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https://www.readbyqxmd.com/read/29414696/dynamics-of-posttranslational-modification-systems-recent-progress-and-future-directions
#1
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
#2
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
#3
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
#4
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...
January 10, 2018: Bio Systems
https://www.readbyqxmd.com/read/29330362/dynamic-modelling-of-the-mtor-signalling-network-reveals-complex-emergent-behaviours-conferred-by-deptor
#5
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
https://www.readbyqxmd.com/read/29330054/deterministic-stability-regimes-and-noise-induced-quasistable-behavior-in-a-pair-of-reciprocally-inhibitory-neurons
#6
Mainak Patel, Badal Joshi
Reciprocal inhibition is a common motif exploited by neuronal networks; an intuitive and tractable way to examine the behaviors produced by reciprocal inhibition is to consider a pair of neurons that synaptically inhibit each other and receive constant or noisy excitatory driving currents. In this work, we examine reciprocal inhibition using two models (a voltage-based and a current-based integrate-and-fire model with instantaneous or temporally structured input), and we use analytic and computational tools to examine the bifurcations that occur and study the various possible monostable, bistable, and tristable regimes that can exist; we find that, depending on system parameters (and on choice of neuron model), there can exist up to 3 distinct monostable regimes (denoted M0, M1, M2), 3 distinct bistable regimes (denoted B, B1, B2), and a single tristable regime (denoted T)...
January 9, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29317645/computational-modelling-of-meiotic-entry-and-commitment
#7
Tanvi Bhola, Orsolya Kapuy, P K Vinod
In response to developmental and environmental conditions, cells exit the mitotic cell cycle and enter the meiosis program to generate haploid gametes from diploid germ cells. Once cells decide to enter the meiosis program they become irreversibly committed to the completion of meiosis irrespective of the presence of cue signals. How meiotic entry and commitment occur due to the dynamics of the regulatory network is not well understood. Therefore, we constructed a mathematical model of the regulatory network that controls the transition from mitosis to meiosis in Schizosaccharomyces pombe...
January 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29272933/parallel-replica-dynamics-method-for-bistable-stochastic-reaction-networks-simulation-and-sensitivity-analysis
#8
Ting Wang, Petr Plecháč
Stochastic reaction networks that exhibit bistable behavior are common in systems biology, materials science, and catalysis. Sampling of stationary distributions is crucial for understanding and characterizing the long-time dynamics of bistable stochastic dynamical systems. However, simulations are often hindered by the insufficient sampling of rare transitions between the two metastable regions. In this paper, we apply the parallel replica method for a continuous time Markov chain in order to improve sampling of the stationary distribution in bistable stochastic reaction networks...
December 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29227103/a-robust-molecular-network-motif-for-period-doubling-devices
#9
Christian Cuba Samaniego, Elisa Franco
Life is sustained by a variety of cyclic processes such as cell division, muscle contraction, and neuron firing. The periodic signals powering these processes often direct a variety of other downstream systems, which operate at different time scales and must have the capacity to divide or multiply the period of the master clock. Period modulation is also an important challenge in synthetic molecular systems, where slow and fast components may have to be coordinated simultaneously by a single oscillator whose frequency is often difficult to tune...
December 11, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29220508/model-based-design-of-bistable-cell-factories-for-metabolic-engineering
#10
Shyam Srinivasan, William R Cluett, Radhakrishnan Mahadevan
Motivation: Metabolism can exhibit dynamic phenomena like bistability due to the presence of regulatory motifs like the positive feedback loop. As cell factories, microorganisms with bistable metabolism can have a high and a low product flux at the two stable steady states, respectively. The exclusion of metabolic regulation and network dynamics limits the ability of pseudo-steady state stoichiometric models to detect the presence of bistability, and reliably assess the outcomes of design perturbations to metabolic networks...
December 6, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29186174/parallel-arrangements-of-positive-feedback-loops-limit-cell-to-cell-variability-in-differentiation
#11
Anupam Dey, Debashis Barik
Cellular differentiations are often regulated by bistable switches resulting from specific arrangements of multiple positive feedback loops (PFL) fused to one another. Although bistability generates digital responses at the cellular level, stochasticity in chemical reactions causes population heterogeneity in terms of its differentiated states. We hypothesized that the specific arrangements of PFLs may have evolved to minimize the cellular heterogeneity in differentiation. In order to test this we investigated variability in cellular differentiation controlled either by parallel or serial arrangements of multiple PFLs having similar average properties under extrinsic and intrinsic noises...
2017: PloS One
https://www.readbyqxmd.com/read/29161843/mathematical-analysis-and-modeling-of-dna-segregation-mechanisms
#12
Bashar Ibrahim
The precise regulation of cell life division is indispensable to the reliable inheritance of genetic material, i.e. DNA, in successive generations of cells. This is governed by dedicated biochemical networks which ensure that all requirements are met before transition from one phase to the next. The Spindle Assembly Checkpoint (SAC) is an evolutionarily mechanism that delays mitotic progression until all chromosomes are properly linked to the mitotic spindle. During some asymmetric cell divisions, such as those observed in budding yeast, an additional mechanism, the Spindle Position Checkpoint (SPOC), is required to delay exit from mitosis until the mitotic spindle is correctly aligned...
April 1, 2018: Mathematical Biosciences and Engineering: MBE
https://www.readbyqxmd.com/read/29159360/integration-of-molecular-machines-into-supramolecular-materials-actuation-between-equilibrium-polymers-and-crystal-like-gels
#13
Giacomo Mariani, Antoine Goujon, Emilie Moulin, Michel Rawiso, Nicolas Giuseppone, Eric Buhler
In this article, the dynamic structure of complex supramolecular polymers composed of bistable [c2]daisy chain rotaxanes as molecular machines that are linked by ureidopyrimidinones (Upy) as recognition moieties was studied. pH actuation of the integrated mechanically active rotaxanes controls the contraction/extension of the polymer chains as well as their physical reticulation. Small-angle neutron and X-ray scattering were used to study in-depth the nanostructure of the contracted and extended polymer aggregates in toluene solution...
November 21, 2017: Nanoscale
https://www.readbyqxmd.com/read/29150615/balancing-a-genetic-toggle-switch-by-real-time-feedback-control-and-periodic-forcing
#14
Jean-Baptiste Lugagne, Sebastián Sosa Carrillo, Melanie Kirch, Agnes Köhler, Gregory Batt, Pascal Hersen
Cybergenetics is a novel field of research aiming at remotely pilot cellular processes in real-time with to leverage the biotechnological potential of synthetic biology. Yet, the control of only a small number of genetic circuits has been tested so far. Here we investigate the control of multistable gene regulatory networks, which are ubiquitously found in nature and play critical roles in cell differentiation and decision-making. Using an in silico feedback control loop, we demonstrate that a bistable genetic toggle switch can be dynamically maintained near its unstable equilibrium position for extended periods of time...
November 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/29120182/designing-single-ion-magnets-and-phosphorescent-materials-with-1-methylimidazole-5-carboxylate-and-transition-metal-ions
#15
Antonio A García-Valdivia, Jose M Seco, Javier Cepeda, Antonio Rodríguez-Diéguez
Detailed structural, magnetic, and photoluminescence (PL) characterization of four new compounds based on 1-methylimidazole-5-carboxylate (mimc) ligand and transition metal ions, namely [Ni(mimc)2(H2O)4] (1), [Co(μ-mimc)2]n (2), {[Cu2(μ-mimc)4(H2O)]·2H2O}n (3), and [Cd(μ-mimc)2(H2O)]n (4) is reported. The structural diversity found in the family of compounds derives from the coordination versatility of the ligand, which coordinates as a terminal ligand to give a supramolecular network of monomeric entities in 1 or acts as a bridging linker to build isoreticular 2D coordination polymers (CPs) in 2-4...
November 9, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/29118381/a-mathematical-model-of-the-impact-of-insulin-secretion-dynamics-on-selective-hepatic-insulin-resistance
#16
Gang Zhao, Dagmar Wirth, Ingo Schmitz, Michael Meyer-Hermann
Physiological insulin secretion exhibits various temporal patterns, the dysregulation of which is involved in diabetes development. We analyzed the impact of first-phase and pulsatile insulin release on glucose and lipid control with various hepatic insulin signaling networks. The mathematical model suggests that atypical protein kinase C (aPKC) undergoes a bistable switch-on and switch-off, under the control of insulin receptor substrate 2 (IRS2). The activation of IRS1 and IRS2 is temporally separated due to the inhibition of IRS1 by aPKC...
November 8, 2017: Nature Communications
https://www.readbyqxmd.com/read/29097666/a-simple-tensor-network-algorithm-for-two-dimensional-steady-states
#17
Augustine Kshetrimayum, Hendrik Weimer, Román Orús
Understanding dissipation in 2D quantum many-body systems is an open challenge which has proven remarkably difficult. Here we show how numerical simulations for this problem are possible by means of a tensor network algorithm that approximates steady states of 2D quantum lattice dissipative systems in the thermodynamic limit. Our method is based on the intuition that strong dissipation kills quantum entanglement before it gets too large to handle. We test its validity by simulating a dissipative quantum Ising model, relevant for dissipative systems of interacting Rydberg atoms, and benchmark our simulations with a variational algorithm based on product and correlated states...
November 3, 2017: Nature Communications
https://www.readbyqxmd.com/read/28973467/a-transcription-network-of-interlocking-positive-feedback-loops-maintains-intracellular-iron-balance-in-archaea
#18
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
#19
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
#20
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
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