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Bistable networks

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https://www.readbyqxmd.com/read/28713623/bistability-and-oscillations-in-co-repressive-synthetic-microbial-consortia
#1
Mehdi Sadeghpour, Alan Veliz-Cuba, Gábor Orosz, Krešimir Josić, Matthew R Bennett
Synthetic microbial consortia are conglomerations of multiple strains of genetically engineered microbes programmed to cooperatively bring about population-level phenotypes. By coordinating their activity, the constituent strains can display emergent behaviors that are difficult to engineer into isogenic populations. To do so, strains are engineered to communicate with one another through intercellular signaling pathways. As a result, the regulatory networks that control gene transcription throughout the population are sensitive to the extracellular concentration of the signaling molecules, and hence the relative densities of constituent strains...
March 2017: Quantitative Biology
https://www.readbyqxmd.com/read/28701732/alpha-power-predicts-persistence-of-bistable-perception
#2
Giovanni Piantoni, Nico Romeijn, German Gomez-Herrero, Ysbrand D Van Der Werf, Eus J W Van Someren
Perception is strongly affected by the intrinsic state of the brain, which controls the propensity to either maintain a particular perceptual interpretation or switch to another. To understand the mechanisms underlying the spontaneous drive of the brain to explore alternative interpretations of unchanging stimuli, we repeatedly recorded high-density EEG after normal sleep and after sleep deprivation while participants observed a Necker cube image and reported the durations of the alternating representations of their bistable perception...
July 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28679225/control-of-birhythmicity-a-self-feedback-approach
#3
Debabrata Biswas, Tanmoy Banerjee, Jürgen Kurths
Birhythmicity occurs in many natural and artificial systems. In this paper, we propose a self-feedback scheme to control birhythmicity. To establish the efficacy and generality of the proposed control scheme, we apply it on three birhythmic oscillators from diverse fields of natural science, namely, an energy harvesting system, the p53-Mdm2 network for protein genesis (the OAK model), and a glycolysis model (modified Decroly-Goldbeter model). Using the harmonic decomposition technique and energy balance method, we derive the analytical conditions for the control of birhythmicity...
June 2017: Chaos
https://www.readbyqxmd.com/read/28667253/inhibitors-alter-the-stochasticity-of-regulatory-proteins-to-force-cells-to-switch-to-the-other-state-in-the-bistable-system
#4
Wun-Sin Jhang, Shih-Chiang Lo, Chen-Chao Yeh, Che-Chi Shu
The cellular behaviors under the control of genetic circuits are subject to stochastic fluctuations, or noise. The stochasticity in gene regulation, far from a nuisance, has been gradually appreciated for its unusual function in cellular activities. In this work, with Chemical Master Equation (CME), we discovered that the addition of inhibitors altered the stochasticity of regulatory proteins. For a bistable system of a mutually inhibitory network, such a change of noise led to the migration of cells in the bimodal distribution...
June 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28659783/multistability-and-long-timescale-transients-encoded-by-network-structure-in-a-model-of-c-elegans-connectome-dynamics
#5
James M Kunert-Graf, Eli Shlizerman, Andrew Walker, J Nathan Kutz
The neural dynamics of the nematode Caenorhabditis elegans are experimentally low-dimensional and may be understood as long-timescale transitions between multiple low-dimensional attractors. Previous modeling work has found that dynamic models of the worm's full neuronal network are capable of generating reasonable dynamic responses to certain inputs, even when all neurons are treated as identical save for their connectivity. This study investigates such a model of C. elegans neuronal dynamics, finding that a wide variety of multistable responses are generated in response to varied inputs...
2017: Frontiers in Computational Neuroscience
https://www.readbyqxmd.com/read/28639170/bistability-and-asynchrony-in-a-boolean-model-of-the-l-arabinose-operon-in-escherichia-coli
#6
Andy Jenkins, Matthew Macauley
The lactose operon in Escherichia coli was the first known gene regulatory network, and it is frequently used as a prototype for new modeling paradigms. Historically, many of these modeling frameworks use differential equations. More recently, Stigler and Veliz-Cuba proposed a Boolean model that captures the bistability of the system and all of the biological steady states. In this paper, we model the well-known arabinose operon in E. coli with a Boolean network. This has several complex features not found in the lac operon, such as a protein that is both an activator and repressor, a DNA looping mechanism for gene repression, and the lack of inducer exclusion by glucose...
June 21, 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/28636629/minimal-oscillating-subnetwork-in-the-huang-ferrell-model-of-the-mapk-cascade
#7
Otto Hadač, František Muzika, Vladislav Nevoral, Michal Přibyl, Igor Schreiber
Prompted by the recent growing evidence of oscillatory behavior involving MAPK cascades we present a systematic approach of analyzing models and elucidating the nature of biochemical oscillations based on reaction network theory. In particular, we formulate a minimal biochemically consistent mass action subnetwork of the Huang-Ferrell model of the MAPK signalling that provides an oscillatory response when a parameter controlling the activation of the top-tier kinase is varied. Such dynamics are either intertwined with or separated from the earlier found bistable/hysteretic behavior in this model...
2017: PloS One
https://www.readbyqxmd.com/read/28600136/an-all-encompassing-global-convergence-result-for-processive-multisite-phosphorylation-systems
#8
Mitchell Eithun, Anne Shiu
Phosphorylation, the enzyme-mediated addition of a phosphate group to a molecule, is a ubiquitous chemical mechanism in biology. Multisite phosphorylation, the addition of phosphate groups to multiple sites of a single molecule, may be distributive or processive. Distributive systems, which require an enzyme and substrate to bind several times in order to add multiple phosphate groups, can be bistable. Processive systems, in contrast, require only one binding to add all phosphate groups, and were recently shown to be globally stable...
June 29, 2017: Mathematical Biosciences
https://www.readbyqxmd.com/read/28582616/molecular-engineering-of-robustness-and-resilience-in-enzymatic-reaction-networks
#9
Albert S Y Wong, Aleksandr A Pogodaev, Ilia N Vialshin, Britta Helwig, Wilhelm T S Huck
Living systems rely on complex networks of chemical reactions to control the concentrations of molecules in space and time. Despite the enormous complexity in biological networks, it is possible to identify network motifs that lead to functional outputs such as bistability or oscillations. One of the greatest challenges in chemistry is the creation of such functionality from chemical reactions. A key limitation is our lack of understanding of how molecular structure impacts on the dynamics of chemical reaction networks, preventing the design of networks that are robust (i...
June 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28525544/bistability-causality-and-complexity-in-cortical-networks-an-in-vitro-perturbational-study
#10
Mattia D'Andola, Beatriz Rebollo, Adenauer G Casali, Julia F Weinert, Andrea Pigorini, Rosa Villa, Marcello Massimini, Maria V Sanchez-Vives
Measuring the spatiotemporal complexity of cortical responses to direct perturbations provides a reliable index of the brain's capacity for consciousness in humans under both physiological and pathological conditions. Upon loss of consciousness, the complex pattern of causal interactions observed during wakefulness collapses into a stereotypical slow wave, suggesting that cortical bistability may play a role. Bistability is mainly expressed in the form of slow oscillations, a default pattern of activity that emerges from cortical networks in conditions of functional or anatomical disconnection...
May 19, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/28505836/stationary-patterns-in-star-networks-of-bistable-units-theory-and-application-to-chemical-reactions
#11
Nikos E Kouvaris, Michael Sebek, Albert Iribarne, Albert Díaz-Guilera, István Z Kiss
We present theoretical and experimental studies on pattern formation with bistable dynamical units coupled in a star network configuration. By applying a localized perturbation to the central or the peripheral elements, we demonstrate the subsequent spreading, pinning, or retraction of the activations; such analysis enables the characterization of the formation of stationary patterns of localized activity. The results are interpreted with a theoretical analysis of a simplified bistable reaction-diffusion model...
April 2017: Physical Review. E
https://www.readbyqxmd.com/read/28505785/noise-induced-polarization-switching-in-complex-networks
#12
Jan O Haerter, Albert Díaz-Guilera, M Ángeles Serrano
The combination of bistability and noise is ubiquitous in complex systems, from biology to social interactions, and has important implications for their functioning and resilience. Here we use a simple three-state dynamical process, in which nodes go from one pole to another through an intermediate state, to show that noise can induce polarization switching in bistable systems if dynamical correlations are significant. In large, fully connected networks, where dynamical correlations can be neglected, increasing noise yields a collapse of bistability to an unpolarized configuration where the three possible states of the nodes are equally likely...
April 2017: Physical Review. E
https://www.readbyqxmd.com/read/28484034/modeling-the-response-of-a-tumor-suppressive-network-to-mitogenic-and-oncogenic-signals
#13
Xinyu Tian, Bo Huang, Xiao-Peng Zhang, Mingyang Lu, Feng Liu, José N Onuchic, Wei Wang
Intrinsic tumor-suppressive mechanisms protect normal cells against aberrant proliferation. Although cellular signaling pathways engaged in tumor repression have been largely identified, how they are orchestrated to fulfill their function still remains elusive. Here, we built a tumor-suppressive network model composed of three modules responsible for the regulation of cell proliferation, activation of p53, and induction of apoptosis. Numerical simulations show a rich repertoire of network dynamics when normal cells are subject to serum stimulation and adenovirus E1A overexpression...
May 23, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28415301/nonlinear-signaling-on-biological-networks-the-role-of-stochasticity-and-spectral-clustering
#14
Gonzalo Hernandez-Hernandez, Jesse Myers, Enrique Alvarez-Lacalle, Yohannes Shiferaw
Signal transduction within biological cells is governed by networks of interacting proteins. Communication between these proteins is mediated by signaling molecules which bind to receptors and induce stochastic transitions between different conformational states. Signaling is typically a cooperative process which requires the occurrence of multiple binding events so that reaction rates have a nonlinear dependence on the amount of signaling molecule. It is this nonlinearity that endows biological signaling networks with robust switchlike properties which are critical to their biological function...
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28397813/nonlinear-dynamics-and-chaos-in-an-optomechanical-beam
#15
Daniel Navarro-Urrios, Néstor E Capuj, Martín F Colombano, P David García, Marianna Sledzinska, Francesc Alzina, Amadeu Griol, Alejandro Martínez, Clivia M Sotomayor-Torres
Optical nonlinearities, such as thermo-optic mechanisms and free-carrier dispersion, are often considered unwelcome effects in silicon-based resonators and, more specifically, optomechanical cavities, since they affect, for instance, the relative detuning between an optical resonance and the excitation laser. Here, we exploit these nonlinearities and their intercoupling with the mechanical degrees of freedom of a silicon optomechanical nanobeam to unveil a rich set of fundamentally different complex dynamics...
April 11, 2017: Nature Communications
https://www.readbyqxmd.com/read/28369623/the-hidden-life-of-integrative-and-conjugative-elements
#16
François Delavat, Ryo Miyazaki, Nicolas Carraro, Nicolas Pradervand, Jan Roelof van der Meer
Integrative and conjugative elements (ICEs) are widespread mobile DNA that transmit both vertically, in a host-integrated state, and horizontally, through excision and transfer to new recipients. Different families of ICEs have been discovered with more or less restricted host ranges, which operate by similar mechanisms but differ in regulatory networks, evolutionary origin and the types of variable genes they contribute to the host. Based on reviewing recent experimental data, we propose a general model of ICE life style that explains the transition between vertical and horizontal transmission as a result of a bistable decision in the ICE-host partnership...
March 25, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28369103/chemical-reaction-network-theory-elucidates-sources-of-multistability-in-interferon-signaling
#17
Irene Otero-Muras, Pencho Yordanov, Joerg Stelling
Bistability has important implications in signaling pathways, since it indicates a potential cell decision between alternative outcomes. We present two approaches developed in the framework of the Chemical Reaction Network Theory for easy and efficient search of multiple steady state behavior in signaling networks (both with and without mass conservation), and apply them to search for sources of bistability at different levels of the interferon signaling pathway. Different type I interferon subtypes and/or doses are known to elicit differential bioactivities (ranging from antiviral, antiproliferative to immunomodulatory activities)...
April 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28280580/organization-of-biogeochemical-nitrogen-pathways-with-switch-like-adjustment-in-fluctuating-soil-redox-conditions
#18
Sanjay Lamba, Soumen Bera, Mubasher Rashid, Alexander B Medvinsky, Gui-Quan Sun, Claudia Acquisti, Amit Chakraborty, Bai-Lian Li
Nitrogen is cycled throughout ecosystems by a suite of biogeochemical processes. The high complexity of the nitrogen cycle resides in an intricate interplay between reversible biochemical pathways alternatively and specifically activated in response to diverse environmental cues. Despite aggressive research, how the fundamental nitrogen biochemical processes are assembled and maintained in fluctuating soil redox conditions remains elusive. Here, we address this question using a kinetic modelling approach coupled with dynamical systems theory and microbial genomics...
January 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28246663/steady-state-statistical-correlations-predict-bistability-in-reaction-motifs
#19
Suchana Chakravarty, Debashis Barik
Various cellular decision making processes are regulated by bistable switches that take graded input signals and convert them to binary all-or-none responses. Traditionally, a bistable switch generated by a positive feedback loop is characterized either by a hysteretic signal response curve with two distinct signaling thresholds or by characterizing the bimodality of the response distribution in the bistable region. To identify the intrinsic bistability of a feedback regulated network, here we propose that bistability can be determined by correlating higher order moments and cumulants (≥2) of the joint steady state distributions of two components connected in a positive feedback loop...
March 1, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28245235/the-role-of-the-hes1-crosstalk-hub-in-notch-wnt-interactions-of-the-intestinal-crypt
#20
Sophie K Kay, Heather A Harrington, Sarah Shepherd, Keith Brennan, Trevor Dale, James M Osborne, David J Gavaghan, Helen M Byrne
The Notch pathway plays a vital role in determining whether cells in the intestinal epithelium adopt a secretory or an absorptive phenotype. Cell fate specification is coordinated via Notch's interaction with the canonical Wnt pathway. Here, we propose a new mathematical model of the Notch and Wnt pathways, in which the Hes1 promoter acts as a hub for pathway crosstalk. Computational simulations of the model can assist in understanding how healthy intestinal tissue is maintained, and predict the likely consequences of biochemical knockouts upon cell fate selection processes...
February 2017: PLoS Computational Biology
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