1
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Frank SA. A biological circuit to anticipate trend. Evol Lett 2024; 8:719-725. [PMID: 39328288 PMCID: PMC11424073 DOI: 10.1093/evlett/qrae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 06/04/2024] [Accepted: 06/10/2024] [Indexed: 09/28/2024] Open
Abstract
Organisms gain by anticipating future changes in the environment. Those environmental changes often follow stochastic trends. The steeper the slope of the trend, the more likely the trend's momentum carries the future trend in the same direction. This article presents a simple biological circuit that measures the momentum, providing a prediction about future trend. The circuit calculates the momentum by the difference between a short-term and a long-term exponential moving average. The time lengths of the two moving averages can be adjusted by changing the decay rates of state variables. Different time lengths for those averages trade off between errors caused by noise and errors caused by lags in predicting a change in the direction of the trend. Prior studies have emphasized circuits that make similar calculations about trends. However, those prior studies embedded their analyses in the details of particular applications, obscuring the simple generality and wide applicability of the approach. The model here contributes to the topic by clarifying the great simplicity and generality of anticipation for stochastic trends. This article also notes that, in financial analysis, the difference between moving averages is widely used to predict future trends in asset prices. The financial measure is called the moving average convergence-divergence indicator. Connecting the biological problem to financial analysis opens the way for future studies in biology to exploit the variety of highly developed trend models in finance.
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Affiliation(s)
- Steven A Frank
- Department of Ecology & Evolutionary Biology, University of California, Irvine, CA, United States
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2
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Carruitero S, Duran AC, Pisegna G, Sturla MB, Grigera TS. Inertial spin model of flocking with position-dependent forces. Phys Rev E 2024; 110:014408. [PMID: 39160993 DOI: 10.1103/physreve.110.014408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 07/10/2024] [Indexed: 08/21/2024]
Abstract
We propose an extension to the inertial spin model (ISM) of flocking and swarming. The model has been introduced to explain certain dynamic features of swarming (second sound, a lower than expected dynamic critical exponent) while preserving the mechanism for onset of order provided by the Vicsek model. The inertial spin model (ISM) has only been formulated with an imitation ("ferromagnetic") interaction between velocities. Here we show how to add position-dependent forces in the model, which allows to consider effects such as cohesion, excluded volume, confinement, and perturbation with external position-dependent field, and thus study this model without periodic boundary conditions. We study numerically a single particle with an harmonic confining field and compare it to a Brownian harmonic oscillator and to a harmonically confined active Browinian particle, finding qualitatively different behavior in the three cases.
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Affiliation(s)
- Sebastián Carruitero
- Instituto de Física de Líquidos y Sistemas Biológicos (IFLySiB), CONICET and Universidad Nacional de La Plata, B1900BTE La Plata, Argentina
- CCT CONICET La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, B1900 La Plata, Argentina
- Departamento de Física, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, B1900 La Plata, Argentina
| | - Alejo Costa Duran
- Instituto de Física de Líquidos y Sistemas Biológicos (IFLySiB), CONICET and Universidad Nacional de La Plata, B1900BTE La Plata, Argentina
- CCT CONICET La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, B1900 La Plata, Argentina
- Departamento de Física, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, B1900 La Plata, Argentina
| | | | | | - Tomás S Grigera
- Instituto de Física de Líquidos y Sistemas Biológicos (IFLySiB), CONICET and Universidad Nacional de La Plata, B1900BTE La Plata, Argentina
- CCT CONICET La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, B1900 La Plata, Argentina
- Departamento de Física, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, B1900 La Plata, Argentina
- Istituto dei Sistemi Complessi, Consiglio Nazionale delle Ricerche, 00185 Rome, Italy
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3
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Ilker E, Hinczewski M. Bioenergetic costs and the evolution of noise regulation by microRNAs. Proc Natl Acad Sci U S A 2024; 121:e2308796121. [PMID: 38386708 PMCID: PMC10907262 DOI: 10.1073/pnas.2308796121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 01/14/2024] [Indexed: 02/24/2024] Open
Abstract
Noise control, together with other regulatory functions facilitated by microRNAs (miRNAs), is believed to have played important roles in the evolution of multicellular eukaryotic organisms. miRNAs can dampen protein fluctuations via enhanced degradation of messenger RNA (mRNA), but this requires compensation by increased mRNA transcription to maintain the same expression levels. The overall mechanism is metabolically expensive, leading to questions about how it might have evolved in the first place. We develop a stochastic model of miRNA noise regulation, coupled with a detailed analysis of the associated metabolic costs. Additionally, we calculate binding free energies for a range of miRNA seeds, the short sequences which govern target recognition. We argue that natural selection may have fine-tuned the Michaelis-Menten constant [Formula: see text] describing miRNA-mRNA affinity and show supporting evidence from analysis of experimental data. [Formula: see text] is constrained by seed length, and optimal noise control (minimum protein variance at a given energy cost) is achievable for seeds of 6 to 7 nucleotides in length, the most commonly observed types. Moreover, at optimality, the degree of noise reduction approaches the theoretical bound set by the Wiener-Kolmogorov linear filter. The results illustrate how selective pressure toward energy efficiency has potentially shaped a crucial regulatory pathway in eukaryotes.
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Affiliation(s)
- Efe Ilker
- Max Planck Institute for the Physics of Complex Systems, Dresden01187, Germany
| | - Michael Hinczewski
- Department of Physics, Case Western Reserve University, Cleveland, OH44106
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4
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Tjalma AJ, Galstyan V, Goedhart J, Slim L, Becker NB, ten Wolde PR. Trade-offs between cost and information in cellular prediction. Proc Natl Acad Sci U S A 2023; 120:e2303078120. [PMID: 37792515 PMCID: PMC10576116 DOI: 10.1073/pnas.2303078120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/23/2023] [Indexed: 10/06/2023] Open
Abstract
Living cells can leverage correlations in environmental fluctuations to predict the future environment and mount a response ahead of time. To this end, cells need to encode the past signal into the output of the intracellular network from which the future input is predicted. Yet, storing information is costly while not all features of the past signal are equally informative on the future input signal. Here, we show for two classes of input signals that cellular networks can reach the fundamental bound on the predictive information as set by the information extracted from the past signal: Push-pull networks can reach this information bound for Markovian signals, while networks that take a temporal derivative can reach the bound for predicting the future derivative of non-Markovian signals. However, the bits of past information that are most informative about the future signal are also prohibitively costly. As a result, the optimal system that maximizes the predictive information for a given resource cost is, in general, not at the information bound. Applying our theory to the chemotaxis network of Escherichia coli reveals that its adaptive kernel is optimal for predicting future concentration changes over a broad range of background concentrations, and that the system has been tailored to predicting these changes in shallow gradients.
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Affiliation(s)
- Age J. Tjalma
- AMOLF, Science Park 104, 1098 XGAmsterdam, The Netherlands
| | - Vahe Galstyan
- AMOLF, Science Park 104, 1098 XGAmsterdam, The Netherlands
| | | | - Lotte Slim
- AMOLF, Science Park 104, 1098 XGAmsterdam, The Netherlands
| | - Nils B. Becker
- Theoretical Systems Biology, German Cancer Research Center, 69120Heidelberg, Germany
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5
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Mattingly HH, Kamino K, Machta BB, Emonet T. Escherichia coli chemotaxis is information limited. NATURE PHYSICS 2021; 17:1426-1431. [PMID: 35035514 PMCID: PMC8758097 DOI: 10.1038/s41567-021-01380-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 09/10/2021] [Indexed: 05/08/2023]
Abstract
Organisms acquire and use information from their environment to guide their behaviour. However, it is unclear whether this information quantitatively limits their behavioural performance. Here, we relate information to the ability of Escherichia coli to navigate up chemical gradients, the behaviour known as chemotaxis. First, we derive a theoretical limit on the speed with which cells climb gradients, given the rate at which they acquire information. Next, we measure cells' gradient-climbing speeds and the rate of information acquisition by their chemotaxis signaling pathway. We find that E. coli make behavioural decisions with much less than the one bit required to determine whether they are swimming up-gradient. Some of this information is irrelevant to gradient climbing, and some is lost in communication to behaviour. Despite these limitations, E. coli climb gradients at speeds within a factor of two of the theoretical bound. Thus, information can limit the performance of an organism, and sensory-motor pathways may have evolved to efficiently use information acquired from the environment.
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Affiliation(s)
- H H Mattingly
- Department of Molecular, Cellular, and Developmental Biology, Yale University
- Quantitative Biology Institute, Yale University
| | - K Kamino
- Department of Molecular, Cellular, and Developmental Biology, Yale University
- Quantitative Biology Institute, Yale University
| | - B B Machta
- Department of Physics, Yale University
- Systems Biology Institute, West Campus, Yale University
| | - T Emonet
- Department of Molecular, Cellular, and Developmental Biology, Yale University
- Quantitative Biology Institute, Yale University
- Department of Physics, Yale University
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6
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Weisenberger C, Hathcock D, Hinczewski M. Cellular Signaling beyond the Wiener-Kolmogorov Limit. J Phys Chem B 2021; 125:12698-12711. [PMID: 34756045 DOI: 10.1021/acs.jpcb.1c07894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Accurate propagation of signals through stochastic biochemical networks involves significant expenditure of cellular resources. The same is true for regulatory mechanisms that suppress fluctuations in biomolecular populations. Wiener-Kolmogorov (WK) optimal noise filter theory, originally developed for engineering problems, has recently emerged as a valuable tool to estimate the maximum performance achievable in such biological systems for a given metabolic cost. However, WK theory has one assumption that potentially limits its applicability: it relies on a linear, continuum description of the reaction dynamics. Despite this, up to now no explicit test of the theory in nonlinear signaling systems with discrete molecular populations has ever seen performance beyond the WK bound. Here we report the first direct evidence of the bound being broken. To accomplish this, we develop a theoretical framework for multilevel signaling cascades, including the possibility of feedback interactions between input and output. In the absence of feedback, we introduce an analytical approach that allows us to calculate exact moments of the stationary distribution for a nonlinear system. With feedback, we rely on numerical solutions of the system's master equation. The results show WK violations in two common network motifs: a two-level signaling cascade and a negative feedback loop. However, the magnitude of the violation is biologically negligible, particularly in the parameter regime where signaling is most effective. The results demonstrate that while WK theory does not provide strict bounds, its predictions for performance limits are excellent approximations, even for nonlinear systems.
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Affiliation(s)
- Casey Weisenberger
- Department of Physics, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - David Hathcock
- Department of Physics, Cornell University, Ithaca, New York 14853, United States
| | - Michael Hinczewski
- Department of Physics, Case Western Reserve University, Cleveland, Ohio 44106, United States
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7
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Trading bits in the readout from a genetic network. Proc Natl Acad Sci U S A 2021; 118:2109011118. [PMID: 34772813 DOI: 10.1073/pnas.2109011118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2021] [Indexed: 11/18/2022] Open
Abstract
In the regulation of gene expression, information of relevance to the organism is represented by the concentrations of transcription factor molecules. To extract this information the cell must effectively "measure" these concentrations, but there are physical limits to the precision of these measurements. We use the gap gene network in the early fly embryo as an example of the tradeoff between the precision of concentration measurements and the transmission of relevant information. For thresholded measurements we find that lower thresholds are more important, and fine tuning is not required for near-optimal information transmission. We then consider general sensors, constrained only by a limit on their information capacity, and find that thresholded sensors can approach true information theoretic optima. The information theoretic approach allows us to identify the optimal sensor for the entire gap gene network and to argue that the physical limitations of sensing necessitate the observed multiplicity of enhancer elements, with sensitivities to combinations rather than single transcription factors.
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8
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Optimal ligand discrimination by asymmetric dimerization and turnover of interferon receptors. Proc Natl Acad Sci U S A 2021; 118:2103939118. [PMID: 34507994 DOI: 10.1073/pnas.2103939118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2021] [Indexed: 11/18/2022] Open
Abstract
In multicellular organisms, antiviral defense mechanisms evoke a reliable collective immune response despite the noisy nature of biochemical communication between tissue cells. A molecular hub of this response, the interferon I receptor (IFNAR), discriminates between ligand types by their affinity regardless of concentration. To understand how ligand type can be decoded robustly by a single receptor, we frame ligand discrimination as an information-theoretic problem and systematically compare the major classes of receptor architectures: allosteric, homodimerizing, and heterodimerizing. We demonstrate that asymmetric heterodimers achieve the best discrimination power over the entire physiological range of local ligand concentrations. This design enables sensing of ligand presence and type, and it buffers against moderate concentration fluctuations. In addition, receptor turnover, which drives the receptor system out of thermodynamic equilibrium, allows alignment of activation points for ligands of different affinities and thereby makes ligand discrimination practically independent of concentration. IFNAR exhibits this optimal architecture, and our findings thus suggest that this specialized receptor can robustly decode digital messages carried by its different ligands.
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9
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Tsuruyama T. Nonlinear thermodynamics of biological signal transduction for predicting conservation of entropy production rate. J Theor Biol 2021; 523:110716. [PMID: 33862093 DOI: 10.1016/j.jtbi.2021.110716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/22/2021] [Accepted: 04/07/2021] [Indexed: 11/26/2022]
Abstract
Cell signal transduction is an example of a nonequilibrium phenomenon. In this study, a nonequilibrium nonlinear thermodynamic model was formulated. First, we obtained a condition in which the Onsager's reciprocity theorem holds in the signal transduction. Second, it was found that the entropy production rate per signal molecule is conserved through signal transduction. Finally, it was determined that when Onsager's reciprocity theorem does not hold, fluctuation circulation is given by the phosphorylation rate of signal molecules. The simple relation implies that the fluctuation circulation can be an essential quantity of the signal transduction amount. These results expand the limit of nonequilibrium thermodynamics and can be used to provide ideas for signal transduction quantification.
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Affiliation(s)
- Tatsuaki Tsuruyama
- Department of Discovery Medicine, Pathology Division, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8315, Japan; Tazukofukai Medical Institute Kitano Hospital, Ogimachi, 2-4-20, Osaka 530-8480, Osaka, Japan.
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10
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Nakamura K, Kobayashi TJ. Connection between the Bacterial Chemotactic Network and Optimal Filtering. PHYSICAL REVIEW LETTERS 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] [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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11
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Meijers M, Ito S, Ten Wolde PR. Behavior of information flow near criticality. Phys Rev E 2021; 103:L010102. [PMID: 33601642 DOI: 10.1103/physreve.103.l010102] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 12/22/2020] [Indexed: 11/07/2022]
Abstract
Recent experiments have indicated that many biological systems self-organize near their critical point, which hints at a common design principle. While it has been suggested that information transmission is optimized near the critical point, it remains unclear how information transmission depends on the dynamics of the input signal, the distance over which the information needs to be transmitted, and the distance to the critical point. Here we employ stochastic simulations of a driven two-dimensional Ising system and study the instantaneous mutual information and the information transmission rate between a driven input spin and an output spin. The instantaneous mutual information varies nonmonotonically with the temperature but increases monotonically with the correlation time of the input signal. In contrast, there exists not only an optimal temperature but also an optimal finite input correlation time that maximizes the information transmission rate. This global optimum arises from a fundamental trade-off between the need to maximize the frequency of independent input messages, the necessity to respond fast to changes in the input, and the need to respond reliably to these changes. The optimal temperature lies above the critical point but moves toward it as the distance between the input and output spin is increased.
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Affiliation(s)
| | - Sosuke Ito
- NWO Institute AMOLF, 1098 XG Amsterdam, The Netherlands.,Universal Biology Institute, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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12
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Malaguti G, ten Wolde PR. Theory for the optimal detection of time-varying signals in cellular sensing systems. eLife 2021; 10:e62574. [PMID: 33594978 PMCID: PMC7946427 DOI: 10.7554/elife.62574] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 02/12/2021] [Indexed: 11/29/2022] Open
Abstract
Living cells often need to measure chemical concentrations that vary in time, yet how accurately they can do so is poorly understood. Here, we present a theory that fully specifies, without any adjustable parameters, the optimal design of a canonical sensing system in terms of two elementary design principles: (1) there exists an optimal integration time, which is determined by the input statistics and the number of receptors; and (2) in the optimally designed system, the number of independent concentration measurements as set by the number of receptors and the optimal integration time equals the number of readout molecules that store these measurements and equals the work to store these measurements reliably; no resource is then in excess and hence wasted. Applying our theory to the Escherichia coli chemotaxis system indicates that its integration time is not only optimal for sensing shallow gradients but also necessary to enable navigation in these gradients.
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13
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Thermal Resonance and Cell Behavior. ENTROPY 2020; 22:e22070774. [PMID: 33286546 PMCID: PMC7517324 DOI: 10.3390/e22070774] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/27/2020] [Accepted: 07/14/2020] [Indexed: 12/11/2022]
Abstract
From a thermodynamic point of view, living cell life is no more than a cyclic process. It starts with the newly separated daughter cells and restarts when the next generations grow as free entities. During this cycle, the cell changes its entropy. In cancer, the growth control is damaged. In this paper, we analyze the role of the volume–area ratio in the cell in relation to the heat exchange between cell and its environment in order to point out its effect on cancer growth. The result holds to a possible control of the cancer growth based on the heat exchanged by the cancer toward its environment and the membrane potential variation, with the consequence of controlling the ions fluxes and the related biochemical reactions. This second law approach could represent a starting point for a possible future support for the anticancer therapies, in order to improve their effectiveness for the untreatable cancers.
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14
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Fang X, Wang J. Nonequilibrium Thermodynamics in Cell Biology: Extending Equilibrium Formalism to Cover Living Systems. Annu Rev Biophys 2020; 49:227-246. [DOI: 10.1146/annurev-biophys-121219-081656] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We discuss new developments in the nonequilibrium dynamics and thermodynamics of living systems, giving a few examples to demonstrate the importance of nonequilibrium thermodynamics for understanding biological dynamics and functions. We study single-molecule enzyme dynamics, in which the nonequilibrium thermodynamic and dynamic driving forces of chemical potential and flux are crucial for the emergence of non-Michaelis-Menten kinetics. We explore single-gene expression dynamics, in which nonequilibrium dissipation can suppress fluctuations. We investigate the cell cycle and identify the nutrition supply as the energy input that sustains the stability, speed, and coherence of cell cycle oscillation, from which the different vital phases of the cell cycle emerge. We examine neural decision-making processes and find the trade-offs among speed, accuracy, and thermodynamic costs that are important for neural function. Lastly, we consider the thermodynamic cost for specificity in cellular signaling and adaptation.
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Affiliation(s)
- Xiaona Fang
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
| | - Jin Wang
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, USA
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15
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Prediction and Dissipation in Nonequilibrium Molecular Sensors: Conditionally Markovian Channels Driven by Memoryful Environments. Bull Math Biol 2020; 82:25. [PMID: 31993762 DOI: 10.1007/s11538-020-00694-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 12/31/2019] [Indexed: 10/25/2022]
Abstract
Biological sensors must often predict their input while operating under metabolic constraints. However, determining whether or not a particular sensor is evolved or designed to be accurate and efficient is challenging. This arises partly from the functional constraints being at cross purposes and partly since quantifying the prediction performance of even in silico sensors can require prohibitively long simulations, especially when highly complex environments drive sensors out of equilibrium. To circumvent these difficulties, we develop new expressions for the prediction accuracy and thermodynamic costs of the broad class of conditionally Markovian sensors subject to complex, correlated (unifilar hidden semi-Markov) environmental inputs in nonequilibrium steady state. Predictive metrics include the instantaneous memory and the total predictable information (the mutual information between present sensor state and input future), while dissipation metrics include power extracted from the environment and the nonpredictive information rate. Success in deriving these formulae relies on identifying the environment's causal states, the input's minimal sufficient statistics for prediction. Using these formulae, we study large random channels and the simplest nontrivial biological sensor model-that of a Hill molecule, characterized by the number of ligands that bind simultaneously-the sensor's cooperativity. We find that the seemingly impoverished Hill molecule can capture an order of magnitude more predictable information than large random channels.
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16
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Manicka S, Levin M. Modeling somatic computation with non-neural bioelectric networks. Sci Rep 2019; 9:18612. [PMID: 31819119 PMCID: PMC6901451 DOI: 10.1038/s41598-019-54859-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 11/13/2019] [Indexed: 02/08/2023] Open
Abstract
The field of basal cognition seeks to understand how adaptive, context-specific behavior occurs in non-neural biological systems. Embryogenesis and regeneration require plasticity in many tissue types to achieve structural and functional goals in diverse circumstances. Thus, advances in both evolutionary cell biology and regenerative medicine require an understanding of how non-neural tissues could process information. Neurons evolved from ancient cell types that used bioelectric signaling to perform computation. However, it has not been shown whether or how non-neural bioelectric cell networks can support computation. We generalize connectionist methods to non-neural tissue architectures, showing that a minimal non-neural Bio-Electric Network (BEN) model that utilizes the general principles of bioelectricity (electrodiffusion and gating) can compute. We characterize BEN behaviors ranging from elementary logic gates to pattern detectors, using both fixed and transient inputs to recapitulate various biological scenarios. We characterize the mechanisms of such networks using dynamical-systems and information-theory tools, demonstrating that logic can manifest in bidirectional, continuous, and relatively slow bioelectrical systems, complementing conventional neural-centric architectures. Our results reveal a variety of non-neural decision-making processes as manifestations of general cellular biophysical mechanisms and suggest novel bioengineering approaches to construct functional tissues for regenerative medicine and synthetic biology as well as new machine learning architectures.
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Affiliation(s)
- Santosh Manicka
- Allen Discovery Center, 200 College Ave., Tufts University, Medford, MA, 02155, USA
| | - Michael Levin
- Allen Discovery Center, 200 College Ave., Tufts University, Medford, MA, 02155, USA.
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17
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Micali G, Endres RG. Maximal information transmission is compatible with ultrasensitive biological pathways. Sci Rep 2019; 9:16898. [PMID: 31729454 PMCID: PMC6858467 DOI: 10.1038/s41598-019-53273-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 10/29/2019] [Indexed: 11/16/2022] Open
Abstract
Cells are often considered input-output devices that maximize the transmission of information by converting extracellular stimuli (input) via signaling pathways (communication channel) to cell behavior (output). However, in biological systems outputs might feed back into inputs due to cell motility, and the biological channel can change by mutations during evolution. Here, we show that the conventional channel capacity obtained by optimizing the input distribution for a fixed channel may not reflect the global optimum. In a new approach we analytically identify both input distributions and input-output curves that optimally transmit information, given constraints from noise and the dynamic range of the channel. We find a universal optimal input distribution only depending on the input noise, and we generalize our formalism to multiple outputs (or inputs). Applying our formalism to Escherichia coli chemotaxis, we find that its pathway is compatible with optimal information transmission despite the ultrasensitive rotary motors.
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Affiliation(s)
- Gabriele Micali
- Department of Life Sciences, Imperial College, London, UK.,Centre for Integrative Systems Biology and Bioinformatics, Imperial College, London, UK.,Department of Environmental Microbiology, Eawag, Dübendorf, Switzerland.,Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Robert G Endres
- Department of Life Sciences, Imperial College, London, UK. .,Centre for Integrative Systems Biology and Bioinformatics, Imperial College, London, UK.
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18
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Jinwoo L. Fluctuation Theorem of Information Exchange within an Ensemble of Paths Conditioned on Correlated-Microstates. ENTROPY 2019; 21:e21050477. [PMID: 33267191 PMCID: PMC7514966 DOI: 10.3390/e21050477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/02/2019] [Accepted: 05/06/2019] [Indexed: 11/16/2022]
Abstract
Fluctuation theorems are a class of equalities that express universal properties of the probability distribution of a fluctuating path functional such as heat, work or entropy production over an ensemble of trajectories during a non-equilibrium process with a well-defined initial distribution. Jinwoo and Tanaka (Jinwoo, L.; Tanaka, H. Sci. Rep.2015, 5, 7832) have shown that work fluctuation theorems hold even within an ensemble of paths to each state, making it clear that entropy and free energy of each microstate encode heat and work, respectively, within the conditioned set. Here we show that information that is characterized by the point-wise mutual information for each correlated state between two subsystems in a heat bath encodes the entropy production of the subsystems and heat bath during a coupling process. To this end, we extend the fluctuation theorem of information exchange (Sagawa, T.; Ueda, M. Phys. Rev. Lett.2012, 109, 180602) by showing that the fluctuation theorem holds even within an ensemble of paths that reach a correlated state during dynamic co-evolution of two subsystems.
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Affiliation(s)
- Lee Jinwoo
- Department of Mathematics, Kwangwoon University, 20 Kwangwoon-ro, Seoul 01897, Korea
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19
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Abstract
The adaptive immune system is able to protect us from a large variety of pathogens, even ones it has not seen yet. Can predicting the future pathogen distribution help in protection? We find that a combination of probabilistic forecasting and occasional sampling of the current environment reduces infection costs—a scheme easily implemented by the memory repertoire. The proposed theoretical framework offers a modular recipe for updating the memory repertoire, which quantitatively predicts the strength of the immune response in flu-vaccination experiments, unlike other update schemes. It also links the observed early life dynamics of the memory pool to the sparseness properties of the pathogen distribution and competitive receptor dynamics for pathogens. An adaptive agent predicting the future state of an environment must weigh trust in new observations against prior experiences. In this light, we propose a view of the adaptive immune system as a dynamic Bayesian machinery that updates its memory repertoire by balancing evidence from new pathogen encounters against past experience of infection to predict and prepare for future threats. This framework links the observed initial rapid increase of the memory pool early in life followed by a midlife plateau to the ease of learning salient features of sparse environments. We also derive a modulated memory pool update rule in agreement with current vaccine-response experiments. Our results suggest that pathogenic environments are sparse and that memory repertoires significantly decrease infection costs, even with moderate sampling. The predicted optimal update scheme maps onto commonly considered competitive dynamics for antigen receptors.
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20
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Fluctuation Theorem of Information Exchange between Subsystems that Co-Evolve in Time. Symmetry (Basel) 2019. [DOI: 10.3390/sym11030433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Sagawa and Ueda established a fluctuation theorem of information exchange by revealing the role of correlations in stochastic thermodynamics and unified the non-equilibrium thermodynamics of measurement and feedback control. They considered a process where a non-equilibrium system exchanges information with other degrees of freedom such as an observer or a feedback controller. They proved the fluctuation theorem of information exchange under the assumption that the state of the other degrees of freedom that exchange information with the system does not change over time while the states of the system evolve in time. Here we relax this constraint and prove that the same form of the fluctuation theorem holds even if both subsystems co-evolve during information exchange processes. This result may extend the applicability of the fluctuation theorem of information exchange to a broader class of non-equilibrium processes, such as a dynamic coupling in biological systems, where subsystems that exchange information interact with each other.
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21
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Carballo-Pacheco M, Desponds J, Gavrilchenko T, Mayer A, Prizak R, Reddy G, Nemenman I, Mora T. Receptor crosstalk improves concentration sensing of multiple ligands. Phys Rev E 2019; 99:022423. [PMID: 30934315 DOI: 10.1103/physreve.99.022423] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Indexed: 06/09/2023]
Abstract
Cells need to reliably sense external ligand concentrations to achieve various biological functions such as chemotaxis or signaling. The molecular recognition of ligands by surface receptors is degenerate in many systems, leading to crosstalk between ligand-receptor pairs. Crosstalk is often thought of as a deviation from optimal specific recognition, as the binding of noncognate ligands can interfere with the detection of the receptor's cognate ligand, possibly leading to a false triggering of a downstream signaling pathway. Here we quantify the optimal precision of sensing the concentrations of multiple ligands by a collection of promiscuous receptors. We demonstrate that crosstalk can improve precision in concentration sensing and discrimination tasks. To achieve superior precision, the additional information about ligand concentrations contained in short binding events of the noncognate ligand should be exploited. We present a proofreading scheme to realize an approximate estimation of multiple ligand concentrations that reaches a precision close to the derived optimal bounds. Our results help rationalize the observed ubiquity of receptor crosstalk in molecular sensing.
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Affiliation(s)
- Martín Carballo-Pacheco
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH9 3FD, United Kingdom
| | - Jonathan Desponds
- Department of Physics, University of California San Diego, La Jolla, CA 92093, USA
| | - Tatyana Gavrilchenko
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andreas Mayer
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Roshan Prizak
- Institute of Science and Technology Austria, Am Campus 1, A-3400, Klosterneuburg, Austria
| | - Gautam Reddy
- Department of Physics, University of California San Diego, La Jolla, CA 92093, USA
| | - Ilya Nemenman
- Department of Physics, Department of Biology, and Initiative in Theory and Modeling of Living Systems, Emory University, Atlanta, GA 30322, USA
| | - Thierry Mora
- Laboratoire de physique de l'École normale supérieure (PSL university), CNRS, Sorbonne University, and University Paris-Diderot, 75005 Paris, France
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22
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Van Vu T, Hasegawa Y. Diffusion-dynamics laws in stochastic reaction networks. Phys Rev E 2019; 99:012416. [PMID: 30780338 DOI: 10.1103/physreve.99.012416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Indexed: 06/09/2023]
Abstract
Many biological activities are induced by cellular chemical reactions of diffusing reactants. The dynamics of such systems can be captured by stochastic reaction networks. A recent numerical study has shown that diffusion can significantly enhance the fluctuations in gene regulatory networks. However, the universal relation between diffusion and stochastic system dynamics remains veiled. Within the approximation of reaction-diffusion master equation (RDME), we find general relation that the steady-state distribution in complex balanced networks is diffusion-independent. Here, complex balance is the nonequilibrium generalization of detailed balance. We also find that for a diffusion-included network with a Poisson-like steady-state distribution, the diffusion can be ignored at steady state. We then derive a necessary and sufficient condition for networks holding such steady-state distributions. Moreover, we show that for linear reaction networks the RDME reduces to the chemical master equation, which implies that the stochastic dynamics of networks is unaffected by diffusion at any arbitrary time. Our findings shed light on the fundamental question of when diffusion can be neglected, or (if nonnegligible) its effects on the stochastic dynamics of the reaction network.
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Affiliation(s)
- Tan Van Vu
- Department of Information and Communication Engineering, Graduate School of Information Science and Technology, The University of Tokyo, Tokyo 113-8656, Japan
| | - Yoshihiko Hasegawa
- Department of Information and Communication Engineering, Graduate School of Information Science and Technology, The University of Tokyo, Tokyo 113-8656, Japan
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23
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Monti M, Lubensky DK, Ten Wolde PR. Optimal entrainment of circadian clocks in the presence of noise. Phys Rev E 2018; 97:032405. [PMID: 29776095 DOI: 10.1103/physreve.97.032405] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Indexed: 01/17/2023]
Abstract
Circadian clocks are biochemical oscillators that allow organisms to estimate the time of the day. These oscillators are inherently noisy due to the discrete nature of the reactants and the stochastic character of their interactions. To keep these oscillators in sync with the daily day-night rhythm in the presence of noise, circadian clocks must be coupled to the dark-light cycle. In this paper, we study the entrainment of phase oscillators as a function of the intrinsic noise in the system. Using stochastic simulations, we compute the optimal coupling strength, intrinsic frequency, and shape of the phase-response curve, that maximize the mutual information between the phase of the clock and time. We show that the optimal coupling strength and intrinsic frequency increase with the noise, but that the shape of the phase-response curve varies nonmonotonically with the noise: in the low-noise regime, it features a dead zone that increases in width as the noise increases, while in the high-noise regime, the width decreases with the noise. These results arise from a tradeoff between maximizing stability-noise suppression-and maximizing linearity of the input-output, i.e., time-phase, relation. We also show that three analytic approximations-the linear-noise approximation, the phase-averaging method, and linear-response theory-accurately describe different regimes of the coupling strength and the noise.
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Affiliation(s)
- Michele Monti
- AMOLF, Science Park 104, 1098 XE Amsterdam, The Netherlands
| | - David K Lubensky
- Department of Physics, University of Michigan, Ann Arbor, Michigan 48109-1040, USA
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Monti M, Lubensky DK, Ten Wolde PR. Robustness of Clocks to Input Noise. PHYSICAL REVIEW LETTERS 2018; 121:078101. [PMID: 30169070 DOI: 10.1103/physrevlett.121.078101] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 03/30/2018] [Indexed: 06/08/2023]
Abstract
To estimate the time, many organisms, ranging from cyanobacteria to animals, employ a circadian clock which is based on a limit-cycle oscillator that can tick autonomously with a nearly 24 h period. Yet, a limit-cycle oscillator is not essential for knowing the time, as exemplified by bacteria that possess an "hourglass": a system that when forced by an oscillatory light input exhibits robust oscillations from which the organism can infer the time, but that in the absence of driving relaxes to a stable fixed point. Here, using models of the Kai system of cyanobacteria, we compare a limit-cycle oscillator with two hourglass models, one that without driving relaxes exponentially and one that does so in an oscillatory fashion. In the limit of low input noise, all three systems are equally informative on time, yet in the regime of high input-noise the limit-cycle oscillator is far superior. The same behavior is found in the Stuart-Landau model, indicating that our result is universal.
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Affiliation(s)
- Michele Monti
- FOM Institute AMOLF, Science Park 104, 1098 XE Amsterdam, Netherlands
| | - David K Lubensky
- Department of Physics, University of Michigan, Ann Arbor, Michigan 48109-1040, USA
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25
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Analysis of Cell Signal Transduction Based on Kullback-Leibler Divergence: Channel Capacity and Conservation of Its Production Rate during Cascade. ENTROPY 2018; 20:e20060438. [PMID: 33265528 PMCID: PMC7512958 DOI: 10.3390/e20060438] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 05/26/2018] [Accepted: 06/03/2018] [Indexed: 11/30/2022]
Abstract
Kullback–Leibler divergence (KLD) is a type of extended mutual entropy, which is used as a measure of information gain when transferring from a prior distribution to a posterior distribution. In this study, KLD is applied to the thermodynamic analysis of cell signal transduction cascade and serves an alternative to mutual entropy. When KLD is minimized, the divergence is given by the ratio of the prior selection probability of the signaling molecule to the posterior selection probability. Moreover, the information gain during the entire channel is shown to be adequately described by average KLD production rate. Thus, this approach provides a framework for the quantitative analysis of signal transduction. Moreover, the proposed approach can identify an effective cascade for a signaling network.
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26
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Hasegawa Y. Multidimensional biochemical information processing of dynamical patterns. Phys Rev E 2018; 97:022401. [PMID: 29548224 DOI: 10.1103/physreve.97.022401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Indexed: 06/08/2023]
Abstract
Cells receive signaling molecules by receptors and relay information via sensory networks so that they can respond properly depending on the type of signal. Recent studies have shown that cells can extract multidimensional information from dynamical concentration patterns of signaling molecules. We herein study how biochemical systems can process multidimensional information embedded in dynamical patterns. We model the decoding networks by linear response functions, and optimize the functions with the calculus of variations to maximize the mutual information between patterns and output. We find that, when the noise intensity is lower, decoders with different linear response functions, i.e., distinct decoders, can extract much information. However, when the noise intensity is higher, distinct decoders do not provide the maximum amount of information. This indicates that, when transmitting information by dynamical patterns, embedding information in multiple patterns is not optimal when the noise intensity is very large. Furthermore, we explore the biochemical implementations of these decoders using control theory and demonstrate that these decoders can be implemented biochemically through the modification of cascade-type networks, which are prevalent in actual signaling pathways.
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Affiliation(s)
- Yoshihiko Hasegawa
- Department of Information and Communication Engineering, Graduate School of Information Science and Technology, The University of Tokyo, Tokyo 113-8656, Japan
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27
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Mutlu A, Trauth S, Ziesack M, Nagler K, Bergeest JP, Rohr K, Becker N, Höfer T, Bischofs IB. Phenotypic memory in Bacillus subtilis links dormancy entry and exit by a spore quantity-quality tradeoff. Nat Commun 2018; 9:69. [PMID: 29302032 PMCID: PMC5754360 DOI: 10.1038/s41467-017-02477-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 12/04/2017] [Indexed: 12/15/2022] Open
Abstract
Some bacteria, such as Bacillus subtilis, withstand starvation by forming dormant spores that revive when nutrients become available. Although sporulation and spore revival jointly determine survival in fluctuating environments, the relationship between them has been unclear. Here we show that these two processes are linked by a phenotypic “memory” that arises from a carry-over of molecules from the vegetative cell into the spore. By imaging life histories of individual B. subtilis cells using fluorescent reporters, we demonstrate that sporulation timing controls nutrient-induced spore revival. Alanine dehydrogenase contributes to spore memory and controls alanine-induced outgrowth, thereby coupling a spore’s revival capacity to the gene expression and growth history of its progenitors. A theoretical analysis, and experiments with signaling mutants exhibiting altered sporulation timing, support the hypothesis that such an intrinsically generated memory leads to a tradeoff between spore quantity and spore quality, which could drive the emergence of complex microbial traits. Bacillus subtilis withstands starvation by forming dormant spores that revive when nutrients become available. Here, Mutlu et al. show that sporulation timing controls spore revival through a phenotypic ‘memory’ that arises from the carry-over of a metabolic enzyme from the vegetative cell into the spore.
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Affiliation(s)
- Alper Mutlu
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Center for Molecular Biology (ZMBH), University of Heidelberg, 69120, Heidelberg, Germany.,Max-Planck-Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Stephanie Trauth
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Center for Molecular Biology (ZMBH), University of Heidelberg, 69120, Heidelberg, Germany.,Max-Planck-Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Marika Ziesack
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Center for Molecular Biology (ZMBH), University of Heidelberg, 69120, Heidelberg, Germany
| | - Katja Nagler
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Max-Planck-Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Jan-Philip Bergeest
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Institute of Pharmacy and Molecular Biotechnology (IPMB), 69120, Heidelberg, Germany.,Department of Bioinformatics and Functional Genomics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Karl Rohr
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Institute of Pharmacy and Molecular Biotechnology (IPMB), 69120, Heidelberg, Germany.,Department of Bioinformatics and Functional Genomics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Nils Becker
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Thomas Höfer
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Ilka B Bischofs
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany. .,Center for Molecular Biology (ZMBH), University of Heidelberg, 69120, Heidelberg, Germany. .,Max-Planck-Institute for Terrestrial Microbiology, 35043, Marburg, Germany.
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28
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Samanta HS, Hinczewski M, Thirumalai D. Optimal information transfer in enzymatic networks: A field theoretic formulation. Phys Rev E 2017; 96:012406. [PMID: 29347079 DOI: 10.1103/physreve.96.012406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Indexed: 06/07/2023]
Abstract
Signaling in enzymatic networks is typically triggered by environmental fluctuations, resulting in a series of stochastic chemical reactions, leading to corruption of the signal by noise. For example, information flow is initiated by binding of extracellular ligands to receptors, which is transmitted through a cascade involving kinase-phosphatase stochastic chemical reactions. For a class of such networks, we develop a general field-theoretic approach to calculate the error in signal transmission as a function of an appropriate control variable. Application of the theory to a simple push-pull network, a module in the kinase-phosphatase cascade, recovers the exact results for error in signal transmission previously obtained using umbral calculus [Hinczewski and Thirumalai, Phys. Rev. X 4, 041017 (2014)2160-330810.1103/PhysRevX.4.041017]. We illustrate the generality of the theory by studying the minimal errors in noise reduction in a reaction cascade with two connected push-pull modules. Such a cascade behaves as an effective three-species network with a pseudointermediate. In this case, optimal information transfer, resulting in the smallest square of the error between the input and output, occurs with a time delay, which is given by the inverse of the decay rate of the pseudointermediate. Surprisingly, in these examples the minimum error computed using simulations that take nonlinearities and discrete nature of molecules into account coincides with the predictions of a linear theory. In contrast, there are substantial deviations between simulations and predictions of the linear theory in error in signal propagation in an enzymatic push-pull network for a certain range of parameters. Inclusion of second-order perturbative corrections shows that differences between simulations and theoretical predictions are minimized. Our study establishes that a field theoretic formulation of stochastic biological signaling offers a systematic way to understand error propagation in networks of arbitrary complexity.
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Affiliation(s)
- Himadri S Samanta
- Department of Chemistry, The University of Texas at Austin, Texas 78712, USA
| | | | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin, Texas 78712, USA
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29
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McGrath T, Jones NS, Ten Wolde PR, Ouldridge TE. Biochemical Machines for the Interconversion of Mutual Information and Work. PHYSICAL REVIEW LETTERS 2017; 118:028101. [PMID: 28128612 DOI: 10.1103/physrevlett.118.028101] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Indexed: 05/18/2023]
Abstract
We propose a physically realizable information-driven device consisting of an enzyme in a chemical bath, interacting with pairs of molecules prepared in correlated states. These correlations persist without direct interaction and thus store free energy equal to the mutual information. The enzyme can harness this free energy, and that stored in the individual molecular states, to do chemical work. Alternatively, the enzyme can use the chemical driving to create mutual information. A modified system can function without external intervention, approaching biological systems more closely.
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Affiliation(s)
- Thomas McGrath
- Department of Mathematics, Imperial College London, London SW7 2AZ, United Kingdom
| | - Nick S Jones
- Department of Mathematics, Imperial College London, London SW7 2AZ, United Kingdom
| | | | - Thomas E Ouldridge
- Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
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30
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Hathcock D, Sheehy J, Weisenberger C, Ilker E, Hinczewski M. Noise Filtering and Prediction in Biological Signaling Networks. ACTA ACUST UNITED AC 2016. [DOI: 10.1109/tmbmc.2016.2633269] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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31
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32
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Hinczewski M, Thirumalai D. Noise Control in Gene Regulatory Networks with Negative Feedback. J Phys Chem B 2016; 120:6166-77. [DOI: 10.1021/acs.jpcb.6b02093] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michael Hinczewski
- Department
of Physics, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - D. Thirumalai
- Department
of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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