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Bistable networks

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https://www.readbyqxmd.com/read/28280580/organization-of-biogeochemical-nitrogen-pathways-with-switch-like-adjustment-in-fluctuating-soil-redox-conditions
#1
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
#2
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
#3
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
https://www.readbyqxmd.com/read/28219776/deactivation-in-the-posterior-mid-cingulate-cortex-reflects-perceptual-transitions-during-binocular-rivalry-evidence-from-simultaneous-eeg-fmri
#4
Abhrajeet V Roy, Keith W Jamison, Sheng He, Stephen A Engel, Bin He
Binocular rivalry is a phenomenon in which perception spontaneously shifts between two different images that are dichoptically presented to the viewer. By elucidating the cortical networks responsible for these stochastic fluctuations in perception, we can potentially learn much about the neural correlates of visual awareness. We obtained concurrent EEG-fMRI data for a group of 20 healthy human subjects during the continuous presentation of dichoptic visual stimuli. The two eyes' images were tagged with different temporal frequencies so that eye specific steady-state visual evoked potential (SSVEP) signals could be extracted from the EEG data for direct comparison with changes in fMRI BOLD activity associated with binocular rivalry...
February 20, 2017: NeuroImage
https://www.readbyqxmd.com/read/28122551/sampling-based-bayesian-approaches-reveal-the-importance-of-quasi-bistable-behavior-in-cellular-decision-processes-on-the-example-of-the-mapk-signaling-pathway-in-pc-12-cell-lines
#5
Antje Jensch, Caterina Thomaseth, Nicole E Radde
BACKGROUND: Positive and negative feedback loops are ubiquitous motifs in biochemical signaling pathways. The mitogen-activated protein kinase (MAPK) pathway module is part of many distinct signaling networks and comprises several of these motifs, whose functioning depends on the cell line at hand and on the particular context. The maintainance of specificity of the response of the MAPK module to distinct stimuli has become a key paradigm especially in PC-12 cells, where the same module leads to different cell fates, depending on the stimulating growth factor...
January 25, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28112462/bistability-and-bifurcation-in-minimal-self-replication-and-nonenzymatic-catalytic-networks
#6
Nathaniel Wagner, Rakesh Mukherjee, Indrajit Maity, Enrique Peacock-Lopez, Gonen Ashkenasy
Bistability and bifurcation, found in a wide range of biochemical networks, are central to the proper function of living systems. We investigate herein recent model systems that show bistable behavior based on nonenzymatic self-replication reactions. Such models were used before to investigate catalytic growth, chemical logic operations, and additional processes of self-organization leading to complexification. By solving for their steady-state solutions by using various analytical and numerical methods, we analyze how and when these systems yield bistability and bifurcation and discover specific cases and conditions producing bistability...
January 23, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/27984903/steady-state-equivalence-among-autocatalytic-peroxidase-oxidase-reactions
#7
José Méndez-González, Ricardo Femat
Peroxidase-oxidase is an enzymatic reaction that can exhibit dynamical scenarios such as bistability, sustained oscillations, and Shilnikov chaos. In this work, we apply the chemical reaction network theory approach to find kinetic constants such that the associated mass action kinetics ordinary differential equations induced by three four dimensional structurally different enzymatic reaction systems can support the same steady states for several chemical species despite differences in their chemical nature...
December 14, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27967004/robustness-of-persistent-spiking-to-partial-synchronization-in-a-minimal-model-of-synaptically-driven-self-sustained-activity
#8
Nikita Novikov, Boris Gutkin
We study the behavior of a minimal model of synaptically sustained persistent activity that consists of two quadratic integrate-and-fire neurons mutually coupled via excitatory synapses. Importantly, each of the neurons is excitable, as opposed to an oscillator; hence when uncoupled it sits at a subthreshold rest state. When the constituent neurons are mutually coupled via sufficiently strong fast excitatory synapses, the system demonstrates bistability between a fixed point (quiescent background state) and a limit cycle (memory state with synaptically driven spiking activity)...
November 2016: Physical Review. E
https://www.readbyqxmd.com/read/27931974/mathematical-modeling-of-atopic-dermatitis-reveals-double-switch-mechanisms-underlying-4-common-disease-phenotypes
#9
Elisa Domínguez-Hüttinger, Panayiotis Christodoulides, Kosuke Miyauchi, Alan D Irvine, Mariko Okada-Hatakeyama, Masato Kubo, Reiko J Tanaka
BACKGROUND: The skin barrier acts as the first line of defense against constant exposure to biological, microbial, physical, and chemical environmental stressors. Dynamic interplay between defects in the skin barrier, dysfunctional immune responses, and environmental stressors are major factors in the development of atopic dermatitis (AD). A systems biology modeling approach can yield significant insights into these complex and dynamic processes through integration of prior biological data...
December 5, 2016: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/27927198/a-computational-method-for-the-investigation-of-multistable-systems-and-its-application-to-genetic-switches
#10
Miriam Leon, Mae L Woods, Alex J H Fedorec, Chris P Barnes
BACKGROUND: Genetic switches exhibit multistability, form the basis of epigenetic memory, and are found in natural decision making systems, such as cell fate determination in developmental pathways. Synthetic genetic switches can be used for recording the presence of different environmental signals, for changing phenotype using synthetic inputs and as building blocks for higher-level sequential logic circuits. Understanding how multistable switches can be constructed and how they function within larger biological systems is therefore key to synthetic biology...
December 7, 2016: BMC Systems Biology
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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...
January 1, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/27768683/intrinsic-noise-profoundly-alters-the-dynamics-and-steady-state-of-morphogen-controlled-bistable-genetic-switches
#17
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
#18
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 29, 2016: Nature
https://www.readbyqxmd.com/read/27593379/determination-of-egfr-signaling-output-by-opposing-gradients-of-bmp-and-jak-stat-activity
#19
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
#20
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...
September 29, 2016: Nature
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