scholarly journals Improvement of the memory function of a mutual repression network in a stochastic environment by negative autoregulation

2018 ◽  
Author(s):  
A B M Shamim Ul Hasan ◽  
Hiroyuki Kurata ◽  
Sebastian Pechmann
Keyword(s):  
Memory Function ◽  
Biological Systems ◽  
Stochastic Simulations ◽  
Rate Equations ◽  
Cellular Memory ◽  
Theoretical Approaches ◽  
Stochastic Fluctuations ◽  
Mutual Repression ◽  
Negative Autoregulation ◽  
Theoretical Analyses

AbstractBackgroundCellular memory is a ubiquitous function of biological systems. By generating a sustained response to a transient inductive stimulus, often due to bistability, memory is central to the robust control of many important biological processes. However, our understanding of the origins of cellular memory remains incomplete. Stochastic fluctuations that are inherent to most biological systems have been shown to hamper memory function. Yet, how stochasticity changes the behavior of genetic circuits is generally not clear from a deterministic analysis of the network alone. Here, we apply deterministic rate equations, stochastic simulations, and theoretical analyses of Fokker-Planck equations to investigate how intrinsic noise affects the memory function in a mutual repression network.ResultsWe find that the addition of negative autoregulation improves the persistence of memory in a small gene regulatory network by reducing stochastic fluctuations. Our theoretical analyses reveal that this improved memory function stems from an increased stability of the steady states of the system. Moreover, we show how the tuning of critical network parameters can further enhance memory.ConclusionsOur work illuminates the power of stochastic and theoretical approaches to understanding biological circuits, and the importance of considering stochasticity to designing synthetic circuits with memory function.

scholarly journals Improvement of the memory function of a mutual repression network in a stochastic environment by negative autoregulation

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
A. B. M. Shamim Ul Hasan ◽  
Hiroyuki Kurata ◽  
Sebastian Pechmann
Keyword(s):  
Memory Function ◽  
Biological Systems ◽  
Stochastic Simulations ◽  
Rate Equations ◽  
Cellular Memory ◽  
Theoretical Approaches ◽  
Stochastic Fluctuations ◽  
Mutual Repression ◽  
Negative Autoregulation ◽  
Theoretical Analyses

Abstract Background Cellular memory is a ubiquitous function of biological systems. By generating a sustained response to a transient inductive stimulus, often due to bistability, memory is central to the robust control of many important biological processes. However, our understanding of the origins of cellular memory remains incomplete. Stochastic fluctuations that are inherent to most biological systems have been shown to hamper memory function. Yet, how stochasticity changes the behavior of genetic circuits is generally not clear from a deterministic analysis of the network alone. Here, we apply deterministic rate equations, stochastic simulations, and theoretical analyses of Fokker-Planck equations to investigate how intrinsic noise affects the memory function in a mutual repression network. Results We find that the addition of negative autoregulation improves the persistence of memory in a small gene regulatory network by reducing stochastic fluctuations. Our theoretical analyses reveal that this improved memory function stems from an increased stability of the steady states of the system. Moreover, we show how the tuning of critical network parameters can further enhance memory. Conclusions Our work illuminates the power of stochastic and theoretical approaches to understanding biological circuits, and the importance of considering stochasticity when designing synthetic circuits with memory function.

Specific ion effects in liquids, in biological systems, and at interfaces

2006 ◽  
Vol 78 (8) ◽  
pp. 1611-1617 ◽  
Author(s):  
Werner Kunz
Keyword(s):  
Current Knowledge ◽  
Biological Systems ◽  
Electrolyte Solutions ◽  
Short Review ◽  
Colloidal Systems ◽  
Theoretical Approaches ◽  
Specific Ion Effects ◽  
Ion Effects ◽  
Self Organizing

A short review is given of current knowledge of ion effects in solutions, at interfaces, and in complex colloidal systems. Further to some key experiments, recent and new theoretical approaches are discussed and references of most important papers are given. Finally, an example of a dissipative, self-organizing system involving electrolyte solutions is mentioned.

Harald Wezler som erindringsforsker: En viderefører af Halbwachs-Assmann-traditionen?

2005 ◽  
Author(s):  
Bernard Eric Jensen
Keyword(s):  
Social Factors ◽  
Cultural Memory ◽  
Social Memory ◽  
Interdisciplinary Approach ◽  
The State ◽  
Memory Research ◽  
Term Memory ◽  
Memory Work ◽  
Theoretical Approaches ◽  
Theoretical Analyses

Bernard Eric Jensen: Harald Welzer’s Approach to Memory Research An analysis of the approach to memory research found in the writings of Harald Welzer is presented. At the present time, Welzer is head of the Centre for Interdisciplinary Memory Research at Kulturwissenschaftliches Institut in Essen, Germany. He has contributed both empirical surveys and theoretical analyses to memory research during the last decade. At a first glance, Welzer’s approach appears to belong neatly within the tradition of memory research that was originally founded by the French sociologist Maurice Halbwachs, and which Aleida and Jan Assmann have been seeking to revive and develop since the 1980’s by introducing concepts such as “communicative and cultural memory” as well as “storage memory” (Speicher-Gedächtnis) and “use memory” (Funktions-Gedächtnis). On closer inspection, however, it transpires that Welzer’s approach cannot be characterised as a mere refinement of the approach taken by the Assmanns. This is partly because Welzer is attempting to develop an interdisciplinary approach, focused on the intricate relationships between biological, psychological and social factors in ongoing memory work. Apart from focussing of the work of Welzer, this article also seeks to highlight the state of “terminological anarchy” that characterises memory research at the present time, making it next to impossible to make direct comparisons between different theoretical approaches. This state of anarchy becomes transparent as soon as one begins to scrutinize the meanings of those adjectives, which nowadays are fixed to the term memory – for instance, “communicative”, “cultural”, “historical” and/or “social” memory. 

scholarly journals Space as the final frontier in stochastic simulations of biological systems

FEBS Letters ◽  
2005 ◽  
Vol 579 (8) ◽  
pp. 1789-1794 ◽  
Author(s):  
Caroline Lemerle ◽  
Barbara Di Ventura ◽  
Luis Serrano
Keyword(s):  
Biological Systems ◽  
Stochastic Simulations

Exhaustivity in It-Clefts

2019 ◽  
pp. 400-417
Author(s):  
Edgar Onea
Keyword(s):  
Experimental Studies ◽  
Semantic Inference ◽  
Theoretical Approaches ◽  
Pragmatic Inference ◽  
Theoretical Analyses

This chapter provides an overview of the most important theoretical positions on the exhaustivity inference often associated with it-clefts in English and comparable structures in other languages alongside with a brief review of the results of a number of experimental studies. There is a surprising discrepancy between the predictions of the theoretical analyses and the empirical findings. While theoretical approaches tend to derive exhaustivity as a necessary semantic inference, most experimental studies suggest that the exhaustivity of it-clefts might be a pragmatic inference. The chapter discusses this discrepancy in some detail and suggests some potential solutions.

scholarly journals Transcription through Intergenic Chromosomal Memory Elements of the Drosophila Bithorax Complex Correlates with an Epigenetic Switch

2002 ◽  
Vol 22 (22) ◽  
pp. 8026-8034 ◽  
Author(s):  
Gerhard Rank ◽  
Matthias Prestel ◽  
Renato Paro
Keyword(s):  
Memory Function ◽  
Polycomb Group ◽  
Published Data ◽  
Homeotic Genes ◽  
Bithorax Complex ◽  
Memory Element ◽  
Cellular Memory ◽  
Response Elements ◽  
Group Response ◽  
Differential Expression Pattern

ABSTRACT The proteins of the trithorax and Polycomb groups maintain the differential expression pattern of homeotic genes established by the early embryonic patterning system during development. These proteins generate stable and heritable chromatin structures by acting via particular chromosomal memory elements. We established a transgenic assay system showing that the Polycomb group response elements bxd and Mcp confer epigenetic inheritance throughout development. With previously published data for the Fab7 cellular memory module, we confirmed the cellular memory function of Polycomb group response elements. In Drosophila melanogaster, several of these memory elements are located in the large intergenic regulatory regions of the homeotic bithorax complex. Using a transgene assay, we showed that transcription through a memory element correlated with the relief of silencing imposed by the Polycomb group proteins and established an epigenetically heritable active chromatin mode. A memory element remodeled by the process of transcription was able to maintain active expression of a reporter gene throughout development. Thus, transcription appears to reset and change epigenetic marks at chromosomal memory elements regulated by the Polycomb and trithorax proteins. Interestingly, in the bithorax complex of D. melanogaster, the segment-specific expression of noncoding intergenic transcripts during embryogenesis seems to fulfill this switching role for memory elements regulating the homeotic genes.

scholarly journals Control of tissue homeostasis, tumorigenesis, and degeneration by coupled bidirectional bistable switches

2021 ◽  
Vol 17 (11) ◽  
pp. e1009606
Author(s):  
Diego Barra Avila ◽  
Juan R. Melendez-Alvarez ◽  
Xiao-Jun Tian
Keyword(s):  
Regulatory Network ◽  
Physiological State ◽  
Critical Role ◽  
Feedback Loops ◽  
Tissue Homeostasis ◽  
State Transitions ◽  
Stochastic Fluctuations ◽  
The One ◽  
Theoretical Analyses ◽  
Complex Regulatory Network

The Hippo-YAP/TAZ signaling pathway plays a critical role in tissue homeostasis, tumorigenesis, and degeneration disorders. The regulation of YAP/TAZ levels is controlled by a complex regulatory network, where several feedback loops have been identified. However, it remains elusive how these feedback loops contain the YAP/TAZ levels and maintain the system in a healthy physiological state or trap the system in pathological conditions. Here, a mathematical model was developed to represent the YAP/TAZ regulatory network. Through theoretical analyses, three distinct states that designate the one physiological and two pathological outcomes were found. The transition from the physiological state to the two pathological states is mechanistically controlled by coupled bidirectional bistable switches, which are robust to parametric variation and stochastic fluctuations at the molecular level. This work provides a mechanistic understanding of the regulation and dysregulation of YAP/TAZ levels in tissue state transitions.

scholarly journals PID Control as a Process of Active Inference with Linear Generative Models

Entropy ◽  
2019 ◽  
Vol 21 (3) ◽  
pp. 257 ◽  
Author(s):  
Manuel Baltieri ◽  
Christopher Buckley
Keyword(s):  
Free Energy ◽  
Biological Systems ◽  
Generative Models ◽  
Pid Controllers ◽  
Mathematical Framework ◽  
Prediction Errors ◽  
Active Inference ◽  
General Process ◽  
Brain Functions ◽  
Theoretical Approaches

In the past few decades, probabilistic interpretations of brain functions have become widespread in cognitive science and neuroscience. In particular, the free energy principle and active inference are increasingly popular theories of cognitive functions that claim to offer a unified understanding of life and cognition within a general mathematical framework derived from information and control theory, and statistical mechanics. However, we argue that if the active inference proposal is to be taken as a general process theory for biological systems, it is necessary to understand how it relates to existing control theoretical approaches routinely used to study and explain biological systems. For example, recently, PID (Proportional-Integral-Derivative) control has been shown to be implemented in simple molecular systems and is becoming a popular mechanistic explanation of behaviours such as chemotaxis in bacteria and amoebae, and robust adaptation in biochemical networks. In this work, we will show how PID controllers can fit a more general theory of life and cognition under the principle of (variational) free energy minimisation when using approximate linear generative models of the world. This more general interpretation also provides a new perspective on traditional problems of PID controllers such as parameter tuning as well as the need to balance performances and robustness conditions of a controller. Specifically, we then show how these problems can be understood in terms of the optimisation of the precisions (inverse variances) modulating different prediction errors in the free energy functional.

scholarly journals Microstructural design for mechanical–optical multifunctionality in the exoskeleton of the flower beetle Torynorrhina flammea

2021 ◽  
Vol 118 (25) ◽  
pp. e2101017118
Author(s):  
Zian Jia ◽  
Matheus C. Fernandes ◽  
Zhifei Deng ◽  
Ting Yang ◽  
Qiuting Zhang ◽  
...  
Keyword(s):  
Damage Tolerance ◽  
Elastic Recovery ◽  
Biological Systems ◽  
Diffraction Order ◽  
Optical Diffraction ◽  
Design Strategies ◽  
Mechanical Stiffness ◽  
Optical Damage ◽  
Theoretical Approaches ◽  
Trade Offs

Biological systems have a remarkable capability of synthesizing multifunctional materials that are adapted for specific physiological and ecological needs. When exploring structure–function relationships related to multifunctionality in nature, it can be a challenging task to address performance synergies, trade-offs, and the relative importance of different functions in biological materials, which, in turn, can hinder our ability to successfully develop their synthetic bioinspired counterparts. Here, we investigate such relationships between the mechanical and optical properties in a multifunctional biological material found in the highly protective yet conspicuously colored exoskeleton of the flower beetle, Torynorrhina flammea. Combining experimental, computational, and theoretical approaches, we demonstrate that a micropillar-reinforced photonic multilayer in the beetle’s exoskeleton simultaneously enhances mechanical robustness and optical appearance, giving rise to optical damage tolerance. Compared with plain multilayer structures, stiffer vertical micropillars increase stiffness and elastic recovery, restrain the formation of shear bands, and enhance delamination resistance. The micropillars also scatter the reflected light at larger polar angles, enhancing the first optical diffraction order, which makes the reflected color visible from a wider range of viewing angles. The synergistic effect of the improved angular reflectivity and damage localization capability contributes to the optical damage tolerance. Our systematic structural analysis of T. flammea’s different color polymorphs and parametric optical and mechanical modeling further suggest that the beetle’s microarchitecture is optimized toward maximizing the first-order optical diffraction rather than its mechanical stiffness. These findings shed light on material-level design strategies utilized in biological systems for achieving multifunctionality and could thus inform bioinspired material innovations.

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