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Bistable networks

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https://www.readbyqxmd.com/read/28973467/a-transcription-network-of-interlocking-positive-feedback-loops-maintains-intracellular-iron-balance-in-archaea
#1
Mar Martinez-Pastor, W Andrew Lancaster, Peter D Tonner, Michael W W Adams, Amy K Schmid
Iron is required for key metabolic processes but is toxic in excess. This circumstance forces organisms across the tree of life to tightly regulate iron homeostasis. In hypersaline lakes dominated by archaeal species, iron levels are extremely low and subject to environmental change; however, mechanisms regulating iron homeostasis in archaea remain unclear. In previous work, we demonstrated that two transcription factors (TFs), Idr1 and Idr2, collaboratively regulate aspects of iron homeostasis in the model species Halobacterium salinarum...
September 29, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28950647/chimeralike-states-in-networks-of-bistable-time-delayed-feedback-oscillators-coupled-via-the-mean-field
#2
V I Ponomarenko, D D Kulminskiy, M D Prokhorov
We study the collective dynamics of oscillators in a network of identical bistable time-delayed feedback systems globally coupled via the mean field. The influence of delay and inertial properties of the mean field on the collective behavior of globally coupled oscillators is investigated. A variety of oscillation regimes in the network results from the presence of bistable states with substantially different frequencies in coupled oscillators. In the physical experiment and numerical simulation we demonstrate the existence of chimeralike states, in which some of the oscillators in the network exhibit synchronous oscillations, while all other oscillators remain asynchronous...
August 2017: Physical Review. E
https://www.readbyqxmd.com/read/28937677/synthesis-and-materialization-of-a-reaction-diffusion-french-flag-pattern
#3
Anton S Zadorin, Yannick Rondelez, Guillaume Gines, Vadim Dilhas, Georg Urtel, Adrian Zambrano, Jean-Christophe Galas, André Estevez-Torres
During embryo development, patterns of protein concentration appear in response to morphogen gradients. These patterns provide spatial and chemical information that directs the fate of the underlying cells. Here, we emulate this process within non-living matter and demonstrate the autonomous structuration of a synthetic material. First, we use DNA-based reaction networks to synthesize a French flag, an archetypal pattern composed of three chemically distinct zones with sharp borders whose synthetic analogue has remained elusive...
October 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28931930/bistability-and-up-down-state-alternations-in-inhibition-dominated-randomly-connected-networks-of-lif-neurons
#4
Elisa M Tartaglia, Nicolas Brunel
Electrophysiological recordings in cortex in vivo have revealed a rich variety of dynamical regimes ranging from irregular asynchronous states to a diversity of synchronized states, depending on species, anesthesia, and external stimulation. The average population firing rate in these states is typically low. We study analytically and numerically a network of sparsely connected excitatory and inhibitory integrate-and-fire neurons in the inhibition-dominated, low firing rate regime. For sufficiently high values of the external input, the network exhibits an asynchronous low firing frequency state (L)...
September 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28931595/cell-cycle-transitions-a-common-role-for-stoichiometric-inhibitors
#5
Michael Hopkins, John J Tyson, Béla Novák
The cell division cycle is the process by which eukaryotic cells replicate their chromosomes and partition them to two daughter cells. To maintain the integrity of the genome, proliferating cells must be able to block progression through the division cycle at key transition points (called 'checkpoints'), if there have been problems in the replication of the chromosomes or their biorientation on the mitotic spindle. These checkpoints are governed by protein-interaction networks, composed of phase-specific cell-cycle activators and inhibitors...
September 20, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28928941/computational-design-of-molecular-motors-as-nanocircuits-in-leishmaniasis
#6
Dipali Kosey, Shailza Singh
Cutaneous leishmaniasis is the most common form of lesihmaniasis, caused by Leishmania major and is spread by the bite of a sandfly .This species infects the macrophages and dendritic cells Due to multi-drug resistance, there is a need for a new therapeutic technique. Recently, a novel molecular motor of Leishmania, Myosin XXI, was classified and characterized. In addition, the drug resistance in this organism has been linked with the overexpression of ABC transporters. Systems biology aims to study the simulation and modeling of natural biological systems whereas synthetic biology deals with building novel and artificial biological parts and devices  Together they have contributed enormously to drug discovery, vaccine design and development, infectious disease detection and diagnostics...
2017: F1000Research
https://www.readbyqxmd.com/read/28902568/interlinked-bistable-mechanisms-generate-robust-mitotic-transitions
#7
Lukas H Hutter, Scott Rata, Helfrid Hochegger, Béla Novák
The transitions between phases of the cell cycle have evolved to be robust and switch-like, which ensures temporal separation of DNA replication, sister chromatid separation, and cell division. Mathematical models describing the biochemical interaction networks of cell cycle regulators attribute these properties to underlying bistable switches, which inherently generate robust, switch-like, and irreversible transitions between states. We have recently presented new mathematical models for two control systems that regulate crucial transitions in the cell cycle: mitotic entry and exit, (1) and the mitotic checkpoint...
October 18, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28845192/grip-on-complexity-in-chemical-reaction-networks
#8
REVIEW
Albert S Y Wong, Wilhelm T S Huck
A new discipline of "systems chemistry" is emerging, which aims to capture the complexity observed in natural systems within a synthetic chemical framework. Living systems rely on complex networks of chemical reactions to control the concentration 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. To truly understand how living systems function, we need a complete understanding of how chemical reaction networks (CRNs) create function...
2017: Beilstein Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28841307/the-timing-of-transcriptional-regulation-in-synthetic-gene-circuits
#9
Yu-Yu Cheng, Andrew J Hirning, Krešimir Josić, Matthew R Bennett
Transcription factors and their target promoters are central to synthetic biology. By arranging these components into novel gene regulatory circuits, synthetic biologists have been able to create a wide variety of phenotypes, including bistable switches, oscillators, and logic gates. However, transcription factors (TFs) do not instantaneously regulate downstream targets. After the gene encoding a TF is turned on, the gene must first be transcribed, the transcripts must be translated, and sufficient TF must accumulate in order to bind operator sites of the target promoter...
September 5, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28826485/up-down-cortical-dynamics-reflect-state-transitions-in-a-bistable-network
#10
Daniel Jercog, Alex Roxin, Peter Barthó, Artur Luczak, Albert Compte, Jaime de la Rocha
In the idling brain, neuronal circuits transition between periods of sustained firing (UP state) and quiescence (DOWN state), a pattern the mechanisms of which remain unclear. Here we analyzed spontaneous cortical population activity from anesthetized rats and found that UP and DOWN durations were highly variable and that population rates showed no significant decay during UP periods. We built a network rate model with excitatory (E) and inhibitory (I) populations exhibiting a novel bistable regime between a quiescent and an inhibition-stabilized state of arbitrarily low rate...
August 4, 2017: ELife
https://www.readbyqxmd.com/read/28804140/vertebrate-sex-determination-evolutionary-plasticity-of-a-fundamental-switch
#11
REVIEW
Blanche Capel
The discovery of the Sry gene in 1990 triggered a revolution in our understanding of sex determination. More recently, advances in non-model organisms have been fuelled by the rapid evolution of affordable genome and transcriptome technologies. This Review considers the unusual plasticity in the bipotential system of sex determination and some of the diverse mechanisms that have evolved to control this critical developmental decision, including strong genetic pathways, environmental influences and epigenetic regulation...
November 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28777728/rat-prefrontal-cortex-inactivations-during-decision-making-are-explained-by-bistable-attractor-dynamics
#12
Alex T Piet, Jeffrey C Erlich, Charles D Kopec, Carlos D Brody
Two-node attractor networks are flexible models for neural activity during decision making. Depending on the network configuration, these networks can model distinct aspects of decisions including evidence integration, evidence categorization, and decision memory. Here, we use attractor networks to model recent causal perturbations of the frontal orienting fields (FOF) in rat cortex during a perceptual decision-making task (Erlich, Brunton, Duan, Hanks, & Brody, 2015 ). We focus on a striking feature of the perturbation results...
November 2017: Neural Computation
https://www.readbyqxmd.com/read/28763188/a-tug-of-war-mechanism-for-pattern-formation-in-a-genetic-network
#13
Marcella M Gomez, Murat Arcak
Synthesizing spatial patterns with genetic networks is an ongoing challenge in synthetic biology. A successful demonstration of pattern formation would imply a better understanding of systems in the natural world and advance applications in synthetic biology. In developmental systems, transient patterning may suffice in order to imprint instructions for long-term development. In this paper we show that transient but persistent patterns can emerge from a realizable synthetic gene network based on a toggle switch...
August 1, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28713623/bistability-and-oscillations-in-co-repressive-synthetic-microbial-consortia
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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