Based on interactions among transcription factors, oncogenes, tumor suppressors and microRNAs, a Boolean model of cancer network regulated by miR-17-92 cluster is constructed, and the network is associated with the control of G1/S transition in the mammalian cell cycle. The robustness properties of this regulatory network are investigated by virtue of the Boolean network theory. It is found that, during G1/S transition in the cell cycle process, the regulatory networks are robustly constructed, and the robustness property is largely preserved with respect to small perturbations to the network. By using the unique process-based approach, the structure of this network is analyzed. It is shown that the network can be decomposed into a backbone motif which provides the main biological functions, and a remaining motif which makes the regulatory system more stable. The critical role of miR-17-92 in suppressing the G1/S cell cycle checkpoint and increasing the uncontrolled proliferation of the cancer cells by targeting a genetic network of interacting proteins is displayed with our model.
We developed a promising SVM-based program, plantMirP, for predicting plant pre-miRNAs by incorporating a set of novel knowledge-based energy features.
Coherent feed-forward loops exist extensively in realistic biological regulatory systems, and are common signaling motifs. Here, we study the characteristics and the propagation mechanism of the output noise in a coherent feed-forward transcriptional regulatory loop that can be divided into a main road and branch. Using the linear noise approximation, we derive analytical formulae for the total noise of the full loop, the noise of the branch, and the noise of the main road, which are verified by the Gillespie algorithm. Importantly, we find that (i) compared with the branch motif or the main road motif, the full motif can effectively attenuate the output noise level; (ii) there is a transition point of system state such that the noise of the main road is dominated when the underlying system is below this point, whereas the noise of the branch is dominated when the system is beyond the point. The entire analysis reveals the mechanism of how the noise is generated and propagated in a simple yet representative signaling module.
Spatially uniform cross-correlated sine-Wiener (CCSW) noises are imposed on each Hodgkin-Huxley (HH) neuron in a twodimensional (2D) regular network. Noise-induced spiral wave destruction and order-disorder spatial pattern transition can be observed by adjusting cross-correlation time or cross-correlation intensity of CCSW noises. The sudden change of the curve of synchronization factor and the time series of average membrane voltage F can be used to semiquantitatively assess this spatial pattern transition and spiral wave destruction induced by CCSW noises, respectively. In addition, moderate cross-correlation time and strong cross-correlation intensity of CCSW noises are both detrimental to survival of spiral wave. Comparing with non-crosscorrelated sine-Wiener noises, CCSW noises can destroy organized spiral wave with lesser noise amplitude.
Spiral waves are observed in the chemical, physical and biological systems, and the emergence of spiral waves in cardiac tissue is linked to some diseases such as heart ventricular fibrillation and epilepsy; thus it has importance in theoretical studies and potential medical applications. Noise is inevitable in neuronal systems and can change the electrical activities of neuron in different ways. Many previous theoretical studies about the impacts of noise on spiral waves focus an unbounded Gaussian noise and even colored noise. In this paper, the impacts of bounded noise and rewiring of network on the formation and instability of spiral waves are discussed in small-world (SW) network of Hodgkin-Huxley (HH) neurons through numerical simulations, and possible statistical analysis will be carried out. Firstly, we present SW network of HH neurons subjected to bounded noise. Then, it is numerically demonstrated that bounded noise with proper intensity σ, amplitude A, or frequency f can facilitate the formation of spiral waves when rewiring probability p is below certain thresholds. In other words, bounded noise-induced resonant behavior can occur in the SW network of neurons. In addition, rewiring probability p always impairs spiral waves, while spiral waves are confirmed to be robust for small p, thus shortcut-induced phase transition of spiral wave with the increase of p is induced. Furthermore, statistical factors of synchronization are calculated to discern the phase transition of spatial pattern, and it is confirmed that larger factor of synchronization is approached with increasing of rewiring probability p, and the stability of spiral wave is destroyed.
A direct sum form is proposed for constructing a composite game from two games, prisoner's dilemma and snowdrift game. This kind of direct sum form game is called a multiple roles game. The replicator dynamics of the multiple roles game with will-mixed populations is explored. The dynamical behaviors on square lattice are investigated by numerical simulation. It is found that the dynamical behaviors of population on square lattice depend on the mixing proportion of the two simple games. Mixing SD activities to pure PD population inhibits the proportion of cooperators in PD, and mixing PD activities to pure SD population stimulates the proportion of cooperators in SD. Besides spatial reciprocity, our results show that there are roles reciprocities between different types of individuals.
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