Biosystems最新文献_第5页

Morphospace engineering: Morphological computation in scaffold design 形态空间工程：支架设计中的形态计算。

IF 1.9 4区生物学

Biosystems Pub Date : 2026-01-01 Epub Date: 2025-12-12 DOI: 10.1016/j.biosystems.2025.105676

C. Galli , M.T. Colangelo , M. Meleti , S. Guizzardi

引用次数: 0

Computational image analysis from the transverse plane of Drosophila embryos 果蝇胚胎横切面的计算图像分析

IF 1.9 4区生物学

Biosystems Pub Date : 2026-01-01 Epub Date: 2025-11-12 DOI: 10.1016/j.biosystems.2025.105656

Daniela J. de Sousa , Maira A. Cardoso , Helena M.M. Araujo , Francisco J.P. Lopes , Bruno A.N. Travençolo

{"title":"Computational image analysis from the transverse plane of Drosophila embryos","authors":"Daniela J. de Sousa , Maira A. Cardoso , Helena M.M. Araujo , Francisco J.P. Lopes , Bruno A.N. Travençolo","doi":"10.1016/j.biosystems.2025.105656","DOIUrl":"10.1016/j.biosystems.2025.105656","url":null,"abstract":"<div><div>The constant improvement in molecular biology techniques, as well as the continuous advances in optical microscopy, has generated an unmet demand for new tools for the analysis and processing of digital images. In this paper, we present and validate a new computational approach for quantitative analysis of mRNA and protein spatial profiles extracted from transverse-plane images of <em>Drosophila melanogaster</em> embryos. These images are used to collect fluorescence signal intensities from protein and RNA staining at the early developmental stages. Six main image processing tasks are addressed: image preprocessing, nuclei segmentation, cytoplasm detection (apical and basal), protein/RNA quantification, detection of the dorsoventral axis, and extraction of expression profiles. This approach enables the simultaneous determination of nuclear and cytoplasmic (both basal and apical) protein and/or RNA expression. In addition, it facilitates data extraction at an unprecedent level, with a potential significant impact to understand the establishment of morphogen gradients, gene regulation mechanisms, and cell signaling in eukaryotic organism. To our knowledge, this is the first of approach this kind. Our results show that the method is fully automated and robust to a variety of confocal image settings.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105656"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145521269","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

Overview of the fifth special issue in Code Biology 《密码生物学》第五期特刊综述。

IF 1.9 4区生物学

Biosystems Pub Date : 2026-01-01 Epub Date: 2025-11-04 DOI: 10.1016/j.biosystems.2025.105643

Marcello Barbieri

引用次数: 0

Anthropogenesis and the origin of human consciousness 人类起源和人类意识的起源。

IF 1.9 4区生物学

Biosystems Pub Date : 2026-01-01 Epub Date: 2025-12-08 DOI: 10.1016/j.biosystems.2025.105668

Pedro C. Marijuán, Abir U. Igamberdiev, Terrence W. Deacon, Giuseppe Iurato

引用次数: 0

Energy transformation and nuclear spin catalysis: From magnetic isotope effects in chemical physics to ATP-dependent molecular motors in bioenergetics 能量转换和核自旋催化：从化学物理中的磁同位素效应到生物能量学中依赖atp的分子马达。

IF 1.9 4区生物学

Biosystems Pub Date : 2026-01-01 Epub Date: 2025-11-13 DOI: 10.1016/j.biosystems.2025.105657

Vitaly K. Koltover

{"title":"Energy transformation and nuclear spin catalysis: From magnetic isotope effects in chemical physics to ATP-dependent molecular motors in bioenergetics","authors":"Vitaly K. Koltover","doi":"10.1016/j.biosystems.2025.105657","DOIUrl":"10.1016/j.biosystems.2025.105657","url":null,"abstract":"<div><div>Cells and tissues are composed from atoms of chemical elements, some of which have two kinds of stable isotopes, magnetic and non-nonmagnetic ones. Not long ago, magnetic isotope effects (MIE) were discovered in living nature, in part, in the experiments with myosin, the important molecular motor of bioenergetics. In this review, the effects of different isotopes of magnesium and zinc on the enzymatic activity of myosin, namely - subfragment-1 of myosin, are presented. The rate of the ATP hydrolysis with the magnetic <sup>25</sup>Mg as the enzyme cofactor is twice higher than the rates of the same reactions with the nonmagnetic <sup>24</sup>Mg or <sup>26</sup>Mg. The similar effect of the nuclear spin catalysis was detected in the enzymatic ATP hydrolysis driven by mitochondrial H<sup>+</sup>-ATPase. Furthermore, MIE has been discovered in the experiments with different stable isotopes of zinc. While Zn<sup>2+</sup> performs the cofactor function less efficiently, than Mg<sup>2+</sup>, it was found that the rate of the enzymatic ATP hydrolysis with magnetic <sup>67</sup>Zn is 40–50 percents higher as compared to the nonmagnetic <sup>64</sup>Zn or <sup>68</sup>Zn. As the kinetics phenomenon, MIE unambiguously indicates that, in the chemo-mechanical process driven by the biomolecular motor, there is a limiting step, and this “bottle-neck” is accelerated by the nuclear spin of the magnetic isotopes of <sup>25</sup>Mg or <sup>67</sup>Zn. Although detailed mechanisms of the discovered effects require further investigations, the findings of the nuclear spin catalysis in the ATP-dependent molecular motors of bioenergetics principally manifest the potentialities of the stable magnetic isotopes in the research aimed at creating the unified theory of ATP synthesis/hydrolysis.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105657"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145530960","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

Anticipation, memory, and top-down causation in living systems 生命系统中的预期、记忆和自上而下的因果关系。

IF 1.9 4区生物学

Biosystems Pub Date : 2026-01-01 Epub Date: 2025-11-04 DOI: 10.1016/j.biosystems.2025.105640

Gordana Dodig-Crnkovic

{"title":"Anticipation, memory, and top-down causation in living systems","authors":"Gordana Dodig-Crnkovic","doi":"10.1016/j.biosystems.2025.105640","DOIUrl":"10.1016/j.biosystems.2025.105640","url":null,"abstract":"<div><div>Many physical systems retain traces of their past, but living systems differ in that they use memory for anticipation. This paper develops the thesis that anticipation depends on memory. In living systems, stored information about past states enables the prediction and modulation of future behavior. Drawing on Robert Rosen's theory of anticipatory systems, Friston's free-energy principle, and recent examples from microbiology, immunology, and cognition, I argue that Rosen's “model” is the organized memory of a system. Memory—whether mechanical, chemical, genetic, epigenetic, bioelectric, neural, or cultural—provides the substrate for anticipation, projecting possible futures and constraining present behavior. Examples across biological scales illustrate how this works in practice. Bacteria record viral encounters and use these genomic memories to defend against reinfection. In E. coli, biochemical traces of past interactions direct chemotaxis. Yeast cells store epigenetic stress memories that accelerate adaptation. With the advent of nervous systems, anticipation becomes centralized in internal neural models, enabling flexible simulations of organism–environment interactions. In all cases, anticipatory memory underlies teleonomy as goal-directedness that emerges from evolutionary and developmental processes. Top-down causation plays a central role in shaping the constraints that give rise to purposive, self-maintaining behavior. System-level goals emerge from past-informed constraints, giving living systems their distinctive autonomy, adaptivity, and creativity.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105640"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145453925","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

EMI model: A scale free biophysical framework for human consciousness, cognition and behaviour EMI模型：人类意识、认知和行为的无标度生物物理框架

IF 1.9 4区生物学

Biosystems Pub Date : 2026-01-01 Epub Date: 2025-12-09 DOI: 10.1016/j.biosystems.2025.105674

Tommaso Firaux , Jack A. Tuszynski , Marco Cavaglià

{"title":"EMI model: A scale free biophysical framework for human consciousness, cognition and behaviour","authors":"Tommaso Firaux , Jack A. Tuszynski , Marco Cavaglià","doi":"10.1016/j.biosystems.2025.105674","DOIUrl":"10.1016/j.biosystems.2025.105674","url":null,"abstract":"<div><div>Understanding consciousness, cognition, and behaviour requires an integrated framework capable of bridging neurobiology, physics, and information theory. In this paper, we propose the Energy-Mass-Information (EMI) framework as a novel paradigm to conceptualize mental phenomena as emergent properties of dynamic, field-based interactions. Rooted in, and direct expression of the Unified Holographic Framework for Neural Coherence and Consciousness (UHF), EMI introduces a transdisciplinary approach that reconceptualizes the brain-mind system as a continuously evolving network of interactions among energetic oscillations, material substrates, and informational patterns. At the heart of the EMI model lies the notion that cognition arises through the formation and modulation of attractor states-stable yet flexible configurations in the brain's energy-information landscape-guided by resonance, plasticity, and self-organizing processes.</div><div>Consciousness is thus interpreted as a holographically organized phenomenon, embedded within the biophysical substrate of the brain-body system and dynamically shaped by both internal and external fields. Behaviour emerges as the macroscopic expression of shifts among informational attractors, driven by energetic gradients and encoded across multiple scales of neural and body organization. By integrating principles from quantum coherence, neural synchronization, and dynamic systems theory, EMI offers a unifying perspective that transcends reductionist models, linking subjective experience to measurable neurophysiological and field-level processes.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105674"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145736540","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

Kinematic linkage models of muscle contraction: A mechanical engineering perspective 肌肉收缩的运动连杆模型：机械工程的观点。

IF 1.9 4区生物学

Biosystems Pub Date : 2026-01-01 Epub Date: 2025-11-22 DOI: 10.1016/j.biosystems.2025.105658

Rama Krishna K

引用次数: 0

Endogenous regulation of selection pressure: A minimal game-theoretical model 选择压力的内源性调节：一个最小博弈论模型。

IF 1.9 4区生物学

Biosystems Pub Date : 2026-01-01 Epub Date: 2025-12-02 DOI: 10.1016/j.biosystems.2025.105666

Bruno Gašperov, Branko Šter

{"title":"Endogenous regulation of selection pressure: A minimal game-theoretical model","authors":"Bruno Gašperov, Branko Šter","doi":"10.1016/j.biosystems.2025.105666","DOIUrl":"10.1016/j.biosystems.2025.105666","url":null,"abstract":"<div><div>Selection pressure, determining which individuals survive and reproduce, is traditionally regarded as an exogenous property of the environment. However, growing evidence from the Extended Evolutionary Synthesis (EES) suggests that the strength of selection can, to some extent, be modulated by the organisms themselves. In this paper, we propose a minimal game-theoretical model that formalizes the concept of <em>endogenous selection pressure</em>. In the model, individuals collectively determine the intensity of selection through their actions: each agent “votes” to either intensify or relax selection depending on its relative fitness rank. The aggregate outcome of these decisions defines the number of reproducers, <span><math><mi>k</mi></math></span>, which is inversely related to the overall strength of selection. We analytically derive all pure strategy Nash equilibria of the game and examine their properties. By internalizing selection as a population-level emergent variable, the framework provides a tractable formalization of key principles from the EES and offers a foundation for exploring evolutionary dynamics that arise under the presence of endogenous selection pressure.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105666"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145679369","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

On the origin of biological teleonomy 论生物目的学的起源

IF 1.9 4区生物学

Biosystems Pub Date : 2026-01-01 Epub Date: 2025-11-20 DOI: 10.1016/j.biosystems.2025.105662

Shaojie Deng

{"title":"On the origin of biological teleonomy","authors":"Shaojie Deng","doi":"10.1016/j.biosystems.2025.105662","DOIUrl":"10.1016/j.biosystems.2025.105662","url":null,"abstract":"<div><div>Biological teleonomy is a concept that reflects the goal-directedness and internal purposiveness characteristics in living systems. It is manifested in the way that the structures, functions, and behaviors of organisms are organized and evolved to achieve specific goals or maintain specific states. Teleonomy is a fundamental attribute of life, and as a biological principle, it stems from the special material structure of living systems. This paper uses the stable complex (evolution) encoding (SCE) model to explain the origin and mechanism of teleonomy. The SCE model represents biological functions as attractors and non-equilibrium dynamic stability structures, revealing how biological systems achieve the autonomous characteristics of self-selection and self-evolution through thermodynamic and kinetic encoding. This autonomy is the core manifestation of teleonomy and the fundamental reason for its self-sustaining and self-stabilizing characteristics. Since the origin of life, its structure has been goal-directed and has internal teleonomy. The structure at the origin of life established specific biological rules. As described by the SCE model, all functional structures are integrated into the system by forming encoded stable complexes. Therefore, life not only follows the laws of physics and chemistry but also has unique biological rules. Teleonomy emphasizes the self-leading and self-adapting aspects of biological evolution, achieving self-organization and self-construction in a way that coordinates with the environment.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105662"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145571843","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