmparison in Low Dimensions (RECOLD) based on TCR sequence information, which can estimate the low-dimensional structure by embedding the pairwise sequence dissimilarities in high-dimensional sequence space. The inter-sample differences between repertoires are then quantified by information-theoretic measures among the distributions of data estimated in the embedded space. Using datasets of mouse and human TCR repertoires, we demonstrate that RECOLD can accurately identify the inter-sample hierarchical structures, which have a good correspondence with our intuitive understanding about sample conditions. Moreover, for the dataset of transgenic mice that have strong restrictions on the diversity of their repertoires, our estimated inter-sample structure was consistent with the structure estimated by previous methods based on abundance or overlapping sequence information. For the dataset of human healthy donors and Sézary syndrome patients, our method also showed robust estimation performance even under the condition of high sparsity in TCR sequences, while previous studies failed to estimate the structure. In addition, we identified the sequences that contribute to the pairwise-sample differences between the repertoires with the different genetic backgrounds of mice. Such identification of the sequences contributing to variation in immune cell repertoires may provide substantial insight for the development of new immunotherapies and vaccines.
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Affiliation(s)
- Ryo Yokota
- Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
| | - Yuki Kaminaga
- Department of Electrical Engineering and Information Systems, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Tetsuya J Kobayashi
- Institute of Industrial Science, The University of Tokyo, Tokyo, Japan.,Department of Electrical Engineering and Information Systems, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.,PRESTO, Japan Science and Technology Agency (JST), Saitama, Japan
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22
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Kajita MK, Aihara K, Kobayashi TJ. Balancing specificity, sensitivity, and speed of ligand discrimination by zero-order ultraspecificity. Phys Rev E 2017; 96:012405. [PMID: 29347185 DOI: 10.1103/physreve.96.012405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Indexed: 06/07/2023]
Abstract
Specific interactions between receptors and their target ligands in the presence of nontarget ligands are crucial for biological processes such as T cell ligand discrimination. To discriminate between the target and nontarget ligands, cells have to increase specificity to the target ligands by amplifying the small differences in affinity among ligands. In addition, sensitivity to the ligand concentration and quick discrimination are also important to detect low amounts of target ligands and facilitate fast cellular decision making after ligand recognition. In this work we propose a mechanism for nonlinear specificity amplification (ultraspecificity) based on zero-order saturating reactions, which was originally proposed to explain nonlinear sensitivity amplification (ultrasensitivity) to the ligand concentration. In contrast to the previously proposed proofreading mechanisms that amplify the specificity by a multistep reaction, our model can produce an optimal balance of specificity, sensitivity, and quick discrimination. Furthermore, we show that a model for insensitivity to a large number of nontarget ligands can be naturally derived from a model with the zero-order ultraspecificity. The zero-order ultraspecificity, therefore, may provide an alternative way to understand ligand discrimination from the viewpoint of nonlinear properties in biochemical reactions.
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Affiliation(s)
- Masashi K Kajita
- Department of Mathematical Informatics, Graduate School of Information Science and Technology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan and Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-Ku, Tokyo 153-8505, Japan
| | - Kazuyuki Aihara
- Department of Mathematical Informatics, Graduate School of Information Science and Technology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan and Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-Ku, Tokyo 153-8505, Japan
| | - Tetsuya J Kobayashi
- Department of Mathematical Informatics, Graduate School of Information Science and Technology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan and Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-Ku, Tokyo 153-8505, Japan
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23
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Kobayashi TJ, Sughiyama Y. Stochastic and information-thermodynamic structures of population dynamics in a fluctuating environment. Phys Rev E 2017; 96:012402. [PMID: 29347239 DOI: 10.1103/physreve.96.012402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Indexed: 06/07/2023]
Abstract
Adaptation in a fluctuating environment is a process of fueling environmental information to gain fitness. Living systems have gradually developed strategies for adaptation from random and passive diversification of the phenotype to more proactive decision making, in which environmental information is sensed and exploited more actively and effectively. Understanding the fundamental relation between fitness and information is therefore crucial to clarify the limits and universal properties of adaptation. In this work, we elucidate the underlying stochastic and information-thermodynamic structure in this process, by deriving causal fluctuation relations (FRs) of fitness and information. Combined with a duality between phenotypic and environmental dynamics, the FRs reveal the limit of fitness gain, the relation of time reversibility with the achievability of the limit, and the possibility and condition for gaining excess fitness due to environmental fluctuation. The loss of fitness due to causal constraints and the limited capacity of real organisms is shown to be the difference between time-forward and time-backward path probabilities of phenotypic and environmental dynamics. Furthermore, the FRs generalize the concept of the evolutionary stable state (ESS) for fluctuating environment by giving the probability that the optimal strategy on average can be invaded by a suboptimal one owing to rare environmental fluctuation. These results clarify the information-thermodynamic structures in adaptation and evolution.
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Affiliation(s)
- Tetsuya J Kobayashi
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku 153-8505, Tokyo, Japan
- PREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Yuki Sughiyama
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku 153-8505, Tokyo, Japan
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24
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Abstract
We report that population dynamics in fluctuating environments is characterized by a mathematically equivalent structure to steady-state thermodynamics. By employing the structure, population growth in fluctuating environments is decomposed into housekeeping and excess parts. The housekeeping part represents the integral of the stationary growth rate for each condition during a history of the environmental change. The excess part accounts for the excess growth induced by environmental fluctuations. Focusing on the excess growth, we obtain a Clausius inequality, which gives the upper bound of the excess growth. The equality is shown to be achieved in quasistatic environmental changes. We also clarify that this bound can be evaluated by the "lineage fitness", which is an experimentally observable quantity.
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Affiliation(s)
- Yuki Sughiyama
- Institute of Industrial Science, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Tetsuya J Kobayashi
- Institute of Industrial Science, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8505, Japan
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25
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Arata Y, Hiroshima M, Pack CG, Ramanujam R, Motegi F, Nakazato K, Shindo Y, Wiseman PW, Sawa H, Kobayashi TJ, Brandão HB, Shibata T, Sako Y. Cortical Polarity of the RING Protein PAR-2 Is Maintained by Exchange Rate Kinetics at the Cortical-Cytoplasmic Boundary. Cell Rep 2016; 17:316. [PMID: 27681440 DOI: 10.1016/j.celrep.2016.09.044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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26
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Abstract
A decrease in system size can induce qualitatively different behavior compared to the macroscopic behavior of the corresponding large-size system. The mechanisms of this transition, which is known as the small-size transition, can be attributed to either a relative increase in the noise intensity or to the discreteness of the state space due to the small system size. The former mechanism has been intensively investigated using several toy and realistic models. However, the latter has rarely been analyzed and is sometimes confused with the former, because a toy model that extracts the essence of the discreteness-induced transition mechanism is lacking. In this work, we propose a one- and three-body reaction system as a minimal model of the discreteness-induced transition and derive the conditions under which this transition occurs in more complex systems. This work enriches our understanding of the influence of small system size on system behavior.
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Affiliation(s)
- Yohei Saito
- Institute of Industrial Science, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8505 Japan
| | - Yuki Sughiyama
- Institute of Industrial Science, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8505 Japan.,Department of Basic Science, School of Arts and Sciences, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Kunihiko Kaneko
- Department of Basic Science, School of Arts and Sciences, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Tetsuya J Kobayashi
- Institute of Industrial Science, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8505 Japan
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27
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Abstract
Phenotype switching with and without sensing environment is a common strategy of organisms to survive in a fluctuating environment. Understanding the evolutionary advantages of switching and sensing requires a quantitative evaluation of their fitness gain and its fluctuation together with the conditions for the switching and sensing strategies being adapted to a given environment. In this work, by using a pathwise formulation of the population dynamics, we show that the optimal switching strategy is characterized by a consistency condition for time-forward and backward path probabilities. The formulation also clarifies the underlying information-theoretic aspect of selection as a passive information compression. The loss of fitness by a suboptimal strategy is also shown to satisfy a fluctuation relation, which provides us with the information on how environmental fluctuation impacts the advantages of the optimal strategy. These results are naturally extended to the situation that organisms can use an environmental signal by actively sensing the environment. The fluctuation relations of the fitness gain by sensing are derived in which the multivariate mutual information among the phenotype, the environment, and the signal plays the role to quantify the relevant information in the signal for the fitness gain.
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Affiliation(s)
- Tetsuya J Kobayashi
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba Meguro-ku, Tokyo 153-8505, Japan
| | - Yuki Sughiyama
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba Meguro-ku, Tokyo 153-8505, Japan
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28
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Hiroi N, Iba K, Tabira A, Okuhara T, Kubojima T, Hiraiwa T, Kobayashi TJ, Oka K, Funahashi A. In vivo oriented modeling with consideration of intracellular crowding. Annu Int Conf IEEE Eng Med Biol Soc 2015; 2013:2716-9. [PMID: 24110288 DOI: 10.1109/embc.2013.6610101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In vivo reaction space is constrained by complex structures which are made of entwined cytoskeletons and organelles; this create the difference between in vivo and in vitro in respect of molecular mobility, and it may affect reaction processes. Our motivation is to reveal the background mechanisms of the properties of molecular behaviors in vivo by numerical approach. For this object, we reassembled a pseudo-intracellular environment in 3D lattice space, and executed Monte Carlo simulation. By changing the relative amount of non-reactive obstacles in the simulation space, we tested the effect of the level of crowdedness to the molecular mobility and reaction processes. Our results showed that molecules demonstrated anomalous diffusion correlating to the restriction level of the reaction space. Reaction processes also showed distinct characteristics, that is increase of reaction rate at the beginning of reactions, with the decrease of the reaction rate at later time frame of reactions. Our results suggested that the anomalous behaviors at singe molecule level in vivo could bring an essential difference to the reaction processes and the results.
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29
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Akiyama T, Tateishi R, Akiyama N, Yoshinaga R, Kobayashi TJ. Positive and Negative Regulatory Mechanisms for Fine-Tuning Cellularity and Functions of Medullary Thymic Epithelial Cells. Front Immunol 2015; 6:461. [PMID: 26441966 PMCID: PMC4568481 DOI: 10.3389/fimmu.2015.00461] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 08/24/2015] [Indexed: 01/10/2023] Open
Abstract
Self-tolerant T cells and regulatory T cells develop in the thymus. A wide variety of cell-cell interactions in the thymus is required for the differentiation, proliferation, and repertoire selection of T cells. Various secreted and cell surface molecules expressed in thymic epithelial cells (TECs) mediate these processes. Moreover, cytokines expressed by cells of hematopoietic origin regulate the cellularity of TECs. Tumor necrosis factor (TNF) family RANK ligand, lymphotoxin, and CD40 ligand, expressed in T cells and innate lymphoid cells (ILCs), promote the differentiation and proliferation of medullary TECs (mTECs) that play critical roles in the induction of immune tolerance. A recent study suggests that interleukin-22 (IL-22) produced by ILCs promotes regeneration of TECs after irradiation. Intriguingly, tumor growth factor-β and osteoprotegerin limit cellularity of mTECs, thereby attenuating regulatory T cell generation. We will review recent insights into the molecular basis for cell-cell interactions regulating differentiation and proliferation of mTECs and also discuss about a perspective on use of mathematical models for understanding this complicated system.
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Affiliation(s)
- Taishin Akiyama
- Division of Cellular and Molecular Biology, Institute of Medical Science, University of Tokyo , Tokyo , Japan
| | - Ryosuke Tateishi
- Division of Cellular and Molecular Biology, Institute of Medical Science, University of Tokyo , Tokyo , Japan
| | - Nobuko Akiyama
- Division of Cellular and Molecular Biology, Institute of Medical Science, University of Tokyo , Tokyo , Japan
| | - Riko Yoshinaga
- Division of Cellular and Molecular Biology, Institute of Medical Science, University of Tokyo , Tokyo , Japan
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30
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Kinoshita K, Kobayashi TJ, Hirano T. Balancing acts of two HEAT subunits of condensin I support dynamic assembly of chromosome axes. Dev Cell 2015; 33:94-106. [PMID: 25850674 DOI: 10.1016/j.devcel.2015.01.034] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Revised: 10/16/2014] [Accepted: 01/29/2015] [Indexed: 11/17/2022]
Abstract
Condensin I is a five-subunit protein complex that plays a central role in mitotic chromosome assembly and segregation in eukaryotes. To dissect its mechanism of action, we reconstituted wild-type and mutant complexes from recombinant subunits and tested their abilities to assemble chromosomes in Xenopus egg cell-free extracts depleted of endogenous condensins. We find that ATP binding and hydrolysis by SMC subunits have distinct contributions to the action of condensin I and that continuous ATP hydrolysis is required for structural maintenance of chromosomes. Mutant complexes lacking either one of two HEAT subunits produce abnormal chromosomes with highly characteristic defects and have contrasting structural effects on chromosome axes preassembled with the wild-type complex. We propose that balancing acts of the two HEAT subunits support dynamic assembly of chromosome axes under the control of the SMC ATPase cycle, thereby governing construction of rod-shaped chromosomes in eukaryotic cells.
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Affiliation(s)
- Kazuhisa Kinoshita
- Chromosome Dynamics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Tetsuya J Kobayashi
- Institute of Industrial Sciences, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Tatsuya Hirano
- Chromosome Dynamics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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31
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Kajita MK, Yokota R, Aihara K, Kobayashi TJ. Experimental and theoretical bases for mechanisms of antigen discrimination by T cells. Biophysics (Nagoya-shi) 2015; 11:85-92. [PMID: 27493520 PMCID: PMC4736787 DOI: 10.2142/biophysics.11.85] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 02/01/2015] [Indexed: 12/01/2022] Open
Abstract
Interaction only within specific molecules is a requisite for accurate operations of a biochemical reaction in a cell where bulk of background molecules exist. While structural specificity is a well-established mechanism for specific interaction, biophysical and biochemical experiments indicate that the mechanism is not sufficient for accounting for the antigen discrimination by T cells. In addition, the antigen discrimination by T cells also accompanies three intriguing properties other than the specificity: sensitivity, speed, and concentration compensation. In this work, we review experimental and theoretical works on the antigen discrimination by focusing on these four properties and show future directions towards understanding of the fundamental principle for molecular discrimination.
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Affiliation(s)
- Masashi K Kajita
- Department of Mathematical Informatics, Graduate School of Information Science and Technology, The University of Tokyo, 4-6-1 Komaba Meguro-ku, Tokyo 153-8505, Japan
| | - Ryo Yokota
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba Meguro-ku, Tokyo 153-8505, Japan
| | - Kazuyuki Aihara
- Department of Mathematical Informatics, Graduate School of Information Science and Technology, The University of Tokyo, 4-6-1 Komaba Meguro-ku, Tokyo 153-8505, Japan; Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba Meguro-ku, Tokyo 153-8505, Japan
| | - Tetsuya J Kobayashi
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba Meguro-ku, Tokyo 153-8505, Japan
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32
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Sughiyama Y, Kobayashi TJ, Tsumura K, Aihara K. Pathwise thermodynamic structure in population dynamics. Phys Rev E Stat Nonlin Soft Matter Phys 2015; 91:032120. [PMID: 25871067 DOI: 10.1103/physreve.91.032120] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Indexed: 06/04/2023]
Abstract
We reveal thermodynamic structure in population dynamics with phenotype switching. Mean fitness for a population of organisms is determined by a thermodynamic variational principle described by the large deviation of phenotype-switching dynamics. Owing to this variational principle, a response relation of the mean fitness with respect to changes of environments and phenotype-switching dynamics is represented as a thermodynamic differential form. Furthermore, we discuss the strength of the selection by using the difference between time-forward and time-backward (retrospective) processes.
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Affiliation(s)
- Yuki Sughiyama
- Department of Basic Science, School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Tetsuya J Kobayashi
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Koji Tsumura
- Department of Information Physics and Computing, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kazuyuki Aihara
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
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33
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Bashar MK, Yamagata K, Kobayashi TJ. Improved and robust detection of cell nuclei from four dimensional fluorescence images. PLoS One 2014; 9:e101891. [PMID: 25020042 PMCID: PMC4096508 DOI: 10.1371/journal.pone.0101891] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 06/12/2014] [Indexed: 11/18/2022] Open
Abstract
Segmentation-free direct methods are quite efficient for automated nuclei extraction from high dimensional images. A few such methods do exist but most of them do not ensure algorithmic robustness to parameter and noise variations. In this research, we propose a method based on multiscale adaptive filtering for efficient and robust detection of nuclei centroids from four dimensional (4D) fluorescence images. A temporal feedback mechanism is employed between the enhancement and the initial detection steps of a typical direct method. We estimate the minimum and maximum nuclei diameters from the previous frame and feed back them as filter lengths for multiscale enhancement of the current frame. A radial intensity-gradient function is optimized at positions of initial centroids to estimate all nuclei diameters. This procedure continues for processing subsequent images in the sequence. Above mechanism thus ensures proper enhancement by automated estimation of major parameters. This brings robustness and safeguards the system against additive noises and effects from wrong parameters. Later, the method and its single-scale variant are simplified for further reduction of parameters. The proposed method is then extended for nuclei volume segmentation. The same optimization technique is applied to final centroid positions of the enhanced image and the estimated diameters are projected onto the binary candidate regions to segment nuclei volumes.Our method is finally integrated with a simple sequential tracking approach to establish nuclear trajectories in the 4D space. Experimental evaluations with five image-sequences (each having 271 3D sequential images) corresponding to five different mouse embryos show promising performances of our methods in terms of nuclear detection, segmentation, and tracking. A detail analysis with a sub-sequence of 101 3D images from an embryo reveals that the proposed method can improve the nuclei detection accuracy by 9 over the previous methods, which used inappropriate large valued parameters. Results also confirm that the proposed method and its variants achieve high detection accuracies ( 98 mean F-measure) irrespective of the large variations of filter parameters and noise levels.
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Affiliation(s)
- Md. Khayrul Bashar
- Leading Graduate School Promotion Center, Ochanomizu University, Tokyo, Japan
- * E-mail:
| | - Kazuo Yamagata
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
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34
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Kobayashi TJ. Information decoding in microscopic biological processes. Annu Int Conf IEEE Eng Med Biol Soc 2013; 2013:2704-7. [PMID: 24110285 DOI: 10.1109/embc.2013.6610098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The cellular and intracellular dynamics are intrinsically stochastic and dynamic. However, whole biological system such as a cell or our body can function very robustly and stably even though they are composed of these stochastic reactions. To account for this riddling relation between macroscopic robustness and microscopic stochasticity, I propose a mechanism that information relevant for stable and reliable operation of a biological system is embedded in apparently stochastic and noisy behavior of their components. To show validity of this possibility, I demonstrates that information can actually be decoded from apparently noisy signal when it is processed by an appropriate dynamics derived by Bayes' rule. Next, I investigate biological relevance of this possibility by showing that several intracellular networks can implement this decoding dynamics. Finally, by focusing its dynamical properties, I show the mechanism how the derived dynamics can separate information and noise.
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35
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Mano Y, Kobayashi TJ, Nakayama JI, Uchida H, Oki M. Single cell visualization of yeast gene expression shows correlation of epigenetic switching between multiple heterochromatic regions through multiple generations. PLoS Biol 2013; 11:e1001601. [PMID: 23843746 PMCID: PMC3699475 DOI: 10.1371/journal.pbio.1001601] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2013] [Accepted: 05/23/2013] [Indexed: 11/25/2022] Open
Abstract
A single-cell method allows the assessment of relationships between the dynamic epigenetic behavior of yeast heterochromatin boundaries over multiple generations. Differences in gene expression between individual cells can be mediated by epigenetic regulation; thus, methods that enable detailed analyses of single cells are crucial to understanding this phenomenon. In this study, genomic silencing regions of Saccharomyces cerevisiae that are subject to epigenetic regulation, including the HMR, HML, and telomere regions, were investigated using a newly developed single cell analysis method. This method uses fluorescently labeled proteins to track changes in gene expression over multiple generations of a single cell. Epigenetic control of gene expression differed depending on the specific silencing region at which the reporter gene was inserted. Correlations between gene expression at the HMR-left and HMR-right regions, as well as the HMR-right and HML-right regions, were observed in the single-cell level; however, no such correlations involving the telomere region were observed. Deletion of the histone acetyltransferase GCN5 gene from a yeast strain carrying a fluorescent reporter gene at the HMR-left region reduced the frequency of changes in gene expression over a generation. The results presented here suggest that epigenetic control within an individual cell is reversible and can be achieved via regulation of histone acetyltransferase activity. Although eukaryotic gene repression usually acts on individual genes, cells can also repress larger chromosomal regions via the establishment of a high order chromatin structure called heterochromatin. Once initiated, heterochromatin spreads until halted by a boundary, and in this study we focus on how this boundary is formed. Because the mechanism is epigenetic and can differ from cell to cell, we wanted to assess the dynamics of the process by tracking individual cells over multiple generations. Here we develop a novel method employing protein fluorescence to monitor gene expression at the boundaries of several yeast heterochromatic regions simultaneously. This allows us to assess whether different boundaries within a single cell fluctuate in concert or independently of each other. In addition, we use histone modification mutants to probe the specific types of epigenetic regulation responsible for fluctuations in heterochromatin boundary positioning. Using this method, we show that epigenetic gene expression within individual cells is reversible and that this process is regulated by histone acetylation state. Future work will identify connections between variation in boundary positioning and novel transcription control systems.
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Affiliation(s)
- Yasunobu Mano
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, Fukui, Japan
- Research Fellow of the Japan Society for the Promotion of Science, Tokyo, Japan
| | - Tetsuya J. Kobayashi
- Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
- PRESTO, Japan Science and Technology Agency (JST), Saitama, Japan
| | - Jun-ichi Nakayama
- Laboratory for Chromatin Dynamics, Center for Developmental Biology, RIKEN, Kobe, Japan
- Graduate School of Natural Sciences, Nagoya City University, Nagoya, Japan
| | - Hiroyuki Uchida
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, Fukui, Japan
| | - Masaya Oki
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, Fukui, Japan
- PRESTO, Japan Science and Technology Agency (JST), Saitama, Japan
- Research and Education Program for Life Science, University of Fukui, Fukui, Japan
- * E-mail:
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36
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Draviam VM, Funahashi A, Hiroi N, Kimura A, Kobayashi TJ. Meeting report of the International Workshop on Quantitative Biology 2012: mesoscopic and microscopic worlds meet. Front Physiol 2013; 3:479. [PMID: 23335898 PMCID: PMC3542476 DOI: 10.3389/fphys.2012.00479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 12/07/2012] [Indexed: 11/23/2022] Open
Affiliation(s)
- Viji M. Draviam
- Department of Genetics, University of CambridgeCambridge, UK
| | - Akira Funahashi
- Department of Biosciences and Informatics, Keio UniversityYokohama, Japan
| | - Noriko Hiroi
- Department of Biosciences and Informatics, Keio UniversityYokohama, Japan
| | - Akatsuki Kimura
- Cell Architecture Laboratory, National Institute of GeneticsMishima, Japan
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37
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Hiroi N, Okuhara T, Kubojima T, Iba K, Tabira A, Yamashita S, Okada Y, Kobayashi TJ, Funahashi A. Physiological Intracellular Crowdedness is Defined by the Perimeter-to-Area Ratio of Sub-Cellular Compartments. Front Physiol 2012; 3:293. [PMID: 22936917 PMCID: PMC3424521 DOI: 10.3389/fphys.2012.00293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 07/04/2012] [Indexed: 11/30/2022] Open
Abstract
The intracellular environment is known to be a crowded and inhomogeneous space. Such an in vivo environment differs from a well-diluted, homogeneous environment for biochemical reactions. However, the effects of both crowdedness and the inhomogeneity of environment on the behavior of a mobile particle have not yet been investigated sufficiently. As described in this paper, we constructed artificial reaction spaces with fractal models, which are assumed to be non-reactive solid obstacles in a reaction space with crevices that function as operating ranges for mobile particles threading the space. Because of the homogeneity of the structures of artificial reaction spaces, the models succeeded in reproducing the physiological fractal dimension of solid structures with a smaller number of non-reactive obstacles than in the physiological condition. This incomplete compatibility was mitigated when we chose a suitable condition of a perimeter-to-area ratio of the operating range to our model. Our results also show that a simulation space is partitioned into convenient reaction compartments as an in vivo environment with the exact amount of solid structures estimated from TEM images. The characteristics of these compartments engender larger mean square displacement of a mobile particle than that of particles in smaller compartments. Subsequently, the particles start to show confined particle-like behavior. These results are compatible with our previously presented results, which predicted that a physiological environment would produce quick response and slow exhaustion reactions.
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Affiliation(s)
- Noriko Hiroi
- Department of Bioscience and Informatics, School of Fundamental Science and Technology, Keio University Yokohama, Japan
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38
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Kamimura A, Kobayashi TJ. Information processing and integration with intracellular dynamics near critical point. Front Physiol 2012; 3:203. [PMID: 22707939 PMCID: PMC3374347 DOI: 10.3389/fphys.2012.00203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 05/23/2012] [Indexed: 11/13/2022] Open
Abstract
Recent experimental observations suggest that cells can show relatively precise and reliable responses to external signals even though substantial noise is inevitably involved in the signals. An intriguing question is the way how cells can manage to do it. One possible way to realize such response for a cell is to evolutionary develop and optimize its intracellular signaling pathways so as to extract relevant information from the noisy signal. We recently demonstrated that certain intracellular signaling reactions could actually conduct statistically optimal information processing. In this paper, we clarify that such optimal reaction operates near bifurcation point. This result suggests that critical-like phenomena in the single-cell level may be linked to efficient information processing inside a cell. In addition, improving the performance of response in the single-cell level is not the only way for cells to realize reliable response. Another possible strategy is to integrate information of individual cells by cell-to-cell interaction such as quorum sensing. Since cell-to-cell interaction is a common phenomenon, it is equally important to investigate how cells can integrate their information by cell-to-cell interaction to realize efficient information processing in the population level. In this paper, we consider roles and benefits of cell-to-cell interaction by considering integrations of obtained information of individuals with the other cells from the viewpoint of information processing. We also demonstrate that, by introducing cell movement, spatial organizations can spontaneously emerge as a result of efficient responses of the population to external signals.
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Affiliation(s)
- Atsushi Kamimura
- Institute of Industrial Science, The University of Tokyo Tokyo, Japan
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39
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Bashar MK, Komatsu K, Fujimori T, Kobayashi TJ. Automatic extraction of nuclei centroids of mouse embryonic cells from fluorescence microscopy images. PLoS One 2012; 7:e35550. [PMID: 22590505 PMCID: PMC3348125 DOI: 10.1371/journal.pone.0035550] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 03/21/2012] [Indexed: 11/18/2022] Open
Abstract
Accurate identification of cell nuclei and their tracking using three dimensional (3D) microscopic images is a demanding task in many biological studies. Manual identification of nuclei centroids from images is an error-prone task, sometimes impossible to accomplish due to low contrast and the presence of noise. Nonetheless, only a few methods are available for 3D bioimaging applications, which sharply contrast with 2D analysis, where many methods already exist. In addition, most methods essentially adopt segmentation for which a reliable solution is still unknown, especially for 3D bio-images having juxtaposed cells. In this work, we propose a new method that can directly extract nuclei centroids from fluorescence microscopy images. This method involves three steps: (i) Pre-processing, (ii) Local enhancement, and (iii) Centroid extraction. The first step includes two variations: first variation (Variant-1) uses the whole 3D pre-processed image, whereas the second one (Variant-2) modifies the preprocessed image to the candidate regions or the candidate hybrid image for further processing. At the second step, a multiscale cube filtering is employed in order to locally enhance the pre-processed image. Centroid extraction in the third step consists of three stages. In Stage-1, we compute a local characteristic ratio at every voxel and extract local maxima regions as candidate centroids using a ratio threshold. Stage-2 processing removes spurious centroids from Stage-1 results by analyzing shapes of intensity profiles from the enhanced image. An iterative procedure based on the nearest neighborhood principle is then proposed to combine if there are fragmented nuclei. Both qualitative and quantitative analyses on a set of 100 images of 3D mouse embryo are performed. Investigations reveal a promising achievement of the technique presented in terms of average sensitivity and precision (i.e., 88.04% and 91.30% for Variant-1; 86.19% and 95.00% for Variant-2), when compared with an existing method (86.06% and 90.11%), originally developed for analyzing C. elegans images.
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Affiliation(s)
- Md Khayrul Bashar
- Institute of Industrial Science, The University of Tokyo, Tokyo, Japan.
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Abstract
Microscopic biological processes have extraordinary complexity and variety at the sub-cellular, intra-cellular, and multi-cellular levels. In dealing with such complex phenomena, conceptual and theoretical frameworks are crucial, which enable us to understand seemingly different intra- and inter-cellular phenomena from unified viewpoints. Decision-making is one such concept that has attracted much attention recently. Since a number of cellular behavior can be regarded as processes to make specific actions in response to external stimuli, decision-making can cover and has been used to explain a broad range of different cellular phenomena [Balázsi et al. (Cell 144(6):910, 2011), Zeng et al. (Cell 141(4):682, 2010)]. Decision-making is also closely related to cellular information-processing because appropriate decisions cannot be made without exploiting the information that the external stimuli contain. Efficiency of information transduction and processing by intra-cellular networks determines the amount of information obtained, which in turn limits the efficiency of subsequent decision-making. Furthermore, information-processing itself can serve as another concept that is crucial for understanding of other biological processes than decision-making. In this work, we review recent theoretical developments on cellular decision-making and information-processing by focusing on the relation between these two concepts.
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Affiliation(s)
- Tetsuya J Kobayashi
- Institute of Industrial Science, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8505, Japan.
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Abstract
A variety of cellular functions are robust even to substantial intrinsic and extrinsic noise in intracellular reactions and the environment that could be strong enough to impair or limit them. In particular, of substantial importance is cellular decision-making in which a cell chooses a fate or behavior on the basis of information conveyed in noisy external signals. For robust decoding, the crucial step is filtering out the noise inevitably added during information transmission. As a minimal and optimal implementation of such an information decoding process, the autocatalytic phosphorylation and autocatalytic dephosphorylation (aPadP) cycle was recently proposed. Here, we analyze the dynamical properties of the aPadP cycle in detail. We describe the dynamical roles of the stationary and short-term responses in determining the efficiency of information decoding and clarify the optimality of the threshold value of the stationary response and its information-theoretical meaning. Furthermore, we investigate the robustness of the aPadP cycle against the receptor inactivation time and intrinsic noise. Finally, we discuss the relationship among information decoding with information-dependent actions, bet-hedging and network modularity.
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Affiliation(s)
- Tetsuya J Kobayashi
- Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan.
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Koyama YM, Kobayashi TJ, Ueda HR. Perturbation analyses of intermolecular interactions. Phys Rev E Stat Nonlin Soft Matter Phys 2011; 84:026704. [PMID: 21929141 DOI: 10.1103/physreve.84.026704] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Revised: 06/19/2011] [Indexed: 05/31/2023]
Abstract
Conformational fluctuations of a protein molecule are important to its function, and it is known that environmental molecules, such as water molecules, ions, and ligand molecules, significantly affect the function by changing the conformational fluctuations. However, it is difficult to systematically understand the role of environmental molecules because intermolecular interactions related to the conformational fluctuations are complicated. To identify important intermolecular interactions with regard to the conformational fluctuations, we develop herein (i) distance-independent and (ii) distance-dependent perturbation analyses of the intermolecular interactions. We show that these perturbation analyses can be realized by performing (i) a principal component analysis using conditional expectations of truncated and shifted intermolecular potential energy terms and (ii) a functional principal component analysis using products of intermolecular forces and conditional cumulative densities. We refer to these analyses as intermolecular perturbation analysis (IPA) and distance-dependent intermolecular perturbation analysis (DIPA), respectively. For comparison of the IPA and the DIPA, we apply them to the alanine dipeptide isomerization in explicit water. Although the first IPA principal components discriminate two states (the α state and PPII (polyproline II) + β states) for larger cutoff length, the separation between the PPII state and the β state is unclear in the second IPA principal components. On the other hand, in the large cutoff value, DIPA eigenvalues converge faster than that for IPA and the top two DIPA principal components clearly identify the three states. By using the DIPA biplot, the contributions of the dipeptide-water interactions to each state are analyzed systematically. Since the DIPA improves the state identification and the convergence rate with retaining distance information, we conclude that the DIPA is a more practical method compared with the IPA. To test the feasibility of the DIPA for larger molecules, we apply the DIPA to the ten-residue chignolin folding in explicit water. The top three principal components identify the four states (native state, two misfolded states, and unfolded state) and their corresponding eigenfunctions identify important chignolin-water interactions to each state. Thus, the DIPA provides the practical method to identify conformational states and their corresponding important intermolecular interactions with distance information.
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Affiliation(s)
- Yohei M Koyama
- Laboratory for Synthetic Biology, Quantitative Biology Center, RIKEN, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
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Kobayashi TJ. Connection between noise-induced symmetry breaking and an information-decoding function for intracellular networks. Phys Rev Lett 2011; 106:228101. [PMID: 21702634 DOI: 10.1103/physrevlett.106.228101] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Indexed: 05/31/2023]
Abstract
The biological function of noise-induced symmetry breaking (NISB) is still unclear even though it may potentially occur in noisy intracellular systems. In this work, I demonstrate that information decoding from a noisy signal is a potential biological function of NISB by revealing that NISB naturally emerges from an optimal information-decoding dynamics and that several intracellular networks can be identified with the information-decoding dynamics. I also propose a mean first passage time profile as a way to experimentally identify NISB.
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Harumoto T, Ito M, Shimada Y, Kobayashi TJ, Ueda HR, Lu B, Uemura T. Atypical cadherins Dachsous and Fat control dynamics of noncentrosomal microtubules in planar cell polarity. Dev Cell 2010; 19:389-401. [PMID: 20817616 PMCID: PMC2951474 DOI: 10.1016/j.devcel.2010.08.004] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Revised: 06/04/2010] [Accepted: 08/11/2010] [Indexed: 01/07/2023]
Abstract
How global organ asymmetry and individual cell polarity are connected to each other is a central question in studying planar cell polarity (PCP). In the Drosophila wing, which develops PCP along its proximal-distal (P-D) axis, we previously proposed that the core PCP mediator Frizzled redistributes distally in a microtubule (MT)-dependent manner. Here, we performed organ-wide analysis of MT dynamics by introducing quantitative in vivo imaging. We observed MTs aligning along the P-D axis at the onset of redistribution and a small but significant excess of + ends-distal MTs in the proximal region of the wing. This characteristic alignment and asymmetry of MT growth was controlled by atypical cadherins Dachsous (Ds) and Fat (Ft). Furthermore, the action of Ft was mediated in part by PAR-1. All these data support the idea that the active reorientation of MT growth adjusts cell polarity along the organ axis.
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Affiliation(s)
- Toshiyuki Harumoto
- Graduate School of Biostudies, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8507, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Masayoshi Ito
- Graduate School of Biostudies, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yuko Shimada
- Graduate School of Biostudies, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Tetsuya J. Kobayashi
- Institute of Industrial Science, the University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Hiroki R. Ueda
- Laboratory for Systems Biology, Center for Developmental Biology, RIKEN, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Bingwei Lu
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Tadashi Uemura
- Graduate School of Biostudies, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8507, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
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Abstract
Decision making in a noisy and dynamically changing environment is a fundamental task for a cell. To choose appropriate decisions over time, a cell must be equipped with intracellular kinetics that can conduct dynamic and efficient decision making. By using the theory of sequential inference, I demonstrate that dynamic Bayesian decision making can be implemented by an intracellular kinetics with a dual positive feedback structure. I also show that the combination of linear instantaneous and nonlinear stationary sensitivities to the input dominantly contributes to decision making efficiency, and that the state-dependent sensitivity change further suppresses noisy response. The statistical principles underlying these two factors are further clarified to be a log-likelihood-dependent quantification of the input information and uncertainty-dependent sensitivity control.
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Affiliation(s)
- Tetsuya J Kobayashi
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba Meguro-ku, Tokyo 153-8505, Japan.
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Koyama YM, Kobayashi TJ, Tomoda S, Ueda HR. Perturbational formulation of principal component analysis in molecular dynamics simulation. Phys Rev E Stat Nonlin Soft Matter Phys 2008; 78:046702. [PMID: 18999556 DOI: 10.1103/physreve.78.046702] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2008] [Revised: 08/18/2008] [Indexed: 05/27/2023]
Abstract
Conformational fluctuations of a molecule are important to its function since such intrinsic fluctuations enable the molecule to respond to the external environmental perturbations. For extracting large conformational fluctuations, which predict the primary conformational change by the perturbation, principal component analysis (PCA) has been used in molecular dynamics simulations. However, several versions of PCA, such as Cartesian coordinate PCA and dihedral angle PCA (dPCA), are limited to use with molecules with a single dominant state or proteins where the dihedral angle represents an important internal coordinate. Other PCAs with general applicability, such as the PCA using pairwise atomic distances, do not represent the physical meaning clearly. Therefore, a formulation that provides general applicability and clearly represents the physical meaning is yet to be developed. For developing such a formulation, we consider the conformational distribution change by the perturbation with arbitrary linearly independent perturbation functions. Within the second order approximation of the Kullback-Leibler divergence by the perturbation, the PCA can be naturally interpreted as a method for (1) decomposing a given perturbation into perturbations that independently contribute to the conformational distribution change or (2) successively finding the perturbation that induces the largest conformational distribution change. In this perturbational formulation of PCA, (i) the eigenvalue measures the Kullback-Leibler divergence from the unperturbed to perturbed distributions, (ii) the eigenvector identifies the combination of the perturbation functions, and (iii) the principal component determines the probability change induced by the perturbation. Based on this formulation, we propose a PCA using potential energy terms, and we designate it as potential energy PCA (PEPCA). The PEPCA provides both general applicability and clear physical meaning. For demonstrating its power, we apply the PEPCA to an alanine dipeptide molecule in vacuum as a minimal model of a nonsingle dominant conformational biomolecule. The first and second principal components clearly characterize two stable states and the transition state between them. Positive and negative components with larger absolute values of the first and second eigenvectors identify the electrostatic interactions, which stabilize or destabilize each stable state and the transition state. Our result therefore indicates that PCA can be applied, by carefully selecting the perturbation functions, not only to identify the molecular conformational fluctuation but also to predict the conformational distribution change by the perturbation beyond the limitation of the previous methods.
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Affiliation(s)
- Yohei M Koyama
- Laboratory for Systems Biology, Center for Developmental Biology, RIKEN, 2-2-3 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan.
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Ukai H, Kobayashi TJ, Nagano M, Masumoto KH, Sujino M, Kondo T, Yagita K, Shigeyoshi Y, Ueda HR. Melanopsin-dependent photo-perturbation reveals desynchronization underlying the singularity of mammalian circadian clocks. Nat Cell Biol 2007; 9:1327-34. [PMID: 17952058 DOI: 10.1038/ncb1653] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2007] [Accepted: 09/27/2007] [Indexed: 11/09/2022]
Abstract
Singularity behaviour in circadian clocks--the loss of robust circadian rhythms following exposure to a stimulus such as a pulse of bright light--is one of the fundamental but mysterious properties of clocks. To quantitatively perturb and accurately measure the dynamics of cellular clocks, we synthetically produced photo-responsiveness within mammalian cells by exogenously introducing the photoreceptor melanopsin and continuously monitoring the effect of photo-perturbation on the state of cellular clocks. Here we report that a critical light pulse drives cellular clocks into singularity behaviour. Our theoretical analysis consistently predicts and subsequent single-cell level observation directly proves that desynchronization of individual cellular clocks underlies singularity behaviour. Our theoretical framework also explains why singularity behaviours have been experimentally observed in various organisms, and it suggests that desynchronization is a plausible mechanism for the observable singularity of circadian clocks. Importantly, these in vitro and in silico findings are further supported by in vivo observations that desynchronization underlies the multicell-level amplitude decrease in the rat suprachiasmatic nucleus induced by critical light pulses.
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Affiliation(s)
- Hideki Ukai
- Laboratory for Systems Biology, Center for Developmental Biology, RIKEN, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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Abstract
Understanding the information processing ability of signal transduction pathways is of great importance because of their crucial roles in triggering various cellular responses. Despite continuing theoretical investigation, some important aspects of signal transduction such as a transient response and its connection to stochasticity originating from a small number of molecules have not yet been well understood. It is, however, through these aspects that unexpected and nontrivial properties of the information processing emerge. In this article, we analyze the transient behavior of a simple signaling cascade by taking into account the stochasticity originating from the small number of molecules. We identify several properties of the signaling cascade that emerge as a result of the interplay between the stochasticity and transient dynamics of the cascade. We specifically demonstrate that each step of the cascade has an optimal number of signaling molecules at which the average signal amplitude becomes maximal. We further investigate the connection between a finite number of molecules and the ability of the cascade to discriminate between true and error signals, which cannot be inferred from deterministic descriptions. The implications of our results are discussed from both biological and mathematical viewpoints.
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Affiliation(s)
- Yoshihiro Morishita
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan.
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Sato TK, Yamada RG, Ukai H, Baggs JE, Miraglia LJ, Kobayashi TJ, Welsh DK, Kay SA, Ueda HR, Hogenesch JB. Feedback repression is required for mammalian circadian clock function. Nat Genet 2006; 38:312-9. [PMID: 16474406 PMCID: PMC1994933 DOI: 10.1038/ng1745] [Citation(s) in RCA: 280] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2005] [Accepted: 01/09/2006] [Indexed: 11/09/2022]
Abstract
Direct evidence for the requirement of transcriptional feedback repression in circadian clock function has been elusive. Here, we developed a molecular genetic screen in mammalian cells to identify mutants of the circadian transcriptional activators CLOCK and BMAL1, which were uncoupled from CRYPTOCHROME (CRY)-mediated transcriptional repression. Notably, mutations in the PER-ARNT-SIM domain of CLOCK and the C terminus of BMAL1 resulted in synergistic insensitivity through reduced physical interactions with CRY. Coexpression of these mutant proteins in cultured fibroblasts caused arrhythmic phenotypes in population and single-cell assays. These data demonstrate that CRY-mediated repression of the CLOCK/BMAL1 complex activity is required for maintenance of circadian rhythmicity and provide formal proof that transcriptional feedback is required for mammalian clock function.
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Affiliation(s)
- Trey K Sato
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, USA
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Morishita Y, Kobayashi TJ, Aihara K. Evaluation of the performance of mechanisms for noise attenuation in a single-gene expression. J Theor Biol 2005; 235:241-64. [PMID: 15862593 DOI: 10.1016/j.jtbi.2005.01.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2004] [Revised: 01/07/2005] [Accepted: 01/13/2005] [Indexed: 11/26/2022]
Abstract
Experiments of synthetic gene regulatory modules and theoretical studies have clarified the stochastic nature of gene expression. The establishment of methods to control the fluctuation in gene expression is an indispensable step to the synthesis of robust and reliable genetic modules. In this study, we evaluate the performances of several major mechanisms to attenuate the fluctuation in a single-gene expression; noise attenuation through the control of the ratio of the transcription rate to the translation one, the interaction between synthesized proteins and background molecules, and an autoregulatory negative feedback. We analytically derive the dependence of the noise intensity on the parameter values related to elementary reaction processes, optimal conditions to attenuate the noise, and the limitation of the attenuation for those mechanisms. Our results can be an important basis for selecting the most efficient combination of the components in the design and synthesis of robust and reliable genetic modules. Furthermore, the knowledge on the performances that we obtain can also play a role in understanding the design principle of the intracellular gene regulatory networks.
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Affiliation(s)
- Yoshihiro Morishita
- Aihara Laboratory, Department of Complexity Science and Engineering, Graduate School of Frontier Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-8656, Japan.
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