Journal of Theoretical Biology最新文献

{"title":"On the misuse of evolutionary theory to bolster the ‘scientific’ case for intelligent design: A cautionary note","authors":"Arne Traulsen , Mikkel Nif Rasmussen , Joachim Krug , Andreas Beyer","doi":"10.1016/j.jtbi.2024.111985","DOIUrl":"10.1016/j.jtbi.2024.111985","url":null,"abstract":"","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"596 ","pages":"Article 111985"},"PeriodicalIF":1.9,"publicationDate":"2024-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142632804","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":"Statistical inference and neural network training based on stochastic difference model for air pollution and associated disease transmission","authors":"Sha He,&nbsp;Mengqi He,&nbsp;Sanyi Tang","doi":"10.1016/j.jtbi.2024.111987","DOIUrl":"10.1016/j.jtbi.2024.111987","url":null,"abstract":"<div><div>A polluted air environment can potentially provoke infections of diverse respiratory diseases. The development of mathematical models can study the mechanism of air pollution and its effect on the spread of diseases. The key is to characterize the intrinsic correlation between the disease infection and the change in air pollutant concentration. In this paper, we establish a coupled discrete susceptible–exposed–infectious–susceptible (SEIS) model with demography to characterize the transmission of disease, and the change in the concentration of air pollutants is described in the form of the Beverton–Holt (BH) model with a time-varying inflow rate of air pollutants. Considering the periodic variation characteristics of data, time-varying parameters are defined as specific functional forms. We estimate the change point at which the parameters switch and the parameter values within the switching interval based on Bayesian statistical theory. The data fitting of the model can reflect the seasonal peaks and annual growth trends of values of air quality index (AQI) and the number of influenza-like illnesses (ILI) cases. However, the bias in data fitting indicates a more complex correlation pattern between disease and pollutant concentration changes. To explore unknown mechanisms, we propose the extended transmission-dynamics-informed neural network (TDINN) algorithm by combining deep learning with difference equations and obtain the curves of the transmission rate and inflow rate functions over time. The results show that neural network models can help us determine time-varying parameters in the model, thereby better reflecting the trend of data changes.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"596 ","pages":"Article 111987"},"PeriodicalIF":1.9,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142632841","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":"Optimal seasonal schedule for producing biogenic volatile organic compounds for tree defense","authors":"Yoh Iwasa,&nbsp;Rena Hayashi,&nbsp;Akiko Satake","doi":"10.1016/j.jtbi.2024.111986","DOIUrl":"10.1016/j.jtbi.2024.111986","url":null,"abstract":"<div><div>The leaves of many trees emit biogenic volatile organic compounds (BVOCs) that protect them from various threats, including herbivory, pathogens, and heat stress. In a previous study, we analyzed the optimal seasonal schedule for producing isoprene, a highly volatile BVOC, in leaves to mitigate heat damage and maximize net carbon gain. In this paper, we investigate the seasonal production schedule of BVOCs stored in leaves, such as monoterpenes and sesquiterpenes, which decay slowly. When the leaves are bitten, these chemicals are emitted and help to prevent further herbivory. The optimal seasonal schedule, analyzed using Pontryagin’s maximum principle, includes a period of singular control. Producing BVOCs for defense is advantageous if their decay rate is slow and the photosynthetic rate is fast. The amount of BVOCs produced increases with slower decay rate and faster photosynthetic rate. But it does not increase monotonically with the magnitude of the threat. BVOCs are produced earlier than the peak period of the threat for which the chemicals are intended. Based on the results of the model, we discuss the reported variations in BVOC production among different chemical species and tree species, as well as the seasonal patterns of gene expression in different pathways for BVOC production.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"596 ","pages":"Article 111986"},"PeriodicalIF":1.9,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142632806","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":"Implementation of actin polymerization and depolymerization in a two-dimensional cell migration model and its implications on mammalian cell morphology and velocity","authors":"Lingxing Yao ,&nbsp;Yizeng Li","doi":"10.1016/j.jtbi.2024.111977","DOIUrl":"10.1016/j.jtbi.2024.111977","url":null,"abstract":"<div><div>Cell migration, a pivotal process in wound healing, immune response, and even cancer metastasis, manifests through intricate interplay between morphology, speed, and cytoskeletal dynamics. Mathematical modeling emerges as a powerful tool to dissect these complex interactions. This work presents a two-dimensional immersed boundary model for mammalian cell migration, incorporating both filamentous actin (F-actin) and monomeric actin (G-actin) to explicitly capture polymerization and depolymerization. This model builds upon our previous one-dimensional efforts, now enabling us to explore the impact of G-actin on not just cell velocity but also morphology. We compare predictions from both models, revealing that while the one-dimensional model captures core dynamics along the cell’s axis, the two-dimensional model excels in portraying cell shape evolution and transverse variations in actin concentration and velocity. Our findings highlight the crucial role of including G-actin in shaping cell morphology. Actin velocity aligned with migration direction elongates the cell, while velocity normal to the membrane promotes spreading. Importantly, the model establishes a link between these microscopic aspects and macroscopic observables like cell shape, offering a deeper understanding of cell migration dynamics. This work not only provides a more comprehensive picture of cell migration but also paves the way for future studies exploring the interplay of actin dynamics, cell morphology, and biophysical parameters in diverse biological contexts.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"596 ","pages":"Article 111977"},"PeriodicalIF":1.9,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142606479","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":"Event-based biological pest control: An LMI approach","authors":"M. Sathishkumar ,&nbsp;Maya Joby ,&nbsp;Srimanta Santra ,&nbsp;Yong-Ki Ma ,&nbsp;S. Marshal Anthoni","doi":"10.1016/j.jtbi.2024.111975","DOIUrl":"10.1016/j.jtbi.2024.111975","url":null,"abstract":"<div><div>This study focuses on the event-triggered control approach for the mathematical model describing the interaction between the sugarcane borer <em>(Diatraea saccharalis)</em> and its egg parasitoid <em>Trichogramma galloi</em>, as well as the combined interaction of <em>Trichogramma galloi</em> and <em>Cotesia flavipes.</em> By employing digital control design, an effective strategy can be devised to minimize the population of natural enemies. Therefore, proposing an event-triggered control mechanism for the sugarcane borer is essential. The primary objective of this study is to develop an event-triggered reliable state feedback controller, ensuring that the states of the sugarcane borer system converge to the desired steady-state equilibrium points. Additionally, this control design significantly reduces control updates and maintains the introduction of natural enemies into the environment. Ultimately, simulations are carried out using sugarcane borer systems to demonstrate the benefits and effectiveness of the proposed event-triggered design technique.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"596 ","pages":"Article 111975"},"PeriodicalIF":1.9,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142553398","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":"A continuous approach of modeling tumorigenesis and axons regulation for the pancreatic cancer","authors":"Marie-Jose Chaaya ,&nbsp;Sophie Chauvet ,&nbsp;Florence Hubert ,&nbsp;Fanny Mann ,&nbsp;Mathieu Mezache ,&nbsp;Pierre Pudlo","doi":"10.1016/j.jtbi.2024.111967","DOIUrl":"10.1016/j.jtbi.2024.111967","url":null,"abstract":"<div><div>The pancreatic innervation undergoes dynamic remodeling during the development of pancreatic ductal adenocarcinoma (PDAC). Denervation experiments have shown that different types of axons can exert either pro- or anti-tumor effects, but conflicting results exist in the literature, leaving the overall influence of the nervous system on PDAC incompletely understood. To address this gap, we propose a continuous mathematical model of nerve-tumor interactions that allows in silico simulation of denervation at different phases of tumor development. This model takes into account the pro- or anti-tumor properties of different types of axons (sympathetic or sensory) and their distinct remodeling dynamics during PDAC development. We observe a “shift effect” where an initial pro-tumor effect of sympathetic axon denervation is later outweighed by the anti-tumor effect of sensory axon denervation, leading to a transition from an overall protective to a deleterious role of the nervous system on PDAC tumorigenesis. Our model also highlights the importance of the impact of sympathetic axon remodeling dynamics on tumor progression. These findings may guide strategies targeting the nervous system to improve PDAC treatment.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111967"},"PeriodicalIF":1.9,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142513166","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":"Pulmonary epithelial wound healing and the immune system. Mathematical modeling and bifurcation analysis of a bistable system","authors":"Clara R. Lotter,&nbsp;Jonathan A. Sherratt","doi":"10.1016/j.jtbi.2024.111968","DOIUrl":"10.1016/j.jtbi.2024.111968","url":null,"abstract":"<div><div>Respiratory diseases such as asthma, acute respiratory distress syndrome (ARDS), influenza or COVID-19 often directly target the epithelium. Elevated immune levels and a ‘cytokine storm’ are directly associated with defective healing dynamics of lung diseases such as COVID-19 or ARDS. The infected cells leave wounded regions in the epithelium which must be healed for the lung to return to a healthy state and carry out its main function of gas-exchange. Due to the complexity of the various interactions between cells of the lung epithelium and surrounding tissue, it is necessary to develop models that can complement experiments to fully understand the healing dynamics. In this mathematical study we model the mechanism of epithelial regeneration. We assume that healing is exclusively driven by progenitor cell proliferation, induced by a chemical activator such as epithelial growth factor (EGF) and cytokines such as interleukin-22 (IL22). Contrary to previous studies of wound healing, we consider the immune system, specifically the T effector cells TH1, TH17, TH22 and Treg to strongly contribute to the healing process, by producing IL22 or regulating the immune response. We therefore obtain a coupled system of two ordinary differential equations for the epithelial and immune cell densities and two functions for the levels of chemicals that either induce epithelial proliferation or recruit immune cells. These functions link the two cell equations. We find that to allow the epithelium to regenerate to a healthy state, the immune system must not exceed a threshold value at the onset of the healing phase. This immune threshold is supported experimentally but was not explicitly built into our equations. Our assumptions are therefore sufficient to reproduce experimental results concerning the ratio TH17/Treg cells as a threshold to predict higher mortality rates in patients. This immune threshold can be controlled by parameters of the model, specifically the base-level growth factor concentration. This conclusion is based on a mathematical bifurcation analysis and linearization of the model equations. Our results suggest treatment of severe cases of lung injury by reducing or suppressing the immune response, in an individual patient, assessed by their disease parameters such as course of lung injury and immune response levels.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"596 ","pages":"Article 111968"},"PeriodicalIF":1.9,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142513168","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":"PULSAR Effect: Revealing potential synergies in combined radiation therapy and immunotherapy via differential equations","authors":"Samiha Rouf ,&nbsp;Casey Moore ,&nbsp;Debabrata Saha ,&nbsp;Dan Nguyen ,&nbsp;MaryLena Bleile ,&nbsp;Robert Timmerman ,&nbsp;Hao Peng ,&nbsp;Steve Jiang","doi":"10.1016/j.jtbi.2024.111974","DOIUrl":"10.1016/j.jtbi.2024.111974","url":null,"abstract":"<div><div>PULSAR (personalized ultrafractionated stereotactic adaptive radiotherapy) is a form of radiotherapy method where a patient is given a large dose or “pulse” of radiation a couple of weeks apart rather than daily small doses. The tumor response is then monitored to determine when the subsequent pulse should be given. Pre-clinical trials have shown better tumor response in mice that received immunotherapy along with pulses spaced 10 days apart. However, this was not the case when the pulses were 1 or 4 days apart. Therefore, a synergistic effect between immunotherapy and PULSAR is observed when the pulses are spaced out by a certain number of days. In our study, we aimed to develop a mathematical model that can capture the synergistic effect by considering a time-dependent weight function that takes into account the spacing between pulses. We determined feasible parameters by fitting murine tumor volume data of six treatment groups via simulated annealing algorithm. Applying these parameters to the model we simulated 4000 trials with varying sequencing of pulses. These simulations indicated that if pulses were spaced apart by at least 9 days the tumor volume was about 200 <span><math><mrow><mi>m</mi><msup><mrow><mi>m</mi></mrow><mn>3</mn></msup></mrow></math></span> to 250 <span><math><mrow><mi>m</mi><msup><mrow><mi>m</mi></mrow><mn>3</mn></msup></mrow></math></span> smaller when treated with PULSAR combined with immunotherapy. We successfully demonstrate that our model is simple to implement and can generate tumor volume data that is consistent with the pre-clinical trial data. Our model has the potential to aid in the development of clinical trials of PULSAR therapy.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"596 ","pages":"Article 111974"},"PeriodicalIF":1.9,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142513069","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":"A theoretical model for focal adhesion and cytoskeleton formation in non-motile cells","authors":"Gordon R. McNicol ,&nbsp;Matthew J. Dalby ,&nbsp;Peter S. Stewart","doi":"10.1016/j.jtbi.2024.111965","DOIUrl":"10.1016/j.jtbi.2024.111965","url":null,"abstract":"<div><div>To function and survive cells need to be able to sense and respond to their local environment through mechanotransduction. Crucially, mechanical and biochemical perturbations initiate cell signalling cascades, which can induce responses such as growth, apoptosis, proliferation and differentiation. At the heart of this process are actomyosin stress fibres (SFs), which form part of the cell cytoskeleton, and focal adhesions (FAs), which bind this cytoskeleton to the extra-cellular matrix (ECM). The formation and maturation of these structures (connected by a positive feedback loop) is pivotal in non-motile cells, where SFs are generally of ventral type, interconnecting FAs and producing isometric tension. In this study we formulate a one-dimensional bio-chemo-mechanical continuum model to describe the coupled formation and maturation of ventral SFs and FAs. We use a set of reaction–diffusion–advection equations to describe three sets of biochemical events: the polymerisation of actin and subsequent bundling into activated SFs; the formation and maturation of cell–substrate adhesions; and the activation of signalling proteins in response to FA and SF formation. The evolution of these key proteins is coupled to a Kelvin–Voigt viscoelastic description of the cell cytoplasm and the ECM. We employ this model to understand how cells respond to external and intracellular cues <em>in vitro</em> and are able to reproduce experimentally observed phenomena including non-uniform cell striation and cells forming weaker SFs and FAs on softer substrates.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"596 ","pages":"Article 111965"},"PeriodicalIF":1.9,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142513167","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":"Simulating irregular symmetry breaking in gut cross sections using a novel energy-optimization approach in growth-elasticity","authors":"Min Wu","doi":"10.1016/j.jtbi.2024.111971","DOIUrl":"10.1016/j.jtbi.2024.111971","url":null,"abstract":"<div><div>Growth-elasticity (also known as morphoelasticity) is a powerful model framework for understanding complex shape development in soft biological tissues. At each instant, by mapping how continuum building blocks have grown geometrically and how they respond elastically to the push-and-pull from their neighbors, the shape of the growing structure is determined from a state of mechanical equilibrium. As mechanical loads continue to be added to the system through growth, many interesting shapes, such as smooth wavy wrinkles, sharp creases, and deep folds, can form on the tissue surface from a relatively flatter geometry.</div><div>Previous numerical simulations of growth-elasticity have reproduced many interesting shapes resembling those observed in reality, such as the foldings on mammalian brains and guts. In the case of mammalian guts, it has been shown that wavy wrinkles, deep folds, and sharp creases on the interior organ surface can be simulated even under a simple assumption of isotropic uniform growth in the interior layer of the organ. Interestingly, the simulated patterns are all regular along the tube’s circumference, with either all smooth or all sharp indentations, whereas some undulation patterns in reality exhibit irregular patterns and a mixture of sharp creases and smooth indentations along the circumference. Can we simulate irregular indentation patterns without further complicating the growth patterning?</div><div>In this paper, we have discovered abundant shape solutions with irregular indentation patterns by developing a Rayleigh–Ritz finite-element method (FEM). In contrast to previous Galerkin FEMs, which solve the weak formulation of the mechanical-equilibrium equations, the new method formulates an optimization problem for the discretized energy functional, whose critical points are equivalent to solutions obtained by solving the mechanical-equilibrium equations. This new method is more robust than previous methods. Specifically, it does not require the initial guess to be near a solution to achieve convergence, and it allows control over the direction of numerical iterates across the energy landscape. This approach enables the capture of more solutions that cannot be easily reached by previous methods. In addition to the previously found regular smooth and non-smooth configurations, we have identified a new transitional irregular smooth shape, new shapes with a mixture of smooth and non-smooth surface indentations, and a variety of irregular patterns with different numbers of creases. Our numerical results demonstrate that growth-elasticity modeling can match more shape patterns observed in reality than previously thought.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111971"},"PeriodicalIF":1.9,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142513070","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}