Journal of Theoretical Biology最新文献_第6页

Optimal resource allocation in micro-organisms under periodic nutrient fluctuations 周期性养分波动下微生物的最佳资源分配。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-09-30 DOI: 10.1016/j.jtbi.2024.111953

J. Innerarity Imizcoz , W. Djema , F. Mairet , J.-L. Gouzé

{"title":"Optimal resource allocation in micro-organisms under periodic nutrient fluctuations","authors":"J. Innerarity Imizcoz , W. Djema , F. Mairet , J.-L. Gouzé","doi":"10.1016/j.jtbi.2024.111953","DOIUrl":"10.1016/j.jtbi.2024.111953","url":null,"abstract":"<div><div>Although microorganisms often live in dynamic environments, most studies, both experimental and theoretical, are carried out under static conditions. In this work, we investigate the issue of optimal resource allocation in bacteria growing in periodic environments. We consider a dynamic model describing the microbial metabolism under varying conditions, involving a control variable quantifying the protein precursors allocation. Our objective is to determine the optimal strategies maximizing the long-term growth of cells under a piecewise-constant periodic environment. Firstly, we perform a theoretical analysis of the resulting optimal control problem (OCP), based on the application the Pontryagin’s Maximum Principle (PMP). We determine that the structure of the optimal control must be bang–bang, with possibly some singular arcs corresponding to optimal equilibria of the system. If the control presents singular arcs, then these can only be reached and left through chattering arcs. We also use a direct optimization method, implemented in the <span>BOCOP</span> software, to solve the studied OCP. Our study reveals that the optimal solution over a large time horizon is related to the one over a single period of the varying environment with periodic constraints. Moreover, we observe that the maximal average growth rate attainable under periodic conditions can be higher than the one under a constant environment. We further extend our analysis to conduct a qualitative comparison between the predictions from our model and some recent biological experiments on <em>E. coli</em>. This analysis particularly highlights the mechanisms of action of the ppGpp signaling molecule, thus providing relevant explanations of the experimental observations. In conclusion, our study corroborates previous research indicating that this molecule plays a crucial role in the regulation of resource allocation of protein precursors in <em>E. coli</em>.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111953"},"PeriodicalIF":1.9,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142367446","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Macroscale vertical power-law distribution of bacteria in dark oceans can emerge from microscale bacteria-particle interactions 暗色海洋中细菌的宏观垂直幂律分布可以从微观的细菌-粒子相互作用中产生。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-09-29 DOI: 10.1016/j.jtbi.2024.111956

Takeshi Miki , Po-Ju Ke

{"title":"Macroscale vertical power-law distribution of bacteria in dark oceans can emerge from microscale bacteria-particle interactions","authors":"Takeshi Miki , Po-Ju Ke","doi":"10.1016/j.jtbi.2024.111956","DOIUrl":"10.1016/j.jtbi.2024.111956","url":null,"abstract":"<div><div>Microbes in the dark oceans are a key determinant of remineralization of sinking carbon particles. However, most marine ecosystem models overlook how microbes aggregate on particles and the microscale interactions between particle-associated microbes, making it difficult to obtain mechanistic insights on their vertical power-law decay pattern. Here, we present a spatial population model where the attachment and detachment processes of bacterial cells depend on local density of particle-associated bacteria. We show that the power-law relationship can emerge when the non-random aggregated distribution of bacteria is considered without any depth-specific environmental parameters. Furthermore, the comparison between model behavior and empirical patterns in the Pacific and Southern Ocean indicated that temperature-dependent hydrolysis rate and nutrient-dependent sinking rate of particles are key parameters to explain the regional variations of the power-law exponent. The mechanistic approach developed here provides a pathway to link micro-scale interactions between individuals to macro-scale food chain structures and carbon cycle.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111956"},"PeriodicalIF":1.9,"publicationDate":"2024-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142367445","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The eco-evolutionary dynamics of two strategic species: From the predator-prey to the innocent-spreader rumor model 两个战略物种的生态进化动态：从捕食者-猎物到无辜传播者的谣言模式。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-09-28 DOI: 10.1016/j.jtbi.2024.111955

Subrata Ghosh , Sourav Roy , Matjaž Perc , Dibakar Ghosh

{"title":"The eco-evolutionary dynamics of two strategic species: From the predator-prey to the innocent-spreader rumor model","authors":"Subrata Ghosh , Sourav Roy , Matjaž Perc , Dibakar Ghosh","doi":"10.1016/j.jtbi.2024.111955","DOIUrl":"10.1016/j.jtbi.2024.111955","url":null,"abstract":"<div><div>Species frequently engage in both competitive and cooperative interactions, delicately balancing these dynamics to optimize their chances of survival and reproduction. While competition drives individuals to compete for limited resources, cooperation can emerge as a strategic response, mitigating risk and enhancing collective payoff. To bridge theoretical game approaches such as payoff, cooperation, and defections in ecological systems, we propose a two-species predator–prey model inspired by the principles and variations of the prisoner’s dilemma game. We comprehensively address and analytically verify all stable strategic states, exploring the role of payoff parameters both individually and collectively. Additionally, we investigate the effect of free space. Beyond ecological contexts, we present a model of rumor propagation within a social system to establish connections with the prisoner’s dilemma game. In both systems, our primary focus is to discuss strategies and enhance the cooperative factor within the system, given its crucial importance across diverse environments.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111955"},"PeriodicalIF":1.9,"publicationDate":"2024-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142332576","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Emergence and stability of endoplasmic reticulum network streaming in plant cells 植物细胞内质网网络流的出现和稳定性。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-09-27 DOI: 10.1016/j.jtbi.2024.111954

Graham M. Donovan , Congping Lin , Imogen Sparkes , Peter Ashwin

引用次数: 0

Agent-based evolutionary game dynamics uncover the dual role of resource heterogeneity in the evolution of cooperation 基于代理的进化博弈动力学揭示了资源异质性在合作进化中的双重作用。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-09-24 DOI: 10.1016/j.jtbi.2024.111952

Qin Yang , Yi Tang , Dehua Gao

{"title":"Agent-based evolutionary game dynamics uncover the dual role of resource heterogeneity in the evolution of cooperation","authors":"Qin Yang , Yi Tang , Dehua Gao","doi":"10.1016/j.jtbi.2024.111952","DOIUrl":"10.1016/j.jtbi.2024.111952","url":null,"abstract":"<div><div>Cooperation is a cornerstone of social harmony and group success. Environmental feedbacks that provide information about resource availability play a crucial role in encouraging cooperation. Previous work indicates that the impact of resource heterogeneity on cooperation depends on the incentive to act in self-interest presented by a situation, demonstrating its potential to both hinder and facilitate cooperation. However, little is known about the underlying evolutionary drivers behind this phenomenon. Leveraging agent-based modeling and game theory, we explore how differences in resource availability across environments influence the evolution of cooperation. Our results show that resource variation hinders cooperation when resources are slowly replenished but supports cooperation when resources are more readily available. Furthermore, simulations in different scenarios suggest that discerning the rate of natural selection acts on strategies under distinct evolutionary dynamics is instrumental in elucidating the intricate nexus between resource variability and cooperation. When evolutionary forces are strong, resource heterogeneity tends to work against cooperation, yet relaxed selection conditions enable it to facilitate cooperation. Inspired by these findings, we also propose a potential application in improving the performance of artificial intelligence systems through policy optimization in multi-agent reinforcement learning. These explorations promise a novel perspective in understanding the evolution of social organisms and the impact of different interactions on the function of natural systems.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111952"},"PeriodicalIF":1.9,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142332577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Optimal control of combination immunotherapy for a virtual murine cohort in a glioblastoma-immune dynamics model 胶质母细胞瘤-免疫动力学模型中虚拟小鼠队列的联合免疫疗法优化控制。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-09-20 DOI: 10.1016/j.jtbi.2024.111951

Hannah G. Anderson , Gregory P. Takacs , Jeffrey K. Harrison , Libin Rong , Tracy L. Stepien

{"title":"Optimal control of combination immunotherapy for a virtual murine cohort in a glioblastoma-immune dynamics model","authors":"Hannah G. Anderson , Gregory P. Takacs , Jeffrey K. Harrison , Libin Rong , Tracy L. Stepien","doi":"10.1016/j.jtbi.2024.111951","DOIUrl":"10.1016/j.jtbi.2024.111951","url":null,"abstract":"<div><div>The immune checkpoint inhibitor anti-PD-1, commonly used in cancer immunotherapy, has not been successful as a monotherapy for the highly aggressive brain cancer glioblastoma. However, when used in conjunction with a CC-chemokine receptor-2 (CCR2) antagonist, anti-PD-1 has shown efficacy in preclinical studies. In this paper, we aim to optimize treatment regimens for this combination immunotherapy using optimal control theory. We extend a treatment-free glioblastoma-immune dynamics ODE model to include interventions with anti-PD-1 and the CCR2 antagonist. An optimized regimen increases the survival of an average mouse from 32 days post-tumor implantation without treatment to 111 days with treatment. We scale this approach to a virtual murine cohort to evaluate mortality and quality of life concerns during treatment, and predict survival, tumor recurrence, or death after treatment. A parameter identifiability analysis identifies five parameters suitable for personalizing treatment within the virtual cohort. Sampling from these five practically identifiable parameters for the virtual murine cohort reveals that personalized, optimized regimens enhance survival: 84% of the virtual mice survive to day 100, compared to 60% survival in a previously studied experimental regimen. Subjects with high tumor growth rates and low T cell kill rates are identified as more likely to die during and after treatment due to their compromised immune systems and more aggressive tumors. Notably, the MDSC death rate emerges as a long-term predictor of either disease-free survival or death.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111951"},"PeriodicalIF":1.9,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142301240","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mathematical consideration of massive estimation of dissociation rate constant for genotype–phenotype linking molecules bound to targets through washing/selection and next-generation sequencing 对通过洗涤/选择和新一代测序与靶标结合的基因型-表型连接分子的解离率常数进行大规模估算的数学考虑。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-09-19 DOI: 10.1016/j.jtbi.2024.111944

Takuyo Aita , Naoto Nemoto

{"title":"Mathematical consideration of massive estimation of dissociation rate constant for genotype–phenotype linking molecules bound to targets through washing/selection and next-generation sequencing","authors":"Takuyo Aita , Naoto Nemoto","doi":"10.1016/j.jtbi.2024.111944","DOIUrl":"10.1016/j.jtbi.2024.111944","url":null,"abstract":"<div><div>As one of methods for <em>in vitro</em> selection, a flow reactor type washing/selection system seems to be effective, where a ligand library is composed of “genotype–phenotype linking molecules”. In this system, high affinity ligands are selected by their respective “residual ratio” given by <span><math><mrow><mo>exp</mo><mrow><mo>(</mo><mo>−</mo><msub><mrow><mi>k</mi></mrow><mrow><mi>off</mi></mrow></msub><mo>×</mo><mi>t</mi><mo>)</mo></mrow></mrow></math></span>, where <span><math><msub><mrow><mi>k</mi></mrow><mrow><mi>off</mi></mrow></msub></math></span> is the dissociation rate constant and <span><math><mi>t</mi></math></span> is the washing time. In this paper, we mathematically considered the following possibility. When the washing/selection dynamics obeys the residual ratio <span><math><mrow><mo>exp</mo><mrow><mo>(</mo><mo>−</mo><msub><mrow><mi>k</mi></mrow><mrow><mi>off</mi></mrow></msub><mo>×</mo><mi>t</mi><mo>)</mo></mrow></mrow></math></span> deterministically and mole fraction measurement for sampled sequences by next-generation sequencing (NGS) is performed ideally, the “relative value” of <span><math><msub><mrow><mi>k</mi></mrow><mrow><mi>off</mi></mrow></msub></math></span> for each of high-ranking sequences can be estimated simultaneously. In addition to these, when the residual ratio for the whole ligand population is measured correctly, the “absolute value” for each sequence can be estimated. We deduced formulas to present the relative and absolute estimates, and mathematically analyzed the effect of fluctuations in the number of NGS reads on the estimates in details. These were confirmed by numerical simulations.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111944"},"PeriodicalIF":1.9,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142301238","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The evolution of fear-acquisition strategies under predation 捕食下恐惧获取策略的进化

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-09-19 DOI: 10.1016/j.jtbi.2024.111949

Megan E. Bishop, Maria R. Servedio, Brian A. Lerch

{"title":"The evolution of fear-acquisition strategies under predation","authors":"Megan E. Bishop, Maria R. Servedio, Brian A. Lerch","doi":"10.1016/j.jtbi.2024.111949","DOIUrl":"10.1016/j.jtbi.2024.111949","url":null,"abstract":"<div><div>Fear is a taxonomically widespread behavioral response that functions to keep individuals out of danger. Empirical research has demonstrated that a diverse set of strategies are used in order to acquire a fear response across animals. Animals often use a mixed strategy: fear is acquired both innately and through learning. Despite the ubiquity of the fear response, and its established importance for shaping predator–prey interactions, little is known about why different fear acquisition strategies evolve or why mixed strategies appear common. Here, we model the evolution of fear acquisition (learning versus innate) under predation. We assume a tradeoff where individuals that learn fear are at higher risk from predators initially, but eventually obtain a lower risk as they survive predation attempts. We find that frequent predator encounters, predators that are not very dangerous, and effective learning favor the evolution of learned fear. Only pure strategies of fear acquisition evolve unless individuals suffer from either a cost to fear or, especially, a cost to learning, either of which can lead to the evolution of mixed strategies. Our results thus shed light onto the evolution of mixed fear acquisition strategies and open the door to further research on the evolution of fear acquisition.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111949"},"PeriodicalIF":1.9,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142301242","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Convergence of reputations under indirect reciprocity 间接互惠下的声誉趋同。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-09-18 DOI: 10.1016/j.jtbi.2024.111947

Bryce Morsky , Joshua B. Plotkin , Erol Akçay

引用次数: 0

Temperature variability regulates the interactive effects of warming and pharmaceutical on aquatic ecosystem dynamics 温度变化调节着气候变暖和制药对水生生态系统动态的交互影响。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-09-17 DOI: 10.1016/j.jtbi.2024.111948

Guangjing Qian , Dan Wu , Lai Zhang , Susanne Kortsch

{"title":"Temperature variability regulates the interactive effects of warming and pharmaceutical on aquatic ecosystem dynamics","authors":"Guangjing Qian , Dan Wu , Lai Zhang , Susanne Kortsch","doi":"10.1016/j.jtbi.2024.111948","DOIUrl":"10.1016/j.jtbi.2024.111948","url":null,"abstract":"<div><div>Climate warming and pharmaceutical contaminants have profound impacts on population dynamics and ecological community structure, yet the consequences of their interactive effects remain poorly understood. Here, we explore how climate warming interacts with pharmaceutical-induced boldness change to affect aquatic ecosystems, built on an empirically well-informed food-chain model, consisting of a size-structured fish consumer, a zooplankton prey, and a fish predator. Climate warming is characterized by both daily mean temperature (DMT) and diurnal temperature range (DTR) in our model. Results show that DMT and high levels of species’ boldness are the primary drivers of community instability. However, their interactive effects can lead to diverse outcomes: from predator collapse to coexistence with seasonality-driven cycles and coexistence with population interaction-driven cycles. The interactive effects are significantly modulated by daily temperature variability, where moderate DTR counteracts the destabilizing interactive effects by increasing consumer reproduction, while large temperature variability considerably reduces consumer biomass<em>,</em> destabilizing the community at high mean temperatures. Our analyses disentangle the respective roles of DMT, DTR and boldness in mediating the response of aquatic ecosystems to the impacts from pharmaceutical contaminants in the context of climate warming. The interactive effects of the environmental stressors reported here underscore the pressing need for studies aimed at quantifying the cumulative impacts of multiple environmental stressors on aquatic ecosystems.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111948"},"PeriodicalIF":1.9,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142301241","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0