IF 1.9 4区生物学

Biosystems Pub Date : 2025-10-01 Epub Date: 2025-08-07 DOI: 10.1016/j.biosystems.2025.105552

Omar Paredes, Robert Prinz

{"title":"The scientometric approach to Code Biology: What the title tells about the field.","authors":"Omar Paredes, Robert Prinz","doi":"10.1016/j.biosystems.2025.105552","DOIUrl":"10.1016/j.biosystems.2025.105552","url":null,"abstract":"<p><p>Code Biology has emerged as a conceptual framework for investigating how information is encoded, transmitted, and interpreted in living systems. Building on recent efforts to catalog biological codes across disciplines, we present the first comprehensive scientometric analysis of the field. Using a curated corpus of publications explicitly invoking the term code, we apply full-text natural language processing and unsupervised topic modeling to map the intellectual landscape of Code Biology. Our analysis reveals 24 distinct thematic clusters, ranging from molecular mechanisms and regulatory architectures to neural information processing and philosophical discourse on meaning and organization. This approach offers insights that conventional literature reviews often miss-uncovering latent patterns, inter-topic correlations, and conceptual blind spots. In doing so, we expose the field's current fragmentation into isolated knowledge niches and highlight the need for integrative models of how biological codes interact across scales. Temporal and geographical analyses reveal distinct phases in the development of Code Biology, shifting from gene-centric and mechanistic views to increasingly symbolic, cognitive, and systems-oriented paradigms. Collaboration network analysis further shows the emergence of modular scientific communities and identifies key interdisciplinary contributors shaping the field. Taken together, our results establish the foundation for a new branch of code biology, dedicated to the empirical and conceptual mapping of coding processes in biology based on literature. We propose key research directions, including the structural grammar of neural codes, the role of prebiotic and evolutionary codes in transitions of life, and the intersection between biological and artificial coding systems. This work provides not only a roadmap for future research but also a call to develop standardized frameworks capable of bridging molecular, neural, and symbolic dimensions of biological information processing.</p>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":" ","pages":"105552"},"PeriodicalIF":1.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144812654","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

Teeth Between the Eyes: Extra-Oral Dentition in Chimaeras as Evidence for Biological Codes. 眼间的牙齿：嵌合体的口外齿作为生物密码的证据。

IF 1.9 4区生物学

Biosystems Pub Date : 2025-09-30 DOI: 10.1016/j.biosystems.2025.105605

João Carlos Major

{"title":"Teeth Between the Eyes: Extra-Oral Dentition in Chimaeras as Evidence for Biological Codes.","authors":"João Carlos Major","doi":"10.1016/j.biosystems.2025.105605","DOIUrl":"https://doi.org/10.1016/j.biosystems.2025.105605","url":null,"abstract":"<p><p>The recent discovery of functional dentition on the cranial tenaculum of male Hydrolagus colliei (spotted ratfish), published in a 2025 issue of the Proceedings of the National Academy of Sciences, provides a compelling empirical example for the theory of biological codes. Described as a reversal of the long-standing assumption that teeth are exclusively oral structures, this case demonstrates how codified developmental programs can be reused in novel anatomical and functional contexts. This paper explores how the appearance of extra-oral teeth illustrates the triadic structure of code, mediator, and artifact as proposed by Code Biology. Drawing on Barbieri's framework and recent research bridging biological, neural, and symbolic systems, the study argues that biological meaning arises through arbitrary yet functional correspondences, activated and modulated by developmentally regulated mediators, leading to adaptive morphological innovations. The framework presented is not merely metaphorical; it is empirically grounded, conceptually robust, and testable - offering a powerful explanation not only for evolutionary novelty but also for how structured meaning arises in living, cognitive, and cultural systems. By tracing how biological codes give rise to artifacts of both functional and formal relevance, this case contributes to a broader theoretical model that connects morphogenesis, neural semiosis, and archetypal patterns within a unified semiotic view of life.</p>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":" ","pages":"105605"},"PeriodicalIF":1.9,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145214279","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

Are there grounded semantics in (model) organisms? 在（模型）生物体中是否存在基础语义？

IF 1.9 4区生物学

Biosystems Pub Date : 2025-09-30 DOI: 10.1016/j.biosystems.2025.105606

Claudio J Rodríguez H

引用次数: 0

Generalized model of closed microecosystem «alga - micro-consumers». 封闭微生态系统“藻类-微消费者”的广义模型。

IF 1.9 4区生物学

Biosystems Pub Date : 2025-09-30 DOI: 10.1016/j.biosystems.2025.105599

V E Zalizniak, O A Zolotov, A I Chusovitina

{"title":"Generalized model of closed microecosystem «alga - micro-consumers».","authors":"V E Zalizniak, O A Zolotov, A I Chusovitina","doi":"10.1016/j.biosystems.2025.105599","DOIUrl":"https://doi.org/10.1016/j.biosystems.2025.105599","url":null,"abstract":"<p><p>Model of closed microecosystem \"alga-micro-consumers\" is proposed in this paper. Mathematical model is the Cauchy problem for system of nonlinear ordinary differential equations. To develop the model Liebig's law of the minimum is consistently used for both specific rate of biomass growth and specific death rate of alga and micro-consumers cells. To describe the specific rate of substrate utilization by alga and micro-consumer the Andrew model (substrate inhibition) is used. It is assumed that specific death rate of alga and micro-consumer cells increases with decreasing substrate concentration. It is also assumed that carbon and nitrogen are main biogenic elements, and in the system they are in the form of mineral substrate and biological substrate. To verify the proposed model experimental data for microecosystems «Chlorella vulgaris-Pseudomonas sp» and «Chlorella vulgaris-Pseudomonas sp-Mycobacterium rubrum» are used. These systems were studied in laboratory conditions, and concentrations of elements of microecosystems in stationary state were obtained. Parameters of functions describing specific rate of utilization of biogenic elements were derived from experimental data for growth kinetics of alga and bacteria. Concentration of the biomass in stationary state obtained with the use of the proposed model is in reasonable agreement with experimental data.</p>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":" ","pages":"105599"},"PeriodicalIF":1.9,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145214367","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

Multi-factor vaccination game and optimal control of a SVIS epidemic model. SVIS流行病模型的多因素疫苗接种对策与最优控制。

IF 1.9 4区生物学

Biosystems Pub Date : 2025-09-29 DOI: 10.1016/j.biosystems.2025.105603

Na Liu, Jia Wang, Jie Fang, Junwei Sun, Qixun Lan, Wei Deng

{"title":"Multi-factor vaccination game and optimal control of a SVIS epidemic model.","authors":"Na Liu, Jia Wang, Jie Fang, Junwei Sun, Qixun Lan, Wei Deng","doi":"10.1016/j.biosystems.2025.105603","DOIUrl":"https://doi.org/10.1016/j.biosystems.2025.105603","url":null,"abstract":"<p><p>Infectious diseases represent a major global health challenge, characterized by their abrupt onset and rapid transmission, leading to millions of deaths annually. Vaccination can not only protect individuals, but also establish a group immune barrier to effectively prevent the spread of diseases, which is crucial in the prevention and control of infectious diseases. However, individual vaccination decisions are affected by many factors, typically to maximize personal benefits. Therefore, a SVIS epidemic network model based on complete information is proposed, and the stability of the equilibrium points is analyzed by using Jacobian matrix and Lyapunov stability theory. This study explores vaccination behavior within the framework of game theory, in which individuals seek to maximize their own benefits through strategic decision-making. However, such self-interested behavior often results in high social costs. Subsequently, to address the gap between individual income and social cost, we propose an optimal control strategy that minimizes societal costs while ensuring sufficient coverage to suppress transmission. Finally, The simulation results not only validate the efficacy of game-theoretic approaches, but also demonstrate their capability to achieve optimal control with minimized social costs. In addition, the simulation results also show that network structure has a significant impact on the speed and scope of disease transmission, and the social benefits are different in different network environments.</p>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":" ","pages":"105603"},"PeriodicalIF":1.9,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145208430","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

Modeling the role of ATP metabolism in articular cartilage and osteoarthritis 模拟ATP代谢在关节软骨和骨关节炎中的作用

IF 1.9 4区生物学

Biosystems Pub Date : 2025-09-24 DOI: 10.1016/j.biosystems.2025.105597

Dhruba Jyoti Mech, Mohd Suhail Rizvi

{"title":"Modeling the role of ATP metabolism in articular cartilage and osteoarthritis","authors":"Dhruba Jyoti Mech, Mohd Suhail Rizvi","doi":"10.1016/j.biosystems.2025.105597","DOIUrl":"10.1016/j.biosystems.2025.105597","url":null,"abstract":"<div><div>Osteoarthritis, a prevalent degenerative joint disease, is characterized by progressive degradation of articular cartilage. The avascular nature of articular cartilage makes it vulnerable to metabolic disruptions under hypoxic conditions. Central to this process is the role of ATP metabolism in chondrocytes, which generally maintains a delicate balance between glycolysis and oxidative phosphorylation. To investigate the balance between these two mechanisms and their regulation, we developed a comprehensive mathematical model simulating ATP metabolism in chondrocytes. The model incorporates key metabolic regulators, capturing the bistable switching between glycolysis and oxidative phosphorylation under varying nutrient conditions. Our simulation also accounts for stochastic fluctuations in oxygen and glucose levels, mimicking physiological conditions during mechanical loading, and their impact on articular cartilage dynamics. The results demonstrate that chronic hypoxia induces an irreversible metabolic shift to glycolysis, leading to sustained reductions in ATP levels and progressive ECM loss. Interestingly, the model predicts that physiological stochasticity in oxygen levels, representative of mechanical loading during physical activity, enhances metabolic flexibility and promotes ATP synthesis. When testing therapeutic interventions, we found that while exogenous ECM supplementation provides transient matrix restoration, only approaches targeting metabolic dysfunction — either through enhanced ATP synthesis or controlled suppression of regulatory factors — successfully reverse the pathological glycolytic shift. Our model suggests that optimal therapeutic approaches should combine ATP metabolic modulation with structural support to maintain beneficial nutrient fluctuations. The framework provides a basis for the development of personalized treatment strategies that address both the metabolic and structural aspects of osteoarthritis, offering new possibilities for restoring cartilage homeostasis and preventing disease progression.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"257 ","pages":"Article 105597"},"PeriodicalIF":1.9,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145158556","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

Using monoids for the integration of genomic and metabolic parameters in the prediction of phenotypes in regulatory cascades 利用monoids整合基因组和代谢参数，预测调节级联中的表型。

IF 1.9 4区生物学

Biosystems Pub Date : 2025-09-22 DOI: 10.1016/j.biosystems.2025.105595

Marco Polo Castillo-Villalba , Yair Romero , Pedro Miramontes

{"title":"Using monoids for the integration of genomic and metabolic parameters in the prediction of phenotypes in regulatory cascades","authors":"Marco Polo Castillo-Villalba , Yair Romero , Pedro Miramontes","doi":"10.1016/j.biosystems.2025.105595","DOIUrl":"10.1016/j.biosystems.2025.105595","url":null,"abstract":"<div><div>Molecular network modeling requires the use of mathematical and computational formalisms for a robust and accurate prediction of phenotypes. Furthermore, there is a need to extend these formalisms to be applied to large-scale molecular networks, thus helping in the understanding of biological complexity. In this work, we propose an extension of the modeling framework known as design principles, developed by M.A. Savageau, which is based on power-law modeling. While power-law modeling has proven valuable for understanding various properties of molecular networks, it does not allow for the inference of kinetic orders, which are typically associated with the number of binding sites present in molecules. We address this limitation by modifying the traditional approach to incorporate the use of monoids, thereby introducing a novel methodological framework we call Genotype Arithmetic. The resulting combinatorial object defines a family of geometric points, whose fixed points in the exponent space impose a set of constraints that determine the appropriate kinetic order to be used in the power law models. This feature enables a prediction of the binding strength and/or the number of DNA binding sites in regulatory sequences, as well as the reaction orders in enzymatic kinetics. To demonstrate the applicability of the present approach, we illustrated how the number of binding sites can be approximated in metabolic pathways formed by 3 to 9 reactions, in allosteric systems of end-product inhibition with intermediate catalytic reactions and one gene inhibition.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"257 ","pages":"Article 105595"},"PeriodicalIF":1.9,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145139188","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

SEMIOSIS IN ACTION: A BIOMOLECULAR PERSPECTIVE. 符号学在行动：一个生物分子的观点。

IF 1.9 4区生物学

Biosystems Pub Date : 2025-09-22 DOI: 10.1016/j.biosystems.2025.105602

Suren Zolyan

{"title":"SEMIOSIS IN ACTION: A BIOMOLECULAR PERSPECTIVE.","authors":"Suren Zolyan","doi":"10.1016/j.biosystems.2025.105602","DOIUrl":"https://doi.org/10.1016/j.biosystems.2025.105602","url":null,"abstract":"<p><p>The consideration of semiotic relations and operations in genetic coding leads to a revision of the accepted understanding of the sign as a kind of substitute associated with some object by social conventions. The new perspective allows us to eliminate the conventional and socially determined characteristics of signs as conditio sine qua non and adopt a broader understanding of sign production as an inherent property of systems that control information processes. An exemplification of such a system is the GC (the genetic code), it encompasses correlation schemes between nucleotides and amino acids. It also includes operations that regulate and interact with the context (environment). The recognition of conventionality as a necessary condition can be reformulated and replaced by interaction schemes. As a first step, we reconsider the representation of the genetic code as a static vocabulary and recognize its dynamic character - in this case a sign as determined association between the signified and the signifier arises every time as a result of an operation performed here and now, as a codepoiesis (or semiopoiesis) in action. At the same time, the nature of semiosis at each stage of the gene expression (DNA - mRNA - tRNA) is changed. These stages can be considered as a transition from hypertext (genome as a set or sequence of texts) to a single text (gene) and sign (tRNA). A full-fledged sign as a triadic relationship (sign vehicle - sense - meaning) is represented by tRNA. Additionally, in association with mRNA, tRNA acts as a second-order signifier for a complex sign: codon of mRNA → {(tRNA anticodon + tRNA) → amino acid}.</p>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":" ","pages":"105602"},"PeriodicalIF":1.9,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145139163","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

Richness of emotion in people with dementia 痴呆症患者的情感丰富性。

IF 1.9 4区生物学

Biosystems Pub Date : 2025-09-22 DOI: 10.1016/j.biosystems.2025.105601

Ayako Onzo , Shinichi Nozawa , Tetsuo Ishikawa , Ken Mogi , Mikiko Oono , Shuji Tsuda , Satoko Hotta

{"title":"Richness of emotion in people with dementia","authors":"Ayako Onzo , Shinichi Nozawa , Tetsuo Ishikawa , Ken Mogi , Mikiko Oono , Shuji Tsuda , Satoko Hotta","doi":"10.1016/j.biosystems.2025.105601","DOIUrl":"10.1016/j.biosystems.2025.105601","url":null,"abstract":"<div><div>It is important to explore not only what is lost with the progression of dementia, but also what is left and what can be compensated or developed by adapting to the special needs of the conditions. Some studies suggest that as dementia progresses, people become less emotionally expressive and have difficulties in distinguishing between other people's facial expressions. On the other hand, it is also said as cognitive function declines, anger and anxiety increase, placing a burden on caregivers. Here we report the richness of emotions in people with dementia expressed in their interviews. We analysed the transcripts of 88 interviews of people with dementia (4.8 years after diagnosis), which lasted about 60–90 min, sometimes even longer. Those transcripts are valuable, as they show that people with dementia can express themselves verbally for a long time. From the analysis of the transcripts using Paul Ekman's basic emotions, we found that the strongest emotion expressed in the interviews was happiness. We also conducted a survey of the general public recruited through X about the emotions of people with dementia, and found that people without dementia imagined that the strongest emotion felt by people with dementia was fear. Our results suggest that the cognitive abilities and emotional states of people with dementia can be more robust than people without dementia typically perceive. It might be possible to augment happiness-related emotions by the support of those around people with dementia, and the cognitive efforts of the affected people themselves.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"257 ","pages":"Article 105601"},"PeriodicalIF":1.9,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145139129","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

Relational model of all genetic codes 所有遗传密码的关系模型。

IF 1.9 4区生物学

Biosystems Pub Date : 2025-09-21 DOI: 10.1016/j.biosystems.2025.105600

Nikola Štambuk , Paško Konjevoda , Albert Štambuk

{"title":"Relational model of all genetic codes","authors":"Nikola Štambuk , Paško Konjevoda , Albert Štambuk","doi":"10.1016/j.biosystems.2025.105600","DOIUrl":"10.1016/j.biosystems.2025.105600","url":null,"abstract":"<div><div>The most common way to display the rules of all genetic codes is the Standard Genetic Code (SGC) table and its variants. This article takes an alternative approach to the genetic code table based on the relational model (Konjevoda and Štambuk, 2021). The relational model (RM) proposes distributed storage of the data into a collection of tables, which are called relations. Basic elements of the SGC table are rows (called records or tuples) and columns (called attributes). The SGC table, according to the RM, represents the so-called unnormalized form of a table, and it can be decomposed or divided into 4 tables using a set of rules called normal forms. The rows and columns of a single table are defined by the first and second base, and individual tables are specified by the third codon base. The result of this model is an approach to managing genetic code data, represented in terms of tuples and grouped into relations, with table structure and language consistent with the first-order logic, and sixteen truth functions defined by IUPAC ambiguity codes for incomplete nucleic acid specification. It is concluded that the relational model is a suitable method to display the rules of the Standard Genetic Code and its 28 variants according to Marcello Barbieri's concepts of ambiguity reduction and codepoiesis.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"257 ","pages":"Article 105600"},"PeriodicalIF":1.9,"publicationDate":"2025-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145132462","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

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