Journal of Theoretical Biology最新文献_第8页

An immuno-epidemiological model with non-exponentially distributed disease stage on complex networks 复杂网络上非指数分布疾病阶段的免疫流行病学模型。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-10-09 DOI: 10.1016/j.jtbi.2024.111964

Junyuan Yang , Xinyi Duan , Guiquan Sun

引用次数: 0

A model for transcription-dependent R-loop formation at double-stranded DNA breaks: Implications for their detection and biological effects 双链 DNA 断裂处转录依赖性 R 环形成模型：对其检测和生物效应的影响

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-10-09 DOI: 10.1016/j.jtbi.2024.111962

Boris P. Belotserkovskii, Philip C. Hanawalt

{"title":"A model for transcription-dependent R-loop formation at double-stranded DNA breaks: Implications for their detection and biological effects","authors":"Boris P. Belotserkovskii, Philip C. Hanawalt","doi":"10.1016/j.jtbi.2024.111962","DOIUrl":"10.1016/j.jtbi.2024.111962","url":null,"abstract":"<div><div>R-loops are structures containing an RNA-DNA duplex and an unpaired DNA strand. During R-loop formation an RNA strand invades the DNA duplex, displacing the homologous DNA strand and binding the complementary DNA strand. Here we analyze a model for transcription-dependent R-loop formation at double-stranded DNA breaks (DSBs). In this model, R-loop formation is preceded by detachment of the non-template DNA strand from the RNA polymerase (RNAP). Then, strand exchange is initiated between the nascent RNA and the non-template DNA strand. During that strand exchange the length of the R-loop could either increase, or decrease in a biased random-walk fashion, in which the bias would depend upon the DNA sequence. Eventually, the restoration of the DNA duplex would completely displace the RNA. However, as long as the RNAP remains bound to the template DNA strand it prevents that displacement. Thus, according to the model, RNAPs stalled at DSBs can increase the lifespan of R-loops, increasing their detectability in experiments, and perhaps enhancing their biological effects.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111962"},"PeriodicalIF":1.9,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142395390","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 development of drug resistance in metastatic tumours under chemotherapy: An evolutionary perspective 化疗下转移性肿瘤耐药性的发展：从进化角度看

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-10-05 DOI: 10.1016/j.jtbi.2024.111957

Federica Padovano , Chiara Villa

引用次数: 0

Global stability of coexistence equilibria for n-species models of facultative mutualism n种互惠模式共存平衡的全局稳定性。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-10-03 DOI: 10.1016/j.jtbi.2024.111961

Paul Georgescu , Hong Zhang

{"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}

引用次数: 0

Exploring the treatment of SARS-CoV-2 with modified vesicular stomatitis virus 探索用改良水泡性口炎病毒治疗 SARS-CoV-2

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-10-02 DOI: 10.1016/j.jtbi.2024.111959

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}

引用次数: 0

Agelessness is possible under the disposable soma theory but system complexity makes it unlikely 根据可抛弃的肉体理论，永恒是有可能的，但系统的复杂性使其不太可能实现。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-10-01 DOI: 10.1016/j.jtbi.2024.111958

Christopher W. Rodriguez, Peter W. Reddien

{"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}

引用次数: 0

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