{"title":"The development of drug resistance in metastatic tumours under chemotherapy: An evolutionary perspective","authors":"Federica Padovano , Chiara Villa","doi":"10.1016/j.jtbi.2024.111957","DOIUrl":"10.1016/j.jtbi.2024.111957","url":null,"abstract":"<div><div>We present a mathematical model of the evolutionary dynamics of a metastatic tumour under chemotherapy, comprising non-local partial differential equations for the phenotype-structured cell populations in the primary tumour and its metastasis. These equations are coupled with a physiologically-based pharmacokinetic model of drug administration and distribution, implementing a realistic delivery schedule. The model is carefully calibrated from the literature, focusing on BRAF-mutated melanoma treated with Dabrafenib as a case study. By means of long-time asymptotic and global sensitivity analyses, as well as numerical simulations, we explore the impact of cell migration from the primary to the metastatic site, physiological aspects of the tumour tissues and drug dose on the development of chemoresistance and treatment efficacy. Our findings provide a possible explanation for empirical evidence indicating that chemotherapy may foster metastatic spread and that metastases may be less impacted by the chemotherapeutic agent.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111957"},"PeriodicalIF":1.9,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142382450","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}
{"title":"Global stability of coexistence equilibria for n-species models of facultative mutualism","authors":"Paul Georgescu , Hong Zhang","doi":"10.1016/j.jtbi.2024.111961","DOIUrl":"10.1016/j.jtbi.2024.111961","url":null,"abstract":"<div><div>We further pursue an investigation on an abstract model characterizing the dynamics of a general class of <span><math><mi>n</mi></math></span>-species facultative mutualisms that was initiated in Georgescu et al. (2017), establishing biologically relevant sufficient conditions for the global asymptotic stability of the coexistence equilibria. These conditions are given in terms of per-species limits of growth-to-loss ratios computed at higher population densities, complemented by either monotonicity or sublinearity inequalities, and are observed to hold for <span><math><mi>n</mi></math></span>-species versions of mutualistic models in current use. The specific modeling details that require either of these conditions being satisfied are outlined and discussed. As mutualisms can enhance species diversification and facilitate stable coexistence via a plethora of mechanisms, it is then important to understand the stability of speciose mutualisms, our results being of potential interest to theoretical ecologists studying the coexistence of many interacting species and to conservationists aiming for rare species preservation.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111961"},"PeriodicalIF":1.9,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142378625","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}
Nishnath Polavarapu , Madison Doty , Hana M. Dobrovolny
{"title":"Exploring the treatment of SARS-CoV-2 with modified vesicular stomatitis virus","authors":"Nishnath Polavarapu , Madison Doty , Hana M. Dobrovolny","doi":"10.1016/j.jtbi.2024.111959","DOIUrl":"10.1016/j.jtbi.2024.111959","url":null,"abstract":"<div><div>SARS-CoV-2 caused a global pandemic and is now an endemic virus that will require continued antiviral and vaccine development. A possible new treatment modality was recently suggested that would use vesicular stomatitis virus (VSV) modified to express the ACE2 receptor. Since the modified VSV expresses the cell surface receptor that is used by the SARS-CoV-2 spike protein, the thought is that SARS-CoV-2 virions would bind to the modified VSV and thus be neutralized. Additionally, since SARS-CoV-2 infected cells also express the spike protein, the modified VSV could potentially infect these cells, allowing for its own replication, but also potentially interfering with replication of SARS-CoV-2. This idea has not yet been tested experimentally, but we can investigate the feasibility of this possible treatment theoretically. In this manuscript, we develop a mathematical model of this suggested treatment and explore conditions under which it might be effective. We find that treatment with modified VSV does little to change the SARS-CoV-2 time course except when the treatment is applied at the onset of the SARS-CoV-2 infection at very high doses. In this case, VSV reduces the peak SARS-CoV-2 viral load, but lengthens the duration of the SARS-CoV-2 infection. Thus, we find that modified VSV treatment is unlikely to be effective largely because it does not prevent infection of cells by SARS-CoV-2.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111959"},"PeriodicalIF":1.9,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142376324","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}
{"title":"Agelessness is possible under the disposable soma theory but system complexity makes it unlikely","authors":"Christopher W. Rodriguez, Peter W. Reddien","doi":"10.1016/j.jtbi.2024.111958","DOIUrl":"10.1016/j.jtbi.2024.111958","url":null,"abstract":"<div><div>Although demographic studies have failed to find evidence of aging in certain animal species, classic evolutionary theories of aging struggle to explain how evolution could favor agelessness in such cases. Here, we develop mathematical models of the disposable soma theory to identify conditions in which agelessness would be evolutionarily favored. For any given type of damage that could accumulate and cause age-accelerating mortality risk, we find that evolution could select for its complete removal if the mortality risk it poses is severe enough and its repair does not pose too large of a penalty to reproduction. Environmental factors such as extrinsic mortality and the form of population density-dependent regulation also play a large role in determining the optimal rate of aging and whether agelessness should be evolutionarily favored. However, in a system with multiple sources of damage and multiple independent repair processes, avoiding aging is rarely evolutionarily favorable. Pleiotropic repair processes, such as those that could be present in asexual fissioning organisms, make agelessness more likely but do not guarantee it. Our results indicate that agelessness could be favored by evolution in narrow contexts but that multiple types of damage and repair make agelessness unlikely to arise in sufficiently complex organisms.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111958"},"PeriodicalIF":1.9,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142373588","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}
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}
{"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}
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}
Graham M. Donovan , Congping Lin , Imogen Sparkes , Peter Ashwin
{"title":"Emergence and stability of endoplasmic reticulum network streaming in plant cells","authors":"Graham M. Donovan , Congping Lin , Imogen Sparkes , Peter Ashwin","doi":"10.1016/j.jtbi.2024.111954","DOIUrl":"10.1016/j.jtbi.2024.111954","url":null,"abstract":"<div><div>The endoplasmic reticulum (ER) network is highly complex and highly dynamic in its geometry, and undergoes extensive remodeling and bulk flow. It is known that the ER dynamics are driven by actin–myosin dependent processes. ER motion through the cytoplasm will cause forces on the cytoplasm that will induce flow. However, ER will also clearly be passively transported by the bulk cytoplasmic streaming. We take the complex ER network structure into account and propose a positive-feedback mechanism among myosin-like motors, actin alignment, ER network dynamics for the emergence of ER flow. Using this model, we demonstrate that ER streaming may be an emergent feature of this three-way interaction and that the persistent-point density may be a key driver of the emergence of ER streaming.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111954"},"PeriodicalIF":1.9,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142332575","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}
{"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}
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}