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Bistable networks

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https://www.readbyqxmd.com/read/27911933/driving-cells-to-the-desired-state-in-a-bimodal-distribution-through-manipulation-of-internal-noise-with-biologically-practicable-approaches
#1
Che-Chi Shu, Chen-Chao Yeh, Wun-Sin Jhang, Shih-Chiang Lo
The stochastic nature of gene regulatory networks described by Chemical Master Equation (CME) leads to the distribution of proteins. A deterministic bistability is usually reflected as a bimodal distribution in stochastic simulations. Within a certain range of the parameter space, a bistable system exhibits two stable steady states, one at the low end and the other at the high end. Consequently, it appears to have a bimodal distribution with one sub-population (mode) around the low end and the other around the high end...
2016: PloS One
https://www.readbyqxmd.com/read/27902489/effects-of-cell-cycle-noise-on-excitable-gene-circuits
#2
Alan Veliz-Cuba, Chinmaya Gupta, Matthew R Bennett, Krešimir Josić, William Ott
We assess the impact of cell cycle noise on gene circuit dynamics. For bistable genetic switches and excitable circuits, we find that transitions between metastable states most likely occur just after cell division and that this concentration effect intensifies in the presence of transcriptional delay. We explain this concentration effect with a three-states stochastic model. For genetic oscillators, we quantify the temporal correlations between daughter cells induced by cell division. Temporal correlations must be captured properly in order to accurately quantify noise sources within gene networks...
November 30, 2016: Physical Biology
https://www.readbyqxmd.com/read/27876879/stimulus-induced-epileptic-spike-wave-discharges-in-thalamocortical-model-with-disinhibition
#3
Denggui Fan, Suyu Liu, Qingyun Wang
Epileptic absence seizure characterized by the typical 2-4 Hz spike-wave discharges (SWD) are known to arise due to the physiologically abnormal interactions within the thalamocortical network. By introducing a second inhibitory neuronal population in the cortical system, here we propose a modified thalamocortical field model to mathematically describe the occurrences and transitions of SWD under the mutual functions between cortex and thalamus, as well as the disinhibitory modulations of SWD mediated by the two different inhibitory interneuronal populations...
November 23, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27845324/boosting-functionality-of-synthetic-dna-circuits-with-tailored-deactivation
#4
Kevin Montagne, Guillaume Gines, Teruo Fujii, Yannick Rondelez
Molecular programming takes advantage of synthetic nucleic acid biochemistry to assemble networks of reactions, in vitro, with the double goal of better understanding cellular regulation and providing information-processing capabilities to man-made chemical systems. The function of molecular circuits is deeply related to their topological structure, but dynamical features (rate laws) also play a critical role. Here we introduce a mechanism to tune the nonlinearities associated with individual nodes of a synthetic network...
November 15, 2016: Nature Communications
https://www.readbyqxmd.com/read/27821768/engineering-dynamical-control-of-cell-fate-switching-using-synthetic-phospho-regulons
#5
Russell M Gordley, Reid E Williams, Caleb J Bashor, Jared E Toettcher, Shude Yan, Wendell A Lim
Many cells can sense and respond to time-varying stimuli, selectively triggering changes in cell fate only in response to inputs of a particular duration or frequency. A common motif in dynamically controlled cells is a dual-timescale regulatory network: although long-term fate decisions are ultimately controlled by a slow-timescale switch (e.g., gene expression), input signals are first processed by a fast-timescale signaling layer, which is hypothesized to filter what dynamic information is efficiently relayed downstream...
November 22, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27810354/human-sensory-cortex-structure-and-top-down-controlling-brain-network-determine-individual-differences-in-perceptual-alternations
#6
Na Sang, Lijie Zhang, Lei Hao, Yongchao Wang, Xiaogang Wang, Fan Zhang, Hui Huang, Xin Hou, Yu Mao, Taiyong Bi, Jiang Qiu
Bistable perception is a type of subjective perception that spontaneously alternates between two perceptual interpretations of an ambiguous sensory input. Past functional magnetic resonance imaging (fMRI) studies have examined the activation patterns underlying bistable perception, yet the variability between individuals in the alternations is not well understood. Therefore, voxel-based morphometry (VBM) was introduced in this study to correlate the GM of the sensory cortex with the alternations of Rubin face-vase illusion in a large group of young adults...
October 31, 2016: Neuroscience Letters
https://www.readbyqxmd.com/read/27768683/intrinsic-noise-profoundly-alters-the-dynamics-and-steady-state-of-morphogen-controlled-bistable-genetic-switches
#7
Ruben Perez-Carrasco, Pilar Guerrero, James Briscoe, Karen M Page
During tissue development, patterns of gene expression determine the spatial arrangement of cell types. In many cases, gradients of secreted signalling molecules-morphogens-guide this process by controlling downstream transcriptional networks. A mechanism commonly used in these networks to convert the continuous information provided by the gradient into discrete transitions between adjacent cell types is the genetic toggle switch, composed of cross-repressing transcriptional determinants. Previous analyses have emphasised the steady state output of these mechanisms...
October 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27680939/autocatalytic-bistable-oscillatory-networks-of-biologically-relevant-organic-reactions
#8
Sergey N Semenov, Lewis J Kraft, Alar Ainla, Mengxia Zhao, Mostafa Baghbanzadeh, Victoria E Campbell, Kyungtae Kang, Jerome M Fox, George M Whitesides
Networks of organic chemical reactions are important in life and probably played a central part in its origin. Network dynamics regulate cell division, circadian rhythms, nerve impulses and chemotaxis, and guide the development of organisms. Although out-of-equilibrium networks of chemical reactions have the potential to display emergent network dynamics such as spontaneous pattern formation, bistability and periodic oscillations, the principles that enable networks of organic reactions to develop complex behaviours are incompletely understood...
September 28, 2016: Nature
https://www.readbyqxmd.com/read/27593379/determination-of-egfr-signaling-output-by-opposing-gradients-of-bmp-and-jak-stat-activity
#9
Mariana Fregoso Lomas, Scott De Vito, Jean-François Boisclair Lachance, Josée Houde, Laura A Nilson
A relatively small number of signaling pathways drive a wide range of developmental decisions, but how this versatility in signaling outcome is generated is not clear. In the Drosophila follicular epithelium, localized epidermal growth factor receptor (EGFR) activation induces distinct cell fates depending on its location. Posterior follicle cells respond to EGFR activity by expressing the T-box transcription factors Midline and H15, while anterior cells respond by expressing the homeodomain transcription factor Mirror...
October 10, 2016: Current Biology: CB
https://www.readbyqxmd.com/read/27580035/single-cell-analysis-of-mixed-lineage-states-leading-to-a-binary-cell-fate-choice
#10
Andre Olsson, Meenakshi Venkatasubramanian, Viren K Chaudhri, Bruce J Aronow, Nathan Salomonis, Harinder Singh, H Leighton Grimes
Delineating hierarchical cellular states, including rare intermediates and the networks of regulatory genes that orchestrate cell-type specification, are continuing challenges for developmental biology. Single-cell RNA sequencing is greatly accelerating such research, given its power to provide comprehensive descriptions of genomic states and their presumptive regulators. Haematopoietic multipotential progenitor cells, as well as bipotential intermediates, manifest mixed-lineage patterns of gene expression at a single-cell level...
August 31, 2016: Nature
https://www.readbyqxmd.com/read/27575167/oscillations-in-the-bistable-regime-of-neuronal-networks
#11
Alex Roxin, Albert Compte
Bistability between attracting fixed points in neuronal networks has been hypothesized to underlie persistent activity observed in several cortical areas during working memory tasks. In network models this kind of bistability arises due to strong recurrent excitation, sufficient to generate a state of high activity created in a saddle-node (SN) bifurcation. On the other hand, canonical network models of excitatory and inhibitory neurons (E-I networks) robustly produce oscillatory states via a Hopf (H) bifurcation due to the E-I loop...
July 2016: Physical Review. E
https://www.readbyqxmd.com/read/27541958/inverse-stochastic-resonance-in-cerebellar-purkinje-cells
#12
Anatoly Buchin, Sarah Rieubland, Michael Häusser, Boris S Gutkin, Arnd Roth
Purkinje neurons play an important role in cerebellar computation since their axons are the only projection from the cerebellar cortex to deeper cerebellar structures. They have complex internal dynamics, which allow them to fire spontaneously, display bistability, and also to be involved in network phenomena such as high frequency oscillations and travelling waves. Purkinje cells exhibit type II excitability, which can be revealed by a discontinuity in their f-I curves. We show that this excitability mechanism allows Purkinje cells to be efficiently inhibited by noise of a particular variance, a phenomenon known as inverse stochastic resonance (ISR)...
August 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27533896/rac1-and-rhoa-networks-loops-and-bistability
#13
Lan K Nguyen, Boris N Kholodenko, Alex von Kriegsheim
Cell migration requires a precise temporal and spatial coordination of several processes which allow the cell to efficiently move. The extension and retraction of membrane protrusion, as well as adhesion are controlled by the Rho-family small GTPases. Two members of the family, Rac1 and RhoA, can show opposite behaviors and spatial localisations, with RhoA being active toward the rear of the cell and regulating its retraction during migration, whereas Rac1 is active toward the front of the cell. In addition to the spatial segregation, RhoA and Rac1 activity at the leading edge of the cells has an element of temporal segregation, with RhoA and Rac1 activities peaking at separate points during the migratory cycle of protrusion and retraction...
August 17, 2016: Small GTPases
https://www.readbyqxmd.com/read/27485552/stochastic-induction-of-long-term-potentiation-and-long-term-depression
#14
G Antunes, A C Roque, F M Simoes-de-Souza
Long-term depression (LTD) and long-term potentiation (LTP) of granule-Purkinje cell synapses are persistent synaptic alterations induced by high and low rises of the intracellular calcium ion concentration ([Ca(2+)]), respectively. The occurrence of LTD involves the activation of a positive feedback loop formed by protein kinase C, phospholipase A2, and the extracellular signal-regulated protein kinase pathway, and its expression comprises the reduction of the population of synaptic AMPA receptors. Recently, a stochastic computational model of these signalling processes demonstrated that, in single synapses, LTD is probabilistic and bistable...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27477623/sensitivity-to-biomechanical-limitations-during-postural-decision-making-depends-on-the-integrity-of-posterior-superior-parietal-cortex
#15
Daniel K Wood, Philippe A Chouinard, Alex J Major, Melvyn A Goodale
Most object-directed limb movements can be carried out with a comfortable grasp posture. However, the orientation of an object relative to our bodies can sometimes lead us to select an uncomfortable or awkward grasp posture due to limitations imposed by the biomechanics of the arm. In a series of experiments, we identified a network of cortical areas that are engaged during the selection of movement strategies. Neurologically intact participants and two brain-damaged patients with overlapping lesions in the right posterior superior parietal lobule (pSPL) performed a grasp posture selection task in which biomechanical constraints were the primary consideration for selecting an action...
July 15, 2016: Cortex; a Journal Devoted to the Study of the Nervous System and Behavior
https://www.readbyqxmd.com/read/27448907/bridging-the-gap-between-modules-in-isolation-and-as-part-of-networks-a-systems-framework-for-elucidating-interaction-and-regulation-of-signalling-modules
#16
Govind Menon, J Krishnan
While signalling and biochemical modules have been the focus of numerous studies, they are typically studied in isolation, with no examination of the effects of the ambient network. In this paper we formulate and develop a systems framework, rooted in dynamical systems, to understand such effects, by studying the interaction of signalling modules. The modules we consider are (i) basic covalent modification, (ii) monostable switches, (iii) bistable switches, (iv) adaptive modules, and (v) oscillatory modules...
July 21, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27442281/high-resolution-mapping-of-bifurcations-in-nonlinear-biochemical-circuits
#17
A J Genot, A Baccouche, R Sieskind, N Aubert-Kato, N Bredeche, J F Bartolo, V Taly, T Fujii, Y Rondelez
Analog molecular circuits can exploit the nonlinear nature of biochemical reaction networks to compute low-precision outputs with fewer resources than digital circuits. This analog computation is similar to that employed by gene-regulation networks. Although digital systems have a tractable link between structure and function, the nonlinear and continuous nature of analog circuits yields an intricate functional landscape, which makes their design counter-intuitive, their characterization laborious and their analysis delicate...
August 2016: Nature Chemistry
https://www.readbyqxmd.com/read/27425609/protein-dimerization-generates-bistability-in-positive-feedback-loops
#18
Chieh Hsu, Vincent Jaquet, Mumun Gencoglu, Attila Becskei
Bistability plays an important role in cellular memory and cell-fate determination. A positive feedback loop can generate bistability if it contains ultrasensitive molecular reactions. It is often difficult to detect bistability based on such molecular mechanisms due to its intricate interaction with cellular growth. We constructed transcriptional feedback loops in yeast. To eliminate growth alterations, we reduced the protein levels of the transcription factors by tuning the translation rates over two orders of magnitude with designed RNA stem loops...
August 2, 2016: Cell Reports
https://www.readbyqxmd.com/read/27395401/mathematical-model-of-galactose-regulation-and-metabolic-consumption-in-yeast
#19
Tina M Mitre, Michael C Mackey, Anmar Khadra
The galactose network has been extensively studied at the unicellular level to broaden our understanding of the regulatory mechanisms governing galactose metabolism in multicellular organisms. Although the key molecular players involved in the metabolic and regulatory processes of this system have been known for decades, their interactions and chemical kinetics remain incompletely understood. Mathematical models can provide an alternative method to study the dynamics of this network from a quantitative and a qualitative perspective...
October 21, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27378101/realization-of-tristability-in-a-multiplicatively-coupled-dual-loop-genetic-network
#20
Bo Huang, Yun Xia, Feng Liu, Wei Wang
Multistability is a crucial recurring theme in cell signaling. Multistability is attributed to the presence of positive feedback loops, but the general condition and essential mechanism for realizing multistability remain unclear. Here, we build a generic circuit model comprising two transcription factors and a microRNA, representing a kind of core architecture in gene regulatory networks. The circuit can be decomposed into two positive feedback loops (PFLs) or one PFL and one negative feedback loop (NFL), which are multiplicatively coupled...
2016: Scientific Reports
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