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Journal of Theoretical Biology

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https://www.readbyqxmd.com/read/28238703/competition-for-light-in-forest-population-dynamics-from-computer-simulator-to-mathematical-model
#1
Pierre Magal, Zhengyang Zhang
In this article we build a mathematical model for forest growth and we compare this model with a computer forest simulator named SORTIE. The main ingredient taken into account in both models is the competition for light between trees. The parameters of the mathematical model are estimated by using SORTIE model, when the parameter values of SORTIE model correspond to the ones previously evaluated for the Great Mountain Forest in USA. We see that the best fit of the parameters of the mathematical model is obtained when the competition for light influences only the growth rate of trees...
February 23, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28237396/darwinizing-gaia
#2
W Ford Doolittle
The Gaia hypothesis of James Lovelock was co-developed with and vigorously promoted by Lynn Margulis, but most mainstream Darwinists scorned and still do not accept the notion. They cannot imagine selection for global stability being realized at the level of the individuals or species that make up the biosphere. Here I suggest that we look at the biogeochemical cycles and other homeostatic processes that might confer stability - rather than the taxa (mostly microbial) that implement them - as the relevant units of selection...
February 22, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28237395/network-connectivity-value
#3
Arnaud Dragicevic, Vincent Boulanger, Max Bruciamacchie, Sandrine Chauchard, Jean-Luc Dupouey, Anne Stenger
In order to unveil the value of network connectivity, we formalize the construction of ecological networks in forest environments as an optimal control dynamic graph-theoretic problem. The network is based on a set of bioreserves and patches linked by ecological corridors. The node dynamics, built upon the consensus protocol, form a time evolutive Mahalanobis distance weighted by the opportunity costs of timber production. We consider a case of complete graph, where the ecological network is fully connected, and a case of incomplete graph, where the ecological network is partially connected...
February 22, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28237394/developmental-changes-in-the-balance-of-glycolytic-atp-production-and-oxidative-phosphorylation-in-ventricular-cells-a-simulation-study
#4
Hitomi I Sano, Tamami Toki, Yasuhiro Naito, Masaru Tomita
The developmental program of the heart requires accurate regulation to ensure continuous circulation and simultaneous cardiac morphogenesis, because any functional abnormalities may progress to congenital heart malformation. Notably, energy metabolism in fetal ventricular cells is regulated in a manner that differs from adult ventricular cells: fetal cardiomyocytes generally have immature mitochondria and fetal ventricular cells show greater dependence on glycolytic ATP production. However, although various characteristics of energy metabolism in fetal ventricular cells have been reported, to our knowledge, a quantitative description of the contributions of these factors to fetal ventricular cell functions has not yet been established...
February 22, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28232123/enumerating-secondary-structures-and-structural-moieties-for-circular-rnas
#5
Jose A Cuesta, Susanna Manrubia
A quantitative characterization of the relationship between molecular sequence and structure is essential to improve our understanding of how function emerges. This particular genotype-phenotype map has been often studied in the context of RNA sequences, with the folded configurations standing as a proxy for the phenotype. Here, we count the secondary structures of circular RNAs of length n and calculate the asymptotic distributions of different structural moieties, such as stems or hairpin loops, by means of symbolic combinatorics...
February 20, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28223171/how-tumour-induced-vascular-changes-alter-angiogenesis-insights-from-a-computational-model
#6
A Stéphanou, A C Lesart, J Deverchère, A Juhem, A Popov, F Estève
A computational model was developed to describe experimentally observed vascular changes induced by the introduction of a tumour on a mouse equipped with a dorsal skinfold chamber. The vascular structure of the host tissue was segmented from in vivo images and transposed into the computational framework. Simulations of tumour-induced vascular changes were performed and include the destabilizing effects of the growth factor VEGF on the integrity of the vessels walls. The integration of those effects, that include alteration of the vessel wall elasticity and wall breaching, were required to realistically reproduce the experimental observations...
February 20, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28223173/interactions-and-constraints-in-model-species-response-to-environmental-heteroscedasticity
#7
George P Malanson
Increasing environmental variability could exacerbate the effects of climate change on ecological processes such as population dynamics, or positive and negative effects (favorable or unfavorable weather) could balance. Such a balance could depend on constraints of the processes. Biological and spatial constraints are represented in a spatially explicit individual based simulation of an ecotone reduced to two species on a single environmental gradient. The effects of climate amelioration are simulated from a plant's-eye-view by increasing the establishment and decreasing the mortality rates...
February 18, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28223172/a-simple-model-of-cardiac-muscle-for-multiscale-simulation-passive-mechanics-crossbridge-kinetics-and-calcium-regulation
#8
Fyodor A Syomin, Andrey K Tsaturyan
A simple model of cardiac muscle was designed for multiscale simulation of heart mechanics. Relaxed cardiac muscle was described as a transversally isotropic hyperelastic material. Active tension caused by actin-myosin crossbridges depends on the ensemble averaged strain of myosin heads bound to actin. Calcium activation was modeled by Ca(2+) binding to troponin-C. To account for the dependence of troponin affinity for Ca(2+) on myosin heads strongly bound to actin, the kinetics of troponin binding to Ca(2+) in the overlap zone of the thin and thick filaments and outside it were separated...
February 18, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28219660/modelling-and-investigation-of-the-cd4-t-cells-macrophages-paradox-in-melanoma-immunotherapies
#9
Raluca Eftimie, Haneen Hamam
It is generally accepted that tumour cells can be eliminated by M1 anti-tumour macrophages and CD8(+) T cells. However, experimental results over the past 10-15 years have shown that B16 mouse melanoma cells can be eliminated by the CD4(+) T cells alone (either Th1 or Th2 sub-types), in the absence of CD8(+) T cells. In some studies, elimination of B16 melanoma was associated with a Th1 immune response (i.e., elimination occurred in the presence of cytokines produced by Th1 cells), while in other studies melanoma elimination was associated with a Th2 immune response (i...
February 17, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28216428/antimicrobial-potency-of-cationic-antimicrobial-peptides-can-be-predicted-from-their-amino-acid-composition-application-to-the-detection-of-cryptic-antimicrobial-peptides
#10
Katia Pane, Lorenzo Durante, Orlando Crescenzi, Valeria Cafaro, Elio Pizzo, Mario Varcamonti, Anna Zanfardino, Viviana Izzo, Alberto Di Donato, Eugenio Notomista
Cationic antimicrobial peptides (CAMPs) are essential components of innate immunity. Here we show that antimicrobial potency of CAMPs is linearly correlated to the product C(m)H(n)L where C is the net charge of the peptide, H is a measure of its hydrophobicity and L its length. Exponents m and n define the relative contribution of charge and hydrophobicity to the antimicrobial potency. Very interestingly the values of m and n are strain specific. The ratio n/(m+n) can vary between ca. 0.5 and 1, thus indicating that some strains are sensitive to highly charged peptides, whereas others are particularly susceptible to more hydrophobic peptides...
February 17, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28216427/utilization-of-the-bootstrap-method-for-determining-confidence-intervals-of-parameters-for-a-model-of-map1b-protein-transport-in-axons
#11
I A Kuznetsov, A V Kuznetsov
This paper develops a model of axonal transport of MAP1B protein. The problem of determining parameter values for the proposed model utilizing limited available experimental data is addressed. We used a global minimum search algorithm to find parameter values that minimize the discrepancy between model predictions and published experimental results. By analyzing the best fit parameter values it was established that some processes can be dropped from the model without losing accuracy, thus a simplified version of the model was formulated...
February 16, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28214543/theoretical-structural-characterization-of-lymphoguanylin-a-potential-candidate-for-the-development-of-drugs-to-treat-gastrointestinal-disorders
#12
Állan S Pires, William F Porto, Pryscilla O Castro, Octavio L Franco, Sérgio A Alencar
Guanylin peptides (GPs) are small cysteine-rich peptide hormones involved in salt absorption, regulation of fluids and electrolyte homeostasis. This family presents four members: guanylin (GN), uroguanylin (UGN), lymphoguanylin (LGN) and renoguanylin (RGN). GPs have been used as templates for the development of drugs for the treatment of gastrointestinal disorders. Currently, LGN is the only GP with only one disulfide bridge, making it a remarkable member of this family and a potential drug template; however, there is no structural information about this peptide...
February 16, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28212786/interplay-between-microbial-trait-dynamics-and-population-dynamics-revealed-by-the-combination-of-laboratory-experiment-and-computational-approaches
#13
Kenta Suzuki, Yuji Yamauchi, Takehito Yoshida
Filament formation is a common bacterial defense mechanism and possibly has a broad impact on microbial community dynamics. In order to examine the impact of filament formation on population dynamics, we developed an experimental system with a filamentous bacterium Flectobacillus sp. MWH38 and a ciliate predator Tetrahymena pyriformis. In this system, the effective defense of Flectobacillus resulted in the extinction of Tetrahymena by allowing almost no population growth. The result of a kairomone experiment suggested the existence of chemical signals for filament formation...
February 16, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28212785/the-role-of-driver-nodes-in-managing-epileptic-seizures-application-of-kuramoto-model
#14
Ali Mohseni, Shahriar Gharibzadeh, Fatemeh Bakouie
Synchronization is an important global phenomenon which could be found in a wide range of complex systems such as brain or electronic devices. However, in some circumstances the synchronized states are not desirable for the system and should be suppressed. For example, excessively synchronized activities in the brain network could be the root of neuronal disorders like epileptic seizures. According to the controllability theory of the complex networks, a minimum set of driver nodes has the ability to control the entire system...
February 15, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28202283/from-typical-sequences-to-typical-genotypes
#15
Omri Tal, Tat Dat Tran, Jacobus Portegies
We demonstrate an application of a core notion of information theory, typical sequences and their related properties, to analysis of population genetic data. Based on the asymptotic equipartition property (AEP) for nonstationary discrete-time sources producing independent symbols, we introduce the concepts of typical genotypes and population entropy and cross entropy rate. We analyze three perspectives on typical genotypes: a set perspective on the interplay of typical sets of genotypes from two populations, a geometric perspective on their structure in high dimensional space, and a statistical learning perspective on the prospects of constructing typical-set based classifiers...
February 12, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28193485/exposing-the-diversity-of-multiple-infection-patterns
#16
Mircea T Sofonea, Samuel Alizon, Yannis Michalakis
Natural populations often have to cope with genetically distinct parasites that can coexist, or not, within the same hosts. Theoretical models addressing the evolution of virulence have considered two within host infection outcomes, namely superinfection and coinfection. The field somehow became limited by this dichotomy that does not correspond to an empirical reality, as other infection patterns, namely sets of within-host infection outcomes, are possible. We indeed formally prove there are over one hundred different infection patterns solely for recoverable chronic infections caused by two genetically distinct horizontally-transmitted microparasites...
February 10, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28192083/anatomical-and-spiral-wave-reentry-in-a-simplified-model-for-atrial-electrophysiology
#17
Yvonne Richter, Pedro G Lind, Gunnar Seemann, Philipp Maass
For modeling the propagation of action potentials in the human atria, various models have been developed in the past, which take into account in detail the influence of the numerous ionic currents flowing through the cell membrane. Aiming at a simplified description, the Bueno-Orovio-Cherry-Fenton (BOCF) model for electric wave propagation in the ventricle has been adapted recently to atrial physiology. Here, we study this adapted BOCF (aBOCF) model with respect to its capability to accurately generate spatio-temporal excitation patterns found in anatomical and spiral wave reentry...
February 10, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28189671/global-sensitivity-analysis-of-a-model-related-to-memory-formation-in-synapses-model-reduction-based-on-epistemic-parameter-uncertainties-and-related-issues
#18
Don Kulasiri, Jingyi Liang, Yao He, Sandhya Samarasinghe
We investigate the epistemic uncertainties of parameters of a mathematical model that describes the dynamics of CaMKII-NMDAR complex related to memory formation in synapses using global sensitivity analysis (GSA). The model, which was published in this journal, is nonlinear and complex with Ca(2+) patterns with different level of frequencies as inputs. We explore the effects of parameter on the key outputs of the model to discover the most sensitive ones using GSA and partial ranking correlation coefficient (PRCC) and to understand why they are sensitive and others are not based on the biology of the problem...
February 9, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28189670/a-model-for-conditional-male-trimorphisms
#19
J Mark Rowland, Clifford R Qualls, Bruno A Buzatto
Conditional dimorphisms are widespread in color, morphology, behavior, and life history. Such traits have been successfully modeled in game theory as conditional strategies, and in quantitative genetics as threshold traits. Conditional trimorphisms have recently been unveiled, and here we combine the rock-paper-scissors (RPS) model of game theory and the environmental threshold (ET) model of quantitative genetics to model trimorphisms that are environmentally induced and result from the expression of two thresholds...
February 9, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28189669/kinetic-order-disorder-transitions-in-a-pause-and-go-swarming-model-with-memory
#20
Oren Rimer, Gil Ariel
A two dimensional model of self-propelled particles combining both a pause-and-go movement pattern and memory is studied in simulations. It is shown, that in contrast to previously studied agent based models in two-dimensions, order and disorder are metastable states that can co-exist at some parameter range. In particular, this implies that the formation and decay of global order in swarms may be kinetic rather than a phase transition. Our results explain metastability recently observed in swarming locust and fish...
February 9, 2017: Journal of Theoretical Biology
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