Journal of Theoretical Biology最新文献

{"title":"Emergence of food webs with a multi-trophic hierarchical structure driven by nonlinear trait-matching.","authors":"Christophe Laplanche, Benjamin Pey, Robin Aguilée","doi":"10.1016/j.jtbi.2025.112091","DOIUrl":"https://doi.org/10.1016/j.jtbi.2025.112091","url":null,"abstract":"<p><p>Food webs are a central subject in community ecology, because consumption supports the flow of matter through the system, which is at the base of many of its functions. Identifying the mechanisms that are at the origin of food web structure is useful, e.g., for restoration purposes. We investigated the extent to which trait-matching, which contributes to defining the strength of trophic interactions, can cause the emergence of food webs with a non-trivial, multi-trophic, hierarchical structure. We compared for that purpose the structural properties of food webs simulated by four food web model variants, depending whether trait-matching was linear or nonlinear and whether population dynamics and evolution were accounted for (dynamical model) or not (static model). Nonlinear trait-matching can restrict interactions in phenotypic space so as to obtain localized interactions (i.e., each species interact with a small subset of species), which is a key element for food web formation. In the static case, nonlinear trait-matching allowed for the emergence of food webs, at a relatively low connectance as with random graphs. In the dynamical case, nonlinear trait-matching combined with population dynamics and evolution allowed for the formation of groups of phenotypically close species, resulting in food webs with a multi-trophic, hierarchical structure.</p>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":" ","pages":"112091"},"PeriodicalIF":1.9,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143588243","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":"An in-depth study of the dynamics of Thornley 's mathematical model in plant biology with a view to an improved model.","authors":"Ati Rostami, Brodie A J Lawson, Kevin Burrage","doi":"10.1016/j.jtbi.2025.112071","DOIUrl":"https://doi.org/10.1016/j.jtbi.2025.112071","url":null,"abstract":"<p><p>Plants are essential for life on Earth, serving as a major source of food supply and contributing to the planet's carbon balance. Mathematical modelling is an important mechanism for predicting and optimising plant growth in agriculture, and Thornley's mathematical model (Thornley, 1997) is one of the most widely used models describing carbon and nitrogen allocation in plants. However, a formal mathematical analysis of the model's behaviour has not been performed. Our analysis of the model provides new insights into how and why the model can be inappropriate. By varying the values of some model parameters, we identify non-physical and even quite chaotic behaviour. In response, we modify Thornley's model by including additional litter terms, resulting in the elimination of these non-physical behaviours.</p>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":" ","pages":"112071"},"PeriodicalIF":1.9,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143588240","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":"The effects of trade-off shape and dimensionality on eco-evolutionary dynamics in resource competition.","authors":"Jonas Wickman, Christopher A Klausmeier","doi":"10.1016/j.jtbi.2025.112087","DOIUrl":"https://doi.org/10.1016/j.jtbi.2025.112087","url":null,"abstract":"<p><p>Organisms invariably experience trade-offs in their capacities for interacting with their environments. In resource competition, this often means that an organism's ability to acquire one resource can only come at the cost of less ability with others. If the traits governing resource acquisition are under selection and heritable, this will induce eco-evolutionary dynamics along the trade-off. For Lotka-Volterra models derived from MacArthur resource competition models and for explicit resource models with two resources, the shape and dimensionality of trade-offs has seen substantial study. However, how the joint effects of trade-off shapes and the number of resources under competition affect eco-evolutionary outcomes has seen relatively little. For example, is diversification through evolutionary branching more or less likely when the number of resources increases? Here, we will present techniques complementary to existing ones for recasting trade-offs in an implicit form. Combining adaptive dynamics and resource-competition theory, we derive expressions for directional and stabilizing/disruptive selection. We apply our techniques to two models of resource competition and investigate how the number of resources and trade-off shapes affect the stability characteristics of the generalist strategy, and how diverse a community of consumers can be assembled through successive evolutionary branching. We find that even for these simple and highly symmetric models, outcomes are surprisingly complex and idiosyncratic. Taken together, our results deepen our understanding of the eco-evolutionary dynamics of resource competition for multiple resources.</p>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":" ","pages":"112087"},"PeriodicalIF":1.9,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143568924","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":"Geometrically balanced model of cell growth","authors":"Alexei Vazquez ,&nbsp;Tomáš Gedeon","doi":"10.1016/j.jtbi.2025.112085","DOIUrl":"10.1016/j.jtbi.2025.112085","url":null,"abstract":"<div><div>The proteome balance constraint in metabolic flux balance analysis asserts that the proteome is constructed by ribosomes, which themselves contain many proteins. This leads to a fundamental question of optimal allocation of limited proteome among different pools of enzymes, which include ribosomes themselves. However, recent work points to additional constraints imposed by the cell geometry. In this paper we deduce the <em>proteogeometric constraint</em><span><math><mrow><msub><mover><mi>π</mi><mo>¯</mo></mover><mi>A</mi></msub><mo>=</mo><msub><mi>π</mi><mi>A</mi></msub><mo>+</mo><mi>θ</mi><msub><mi>π</mi><mi>L</mi></msub><mo>/</mo><msub><mi>π</mi><mi>P</mi></msub></mrow></math></span>, where <span><math><msub><mi>π</mi><mi>A</mi></msub></math></span>, <span><math><msub><mi>π</mi><mi>P</mi></msub></math></span> and <span><math><msub><mi>π</mi><mi>L</mi></msub></math></span> are the proteomic fractions allocated to the cell surface area, protein synthesis and cell membrane phospholipids synthesis and <span><math><msub><mover><mi>π</mi><mo>¯</mo></mover><mi>A</mi></msub></math></span> and <span><math><mi>θ</mi></math></span> are constants imposed by geometry of the cell. We illustrate the relevance of this constraint using a reduced model of cell metabolism, illuminating the interplay between cell metabolism and cell geometry.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"604 ","pages":"Article 112085"},"PeriodicalIF":1.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143544481","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":"Incorporating adult age into mosquito population models: implications for predicting abundances in changing climates.","authors":"Renato Andrade, Steven M White, Christina A Cobbold","doi":"10.1016/j.jtbi.2025.112084","DOIUrl":"https://doi.org/10.1016/j.jtbi.2025.112084","url":null,"abstract":"<p><p>Mosquito-borne diseases (MBDs) pose increasing threats under future climate change scenarios and an understanding of mosquito population dynamics is pivotal to predicting future risk of MBDs. Most models that describe mosquito population dynamics often assume that adult life-history is independent of adult age and yet mosquito senescence is known to affect mosquito mortality, fecundity and other key biological traits. Despite this, little is known about the effects of adult age at the level of the mosquito population, especially under varying temperature scenarios. We develop a stage-structured delayed differential equations (DDEs) model incorporating the effects of the abiotic environment and adult age to shed light on the complex interactions between age, temperature, and mosquito population dynamics. Taking Culex pipiens, a major vector of West Nile Virus, as our study species our results show that failing to consider mosquito senescence can lead to underestimates of future mosquito abundances predicted under climate change scenarios. We also find that the age-dependent mechanisms combined with the effects of density-dependent mortality on the immature stages can result in mosquito abundances decreasing at extreme temperatures. With our work, we underscore the need for more studies to consider the effects of mosquito age. Not accounting for senescence can compromise the accuracy of abundance estimates and has implications for predicting the risk of future MBD outbreaks.</p>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":" ","pages":"112084"},"PeriodicalIF":1.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143544483","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":"Kir4.1 channel and voltage-gated calcium channel of astrocyte account for the transition dynamics of seizures","authors":"Yu Rui ,&nbsp;Shu Liu ,&nbsp;Suyu Liu","doi":"10.1016/j.jtbi.2025.112082","DOIUrl":"10.1016/j.jtbi.2025.112082","url":null,"abstract":"<div><div>Astrocytes have an important role in the indirect regulation of neuronal excitability. The abnormalities of their ion channels cause neurons to discharge abnormally, which may induce seizures. The inwardly rectifying potassium channel 4.1 (Kir4.1 channel) and the voltage-gated calcium channel (VGCC) of an astrocyte play important roles in maintaining the homeostasis of these potassium and calcium ions, and have been found to be associated with seizures. However, the underlying mechanisms by which they induce seizures remain unclear. This paper established a neuron-astrocyte network model, which is a model consisting of a neuron and an astrocyte, to explore some mechanisms of epileptic seizures. Through a series of simulations based on this model, the results showed that low conductance of Kir4.1 channel can induce spontaneous periodic epileptic activity (SPEA) whereas higher conductance results in spontaneous periodic bursting event (SPBE) and high-frequency tonic discharges (HFTD). The abnormalities of VGCC also lead to the generation of SPEA and SPBE. As the changes of potassium concentration in the largest nearby reservoir which is analogous to a bath solution that contains a specific concentration of potassium, SPEA can undergo a process from appearance to disappearance. Thus, the research findings showed that the transitions of seizure-like discharges provide further theoretical analyses to clarify the complex mechanism of seizures.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"604 ","pages":"Article 112082"},"PeriodicalIF":1.9,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143538054","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":"Understanding the regulation of chronic wounds by tissue inhibitors of matrix metalloproteinases through mathematical modelling","authors":"Sonia Dari,&nbsp;Reuben D. O’dea,&nbsp;Nabil T. Fadai","doi":"10.1016/j.jtbi.2025.112083","DOIUrl":"10.1016/j.jtbi.2025.112083","url":null,"abstract":"<div><div>Understanding the biochemistry and pharmacodynamics of chronic wounds is of key importance, due to the millions of people in the UK affected and the significant cost to the NHS. Chronic wounds are characterised by elevated concentrations of matrix metalloproteinases (MMPs) that destroy the surrounding extracellular matrix (ECM). However, fibroblasts can produce tissue inhibitors of MMPs (TIMPs) in order to regulate wound healing. Therefore, the role of TIMPs in both acute and chronic wounds needs to be properly understood in order to develop therapeutic treatments. In this work, we propose a reaction-diffusion system of four partial differential equations that describe the interaction of the ECM, fibroblasts, MMPs, and TIMPs in a wound. We observe that, subject to parameter sets corresponding to both acute and chronic wound healing, this mathematical model gives rise to travelling wave solutions. Using bifurcation analysis, we demonstrate that excessive degradation of the ECM results in the emergence of chronic wounds, and the reversal of these chronic wounds is prohibited for lower TIMP production values. These results are replicated within a simplified model obtained via a parameter sensitivity analysis. This model is further extended to more realistic spatial domains where we demonstrate the effectiveness of a therapeutic hydrogel containing TIMPs as a treatment for chronic wounds.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"604 ","pages":"Article 112083"},"PeriodicalIF":1.9,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143532215","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":"Co-evolution of pathogen–host interactions with vertical transmission can produce bistable outcomes","authors":"Samantha Brotman,&nbsp;Geoff Wild","doi":"10.1016/j.jtbi.2025.112073","DOIUrl":"10.1016/j.jtbi.2025.112073","url":null,"abstract":"<div><div>Vertical transmission is widely predicted to select for reduced virulence of pathogens. Recent theory cast doubt on this prediction by showing that the evolutionary response of the host to vertical transmission can lead to severe disease outcomes. That theory, however, takes a simplified view of host population dynamics by assuming pathogen-induced mortality alone inhibits host population growth. The assumption limits our ability to uncover benign co-evolutionary outcomes characterized by low levels of pathogen-induced mortality. Here, we revisit the role of vertical transmission using a model that assumes host population growth is self-regulated. Our model tracks the co-evolution of pathogen-induced mortality and host recovery until both have reached an evolutionarily stable level. For any given set of model conditions, we could identify as many as two distinct pairs of stable mortality-recovery traits. Mortality and recovery were higher for one of the pairs (the ‘escalated’ one) and lower for the other of the pairs (the ‘de-escalated’ one). As the rate of vertical transmission rose, stable expression of the pathogen-induced mortality trait always decreased, while stable expression of the host-recovery trait increased for ‘escalated’ pairs and decreased for ‘de-escalated’ ones. In addition, (i) increasing the intrinsic rate of host population growth, (ii) increasing the cost of host recovery, and (iii) decreasing the efficiency of horizontal disease transmission all led to lower levels of stable trait expression for both pathogen and host. Factors (i)-(iii) also led to lower virulence, more frequent occurrence of the de-escalated (almost commensal) stable outcome, and greater disease prevalence. We conclude that (i)-(iii) promote the co-evolution of more benign interactions in keeping with previous findings. However, our new insight is that the benign nature of the host-pathogen interaction can now be understood as the more frequent occurrence of the de-escalated outcome. We discuss our findings in light of previous theory and experimental work.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"604 ","pages":"Article 112073"},"PeriodicalIF":1.9,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143509841","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":"PD-based ADRC using time-varying gains: An application to microalgal-based bioprocess","authors":"Viyils Sangregorio-Soto ,&nbsp;Edgar Yesid Mayorga Lancheros ,&nbsp;Gianfranco Mazzanti ,&nbsp;Claudia L. Garzón-Castro","doi":"10.1016/j.jtbi.2025.112074","DOIUrl":"10.1016/j.jtbi.2025.112074","url":null,"abstract":"<div><div>Microalgae cultivation has gained significant attention in recent years due to its potential applications in various fields. However, achieving high productivity in these bioprocesses requires efficient process control. The dynamics of growth models typically comprise both known and unknown components due to mismatches between the nonlinear dynamics and their mathematical representations. Additionally, microalgal culture is subject to external disturbances. To address these issues, a classical proportional-derivative (PD) providing the feedback error, assisted by a time-varying gain extended state observer (ESO), maintaining the structure of an Active Disturbance Rejection Control (ADRC), was implemented. The formulation is aided by a time-varying gain extended state observer to avoid high-peaking estimation values. The optimal operating conditions were identified using the GEKKO Python package. The proposed controller was applied to the growth model of the microalga <em>Isochrysis galbana</em>, and numerical results demonstrated the effectiveness of the control strategy in eliminating steady-state error and ensuring asymptotic convergence to the optimal equilibrium despite unknown disturbances. A detailed analysis of the photobioreactor model, including stability under steady-state conditions, was also conducted. The results indicated that the model exhibits one, two, or no stable steady-state solutions when the dilution rate (<span><math><mrow><mi>D</mi><mo>(</mo><mi>t</mi><mo>)</mo></mrow></math></span>) is manipulated.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"604 ","pages":"Article 112074"},"PeriodicalIF":1.9,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143517586","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":"Cell position-based evaluation of mechanical features of cells in multicellular systems","authors":"Hiroshi Koyama ,&nbsp;Atsushi M. Ito ,&nbsp;Hisashi Okumura ,&nbsp;Tetsuhisa Otani ,&nbsp;Kazuyuki Nakamura ,&nbsp;Toshihiko Fujimori","doi":"10.1016/j.jtbi.2025.112070","DOIUrl":"10.1016/j.jtbi.2025.112070","url":null,"abstract":"<div><div>Measurement of mechanical forces of cell–cell interactions is important for studying the emergence of diverse three-dimensional morphologies of multicellular organisms. We previously reported an image-based statistical method for inferring effective pairwise forces of cell–cell interactions (i.e., attractive/repulsive forces), where a cell particle model was fitted to cell tracking data acquired by live imaging. However, because the particle model is a coarse-grained model, it remains unclear how the pairwise forces relates to sub-cellular mechanical components including cell–cell adhesive forces. Here we applied our inference method to cell tracking data generated by vertex models that assumed sub-cellular components. Through this approach, we investigated the relationship between the effective pairwise forces and various sub-cellular components: cell–cell adhesion forces, cell surface tensions, cell–extracellular matrix (ECM) adhesion, traction forces between cells and ECM, cell growth, etc. We found that the cell–cell adhesion forces were attractive, and both the cell surface tensions and cell–ECM adhesive forces were repulsive, etc. These results indicate that sub-cellular mechanical components can contribute to the effective attractive/repulsive forces of cell–cell interactions. This comprehensive analysis provides theoretical bases for linking the pairwise forces to the sub-cellular mechanical components: this showcase is useful for speculating the sub-cellular mechanical components from the information of cell positions, and for interpreting simulation results based on particle models.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"604 ","pages":"Article 112070"},"PeriodicalIF":1.9,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143453560","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}