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Low-Level Cefepime Exposure Induces High-Level Resistance in Environmental Bacteria: Molecular Mechanism and evolutionary dynamics

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ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022年第21期56卷 15074-15083页

作者： Wang, Hanqing Feng, Youjun Lu, Huijie Zhejiang Univ Coll Environm & Resource Sci Hangzhou 310058 Zhejiang Peoples R China Zhejiang Univ Affiliated Hosp 2 Dept Microbiol Sch Med Hangzhou 310058 Zhejiang Peoples R China Zhejiang Univ Affiliated Hosp 2 Gen Intens Care Unit Sch Med Hangzhou 310058 Zhejiang Peoples R China Zhejiang Univ Acad Ecol Civilizat Hangzhou 310058 Zhejiang Peoples R China

Antibiotics exert selective pressures on clinically relevant antibiotic resistance. It is critical to understand how antibiotic resistance evolves in environmental microbes exposed to subinhibitory concentrations of antibiotics and whether evolutionary dynamics and emergence of resistance are predictable. In this study, Comamonas testosteroni isolated from wastewater activated sludge were subcultured in a medium containing 10 ng/mL cefepime for 40 days (similar to 300 generations). Stepwise mutations were accumulated, leading to an ultimate 200-fold increase in the minimum inhibitory concentration (MIC) of cefepime. Early stage mutation in DNA polymerase-encoding gene dnaE2 played an important role in antibiotic resistance evolution. Diverse resistance mechanisms were employed and validated experimentally, including increased efflux, biofilm formation, reduced antibiotic uptake, and drug inactivation. The cefepime minimal selective concentrations (MSCs) and relative fitness of susceptible, intermediate, and resistant mutants were determined. Agent-based modeling of the modified Moran process enabled simulations of resistance evolution and predictions of the emergence time and frequency of resistant mutants. The unraveled cefepime resistance mechanisms could be employed by broader bacteria, and the newly developed model is applicable to the predictions of general resistance evolution. The improved knowledge facilitates the assessment, prediction, and mitigation of antibiotic resistance progression in antibiotic-polluted environments.

关键词： antibiotic resistance evolutionary dynamics fitness landscape agent-based modeling modified Moran process

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A novel approach on evolutionary dynamics analysis - A progress report

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JOURNAL OF COMPUTATIONAL SCIENCE 2018年 25卷 437-445页

作者： Zelinka, Ivan Tomaszek, Lukas Vasant, Pandian Dao, Tran Trong Hoang, Duy Vo Ton Duc Thang Univ Fac Elect & Elect Engn Modeling Evolutionary Algorithms Simulat & Artifi Ho Chi Minh City Vietnam VSB Tech Univ Ostrava Dept Comp Sci FEI Tr 17 Listopadu 15 Ostrava Czech Republic Univ Teknol PETRONAS Dept Fundamental & Appl Sci Seri Iskandar 32610 Malaysia

In this paper, we discuss the possibility of unique mutual fusion of evolutionary algorithms, complex networks, strange dynamics and hidden attractors. As demonstrated in many research papers, evolutionary algorithms are capable of very complex tasks such as chaotic system control, identification or synthesis and vice versa;chaos can also be observed in the evolutionary dynamics, as originally demonstrated by various researchers. We propose a novel approach on how to analyze and control dynamic of the evolutionary algorithm and also discuss the possibility of strange dynamics analysis that can be a part of dynamic of evolutionary algorithms. In any words, we propose to understand algorithms as a discrete dynamical system that exhibits a wide spectrum of the behavior that can be controlled and analyzed. (C) 2017 Elsevier B.V. All rights reserved.

关键词： evolutionary dynamics Strange dynamics Hidden attractors Complex network evolutionary algorithms Control Chaos

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Stability analysis of evolutionary dynamics of 2 x 2 x 2 asymmetric games

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PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES 2024年第2282期480卷 20230478-20230478页

作者： Song, Sha Pan, Qiuhui Gao, Xubin He, Mingfeng Dalian Univ Technol Sch Math Sci Dalian 116024 Peoples R China Dalian Univ Technol Sch Innovat & Entrepreneurship Dalian 116024 Peoples R China Dalian Univ Sch Informat Engn Dalian 116622 Peoples R China

In biology, economics, sociology as well as other fields, there is often a 2x2x2 asymmetric evolutionary game problem in which each party has a set of strategies, and different strategy combinations correspond to the specific pay-offs of each party. Since each participant dynamically adjusts the strategy for maximizing their own interests, the pay-off matrix plays an important role in the evolution of the game system. Based on the pay-off matrix, we probe into the resulting state of 2x2x2 asymmetric evolutionary games. The results show that from the information of the pay-off matrix, the judgement conditions for the system to evolve into three pure strategies, two pure strategies and one pure strategy can be determined directly. What is more, under a certain type of fixed pay-off matrix, the strategy combinations observed at different evolution times is always varying. Here, we explore the connection between the pay-off matrix and the evolution of behaviours through stability theory, and results obtained are conducive to deeply understand and predict the dynamic evolution of behaviour in game systems.

关键词： 2 x 2 x 2 asymmetric games evolutionary dynamics equilibrium stability

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Temporal behavior of evolutionary dynamics in finite dimensional population

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PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS 2012年第4期391卷 1234-1242页

作者： Tian, Liang Nanjing Univ Aeronaut & Astronaut Coll Sci Nanjing 210016 Peoples R China

We systematically study the temporal behavior of evolutionary dynamics in finite dimensional population based on evolutionary graph theory. Besides the spread of mutants, we also consider the spread of the impact of the initial mutant seed. The time-dependent behavior of these two spreading processes and their relationship are theoretically and computationally investigated. The ingredients and scaling behaviors of the interface between mutants and wild-type individuals are analyzed in detail, which have significant impact on temporal behavior of evolutionary dynamics. Since the evolutionary systems in nature are generally local and spatial, this research provides further understanding of temporal behavior in evolutionary dynamics at the theoretical level. (C) 2011 Published by Elsevier B.V.

关键词： evolutionary dynamics evolutionary graph theory Finite dimensional population Scaling

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To Trust or Not to Trust: evolutionary dynamics of an Asymmetric N-Player Trust Game

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IEEE TRANSACTIONS ON evolutionary COMPUTATION 2024年第1期28卷 117-131页

作者： Lim, Ik Soo Masuda, Naoki Univ Greenwich Sch Comp & Math Sci London SE10 9LS England SUNY Buffalo Dept Math Buffalo NY 14260 USA SUNY Buffalo Computat & Data Enabled Sci & Engn Program Buffalo NY 14260 USA Waseda Univ Fac Sci & Engn Shinjuku Tokyo 1698555 Japan

Trusting others and reciprocating the received trust with trustworthy actions are fundaments of economic and social interactions. The trust game (TG) is widely used for studying trust and trustworthiness and entails a sequential interaction between two players, an investor and a trustee. It requires at least two strategies or options for an investor (e.g., to trust versus not to trust a trustee). According to the evolutionary game theory, the antisocial strategies (e.g., not to trust) evolve such that the investor and trustee end up with lower payoffs than those that they would get with the prosocial strategies (e.g., to trust). A generalization of the TG to a multiplayer (i.e., more than two players) TG was recently proposed. However, its outcomes hinge upon two assumptions that various real situations may substantially deviate from: 1) investors are forced to trust trustees and 2) investors can turn into trustees by imitation and vice versa. We propose an asymmetric multiplayer TG that allows investors not to trust and prohibits the imitation between players of different roles;instead, investors learn from other investors and the same for trustees. We show that the evolutionary game dynamics of the proposed TG qualitatively depends on the non-linearity of the payoff function and the amount of incentives collected from and distributed to players through an institution. We also show that incentives given to trustees can be useful and sufficient to cost-effectively promote trust and trustworthiness among self-interested players.

关键词： evolutionary dynamics evolutionary game theory incentives replicator dynamics trust game (TG)

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Colony and evolutionary dynamics of a two-stage model with brood cannibalism and division of labor in social insects

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NATURAL RESOURCE MODELING 2016年第4期29卷 633-662页

作者： Rodriguez-Rodriguez, Marisabel Kang, Yun Arizona State Univ Sch Math & Stat Sci Tempe AZ 85281 USA Arizona State Univ Sci & Math Fac Coll Integrat Sci & Arts Mesa AZ 85212 USA

Division of labor (DOL) is a major factor for the great success of social insects because it increases the efficiency of a social group where different individuals perform different tasks repeatedly and presumably with increased performance. Cannibalism plays an important role in regulating colony growth and development by regulating the number of individuals in a colony and increasing survival by providing access to essential nutrients and minimizing competition among colony mates. To understand the synergy effects of DOL and cannibalistic behavior on colony dynamic outcomes, we propose and study a compartmental two-stage model using ecological and evolutionary game theory settings. Our analytical results of the ecological and evolutionary models suggest that: (1) A noncannibalistic colony can survive if the efficiency of energy investment reflecting the DOL is greater than the relative death rate of the older population. (2) A cannibalistic colony can die out if both the efficiency of energy investment and the relative cannibalism rate (where each is also reflecting the DOL) are too large;or if the relative cannibalism rate alone is too small. (3) From our numerical analysis, cannibalism can increase or reduce the colony's total population size, which greatly depends on the benefit of egg cannibalism increasing or decreasing of adult's lifespan. (4) A cannibalistic and noncannibalistic colony can experience bistability due to cooperative behavior. (5) In the evolutionary settings, DOL can prevent colony death and natural selection can preserve strong Allee effects by selecting the traits with the largest investment on brood care and the lowest cannibalism rate. (6) evolutionary dynamics may increase the fitness of the colony, i.e., the successful production of workforce which results in the increase of total worker population size, colony survival, and reproduction. Our results suggest both cannibalism and DOLs are adaptive strategies that increase the size of the

关键词： Division of labor egg cannibalism brood care evolutionary dynamics colony dynamics stage-structure model

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Using likelihood-free inference to compare evolutionary dynamics of the protein networks of H. pylori and P. falciparum

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PLOS COMPUTATIONAL BIOLOGY 2007年第11期3卷 2266-2278页

作者： Ratmann, Oliver Jorgensen, Ole Hinkley, Trevor Stumpf, Michael Richardson, Sylvia Wiuf, Carsten Imperial Coll London Dept Publ Hlth & Epidemiol London England Univ Aarhus Bioinformat Res Ctr DK-8000 Aarhus C Denmark Swiss Fed Inst Technol Inst Integrat Biol Zurich Switzerland Imperial Coll London Ctr Bioinformat Div Mol Biosci Theoret Genom Grp London England Imperial Coll London Inst Math Sci London England Imperial Coll London Ctr Biostat London England Aarhus Univ Hosp Mol Diagnost Lab Aarhus Denmark

Gene duplication with subsequent interaction divergence is one of the primary driving forces in the evolution of genetic systems. Yet little is known about the precise mechanisms and the role of duplication divergence in the evolution of protein networks from the prokaryote and eukaryote domains. We developed a novel, model-based approach for Bayesian inference on biological network data that centres on approximate Bayesian computation, or likelihood-free inference. Instead of computing the intractable likelihood of the protein network topology, our method summarizes key features of the network and, based on these, uses a MCMC algorithm to approximate the posterior distribution of the model parameters. This allowed us to reliably fit a flexible mixture model that captures hallmarks of evolution by gene duplication and subfunctionalization to protein interaction network data of Helicobacter pylori and Plasmodium falciparum. The 80% credible intervals for the duplication-divergence component are [ 0.64, 0.98] for H. pylori and [ 0.87, 0.99] for P. falciparum. The remaining parameter estimates are not inconsistent with sequence data. An extensive sensitivity analysis showed that incompleteness of PIN data does not largely affect the analysis of models of protein network evolution, and that the degree sequence alone barely captures the evolutionary footprints of protein networks relative to other statistics. Our likelihood-free inference approach enables a fully Bayesian analysis of a complex and highly stochastic system that is otherwise intractable at present. Modelling the evolutionary history of PIN data, it transpires that only the simultaneous analysis of several global aspects of protein networks enables credible and consistent inference to be made from available datasets. Our results indicate that gene duplication has played a larger part in the network evolution of the eukaryote than in the prokaryote, and suggests that single gene duplications with immediate d

关键词： .approximate evolutionary dynamics Protein networks MCMC Network Data interaction divergence duplication divergence

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EvoDyn-3s: A Mathematica computable document to analyze evolutionary dynamics in 3-strategy games

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SOFTWAREX 2018年 7卷 226-233页

作者： Izquierdo, Luis R. Izquierdo, Segismundo S. Sandholm, William H. Univ Burgos Dept Civil Engn Ed AAvda Cantabria S-N Burgos 09006 Spain Univ Valladolid Dept Ind Org Paseo Cauce 59 E-47011 Valladolid 47011 Spain Univ Wisconsin Dept Econ 1180 Observ Dr Madison WI 53706 USA

EvoDyn-3s generates phase portraits of evolutionary dynamics, as well as data for the analysis of their equilibria. The considered evolutionary dynamics are ordinary differential equations based on adaptive processes taking place in a population of players who are randomly and repeatedly matched in couples to play a 2-player symmetric normal-form game with three strategies. EvoDyn-3s calculates the rest points of the dynamics using exact arithmetic, and represents them. It also provides the eigenvalues of the Jacobian of the dynamics at the isolated rest points, which are useful to evaluate their local stability. The user only needs to specify the 3 x 3 payoff matrix of the game and choose the dynamics. (c) 2018 The Authors. Published by Elsevier B.V.

关键词： evolutionary dynamics Game theory Mathematica Phase portrait Stability

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evolutionary dynamics of the infinitely repeated Minority Game

Evolutionary dynamics of the infinitely repeated Minority Ga...

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作者： Jens Klooster University of Amsterdam

学位级别：硕士

In this thesis we study the evolutionary dynamics of the infinitely repeated Minority Game. We start by introducing the game and equilibrium concepts in a formal matter. Next, we prove the existence of strategies that are Nash and/or NSS in the undiscounted case. We also present some results regarding the properties of strategies that are ESS in the undiscounted case. We conclude by studying the evolutionary dynamics of the infinitely repeated Minority Game with discounting. We introduce a conjecture and show that, if this conjecture is true, there are no strategies that are evolutionary stable in the infinitely repeated minority game with discounting.

关键词： evolutionary Game Theory Minority Game evolutionary dynamics

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On discrete evolutionary dynamics driven by quadratic interactions

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THEORY IN BIOSCIENCES 2016年第4期135卷 187-200页

作者： Grosjean, N. Huillet, T. Rollet, G. CNRS UMR 8089 Lab Phys Theor & Modelisat 2 Ave Adolphe Chauvin F-95302 Cergy Pontoise France Univ Cergy Pontoise 2 Ave Adolphe Chauvin F-95302 Cergy Pontoise France

After an introduction to the general topic of models for a given locus of a diploid population whose quadratic dynamics is determined by a fitness landscape, we consider more specifically the models that can be treated using genetic (or train) algebras. In this setup, any quadratic offspring interaction can produce any type of offspring and after the use of specific changes of basis, we study the evolution and possible stability of some examples. We also consider some examples that cannot be treated using the framework of genetic algebras. Among these are bistochastic matrices.

关键词： evolutionary dynamics Quadratic interactions Genetic algebras Polymorphism Bistochastic interaction

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