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Bistable networks

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https://www.readbyqxmd.com/read/29914480/single-molecules-can-operate-as-primitive-biological-sensors-switches-and-oscillators
#1
Rosa D Hernansaiz-Ballesteros, Luca Cardelli, Attila Csikász-Nagy
BACKGROUND: Switch-like and oscillatory dynamical systems are widely observed in biology. We investigate the simplest biological switch that is composed of a single molecule that can be autocatalytically converted between two opposing activity forms. We test how this simple network can keep its switching behaviour under perturbations in the system. RESULTS: We show that this molecule can work as a robust bistable system, even for alterations in the reactions that drive the switching between various conformations...
June 18, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29898720/landscape-reveals-critical-network-structures-for-sharpening-gene-expression-boundaries
#2
Chunhe Li, Lei Zhang, Qing Nie
BACKGROUND: Spatial pattern formation is a critical issue in developmental biology. Gene expression boundary sharpening has been observed from both experiments and modeling simulations. However, the mechanism to determine the sharpness of the boundary is not fully elucidated. RESULTS: We investigated the boundary sharpening resulted by three biological motifs, interacting with morphogens, and uncovered their probabilistic landscapes. The landscape view, along with calculated average switching time between attractors, provides a natural explanation for the boundary sharpening behavior relying on the noise induced gene state switchings...
June 13, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29773979/efficient-coding-and-energy-efficiency-are-promoted-by-balanced-excitatory-and-inhibitory-synaptic-currents-in-neuronal-network
#3
Lianchun Yu, Zhou Shen, Chen Wang, Yuguo Yu
Selective pressure may drive neural systems to process as much information as possible with the lowest energy cost. Recent experiment evidence revealed that the ratio between synaptic excitation and inhibition (E/I) in local cortex is generally maintained at a certain value which may influence the efficiency of energy consumption and information transmission of neural networks. To understand this issue deeply, we constructed a typical recurrent Hodgkin-Huxley network model and studied the general principles that governs the relationship among the E/I synaptic current ratio, the energy cost and total amount of information transmission...
2018: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/29765314/underlying-mechanisms-of-cooperativity-input-specificity-and-associativity-of-long-term-potentiation-through-a-positive-feedback-of-local-protein-synthesis
#4
Lijie Hao, Zhuoqin Yang, Jinzhi Lei
Long-term potentiation (LTP) is a specific form of activity-dependent synaptic plasticity that is a leading mechanism of learning and memory in mammals. The properties of cooperativity, input specificity, and associativity are essential for LTP; however, the underlying mechanisms are unclear. Here, based on experimentally observed phenomena, we introduce a computational model of synaptic plasticity in a pyramidal cell to explore the mechanisms responsible for the cooperativity, input specificity, and associativity of LTP...
2018: Frontiers in Computational Neuroscience
https://www.readbyqxmd.com/read/29758769/modulation-of-dynamic-modes-by-interplay-between-positive-and-negative-feedback-loops-in-gene-regulatory-networks
#5
Liu-Suo Wang, Ning-Xi Li, Jing-Jia Chen, Xiao-Peng Zhang, Feng Liu, Wei Wang
A positive and a negative feedback loop can induce bistability and oscillation, respectively, in biological networks. Nevertheless, they are frequently interlinked to perform more elaborate functions in many gene regulatory networks. Coupled positive and negative feedback loops may exhibit either oscillation or bistability depending on the intensity of the stimulus in some particular networks. It is less understood how the transition between the two dynamic modes is modulated by the positive and negative feedback loops...
April 2018: Physical Review. E
https://www.readbyqxmd.com/read/29720679/spillover-modes-in-multiplex-games-double-edged-effects-on-cooperation-and-their-coevolution
#6
Tommy Khoo, Feng Fu, Scott Pauls
In recent years, there has been growing interest in studying games on multiplex networks that account for interactions across linked social contexts. However, little is known about how potential cross-context interference, or spillover, of individual behavioural strategy impact overall cooperation. We consider three plausible spillover modes, quantifying and comparing their effects on the evolution of cooperation. In our model, social interactions take place on two network layers: repeated interactions with close neighbours in a lattice, and one-shot interactions with random individuals...
May 2, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29712783/conditional-bistability-a-generic-cellular-mnemonic-mechanism-for-robust-and-flexible-working-memory-computations
#7
Guillaume Rodriguez, Matthieu Sarazin, Alexandra Clemente, Stephanie Holden, Jeanne T Paz, Bruno Delord
Persistent neural activity, the substrate of working memory, is thought to emerge from synaptic reverberation within recurrent networks. However, reverberation models do not robustly explain fundamental dynamics of persistent activity, including high-spiking irregularity, large intertrial variability, and state transitions. While cellular bistability may contribute to persistent activity, its rigidity appears incompatible with persistent activity labile characteristics. Here, we unravel in a cellular model a form of spike-mediated conditional bistability that is robust, generic and provides a rich repertoire of mnemonic computations...
April 30, 2018: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/29684007/identifying-robust-hysteresis-in-networks
#8
Tomáš Gedeon, Bree Cummins, Shaun Harker, Konstantin Mischaikow
We present a new modeling and computational tool that computes rigorous summaries of network dynamics over large sets of parameter values. These summaries, organized in a database, can be searched for observed dynamics, e.g., bistability and hysteresis, to discover parameter regimes over which they are supported. We illustrate our approach on several networks underlying the restriction point of the cell cycle in humans and yeast. We rank networks by how robustly they support hysteresis, which is the observed phenotype...
April 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29669897/axon-growth-regulation-by-a-bistable-molecular-switch
#9
Pranesh Padmanabhan, Geoffrey J Goodhill
For the brain to function properly, its neurons must make the right connections during neural development. A key aspect of this process is the tight regulation of axon growth as axons navigate towards their targets. Neuronal growth cones at the tips of developing axons switch between growth and paused states during axonal pathfinding, and this switching behaviour determines the heterogeneous axon growth rates observed during brain development. The mechanisms controlling this switching behaviour, however, remain largely unknown...
April 25, 2018: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29620527/a-robust-and-tunable-mitotic-oscillator-in-artificial-cells
#10
Ye Guan, Zhengda Li, Shiyuan Wang, Patrick M Barnes, Xuwen Liu, Haotian Xu, Minjun Jin, Allen P Liu, Qiong Yang
Single-cell analysis is pivotal to deciphering complex phenomena like heterogeneity, bistability, and asynchronous oscillations, where a population ensemble cannot represent individual behaviors. Bulk cell-free systems, despite having unique advantages of manipulation and characterization of biochemical networks, lack the essential single-cell information to understand a class of out-of-steady-state dynamics including cell cycles. Here, by encapsulating Xenopus egg extracts in water-in-oil microemulsions, we developed artificial cells that are adjustable in sizes and periods, sustain mitotic oscillations for over 30 cycles, and function in forms from the simplest cytoplasmic-only to the more complicated ones involving nuclear dynamics, mimicking real cells...
April 5, 2018: ELife
https://www.readbyqxmd.com/read/29619463/constrained-stoichiometric-network-analysis
#11
Vuk Radojković, Igor Schreiber
Stoichiometric network analysis (SNA) is a method for studying the stability of steady states of stoichiometric systems by decomposing the corresponding network into elementary subnetworks (also known as extreme currents) and identifying those that may cause loss of a network's stability via interplay of positive and negative feedback. Experimentally studied complex (bio)chemical reactions often display dynamical instabilities leading to oscillations or bistable switches. When modelling such systems, a frequently met case is that an assumed detailed mechanism in terms of power law kinetics is available, but some of the rate coefficients are unknown and obtaining them by traditional kinetic methods based on a least-square fit is cumbersome or unfeasible...
April 18, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29604631/artificial-neural-network-detects-human-uncertainty
#12
Alexander E Hramov, Nikita S Frolov, Vladimir A Maksimenko, Vladimir V Makarov, Alexey A Koronovskii, Juan Garcia-Prieto, Luis Fernando Antón-Toro, Fernando Maestú, Alexander N Pisarchik
Artificial neural networks (ANNs) are known to be a powerful tool for data analysis. They are used in social science, robotics, and neurophysiology for solving tasks of classification, forecasting, pattern recognition, etc. In neuroscience, ANNs allow the recognition of specific forms of brain activity from multichannel EEG or MEG data. This makes the ANN an efficient computational core for brain-machine systems. However, despite significant achievements of artificial intelligence in recognition and classification of well-reproducible patterns of neural activity, the use of ANNs for recognition and classification of patterns in neural networks still requires additional attention, especially in ambiguous situations...
March 2018: Chaos
https://www.readbyqxmd.com/read/29593608/no-evidence-for-phase-specific-effects-of-40-hz-hd-tacs-on-multiple-object-tracking
#13
Nicholas S Bland, Jason B Mattingley, Martin V Sale
Phase synchronization drives connectivity between neural oscillators, providing a flexible mechanism through which information can be effectively and selectively routed between task-relevant cortical areas. The ability to keep track of objects moving between the left and right visual hemifields, for example, requires the integration of information between the two cerebral hemispheres. Both animal and human studies have suggested that coherent (or phase-locked) gamma oscillations (30-80 Hz) might underlie this ability...
2018: Frontiers in Psychology
https://www.readbyqxmd.com/read/29531035/stabilized-supralinear-network-can-give-rise-to-bistable-oscillatory-and-persistent-activity
#14
Nataliya Kraynyukova, Tatjana Tchumatchenko
A hallmark of cortical circuits is their versatility. They can perform multiple fundamental computations such as normalization, memory storage, and rhythm generation. Yet it is far from clear how such versatility can be achieved in a single circuit, given that specialized models are often needed to replicate each computation. Here, we show that the stabilized supralinear network (SSN) model, which was originally proposed for sensory integration phenomena such as contrast invariance, normalization, and surround suppression, can give rise to dynamic cortical features of working memory, persistent activity, and rhythm generation...
March 27, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29499434/systems-level-feedback-regulation-of-cell-cycle-transitions-in-ostreococcus-tauri
#15
Orsolya Kapuy, P K Vinod, Gábor Bánhegyi, Béla Novák
Ostreococcus tauri is the smallest free-living unicellular organism with one copy of each core cell cycle genes in its genome. There is a growing interest in this green algae due to its evolutionary origin. Since O. tauri is diverged early in the green lineage, relatively close to the ancestral eukaryotic cell, it might hold a key phylogenetic position in the eukaryotic tree of life. In this study, we focus on the regulatory network of its cell division cycle. We propose a mathematical modelling framework to integrate the existing knowledge of cell cycle network of O...
May 2018: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29414696/dynamics-of-posttranslational-modification-systems-recent-progress-and-future-directions
#16
REVIEW
Carsten Conradi, Anne Shiu
Posttranslational modification of proteins is important for signal transduction, and hence significant effort has gone toward understanding how posttranslational modification networks process information. This involves, on the theory side, analyzing the dynamical systems arising from such networks. Which networks are, for instance, bistable? Which networks admit sustained oscillations? Which parameter values enable such behaviors? In this Biophysical Perspective, we highlight recent progress in this area and point out some important future directions...
February 6, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29380073/threshold-response-and-bistability-in-gene-regulation-by-small-noncoding-rna
#17
Sutapa Mukherji
In this paper, we study through mathematical modelling the combined effect of transcriptional and translational regulation by proteins and small noncoding RNAs (sRNA) in a genetic feedback motif that has an important role in the survival of E. coli under stress associated with oxygen and energy availability. We show that subtle changes in this motif can bring in drastically different effects on the gene expression. In particular, we show that a threshold response in the gene expression changes to a bistable response as the regulation on sRNA synthesis or degradation is altered...
January 31, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29347512/symmetry-breaking-in-two-interacting-populations-of-quadratic-integrate-and-fire-neurons
#18
Irmantas Ratas, Kestutis Pyragas
We analyze the dynamics of two coupled identical populations of quadratic integrate-and-fire neurons, which represent the canonical model for class I neurons near the spiking threshold. The populations are heterogeneous; they include both inherently spiking and excitable neurons. The coupling within and between the populations is global via synapses that take into account the finite width of synaptic pulses. Using a recently developed reduction method based on the Lorentzian ansatz, we derive a closed system of equations for the neuron's firing rates and the mean membrane potentials in both populations...
October 2017: Physical Review. E
https://www.readbyqxmd.com/read/29331630/mrna-function-after-intracellular-delivery-and-release
#19
Vladimir P Zhdanov
Nanocarrier-mediated mRNA delivery and release into the cells with subsequent translation to protein is of interest in the context of the development of a new generation of drugs. In particular, this protein can play a role of a transcription factor and be used as a tool to regulate temporarily the genetic networks. The corresponding transient kinetics of gene expression are expected to depend on the mechanism and duration of mRNA release. Assuming the release to be rapid on the time scale of other steps, the author shows theoretically the mRNA-related transient features of gene expression occurring in stable, bistable, and oscillatory regimes in a single cell...
March 2018: Bio Systems
https://www.readbyqxmd.com/read/29330362/dynamic-modelling-of-the-mtor-signalling-network-reveals-complex-emergent-behaviours-conferred-by-deptor
#20
Thawfeek M Varusai, Lan K Nguyen
The mechanistic Target of Rapamycin (mTOR) signalling network is an evolutionarily conserved network that controls key cellular processes, including cell growth and metabolism. Consisting of the major kinase complexes mTOR Complex 1 and 2 (mTORC1/2), the mTOR network harbours complex interactions and feedback loops. The DEP domain-containing mTOR-interacting protein (DEPTOR) was recently identified as an endogenous inhibitor of both mTORC1 and 2 through direct interactions, and is in turn degraded by mTORC1/2, adding an extra layer of complexity to the mTOR network...
January 12, 2018: Scientific Reports
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