Journal of Biological Physics最新文献

We have analysed the synchronisation scenario and the rich spatiotemporal patterns in the network of Hindmarsh-Rose neurons under the influence of self, mixed and cross coupling of state variables which are realised by varying coupling phase. We have introduced a coupling matrix in the model to vary coupling phase. The excitatory and inhibitory couplings in the membrane potential induce in-phase and anti-phase bursting dynamics, respectively, in the two coupled system. When the off-diagonal elements of the matrix are zero, the system shows self coupling of the three variables, which helps to attain synchrony. The off-diagonal elements give cross interactions between the variables, which reduces synchrony. The stability of the synchrony attained is analysed using Lyapunov function approach. In our study, we found that self coupling in three variables is sufficient to induce chimera states in non-local coupling. The strength of incoherence and discontinuity measure validates the existence of chimera and multichimera states. The inhibitor self coupling in local interaction induces interesting patterns like Mixed Oscillatory State and clusters. The results may help in understanding the spatiotemporal communications of the brain, within the limitations of the size of the network analysed in this study.

We present an analysis of an epidemic spreading process on an Apollonian network that can describe an epidemic spreading in a non-sedentary population. We studied the modified diffusive epidemic process using the Monte Carlo method by computational analysis. Our model may be helpful for modeling systems closer to reality consisting of two classes of individuals: susceptible (A) and infected (B). The individuals can diffuse in a network according to constant diffusion rates (D_{A}) and (D_{B}), for the classes A and B, respectively, and obeying three diffusive regimes, i.e., (D_{A}<D_{B}), (D_{A}=D_{B}), and (D_{A}>D_{B}). Into the same site i, the reaction occurs according to the dynamical rule based on Gillespie’s algorithm. Finite-size scaling analysis has shown that our model exhibits continuous phase transition to an absorbing state with a set of critical exponents given by (beta /nu =0.66(1)), (1/nu =0.46(2)), and (gamma '/nu =-0.24(2)) familiar to every investigated regime. In summary, the continuous phase transition, characterized by this set of critical exponents, does not have the same exponents of the mean-field universality class in both regular lattices and complex networks.

Copper (Cu), one of the heavy metals, plays a vital role in many complex biochemical reactions as a trace element. However, it often becomes toxic when its concentration in the cell exceeds a certain level. Homeostasis of metals in the cell is primarily related to regulating metal transport into and out of the cell. Therefore, it is thought that porin proteins, which have a role in membrane permeability, may also play a role in developing Cu resistance. This study identified the differences between the molecular profiles of wild-type Escherichia coli W3110 and its seven different porin mutants exposed to Cu ions using attenuated total reflectance (ATR)–Fourier transform infrared (FTIR) spectroscopy. The results showed that the absence of porin genes elicits global changes in the structure and composition of membrane lipids and proteins, in both the absence and presence of Cu. The lack of porin genes significantly elevated the amounts of fatty acids and phospholipids. When the alterations in protein secondary structures were compared, the quantity of amide I proteins was diminished by the presence of Cu. However, the amount of amide II proteins increased in porin mutant groups independent of Cu presence or absence. The DNAs are transformed from B- and Z-form to A-form due to porin mutations and the presence of Cu ions. The lack of porin genes increased polysaccharide content independent of Cu presence. This study can help characterize Cu detoxification efficiency and guide for obtaining active living cells to be used in bioremediation.

Abstract

The occurrence and development of tumors depend on a complex regulation by not only biochemical cues, but also biomechanical factors in tumor microenvironment. With the development of epigenetic theory, the regulation of biomechanical stimulation on tumor progress genetically is not enough to fully illustrate the mechanism of tumorigenesis. However, biomechanical regulation on tumor progress epigenetically is still in its infancy. Therefore, it is particularly important to integrate the existing relevant researches and develop the potential exploration. This work sorted out the existing researches on the regulation of tumor by biomechanical factors through epigenetic means, which contains summarizing the tumor epigenetic regulatory mode by biomechanical factors, exhibiting the influence of epigenetic regulation under mechanical stimulation, illustrating its existing applications, and prospecting the potential. This review aims to display the relevant knowledge through integrating the existing studies on epigenetic regulation in tumorigenesis under mechanical stimulation so as to provide theoretical basis and new ideas for potential follow-up research and clinical applications.

Graphical Abstract

Mechanical factors under physiological conditions stimulate the tumor progress through epigenetic ways, and new strategies are expected to be found with the development of epidrugs and related delivery systems.

Growth curve models play an instrumental role in quantifying the growth of biological processes and have immense practical applications across all disciplines. The most popular growth metric to capture the species fitness is the “Relative Growth Rate” in this domain. The different growth laws, such as exponential, logistic, Gompertz, power, and generalized Gompertz or generalized logistic, can be characterized based on the monotonic behavior of the relative growth rate (RGR) to size or time. Thus, in this case, species fitness can be determined truly through RGR. However, in nature, RGR is often non-monotonic and specifically bell-shaped, especially in the situation when a species is adapting to a new environment [1]. In this case, species may experience with the same fitness (RGR) for two different time points. The species precise growth and maturity status cannot be determined from this RGR function. The instantaneous maturity rate (IMR), as proposed by [2], helps to determine the correct maturity status of the species. Nevertheless, the metric IMR suffers from severe drawbacks; (i) IMR is intractable for all non-integer values of a specific parameter. (ii) The measure depends on a model parameter. The mathematical expression of IMR possesses the term “carrying capacity” which is unknown to the experimenter. (iii) Note that for identifying the precise growth status of a species, it is also necessary to understand its response when the populations are deflected from their equilibrium position at carrying capacity. This is an established concept in population biology, popularly known as the return rate. However, IMR does not provide information on the species deflection rate at the steady state. Hence, we propose a new growth measure connected with the species return rate, termed the “reverse of relative of relative growth rate” (henceforth, RRRGR), which is treated as a proxy for the IMR, having similar mathematical properties. Finally, we introduce a stochastic RRRGR model for specifying precise species growth and status of maturity. We illustrate the model through numerical simulations and real fish data. We believe that this study would be helpful for fishery biologists in regulating the favorable conditions of growth so that the species can reach a steady state with optimum effort.

Abstract

Alpha-2-macroglobulin (α₂M) is an essential antiproteinase that is widely distributed in human plasma. The present study was aimed at investigating the binding of a potential therapeutic dietary flavonol, morin, with human α₂M using a multi-spectroscopic and molecular docking approach. Recently, flavonoid-protein interaction has gained significant attention, because a majority of dietary bioactive components interact with proteins, thereby altering their structure and function. The results of the activity assay exhibited a 48% reduction in the antiproteolytic potential of α₂M upon interaction with morin. Fluorescence quenching tests unequivocally confirmed quenching in the fluorescence of α₂M in the presence of morin, conforming complex formation and demonstrating that the binding mechanism involves a dynamic mode of interaction. Synchronous fluorescence spectra of α₂M with morin showed perturbation in the microenvironment around tryptophan residues. Furthermore, structural changes were observed through CD and FT-IR, showing alterations in the secondary structure of α₂M induced by morin. FRET further supports the results of the dynamic mode of quenching. Moderate interaction is shown by binding constant values using Stern–Volmer’s fluorescence spectroscopy. Morin binds to α₂M at 298 K with a binding constant of 2.7 × 10⁴ M⁻¹, indicating the strength of the association. The α₂M-morin system was found to have negative ΔG values, which suggests that the binding process was spontaneous. Molecular docking also reveals the different amino acid residues involved in this binding process, revealing that the binding energy is -8.1 kcal/mol.

We show that recognizable neural waveforms are reproduced in the model described in previous work. In so doing, we reproduce close matches to certain observed, though filtered, EEG-like measurements in closed mathematical form, to good approximations. Such neural waves represent the responses of individual networks to external and endogenous inputs and are presumably the carriers of the information used to perform computations in actual brains, which are complexes of interconnected networks. Then, we apply these findings to a question arising in short-term memory processing in humans. Namely, we show how the anomalously small number of reliable retrievals from short-term memory found in certain trials of the Sternberg task is related to the relative frequencies of the neural waves involved. This finding justifies the hypothesis of phase-coding, which has been posited as an explanation of this effect.

Calcium ((Ca^{2+})), inositol trisphosphate ((IP_3)), and nitric oxide (NO) signaling are essential to maintain the structural integrity and physiological activity of fibroblast cells. The accumulation of excess quantity of NO for longer periods can lead to a variety of fibrotic disorders, including heart disease, penile fibrosis in Peyronie’s disease (PD), and cystic fibrosis. The dynamics of these three signaling processes and their interdependence in fibroblast cells are not clearly known to date. A systems biology model is proposed using reaction-diffusion equations for calcium, (IP_3), and calcium-dependent NO synthesis in fibroblast cells. The finite element method (FEM) is used to examine (Ca^{2+}), (IP_3), and NO regulation and dysregulation in cells. The results throw light on the conditions that disturb the coupled (Ca^{2+}) and (IP_3) dynamics and the influence of these factors on the levels of NO concentration in the fibroblast cell. The findings suggest that changes in source inflow, buffers, and diffusion coefficient might induce an increase or reduction in nitric oxide and (IP_3) synthesis, resulting in fibroblast cell diseases. Furthermore, the findings provide new information regarding the size and intensity of diseases in response to changes in several factors of their dynamics, which has been linked to the development of cystic fibrosis and cancer. This knowledge could be valuable for developing novel approaches to the diagnosis of diseases and therapies for various disorders of fibroblast cells.