Biosystems最新文献

{"title":"Light-induced ATP production and proton translocation, two independent phenomena in Halobacterium salinarum archaea cells","authors":"Gabi Drochioiu","doi":"10.1016/j.biosystems.2025.105633","DOIUrl":"10.1016/j.biosystems.2025.105633","url":null,"abstract":"<div><div>Bacteriorhodopsin (BR) is involved in the process of light-induced release of ATP molecules from F₁F₀-ATP synthase in the simplest bacterial cells. We have identified the M₄₁₂ intermediate of BR to be a key for understanding the phenomena related to ATP production in <em>Halobacterium salinarum</em> cells. In addition, the release of protons and, consequently, the increase in BR acidity upon illumination can be explained by its fluorescence, and the Förster cycle allows the calculation of pKa changes. The light-induced excitation of electrons in unprotonated M₄₁₂ intermediate can serve as an energy source and not protons. To reinforce our conclusions, we reexamined data from recent literature as well as older findings.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105633"},"PeriodicalIF":1.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145418437","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prevalence of prime mass residues in single point mutations and their importance to protein stability, function and evolution","authors":"Matthew Wright,&nbsp;Kevin M. Downard","doi":"10.1016/j.biosystems.2025.105638","DOIUrl":"10.1016/j.biosystems.2025.105638","url":null,"abstract":"<div><div>Prime mass amino acids residues, assigned based upon the nominal mass of their repeating structure in peptides and proteins, provide a more rigid physicochemical definition not achieved with other more common classifiers. Found to occur more often than by chance, the nine prime residues are predominantly hydrophobic in character that play an important role in protein stability and folding. A global study of the prevalence of particular single point mutations across several hundred proteins has revealed that mutations which retain a prime mass residue are favoured over those that lose them. Further, the mutation of a non-prime to prime residue is favoured over the retention of a non-prime residue. The introduction of the prime alanine residue, in particular, is found to occur in over 50 % of cases when a prime or non-prime residue mutates, based on data extracted across almost 16,000 mutations for within a wide range of proteins. Mutation to the prime residues isoleucine (I) and leucine (L), threonine (T) and proline (P) are also found to predominate. This is evident across the many hundreds of database entries and within a single transmembrane protein previously identified to be among the richest-prime residue protein known. Consideration is given to the impact of these observations on protein stability and the advantages they confer to protein evolution. It is shown that the majority of prime residues are recruited early in the development of the genetic code. Last common universal ancestral (LUCA) proteins are enriched in smaller molecular weight, hydrophobic prime amino acids rather than larger aliphatic non-prime ones.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105638"},"PeriodicalIF":1.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145427163","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cooperation in structured populations via coupled reputation and learning: A spatial evolutionary game approach","authors":"Shouwei Li ,&nbsp;Bo Peng ,&nbsp;Baochen Li ,&nbsp;Yan Shi","doi":"10.1016/j.biosystems.2025.105630","DOIUrl":"10.1016/j.biosystems.2025.105630","url":null,"abstract":"<div><div>This study presents an agent-based model to investigate cooperation dynamics in spatial evolutionary games by integrating memory-based reputation tracking with heterogeneous adaptive learning. Agents interact on a lattice network and update their strategies based on both neighbors’ historical cooperation rates and payoff differences, governed by a modified Fermi rule with individual sensitivity parameters. Simulation results demonstrate that this dual-layered mechanism sustains cooperation even under strong defection incentives and limited interaction ranges. The model also reveals how memory length and learning heterogeneity jointly influence spatial cooperation patterns and strategy diversity. These findings offer new insights into decentralized mechanisms that promote cooperation in structured populations, with implications for evolutionary biology, distributed systems, and behavioral economics.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105630"},"PeriodicalIF":1.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145365332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Maladaptation diseases as disorders of intraorganismal individuation","authors":"Thomas Lissek","doi":"10.1016/j.biosystems.2025.105621","DOIUrl":"10.1016/j.biosystems.2025.105621","url":null,"abstract":"<div><div>The present work introduces the hypothesis that various human maladaptation diseases including addiction, cancer, autoimmunity, fibrosis, depression, chronic pain and post-traumatic stress disorder share a universal functional pattern in that they are caused by defects in goal state integration of physiological subsystems into whole-organism goal states and by the resulting emergence of new levels of individuality within the organism. In this framework, a general mechanism in ontogenetic maladaptation is the intraorganismal individuation of subsystems via physiological adaptation mechanisms, which results in these systems becoming uncoupled from the rest of the organism and developing disproportional autonomy at the cost of whole organism health. A central mechanism for mediating continued dysfunction in these disorders is the formation and maintenance of maladaptive memories. A potential universal therapeutic principle for maladaptation disorders is to provide physiological integration pressure to force subsystems to integrate back into the functional organization of the whole organism.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105621"},"PeriodicalIF":1.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145281628","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Homeostatic set-points are physical and foundational to organism autonomy","authors":"Keith D. Farnsworth","doi":"10.1016/j.biosystems.2025.105634","DOIUrl":"10.1016/j.biosystems.2025.105634","url":null,"abstract":"<div><div>Living systems pose the problem of how a physical system not only maintains itself in a ‘far from equilibrium’ state, but how it determines what state that should be and how it could take the initiative over setting the state, in an act of autonomy that confounds standard physical description. Here I show that the homeostatic set-point is physical information embodied in the structure of evolved enzymes, acting through a series of code and cypher transformations from gene translation, through single molecule dynamics, reaction kinetics, to control system topology and finally physical control. In ‘kinetic regulation’, network topology is determined by the parameters of reaction kinetics and jointly with them, specifies the set-point. Control is added via allosteric manipulation of enzymes based on evolved, not physically inevitable, relationships with effector molecules. This way, enzyme properties alone can determine the set-point. Thus the allosteric enzyme is to homeostasis what the adaptor molecule is to biological code. All the parameters of biochemical regulation result from the way protein structure determines binding affinity and dissociation rates via the shape of electrical forcefields, especially around active sites and effector pockets. In general, the set-point is a highly evolved phenotype having a complicated, but logically inevitable dependence on genotype. By embodying particularising information (the set-point) and using it to do organisational work (homeostasis), even the simplest living system enacts cybernetic independence, characterised by goal-directed behavior, not found in natural abiotic systems.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105634"},"PeriodicalIF":1.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145418438","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A hybrid phase-synchronization framework for rotary motors: Discrete dynamics in ATP synthase and continuous dynamics in the bacterial flagellar motor","authors":"Carey Witkov","doi":"10.1016/j.biosystems.2025.105617","DOIUrl":"10.1016/j.biosystems.2025.105617","url":null,"abstract":"<div><div>ATP synthase functions as a dual-rotor molecular motor, with the F<span><math><msub><mrow></mrow><mrow><mn>0</mn></mrow></msub></math></span> and F<span><math><msub><mrow></mrow><mrow><mn>1</mn></mrow></msub></math></span> units stepping in mismatched increments, yet achieving near 100% chemomechanical efficiency of the F<span><math><msub><mrow></mrow><mrow><mn>1</mn></mrow></msub></math></span> motor under near-reversible conditions. This raises the question of how stable phase synchronization is maintained despite such symmetry mismatch. We address this problem by modeling ATP synthase as a driven oscillator system in which the central elastic stalk acts as a torsional filter, transmitting and modulating torque. We propose a hybrid synchronization model that integrates continuous and discrete dynamics, governed by a torsional energy-dependent mixing parameter that determines interpolation between limits. The resulting single hybrid phase synchronization equation captures both gradual continuous phase drift and discrete pulsed entrainment. This framework reproduces key experimental features, including stable synchronization, intermittent slip events in ATP synthase, and recovery dynamics under varying loads, and offers testable predictions. In the discrete limit, the model specializes to a van Slooten-type pulse map that accords with the well-established 120° stepping of F<span><math><msub><mrow></mrow><mrow><mn>1</mn></mrow></msub></math></span>-ATPase; in the continuous limit, it reduces to an Adler-type equation appropriate for the near-constant-torque behavior of the bacterial flagellar motor. This framing unifies two historically separate descriptions without requiring a literal mode change within a single molecule and clarifies how elastic energy can interpolate between limits via the mixing parameter <span><math><mrow><mi>σ</mi><mrow><mo>(</mo><mi>E</mi><mo>)</mo></mrow></mrow></math></span>. The hybrid model proposes that ATP synthase and the bacterial flagellar motor exploit elastic filtering and energy-regulated regime interpolation between limits to achieve robust rotational coordination, providing new insights into the dynamics of biological rotary motors.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105617"},"PeriodicalIF":1.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145287714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Scale-invariant dissipation underlies enzyme catalytic performance","authors":"Davor Juretić ,&nbsp;Branka Bruvo Mađarić","doi":"10.1016/j.biosystems.2025.105568","DOIUrl":"10.1016/j.biosystems.2025.105568","url":null,"abstract":"<div><div>The role of energy dissipation in the evolution of living systems remains a subject of ongoing debate. Here, we quantify the dissipation associated with enzyme catalysis using minimalistic models of enzyme kinetics and a complete set of microscopic rate constants. We identify a power-law proportionality between total dissipated energy and key kinetic parameters— specifically, the catalytic constant and the specificity constant. These scale-invariant relationships hold across enzyme classes, biological domains, and natural or engineered enzymes. Consistent with Jensen's hypothesis, specialized enzymes display greater catalytic efficiency and higher dissipation. Yet, the wide range of observed efficiencies and dissipation values suggests that scale-independent organizational principles govern enzyme catalysis. Our findings indicate that biological evolution has not merely tolerated dissipation but has actively harnessed and regulated it within constraints imposed by functional and environmental demands. The scale-invariant perspective provides a unifying view of physical (dissipative) and biological (adaptive) evolutionary processes in the emergence of enzymatic function.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105568"},"PeriodicalIF":1.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144977437","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Timing inaccessibility and the projection bound: Resolving Maxwell’s demon for continuous biological substrates","authors":"Ian Todd","doi":"10.1016/j.biosystems.2025.105632","DOIUrl":"10.1016/j.biosystems.2025.105632","url":null,"abstract":"&lt;div&gt;&lt;div&gt;We show that the thermodynamic advantage of biological, continuous substrates over digital simulators arises from &lt;em&gt;timing inaccessibility&lt;/em&gt;: below the Landauer threshold, temporal order cannot be irreversibly registered without dissipating &lt;span&gt;&lt;math&gt;&lt;mrow&gt;&lt;mo&gt;≥&lt;/mo&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;k&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;B&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;mi&gt;T&lt;/mi&gt;&lt;mo&gt;ln&lt;/mo&gt;&lt;mn&gt;2&lt;/mn&gt;&lt;/mrow&gt;&lt;/math&gt;&lt;/span&gt; per binary decision. Consequently, exponentially many micro-trajectories map to the same observable outcome (&lt;em&gt;path degeneracy&lt;/em&gt;). Continuous high-dimensional substrates exploit this by integrating sub-Landauer couplings during evolution and paying only at &lt;em&gt;projection&lt;/em&gt; (dimensional collapse to a low-dimensional output).&lt;/div&gt;&lt;div&gt;We derive a &lt;strong&gt;Projection Bound&lt;/strong&gt; for quasistatic projection at effective temperature &lt;span&gt;&lt;math&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;T&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;eff&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;/math&gt;&lt;/span&gt;: &lt;span&gt;&lt;span&gt;&lt;span&gt;(0.1)&lt;/span&gt;&lt;span&gt;&lt;math&gt;&lt;mrow&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;E&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;collapse&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;mo&gt;≥&lt;/mo&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;k&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;B&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;T&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;eff&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;mfenced&gt;&lt;mrow&gt;&lt;mo&gt;ln&lt;/mo&gt;&lt;mfrac&gt;&lt;mrow&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;N&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;ɛ&lt;/mi&gt;&lt;mo&gt;,&lt;/mo&gt;&lt;mi&gt;pre&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;N&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;ɛ&lt;/mi&gt;&lt;mo&gt;,&lt;/mo&gt;&lt;mi&gt;post&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;/mrow&gt;&lt;/mfrac&gt;&lt;mo&gt;−&lt;/mo&gt;&lt;mi&gt;KL&lt;/mi&gt;&lt;mspace&gt;&lt;/mspace&gt;&lt;mfenced&gt;&lt;mrow&gt;&lt;msup&gt;&lt;mrow&gt;&lt;mi&gt;p&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;pre&lt;/mi&gt;&lt;/mrow&gt;&lt;/msup&gt;&lt;mspace&gt;&lt;/mspace&gt;&lt;mo&gt;∥&lt;/mo&gt;&lt;mspace&gt;&lt;/mspace&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;U&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;pre&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;/mrow&gt;&lt;/mfenced&gt;&lt;mo&gt;+&lt;/mo&gt;&lt;mi&gt;KL&lt;/mi&gt;&lt;mspace&gt;&lt;/mspace&gt;&lt;mfenced&gt;&lt;mrow&gt;&lt;msup&gt;&lt;mrow&gt;&lt;mi&gt;p&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;post&lt;/mi&gt;&lt;/mrow&gt;&lt;/msup&gt;&lt;mspace&gt;&lt;/mspace&gt;&lt;mo&gt;∥&lt;/mo&gt;&lt;mspace&gt;&lt;/mspace&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;U&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;post&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;/mrow&gt;&lt;/mfenced&gt;&lt;/mrow&gt;&lt;/mfenced&gt;&lt;/mrow&gt;&lt;/math&gt;&lt;/span&gt;&lt;/span&gt;&lt;/span&gt;which reduces under typical-set conditions to &lt;span&gt;&lt;math&gt;&lt;mrow&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;E&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;collapse&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;mo&gt;≥&lt;/mo&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;k&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;B&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;T&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;eff&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;mo&gt;ln&lt;/mo&gt;&lt;mrow&gt;&lt;mo&gt;(&lt;/mo&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;N&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;ɛ&lt;/mi&gt;&lt;mo&gt;,&lt;/mo&gt;&lt;mi&gt;pre&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;mo&gt;/&lt;/mo&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;N&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;ɛ&lt;/mi&gt;&lt;mo&gt;,&lt;/mo&gt;&lt;mi&gt;post&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;mo&gt;)&lt;/mo&gt;&lt;/mrow&gt;&lt;/mrow&gt;&lt;/math&gt;&lt;/span&gt;. Combined with a &lt;strong&gt;Temporal Registration Bound&lt;/strong&gt; (order over &lt;span&gt;&lt;math&gt;&lt;mi&gt;M&lt;/mi&gt;&lt;/math&gt;&lt;/span&gt; bins needs &lt;span&gt;&lt;math&gt;&lt;mrow&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mo&gt;log&lt;/mo&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mn&gt;2&lt;/mn&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;mi&gt;M&lt;/mi&gt;&lt;mo&gt;!&lt;/mo&gt;&lt;/mrow&gt;&lt;/math&gt;&lt;/span&gt; bits), we quantify the gap: enumerative digital tracking scales exponentially with dimension, whereas projection cost scales like &lt;span&gt;&lt;math&gt;&lt;mrow&gt;&lt;mo&gt;ln&lt;/mo&gt;&lt;mi&gt;G&lt;/mi&gt;&lt;mo&gt;∼&lt;/mo&gt;&lt;mi&gt;D&lt;/mi&gt;&lt;/mrow&gt;&lt;/math&gt;&lt;/span&gt;.&lt;/div&gt;&lt;div&gt;For biologically plausible parameters, we estimate degeneracies of &lt;span&gt;&lt;math&gt;&lt;mrow&gt;&lt;mn&gt;1&lt;/mn&gt;&lt;msup&gt;&lt;mrow&gt;&lt;m","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105632"},"PeriodicalIF":1.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145446570","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Antagonistic coinfection in rock–paper–scissors models during concurrent epidemics","authors":"J. Menezes ,&nbsp;R. Menezes ,&nbsp;S. Batista ,&nbsp;E. Rangel","doi":"10.1016/j.biosystems.2025.105616","DOIUrl":"10.1016/j.biosystems.2025.105616","url":null,"abstract":"<div><div>We investigate the dynamics of dual disease epidemics within the spatial rock–paper–scissors model. In this framework, individuals from all species are equally susceptible to infection by two distinct pathogens transmitted via person-to-person contact. We assume antagonistic mortality, where the simultaneous occurrence of coinfection reduces the probability of host mortality due to complications arising from either coexisting disease. Specifically, we explore two scenarios: global antagonism, where the presence of one pathogen inhibits the progression of the other in coinfected hosts, and uneven antagonism, where only one pathogen affects the development of the other. Using stochastic simulations, we show that the characteristic length scale of the spatial patterns emerging from random initial conditions diminishes as antagonism becomes more significant. We find that antagonism enhances species population growth and reduces the average probability of healthy organisms becoming infected. Additionally, introducing individuals’ mobility restrictions significantly decreases both organisms’ infection risk and selection pressures. Our results demonstrate that combining mobility restrictions with antagonistic coinfection can increase organisms’ life expectancy by up to 54%. Our findings show that integrating antagonistic coinfection and mobility restriction strategies into ecological models may provide insights into designing interventions for managing concurrent epidemics in complex systems.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105616"},"PeriodicalIF":1.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145278062","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SBDyNetVis: a visualization tool of dynamic network for systems biology model","authors":"Kentaro Inoue","doi":"10.1016/j.biosystems.2025.105644","DOIUrl":"10.1016/j.biosystems.2025.105644","url":null,"abstract":"<div><div>Understanding complex molecular interactions in biological systems requires both precise simulation and effective visualization of dynamic processes. Traditional tools have often presented static network diagrams and segregated simulation results, making it challenging to concurrently interpret network structure and temporal dynamics. In this study, we introduce SBDyNetVis, a novel Python-based library that transforms network and time-course data into interactive JavaScript visualizations using Cytoscape.js. SBDyNetVis integrates multiple network layout algorithms with animated representations of nodes and edges, allowing users to intuitively explore reaction kinetics, flux equations, and dynamic changes all on a single platform. We demonstrate the utility of SBDyNetVis by successfully converting 913 models from BioModels and by applying the tool in a detailed case study of the IKK-NFκB-IκB reaction. Its web-based interface promotes seamless data sharing and collaboration among researchers with varying levels of technical expertise. By bridging the gap between static network representation and dynamic simulation visualization, SBDyNetVis paves the way for deeper insights into cellular processes and holds significant potential for advancing systems biology research. SBDyNetVis is available at <span><span>https://github.com/kntrinoue/SBDyNetVis</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105644"},"PeriodicalIF":1.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145472211","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}