Biosystems最新文献_第4页

Deciphering the dynamic binding of spicy odorants to human olfactory receptors 解读辛辣气味与人类嗅觉受体的动态结合。

IF 1.9 4区生物学

Biosystems Pub Date : 2026-02-01 Epub Date: 2026-01-07 DOI: 10.1016/j.biosystems.2026.105703

Jingtao Wang , Chenglei Zhang , Juncang Peng , Jian Wu , Shan Wang , Wu Fan , Qingzhao Shi , Qidong Zhang , Guobi Chai

{"title":"Deciphering the dynamic binding of spicy odorants to human olfactory receptors","authors":"Jingtao Wang , Chenglei Zhang , Juncang Peng , Jian Wu , Shan Wang , Wu Fan , Qingzhao Shi , Qidong Zhang , Guobi Chai","doi":"10.1016/j.biosystems.2026.105703","DOIUrl":"10.1016/j.biosystems.2026.105703","url":null,"abstract":"<div><div>In this study, we compiled three categories of odorants with spicy aromas: anise class, clove class, and cinnamon class. We aimed to use molecular dynamics simulation techniques to uncover potential regularities in the activation mechanisms of the same odorant across different olfactory receptors, or vice versa, the activation mechanisms of different odorants on the same olfactory receptor. Here, molecular dynamics simulation results reveal that anisaldehyde and estragole preferentially bind to TYR residues, thereby activating the corresponding olfactory receptors. Both eugenol and isoeugenol activate OR5D18 at similar binding sites, but ultimately lead to differential conformational changes in the olfactory receptor. Additionally, the binding conformations of eugenol and methyl eugenol are nearly identical, whereas cinnamaldehyde and cinnamyl alcohol, methyl cinnamaldehyde, exhibit distinct binding conformations with the olfactory receptor. These results underscore how subtle structural changes can impact the binding mechanism of odorants.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"260 ","pages":"Article 105703"},"PeriodicalIF":1.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145946488","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}

引用次数: 0

Quantum formalism for indeterminate preferences in decision theory 决策理论中不确定偏好的量子形式论。

IF 1.9 4区生物学

Biosystems Pub Date : 2026-01-01 Epub Date: 2025-11-20 DOI: 10.1016/j.biosystems.2025.105659

Hervé Zwirn

引用次数: 0

Least ranked human individuals exhibit scale free behavioral responses in hierarchical social systems 排名最低的人类个体在等级社会系统中表现出无尺度的行为反应。

IF 1.9 4区生物学

Biosystems Pub Date : 2026-01-01 Epub Date: 2025-12-08 DOI: 10.1016/j.biosystems.2025.105678

Chetan K. Yadav

{"title":"Least ranked human individuals exhibit scale free behavioral responses in hierarchical social systems","authors":"Chetan K. Yadav","doi":"10.1016/j.biosystems.2025.105678","DOIUrl":"10.1016/j.biosystems.2025.105678","url":null,"abstract":"<div><div>Human behavior is the most complex system generated and represented by the cognitive brain. It is a function of highly adaptive dynamic cognitive states receiving sensory inputs and generating the behavioral responses. Social inputs belong to a class of sensory information affecting individual and collective human behavior for various purposes including a rewarded survival. Many models and theories have been proposed for understanding phenomenological dynamics of collective behavior, however most of them considered a group size effect possibly limiting cognitive scales of a given individual. Inter-element connectivity is an exclusive feature of the self-organized groups, getting optimized in the larger groups, and is a reason for better decision making in the smaller groups. We consider this as a preprocessing step in social information processing by an individual, narrowing down its own cognitive capabilities during a decision making process. Hence, in this perspective, We are considering an alternative form of social connectivity, the hierarchical social system, like in the corporate systems, allowing an individual to make decisions in light of singular instruction coming from its social partners at a higher rank. This model is proposed to unravel hidden cognitive scales in an individual's cognition as its confidence in social suggestions during decision making is expected to exhibit scale free dynamics emerging towards a critical point. Either side of this critical point can be a phase of random dynamics in absence of social information and a highly ordered phase of making limited decisions in light of aforesaid group size effect. We put forward a hypothesis that hierarchical social systems increase productivity and facilitate fruitful decision making allowing more scope to the individual cognition. Four behavioral experiments are proposed for testing this hypothesis in light of exciting scientific evidence discussed in the discussion section.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105678"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145726666","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}

引用次数: 0

Variability in resource productivity drives community dynamics in intraguild predation systems 资源生产力的变化驱动着群落内部捕食系统的动态。

IF 1.9 4区生物学

Biosystems Pub Date : 2026-01-01 Epub Date: 2025-12-22 DOI: 10.1016/j.biosystems.2025.105684

Liyun Hou

{"title":"Variability in resource productivity drives community dynamics in intraguild predation systems","authors":"Liyun Hou","doi":"10.1016/j.biosystems.2025.105684","DOIUrl":"10.1016/j.biosystems.2025.105684","url":null,"abstract":"<div><div>Energy transfer across trophic levels underpins community structure and stability, yet fluctuations in primary productivity challenge the persistence of species at higher trophic levels. We use an intraguild predation model—with resource, consumer, and a stage-structured predator—to show that variability in resource productivity profoundly reshapes trophic interactions and biomass distribution. We find that the amplitude of resource productivity fluctuations (<em>ψ</em>), rather than its period (<em>Y</em>), is the primary driver of dynamics. As <em>ψ</em> increases, the predator biomass shifts from juvenile to adult dominance and undergoes recurrent starvation-recovery cycles, which in turn regulate consumer biomass. Trophic responses to <em>ψ</em> are highly asymmetric: resources biomass remain largely stable, consumers biomass gain modestly, but total predator biomass declines consistently with <em>ψ</em> and collapses once <em>ψ</em> > 0.5. Both deterministic and stochastic resource variability yielded consistent results on population biomass and fluctuation amplitude. Furthermore, the system's equilibrium state—whether resource-only, consumer-resource, full coexistence, or predator-resource—was determined by the interaction between maximum resource density (<em>R</em><sub>max</sub>) and the predator's ontogenetic diet shift (<em>θ</em>). Critically, the amplitude <em>ψ</em> modulates this <em>R</em><sub>max</sub> – <em>θ</em> interaction, expanding or contracting the parameter regions supporting these distinct states.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105684"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145828929","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}

引用次数: 0

Optimal information transmission in a non-Markovian auto-regulatory gene expression system 非马尔可夫自调节基因表达系统中的最优信息传递。

IF 1.9 4区生物学

Biosystems Pub Date : 2026-01-01 Epub Date: 2025-12-08 DOI: 10.1016/j.biosystems.2025.105675

Zihao Wang , Meiling Chen , Zhenquan Zhang , Xiyan Yang , Tianshou Zhou , Changhong Shi , Jiajun Zhang

{"title":"Optimal information transmission in a non-Markovian auto-regulatory gene expression system","authors":"Zihao Wang , Meiling Chen , Zhenquan Zhang , Xiyan Yang , Tianshou Zhou , Changhong Shi , Jiajun Zhang","doi":"10.1016/j.biosystems.2025.105675","DOIUrl":"10.1016/j.biosystems.2025.105675","url":null,"abstract":"<div><div>Gene expression is a multistep and inherently noisy process. Such multistep reactions introduces memory between molecular events, giving rise to non-Markovian dynamics. Simultaneously, noise in the gene regulatory network limits the fidelity with which input signals can be transmitted to gene expression outputs. These considerations raise a key unresolved question: how does molecular memory influence the maximum information transmission capacity of regulatory networks under varying physical conditions? To address this, we develop a theoretical framework for a non-Markovian auto-regulatory gene expression system with arbitrary feedback form. By introducing effective transition rates, we transform the original non-Markovian model into an equivalent Markovian formulation, enabling analytical treatment. We find that non-Markovianity confers a significantly stronger regulatory capacity than feedback alone. In monostable regimes, feedback strength shapes the pattern of optimal information transmission, giving rise to monotonic or non-monotonic dependencies on memory. In bistable regimes, increasing non-Markovianity leads to a consistent decrease in the upper bound of information transmission. Beyond these results, our approach establishes a generalizable strategy for analyzing information flow in complex gene regulatory systems involving memory, feedback, and noise.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105675"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145726692","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}

引用次数: 0

Effects along the epithelial-mesenchymal biointerface in direct cell self-organisation: Multiscale theoretical analysis 细胞自组织中上皮-间充质生物界面的影响：多尺度理论分析。

IF 1.9 4区生物学

Biosystems Pub Date : 2026-01-01 DOI: 10.1016/j.biosystems.2025.105690

Ivana Pajic-Lijakovic , Milan Milivojevic , Peter V.E. McClintock

{"title":"Effects along the epithelial-mesenchymal biointerface in direct cell self-organisation: Multiscale theoretical analysis","authors":"Ivana Pajic-Lijakovic , Milan Milivojevic , Peter V.E. McClintock","doi":"10.1016/j.biosystems.2025.105690","DOIUrl":"10.1016/j.biosystems.2025.105690","url":null,"abstract":"<div><div>Epithelial cancer ranks among the most deadly types of cancer globally. Focusing on the disease's early stages could lead to significant enhancements in the survival rates of cancer patients. The initial phase of the disease is associated with the dissemination of cancer cells into the adjacent healthy epithelium. Therefore, a more profound understanding of cell dynamics at the biointerface between epithelial and cancer (mesenchymal) cells is essential for managing the disease promptly. The dynamics of cells at this epithelial-cancer biointerface arises through interplay between a variety of biological and physical mechanisms. Although considerable research has been dedicated to examining the spread of cancer cells across the epithelium, the physical mechanisms that govern the dynamics at the biointerface remain poorly understood. The main goal of this multi-scale theoretical consideration is to emphasize the influence of physical factors, such as the viscoelasticity of the subpopulations and the dilational viscoelasticity of the biointerface, on the efficiency with which cancer spreads through the epithelium. We do so by consideration of the mechanical coupling between the epithelial and cancer mesenchymal-like subpopulations. In this review, we consider this complex phenomenon from a multiscale mechanical perspective that has not been explicitly addressed in earlier studies, using model systems such as the segregation of co-cultured epithelial–mesenchymal spheroids. The mechanical-coupling between the subpopulations arising from the system's viscoelasticity is discussed from the cellular to supracellular levels in order to recognize the main physical factors responsible for the spreading of cancer.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105690"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145896883","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}

引用次数: 0

Integrating fuzzy DEMATEL and Constructal Law for biofouling dynamics in Marine Growth Prevention Systems 海洋防生长系统中生物污染动力学的模糊DEMATEL和构形律集成。

IF 1.9 4区生物学

Biosystems Pub Date : 2026-01-01 Epub Date: 2025-11-29 DOI: 10.1016/j.biosystems.2025.105663

Veysi Başhan

{"title":"Integrating fuzzy DEMATEL and Constructal Law for biofouling dynamics in Marine Growth Prevention Systems","authors":"Veysi Başhan","doi":"10.1016/j.biosystems.2025.105663","DOIUrl":"10.1016/j.biosystems.2025.105663","url":null,"abstract":"<div><div>Marine Growth Prevention Systems (MGPS) are vital for maintaining vessel efficiency, reducing biofouling, and ensuring sustainable operation under variable marine conditions. However, their performance is often challenged by complex interdependencies among design, thermodynamic, and operational factors. In this study, a fuzzy DEMATEL (Decision Making Trial and Evaluation Laboratory) approach is employed to systematically evaluate and prioritize fifteen critical factors affecting MGPS effectiveness. The analysis integrates Constructal Law principles and bio-inspired design concepts to capture the dynamic interplay between entropy generation, copper ion distribution, electrode configuration, and structural adaptability. Expert evaluations from oceangoing chief engineers with academic and operational experience were used to construct the causal model. The results show that Structural Topology Efficiency (C13) and Evolutionary Robustness under Changing Conditions (C15) exhibited the highest causal influence (rᵢ – cⱼ > 0.35), whereas Biological Antifouling Analogy Consistency (C10) was found to be the most dependent factor (rᵢ – cⱼ < −0.28). Incorporating Constructal alignment principles reduced estimated entropy generation suggesting that thermodynamically optimized configurations can substantially enhance antifouling performance and energy efficiency. The cause–effect diagram highlights that adaptive topology and control responsiveness act as dominant design drivers, shaping electrochemical and flow-related outcomes. This study contributes to the literature by bridging fuzzy multi-criteria decision-making with thermodynamic and bio-organizational perspectives, offering both theoretical insights and practical design guidance. Furthermore, the findings open new research avenues toward integrating Constructal Law optimization with AI-based predictive control, CFD–multi-physics coupling, and self-healing MGPS architectures for next-generation sustainable marine systems.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105663"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145650101","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}

引用次数: 0

Bayesian consolidation of retinal micro(nano)plastic hypothesis: From existential confirmation to spatial–phenotypic inference 视网膜微（纳米）塑性假说的贝叶斯巩固：从存在确认到空间表型推断。

IF 1.9 4区生物学

Biosystems Pub Date : 2026-01-01 Epub Date: 2025-12-23 DOI: 10.1016/j.biosystems.2025.105685

Tan Aik Kah

{"title":"Bayesian consolidation of retinal micro(nano)plastic hypothesis: From existential confirmation to spatial–phenotypic inference","authors":"Tan Aik Kah","doi":"10.1016/j.biosystems.2025.105685","DOIUrl":"10.1016/j.biosystems.2025.105685","url":null,"abstract":"<div><div>Recent empirical confirmation of polymeric micro- and nanoplastics (MNPs) in human retinal tissue marks a decisive epistemic shift—from theoretical plausibility to verified biological occurrence. Five months before this discovery, a Bayesian hypothesis framework published in <em>BioSystems</em> proposed that MNPs may exist in the human retina and could plausibly explain certain imaging anomalies, despite the absence of direct evidence. The present work extends that framework by formalizing how definitive empirical detection collapses existential uncertainty and advances the Bayesian model toward its next inferential stage.</div><div>Using the posterior probability (P = 0.023) derived in the original model as a new prior, strong empirical evidence (P (E | H) = 0.99; P (E | ￢H) = 0.01 or 0.001) yields posteriors between 0.7 and 0.96—representing more than a thirty-fold increase in belief. Sensitivity analysis demonstrates that above a 90 % detection rate, posterior belief asymptotically approaches unity, signifying epistemic closure of the existential hypothesis (H<sub>1</sub>: retinal MNPs exist). This quantitative update does not re-analyze laboratory data but illustrates the formal process by which definitive evidence transforms a probabilistic conjecture into an empirically anchored premise. The resulting posterior of H<sub>1</sub> becomes the prior for a second-stage hypothesis (H<sub>2</sub>): retinal MNP distribution and polymer profile correlate with specific imaging or pathological phenotypes. Framed within an iterative Bayesian logic, this transition exemplifies how probabilistic reasoning can integrate theoretical prediction and empirical validation—converting a speculative biological proposition into a structured platform for future mechanistic exploration.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105685"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145834194","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}

引用次数: 0

Nikolai Koltsov and his work, which anticipated many ideas in modern cellular and molecular biology, genetics, and epigenetics. Toward the 100th anniversary of the concept of template biosynthesis Nikolai Koltsov和他的工作，它预测了现代细胞和分子生物学，遗传学和表观遗传学的许多思想。迈向模板生物合成概念的100周年。

IF 1.9 4区生物学

Biosystems Pub Date : 2026-01-01 Epub Date: 2025-11-08 DOI: 10.1016/j.biosystems.2025.105646

Alexander S. Ermakov

引用次数: 0

Immune response precision customized to tumor adaptive kinetics 免疫反应精确定制肿瘤适应动力学。

IF 1.9 4区生物学

Biosystems Pub Date : 2026-01-01 Epub Date: 2025-12-01 DOI: 10.1016/j.biosystems.2025.105665

Yifan Li , Denisa Vlasceanu , Ruby Kim

{"title":"Immune response precision customized to tumor adaptive kinetics","authors":"Yifan Li , Denisa Vlasceanu , Ruby Kim","doi":"10.1016/j.biosystems.2025.105665","DOIUrl":"10.1016/j.biosystems.2025.105665","url":null,"abstract":"<div><div>Tumor heterogeneity results from the continuous accumulation of mutations in cancer cells. High phenotypic diversity in cancer can reduce the efficacy of precisely targeted adaptive immune responses. To investigate the conditions under which tumor heterogeneity is sufficient for immune evasion, we developed an agent-based model at the level of individual cells. In this model, cancer phenotypes are represented as vectors, with mutation as a random walk on the corresponding phenotypic space. We evaluated various immune activation strategies by modulating the affinity threshold for activation and assessed their impact on tumor clearance rates. First, the model exhibited oscillatory behavior consistent with empirical observation, that we hypothesized was driven by negative frequency dependent selection. Further supporting this mechanism, the variance of cancer phenotypes consistently increases as the cancer population collapses. Finally, we identified conditions favoring either narrow or broad immune activation profiles, in accordance with theoretical predictions. These findings suggest potential strategies for optimizing immunotherapies, such as adoptive cell therapy, by tailoring the antigenic repertoire used to prime immune cells according to the adaptive dynamics of the target tumor population.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105665"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145670557","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}

引用次数: 0