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Journal of Theoretical Biology

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https://www.readbyqxmd.com/read/30227116/hybrid-models-of-genetic-networks-mathematical-challenges-and-biological-relevance
#1
Leon Glass, Roderick Edwards
We review results concerning dynamics in a class of hybrid ordinary differential equations which incorporates logical control to yield piecewise linear equations. These equations relate qualitative features of the structure of networks to qualitative properties of the dynamics. Because of their simple structure, they have been studied using techniques from discrete mathematics and nonlinear dynamics. Initially developed as a qualitataive description of gene regulatory networks, many generalizations of the basic approach have been developed...
September 15, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30222964/modeling-the-crosstalk-between-the-circadian-clock-and-ros-in-neurospora-crassa
#2
Yun Xia, Zhang Cheng, Shaobing Wang, Di Guan, Feng Liu
The circadian clock regulates the expression of clock-controlled genes and adapts to environmental changes. Reactive oxygen species (ROS) also undergo circadian rhythms and have a role in circadian timekeeping. To elucidate crosstalk between ROS and the circadian clock in Neurospora crassa, we build an integrative network model, characterizing the circadian oscillator, ROS system and their interactions. Notably, the (de)phosphorylation and nuclear-cytoplasmic shuttling of clock proteins are modeled in detail...
September 14, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30222963/basic-reproduction-number-for-the-brazilian-spotted-fever
#3
Gina Polo, Marcelo B Labruna, Fernando Ferreira
Brazilian Spotted Fever (BSF) is an emerging and lethal disease in South America which basic reproduction number (R0 ) is unknown. Calculating R0 for this disease is crucial to design control interventions and prevent human deaths. BSF endemic areas are related to the presence of capybaras Hydrochoerus hydrochaeris, amplifier hosts of Rickettsia rickettsii and primary hosts of the tick Amblyomma sculptum, main vector of the agent in this area. Because of the complexity of its dynamics, we calculated R0 for the BSF system by constructing a next-generation matrix considering different categories of vectors and hosts...
September 14, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30219568/the-invasion-speed-of-cell-migration-models-with-realistic-cell-cycle-time-distributions
#4
Enrico Gavagnin, Matthew J Ford, Richard L Mort, Tim Rogers, Christian A Yates
Cell proliferation is typically incorporated into stochastic mathematical models of cell migration by assuming that cell divisions occur after an exponentially distributed waiting time. Experimental observations, however, show that this assumption is often far from the real cell cycle time distribution (CCTD). Recent studies have suggested an alternative approach to modelling cell proliferation based on a multi-stage representation of the CCTD. In this paper we investigate the connection between the CCTD and the speed of the collective invasion...
September 13, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30218648/stochastic-modeling-of-tumor-progression-and-immune-evasion
#5
Jason T George, Herbert Levine
It is now well-established that the host's adaptive immune system plays an important role in identifying and eliminating cancer cells in much the same way that intracellular pathogens are cleared during an adaptive immune response to infection. From a therapeutic standpoint, the adaptive immune system is unique in that it can co-evolve alongside a developing tumor. Tumor acquisition of immune evasive phenotypes, such as class-I MHC down-regulation, remains a major limitation of successful T-cell immunotherapy...
September 12, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30213665/metapopulation-model-of-rock-scissors-paper-game-with-subpopulation-specific-victory-rates-stabilized-by-heterogeneity
#6
Takashi Nagatani, Kei-Ichi Tainaka, Genki Ichinose
Recently, metapopulation models for rock-paper-scissors games have been presented. Each subpopulation is represented by a node on a graph. An individual is either rock (R), scissors (S) or paper (P); it randomly migrates among subpopulations. In the present paper, we assume victory rates differ in different subpopulations. To investigate the dynamic state of each subpopulation (node), we numerically obtain the solutions of reaction-diffusion equations on the graphs with two and three nodes. In the case of homogeneous victory rates, we find each subpopulation has a periodic solution with neutral stability...
September 10, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30205095/a-coupled-bulk-surface-model-for-cell-polarisation
#7
D Cusseddu, L Edelstein-Keshet, J A Mackenzie, S Portet, A Madzvamuse
Several cellular activities, such as directed cell migration, are coordinated by an intricate network of biochemical reactions which lead to a polarised state of the cell, in which cellular symmetry is broken, causing the cell to have a well defined front and back. Recent work on balancing biological complexity with mathematical tractability resulted in the proposal and formulation of a famous minimal model for cell polarisation, known as the wave pinning model. In this study, we present a three-dimensional generalisation of this mathematical framework through the maturing theory of coupled bulk-surface semilinear partial differential equations in which protein compartmentalisation becomes natural...
September 8, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30205094/macro-scale-modelling-of-cortical-spreading-depression-and-the-role-of-astrocytic-gap-junctions
#8
Allanah Kenny, Michael J Plank, Tim David
Neuronal activity evokes a localised increase in cerebral blood flow in a response known as neurovascular coupling (NVC), achieved through communication between a group of cells known as a neurovascular unit (NVU). Dysfunctional NVC can lead to pathologies such as cortical spreading depression (CSD), characterised by a slow moving wave of neuronal depolarisation and high extracellular K+ levels. This phenomenon can be affected by the presence of an astrocytic gap junction network which is able to transport K+ away from areas of high concentrations, however the precise role of these gap junctions remains controversial...
September 8, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30201434/ploc_bal-mgneg-predict-subcellular-localization-of-gram-negative-bacterial-proteins-by-quasi-balancing-training-dataset-and-general-pseaac
#9
Xiang Cheng, Xuan Xiao, Kuo-Chen Chou
One of the hottest topics in molecular cell biology is to determine the subcellular localization of proteins from various different organisms. This is because it is crucially important for both basic research and drug development. Recently, a predictor called "pLoc-mGneg" was developed for identifying the subcellular localization of Gram-negative bacterial proteins. Its performance is overwhelmingly better than that of the other predictors for the same purpose, particularly in dealing with multi-label systems in which some proteins, called "multiplex proteins", may simultaneously occur in two or more subcellular locations...
September 7, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30196064/parasitism-effects-on-coexistence-and-stability-within-simple-trophic-modules
#10
Loïc Prosnier, Vincent Médoc, Nicolas Loeuille
Parasites are important components of food webs. Although their direct effects on hosts are well-studied, indirect impacts on trophic networks, thus on non-host species, remain unclear. In this study, we investigate the consequences of parasitism on coexistence and stability within a simple trophic module: one predator consuming two prey species in competition. We test how such effects depend on the infected species (prey or predator). We account for two effects of parasitism: the virulence effect (parasites affect the infected species intrinsic growth rate through direct effects on fecundity or mortality) and the interaction effect (increased vulnerability of infected prey or increased food intake of infected predators)...
September 7, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30196063/theoretical-modeling-of-pre-and-postnatal-growth
#11
Marcin Molski
A simultaneous analysis of the pre and postnatal growth data obtained for five exemplary animals (zebra, rat, guinea pig, chicken, tilapia) is performed. To this aim, the generalized von Bertalanffy (VB) model is employed in which one of the fitted parameters is related to the gestation or incubation period of the system under consideration. The results obtained reveal a descriptive power of the VB model in both the pre and postnatal stages for a wide range of the data analyzed using several goodness-of-fit metrics and biologically meaningful parameters fitted...
September 6, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30194968/predator-prey-equations-with-constant-harvesting-and-planting
#12
Jieun Choi, Yong-Jung Kim
We propose Lotka-Volterra type predator-prey equations which include small constant terms. Depending on its sign, the constant may model various things. To see the effect of the constants clearly we drop all other functional responses except the ones in the original Lotka-Volterra equations. We add a small negative constant for the harvesting or the Allee effect. A positive constant is added to model the planting or external influx. We find the predator-prey equations with constant terms produce most of dynamic and static patterns observed from other predator-prey models with various functional responses...
September 5, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30194045/global-stability-analysis-and-optimal-control-therapy-of-blood-cell-production-process-hematopoiesis-in-acute-myeloid-leukemia
#13
Abdelhafid Zenati, Messaoud Chakir, Mohamed Tadjine
In this paper we analyze the global stability of a coupled model for Acute Myeloid Leukemia and propose a therapy approach based on an optimal control strategy. Firstly, based on the positivity of the model, stability of trivial solutions for healthy and cancerous cell subsystems is assessed. To this end we use new Lyapunov functionals and take into account the interconnection between cell populations. Secondly, stability conditions for healthy situation in interconnected model are established by using Nyquist criterion...
September 5, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30194044/vegetation-pattern-formation-in-seminal-systems-due-to-internal-competition-reaction-between-plants
#14
Xiaoli Wang, Guohong Zhang
Self-organised patterns of vegetation are a characteristic feature of semi-deserts. In this paper, we find the internal competition reaction between plants can lead to the formation of spatial vegetation patterns, which is different from the normal formation mechanism of long-range competition and short-range facilitation. It is also found that the internal competition between biomass has an effect on the characters of banded vegetation. In particular, it is shown that the internal competition reaction leads to the decrease of the migration speed and the increase of the wavelength of the stripe patterns...
September 5, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30179589/predicting-apoptosis-protein-subcellular-localization-by-integrating-auto-cross-correlation-and-pssm-into-chou-s-pseaac
#15
Shengli Zhang, Yunyun Liang
The prediction of subcellular localization of an apoptosis protein is still a challenging task, and existing methods mainly based on protein primary sequences. In this study, we propose a novel model called MACC-PSSM by integrating Moran autocorrelation and cross correlation with PSSM. Then a 3600-dimensional feature vector is constructed to predict apoptosis protein subcellular localization. Finally, 210 features are selected using principal component analysis (PCA) on the ZW225 dataset, and support vector machine is adopted as classifier...
September 1, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30176249/species-dispersal-and-biodiversity-in-human-dominated-metacommunities
#16
David W Shanafelt, Jean Clobert, Eli P Fenichel, Michael E Hochberg, Ann Kinzig, Michel Loreau, Pablo A Marquet, Charles Perrings
The concept of the Anthropocene is based on the idea that human impacts are now the primary drivers of changes in the earth's systems, including ecological systems. In many cases, the behavior that causes ecosystem change is itself triggered by ecological factors. Yet most ecological models still treat human impacts as given, and frequently as constant. This undermines our ability to understand the feedbacks between human behavior and ecosystem change. Focusing on the problem of species dispersal, we evaluate the effect of dispersal on biodiversity in a system subject to predation by humans...
September 1, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30172690/feedbacks-nonlinearities-and-nonequilibria-a-thermodynamic-perspective
#17
G Nicolis, S C Nicolis
The feedback circuit approach to nonlinear dynamical systems pioneered by Thomas and coworkers is revisited in a thermodynamical perspective. The role of nonequilibrium conditions and of other types of constraints such as mass action kinetics or microscopic reversibility around thermodynamic equilibrium in the way positive feedback circuits are operating is analyzed. It is shown that the appearance of non-trivial steady-state and time-dependent behaviors necessitates that the strengths of the feedback loops present exceed some well-defined critical values...
August 31, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30172688/quantifying-the-impact-of-a-periodic-presence-of-antimicrobial-on-resistance-evolution-in-a-homogeneous-microbial-population-of-fixed-size
#18
Loïc Marrec, Anne-Florence Bitbol
The evolution of antimicrobial resistance generally occurs in an environment where antimicrobial concentration is variable, which has dramatic consequences on the microorganisms' fitness landscape, and thus on the evolution of resistance. We investigate the effect of these time-varying patterns of selection within a stochastic model. We consider a homogeneous microbial population of fixed size subjected to periodic alternations of phases of absence and presence of an antimicrobial that stops growth. Combining analytical approaches and stochastic simulations, we quantify how the time necessary for fit resistant bacteria to take over the microbial population depends on the alternation period...
August 31, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30172691/selection-for-synchronized-cell-division-in-simple-multicellular-organisms
#19
Jason Olejarz, Kamran Kaveh, Carl Veller, Martin A Nowak
The evolution of multicellularity was a major transition in the history of life on earth. Conditions under which multicellularity is favored have been studied theoretically and experimentally. But since the construction of a multicellular organism requires multiple rounds of cell division, a natural question is whether these cell divisions should be synchronous or not. We study a population model in which there compete simple multicellular organisms that grow by either synchronous or asynchronous cell divisions...
August 30, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30172689/methods-for-determining-key-components-in-a-mathematical-model-for-tumor-immune-dynamics-in-multiple-myeloma
#20
Jill Gallaher, Kamila Larripa, Marissa Renardy, Blerta Shtylla, Nessy Tania, Diana White, Karen Wood, Li Zhu, Chaitali Passey, Michael Robbins, Natalie Bezman, Suresh Shelat, Hearn Jay Cho, Helen Moore
In this work, we analyze a mathematical model we introduced previously for the dynamics of multiple myeloma and the immune system. We focus on four main aspects: (1) obtaining and justifying ranges and values for all parameters in the model; (2) determining a subset of parameters to which the model is most sensitive; (3) determining which parameters in this subset can be uniquely estimated given certain types of data; and (4) exploring the model numerically. Using global sensitivity analysis techniques, we found that the model is most sensitive to certain growth, loss, and efficacy parameters...
August 30, 2018: Journal of Theoretical Biology
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