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Journal of Theoretical Biology

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https://www.readbyqxmd.com/read/28322874/reconstructing-the-genotype-to-fitness-map-for-the-bacterial-chemotaxis-network-and-its-emergent-behavioural-phenotypes
#1
Alberto Nakauma, G Sander van Doorn
The signal-transduction network responsible for chemotaxis in Escherichia coli has been characterised in extraordinary detail. Yet, relatively little is known about eco-evolutionary aspects of chemotaxis, such as how the network has been shaped by selection and to what extent natural populations may fine-tune their chemotactic behaviour to the ecological conditions. To address these questions, we here develop an evolutionary-systems-biology model of the chemotaxis network of E. coli, which we apply to estimate the resource accumulation rate (here used as a proxy for fitness) of wildtype and a large number of potential mutant genotypes...
March 18, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28322876/predator-prey-subsidy-population-dynamics-on-stepping-stone-domains
#2
Lulan Shen, Robert A Van Gorder
Predator-prey-subsidy dynamics on stepping-stone domains are examined using a variety of network configurations. Our problem is motivated by the interactions between arctic foxes (predator) and lemmings (prey) in the presence of seal carrion (subsidy) provided by polar bears. We use the n-Patch Model, which considers space explicitly as a "Stepping Stone" system. We consider the role that the carrying capacity, predator migration rate, input subsidy rate, predator mortality rate, and proportion of predators surviving migration play in the predator-prey-subsidy population dynamics...
March 16, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28322875/effects-of-population-growth-on-the-success-of-invading-mutants
#3
Peter Ashcroft, Cassandra E R Smith, Matthew Garrod, Tobias Galla
Understanding if and how mutants reach fixation in populations is an important question in evolutionary biology. We study the impact of population growth has on the success of mutants. To systematically understand the effects of growth we decouple competition from reproduction; competition follows a birth-death process and is governed by an evolutionary game, while growth is determined by an externally controlled branching rate. In stochastic simulations we find non-monotonic behaviour of the fixation probability of mutants as the speed of growth is varied; the right amount of growth can lead to a higher success rate...
March 16, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28322873/fortune-favours-the-brave-movement-responses-shape-demographic-dynamics-in-strongly-competing-populations
#4
Jonathan R Potts, Sergei V Petrovskii
Animal movement is a key mechanism for shaping population dynamics. The effect of interactions between competing animals on a population's survival has been studied for many decades. However, interactions also affect an animal's subsequent movement decisions. Despite this, the indirect effect of these decisions on animal survival is much less well-understood. Here, we incorporate movement responses to foreign animals into a model of two competing populations, where inter-specific competition is greater than intra-specific competition...
March 16, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28302492/from-endosymbiosis-to-holobionts-evaluating-a-conceptual-legacy
#5
Maureen A O'Malley
In her influential 1967 paper, Lynn Margulis synthesized a range of data to support the idea of endosymbiosis. Building on the success of this work, she applied the same methodology to promote the role of symbiosis more generally in evolution. As part of this broader project, she coined the term 'holobiont' to refer to a unified entity of symbiont and host. This concept is now applied with great gusto in microbiome research, and often implies not just a physiological unit but also various senses of an evolving system...
March 13, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28300596/combined-virtual-screening-mmpbsa-molecular-docking-and-dynamics-studies-against-deadly-anthrax-an-in-silico-effort-to-inhibit-bacillus-anthracis-nucleoside-hydrolase
#6
Masoumeh Karami, Chiya Jalali, Sako Mirzaie
Anthrax is a deadly disease caused by Bacillus anthracis, a dangerous biological warfare agent employed for both military and terrorist purposes. A critical selective target for chemotherapy against this disease is nucleoside hydrolase (NH), an enzyme still not found in mammals. In the current study, we have performed molecular docking and dynamics studies, aiming to propose the new potent inhibitors of B. anthracis NH among National Cancer Institute (NCI) Diversity Set. We also analyzed the principal interactions of proposed compounds with the active site residues of NH and the relevant factors to biological activity...
March 12, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28300595/a-biophysical-model-of-how-%C3%AE-tubulin-carboxy-terminal-tails-tune-kinesin-1-processivity-along-microtubule
#7
Miljko V Sataric, Dalibor L Sekulic, Slobodan Zdravkovic, Nebojsa M Ralevic
It appears that so-called post-translational modifications of tubulin heterodimers are mostly focussed at positions of amino acid sequences of carboxy-terminal tails. These changes have very profound effects on microtubule functions especially in connection with cellular traffic in terms of motor proteins. In this study, we elaborated the biophysical model aimed to explain the strategy governing these subtle interplays between structural and functional properties of microtubules. We relied onto Langevin equations including fluctuation-dissipation processes...
March 12, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28288794/stress-mediated-allee-effects-can-cause-the-sudden-collapse-of-honey-bee-colonies
#8
Ross D Booton, Yoh Iwasa, James A R Marshall, Dylan Z Childs
The recent rapid decline in global honey bee populations could have significant implications for ecological systems, economics and food security. No single cause of honey bee collapse has yet to be identified, although pesticides, mites and other pathogens have all been shown to have a sublethal effect. We present a model of a functioning bee hive and introduce external stress to investigate the impact on the regulatory processes of recruitment to the forager class, social inhibition and the laying rate of the queen...
March 10, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28286217/full-reconstruction-of-non-stationary-strand-symmetric-models-on-rooted-phylogenies
#9
Benjamin D Kaehler
Understanding the evolutionary relationship among species is of fundamental importance to the biological sciences. The location of the root in any phylogenetic tree is critical as it gives an order to evolutionary events. None of the popular models of nucleotide evolution currently used in likelihood or Bayesian methods are able to infer the location of the root without exogenous information. It is known that the most general Markov models of nucleotide substitution also cannot identify the location of the root or be fitted to multiple sequence alignments with fewer than three sequences...
March 9, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28286216/a-resource-dependent-protein-synthesis-model-for-evaluating-synthetic-circuits
#10
Wolfgang Halter, Jan Maximilian Montenbruck, Zoltan A Tuza, Frank Allgöwer
Reliable in silico design of synthetic gene networks necessitates novel approaches to model the process of protein synthesis under the influence of limited resources. We present such a novel protein synthesis model which originates from the Ribosome Flow Model and among other things describes the movement of RNA-polymerase and ribosomes on mRNA and DNA templates, respectively. By analyzing the convergence properties of this model based upon geometric considerations, we present additional insights into the dynamic mechanisms of the process of protein synthesis...
March 9, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28284989/punishment-in-the-form-of-shared-cost-promotes-altruism-in-the-cooperative-dilemma-games
#11
Chunyan Zhang, Yuying Zhu, Zengqiang Chen, Jianlei Zhang
One phenomenon or social institution often observed in multi-agent interactions is the altruistic punishment, i.e. the punishment of unfair behavior by others at a personal cost. Inspired by the works focusing on punishment and the intricate mechanism behind it, we theoretically study the strategy evolution in the framework of two-strategy game models with the punishment on defectors, moreover, the cost of punishing will be evenly shared among the cooperators. Theoretical computations suggest that larger punishment on defectors or smaller punishment cost incurred by cooperators will enhance the fixation of altruistic cooperation in the population...
March 9, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28284992/nest-site-lottery-revisited-towards-a-mechanistic-model-of-population-growth-suppressed-by-the-availability-of-nest-sites
#12
Krzysztof Argasinski, Ryszard Rudnicki
In the "nest site lottery" mechanism, newborns form a pool of candidates and randomly drawn candidates replace the dead adults in their nest sites. However, the selection process has only been analyzed under the assumption of an equilibrium population size. In this study, we extend this model to cases where the population size is not at an equilibrium, which yields a simplified (but fully mechanistic) biphasic population growth model, where the suppression of growth is driven only by the availability of free nest sites for newborns...
March 8, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28284991/a-novel-multitarget-model-of-radiation-induced-cell-killing-based-on-the-gaussian-distribution
#13
Lei Zhao, Dong Mi, Yeqing Sun
The multitarget version of the traditional target theory based on the Poisson distribution is still used to describe the dose-survival curves of cells after ionizing radiation in radiobiology and radiotherapy. However, noting that the usual ionizing radiation damage is the result of two sequential stochastic processes, the probability distribution of the damage number per cell should follow a compound Poisson distribution, like e.g. Neyman's distribution of type A (N. A.). In consideration of that the Gaussian distribution can be considered as the approximation of the N...
March 8, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28284990/modeling-the-photoperiodic-entrainment-of-the-plant-circadian-clock
#14
Joëlle De Caluwé, José Romário Fernandes de Melo, Alen Tosenberger, Christian Hermans, Nathalie Verbruggen, Jean-Christophe Leloup, Didier Gonze
The circadian clock is an endogenous 24hour rhythm that helps organisms anticipate and adapt to daily and seasonal variations in environment, such as the day/night cycle or changing temperatures. The plant clock is a complex network of transcription factors that regulate each other, forming interlocked feedback loops. Most of its components are light-regulated in some way, making the system highly sensitive to changes in light conditions. Here, we explore the mechanisms by which the plant clock adapts to changing day length...
March 8, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28263815/the-optimal-rate-for-resolving-a-near-polytomy-in-a-phylogeny
#15
Mike Steel, Christoph Leuenberger
The reconstruction of phylogenetic trees from discrete character data typically relies on models that assume the characters evolve under a continuous-time Markov process operating at some overall rate λ. When λ is too high or too low, it becomes difficult to distinguish a short interior edge from a polytomy (the tree that results from collapsing the edge). In this note, we investigate the rate that maximizes the expected log-likelihood ratio (i.e. the Kullback-Leibler separation) between the four-leaf unresolved (star) tree and a four-leaf binary tree with interior edge length ϵ...
March 3, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28263816/cases-in-which-ancestral-maximum-likelihood-will-be-confusingly-misleading
#16
Tomer Handelman, Benny Chor
Ancestral maximum likelihood (AML) is a phylogenetic tree reconstruction criteria that "lies between" maximum parsimony (MP) and maximum likelihood (ML). ML has long been known to be statistically consistent. On the other hand, Felsenstein (1978) showed that MP is statistically inconsistent, and even positively misleading: There are cases where the parsimony criteria, applied to data generated according to one tree topology, will be optimized on a different tree topology. The question of weather AML is statistically consistent or not has been open for a long time...
March 2, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28263814/convergence-of-a-moran-model-to-eigen-s-quasispecies-model
#17
Joseba Dalmau
We prove that a Moran model converges in probability to Eigen's quasispecies model in the infinite population limit. We show further that the invariant probability measure of the Moran model converges to the unique stationary solution of Eigen's quasispecies model.
March 2, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28259661/interplay-between-epidemic-spread-and-information-propagation-on-metapopulation-networks
#18
Bing Wang, Yuexing Han, Gouhei Tanaka
The spread of an infectious disease has been widely found to evolve with the propagation of information. Many seminal works have demonstrated the impact of information propagation on the epidemic spreading, assuming that individuals are static and no mobility is involved. Inspired by the recent observation of diverse mobility patterns, we incorporate the information propagation into a metapopulation model based on the mobility patterns and contagion process, which significantly alters the epidemic threshold...
March 1, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28259660/a-simple-rule-of-direct-reciprocity-leads-to-the-stable-coexistence-of-cooperation-and-defection-in-the-prisoner-s-dilemma-game
#19
Xiu-Deng Zheng, Cong Li, Jie-Ru Yu, Shi-Chang Wang, Song-Jia Fan, Bo-Yu Zhang, Yi Tao
The long-term coexistence of cooperation and defection is a common phenomenon in nature and human society. However, none of the theoretical models based on the Prisoner's Dilemma (PD) game can provide a concise theoretical model to explain what leads to the stable coexistence of cooperation and defection in the long-term even though some rules for promoting cooperation have been summarized (Nowak, 2006, Science 314, 1560-1563). Here, based on the concept of direct reciprocity, we develop an elementary model to show why stable coexistence of cooperation and defection in the PD game is possible...
March 1, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28257764/by-product-mutualism-with-evolving-common-enemies
#20
Kris De Jaegher
The common-enemy hypothesis of by-product mutualism states that organisms cooperate when it is in their individual interests to do so, with benefits for other organisms arising as a by-product; in particular, such cooperation is hypothesized to arise when organisms face the common enemy of a sufficiently adverse environment. In an evolutionary game where two defenders can cooperate to defend a common resource, this paper analyzes the common-enemy hypothesis when adversity is endogenous, in that an attacker sets the number of attacks...
March 1, 2017: Journal of Theoretical Biology
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