IF 1.9 4区生物学

Biosystems Pub Date : 2025-07-31 DOI: 10.1016/j.biosystems.2025.105546

Abir U. Igamberdiev

{"title":"The development of code systems during eukaryogenesis and the rise of multicellularity","authors":"Abir U. Igamberdiev","doi":"10.1016/j.biosystems.2025.105546","DOIUrl":"10.1016/j.biosystems.2025.105546","url":null,"abstract":"<div><div>The expansion of the set of biological codes associated with the appearance and complexification of eukaryotic cells (eukaryogenesis) and the evolution of multicellularity is based on the development of higher codes operating over the genetic system. In the course of evolution, the perception-action functional cycles described by Jakob von Uexküll become complemented by the secondary meta-cycles, which perceive the work of the primary cycles, and finally by tertiary cycles of meta-reflexivity, which perceive and evaluate the previous activity of the secondary functional cycles and generate a new field of meanings associated with conscious experience. The development of secondary and tertiary cycles forms the basis of higher-level codes operating over the genetic system and resulting in the evolutionary separation between unikonts and bikonts, in the divergence between protostomes and deuterostomes, in all events of cellular differentiation manifested as differentiation trees, and finally in the appearance of consciousness. The expansion of codes associated with the rise of eukaryotic organelles and with the cytoskeleton rearrangements in the ontogenesis of multicellular organisms determines the course of the evolutionary process toward complexification. The internally controlled recombination process, in particular, in the course of meiotic cell division and ontogenetic differentiation, becomes the driving factor of progressive evolution. It corresponds to the growing role of the epigenome and epigenetic regulation in the complexification of biological organization. It is concluded that the evolutionary process unfolds as a propagating non-deducible construction following the generation of functional redundancy, which is achieved through gene duplication, symbiosis, and cell-cell interactions, and becomes an important precondition for the appearance of new evolutionary acquisitions.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"255 ","pages":"Article 105546"},"PeriodicalIF":1.9,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144758034","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

Uncovering dual oscillatory regimes in p53-mdm2 dynamics: A data-driven modeling approach with implications for cancer progression. 揭示p53-mdm2动力学中的双振荡机制：一种数据驱动的建模方法，具有癌症进展的意义。

IF 1.9 4区生物学

Biosystems Pub Date : 2025-07-29 DOI: 10.1016/j.biosystems.2025.105540

Kathryn K Menta, Majid Bani-Yaghoub, Bi-Botti C Youan

{"title":"Uncovering dual oscillatory regimes in p53-mdm2 dynamics: A data-driven modeling approach with implications for cancer progression.","authors":"Kathryn K Menta, Majid Bani-Yaghoub, Bi-Botti C Youan","doi":"10.1016/j.biosystems.2025.105540","DOIUrl":"https://doi.org/10.1016/j.biosystems.2025.105540","url":null,"abstract":"<p><p>Quantifying the dynamic interplay between p53 and Mdm2 is critical for uncovering their roles in cancer progression and therapeutic targeting. Experimental studies have shown that p53-Mdm2 interactions exhibit oscillatory behavior in response to DNA damage. However, several mathematical models fail to sustain these oscillations or do not fit well with the experimental data, instead converging to constant steady-state values of p53 and Mdm2, which is unrealistic. In this study, we develop a simple yet robust ordinary differential equation model that accurately quantifies different stable periodic solutions (limit cycles) for p53-Mdm2 dynamics. Specifically, using a two-step numerical calibration algorithm, we validate the model against four experimental datasets. The calibrated model demonstrates strong data fit and reveals two distinct oscillatory regimes: one where Mdm2 oscillates with an amplitude 2.67 times greater than that of p53, and another where Mdm2 shows variable but consistently smaller oscillations than p53. The observed variability in oscillatory behavior may contribute to tumor progression by shortening overall p53 activity windows, thereby limiting the time available to initiate apoptosis and DNA repair.</p>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":" ","pages":"105540"},"PeriodicalIF":1.9,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144762218","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

Coupling of the energetic and purinergic activities of ATP in ischemic and hypoxic disease states 缺血和缺氧疾病状态下ATP的能量和嘌呤能活性的耦合。

IF 1.9 4区生物学

Biosystems Pub Date : 2025-07-23 DOI: 10.1016/j.biosystems.2025.105544

William D. Ehringer, Kristyn H. Smith

{"title":"Coupling of the energetic and purinergic activities of ATP in ischemic and hypoxic disease states","authors":"William D. Ehringer, Kristyn H. Smith","doi":"10.1016/j.biosystems.2025.105544","DOIUrl":"10.1016/j.biosystems.2025.105544","url":null,"abstract":"<div><div>Adenosine-5′-triphosphate (ATP) is the single most important molecule in life. It is the universal energy currency of all living things. The energy from ATP is used in the synthesis of RNA/DNA, proteins, and lipids. The energy is used in signal transduction, ion pumping, intracellular and extracellular movement, and heat production. To meet the metabolic demand for ATP, cells utilize oxygen to extract maximal energy from substrates. The dependence on oxygen over the course of evolution allowed cells to grow in size and complexity, but at the same time cells became dependent upon oxygen for cell function and survival. During periods of ischemia or hypoxia, ATP produced by oxidative phosphorylation decreases, cells compensate by increasing glycolytic and substrate level phosphorylation, as well as prioritizing ATP consuming processes. If ischemia or hypoxia continues, extracellular ATP levels increase due to leakage and cell death, and ATP becomes an endogenous ligand that activates purinergic receptors located on cells throughout the body. ATP induces a purinergic response that can vary from cell death to cell proliferation, depending on the concentration of extracellular ATP. The coupling of the energetic and purinergic roles of ATP in ischemia or hypoxia is well illustrated in the leading causes of death in humans in the United States. Intracellular ATP depletion leads to cellular dysfunction and extracellular ATP leads to purinergic mediated responses that attempt to rectify the ischemia or hypoxia issue. Understanding the connections between the energetic and purinergic roles of ATP could be useful in future therapies.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"255 ","pages":"Article 105544"},"PeriodicalIF":1.9,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144719073","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

Learning and memory in soldier crabs: Evidence from escape task trials. 士兵蟹的学习和记忆：来自逃跑任务试验的证据。

IF 2 4区生物学

Biosystems Pub Date : 2025-07-23 DOI: 10.1016/j.biosystems.2025.105529

Takeshi Kawai, Yukio Pegio Gunji

引用次数: 0

Two coherent definitions of the life process derived from the half-chaos theory and the (unintentional) purposeful information theory. 半混沌理论和（无意的）目的信息论对生命过程的两个连贯定义。

IF 2 4区生物学

Biosystems Pub Date : 2025-07-21 DOI: 10.1016/j.biosystems.2025.105533

Andrzej Gecow

{"title":"Two coherent definitions of the life process derived from the half-chaos theory and the (unintentional) purposeful information theory.","authors":"Andrzej Gecow","doi":"10.1016/j.biosystems.2025.105533","DOIUrl":"https://doi.org/10.1016/j.biosystems.2025.105533","url":null,"abstract":"<p><p>Most attempts to define life to date have consisted in indicating several features that, according to the author of the definition, occur in all cases that he considers life. Such an analytical path should have existed at the beginning. To this day, we do not have a \"good\" definition from which as many observed features of life result as possible. The derivation of specific features from the definition and additional assumptions is the structure of a deductive theory, which primarily explains and allows for understanding. The initial proposal for the framework of such a theory is presented in the book \"Draft of the Deductive Theory of Life\". There two coherent definitions of life are derived from ordered foundations - the half-chaos theory and unintentional purposeful information theory built for this task. These definitions can be classified as Darwinian. Both of these theories offer new perspectives on the issues described, and are briefly described in the article. Without these theories, the formulations of the given definitions are incomprehensible. Also, without deeper arguments that can be found in the book, the scope of the derived features of the life process and their place in the structure of the proposed theory is shown.</p>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":" ","pages":"105533"},"PeriodicalIF":2.0,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144700262","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

Ecosystem-based reservoir computing. Hypothesis paper 基于生态系统的油藏计算。假设。

IF 2 4区生物学

Biosystems Pub Date : 2025-07-19 DOI: 10.1016/j.biosystems.2025.105525

Alessandro Chiolerio , Zoran Konkoli , Andrew Adamatzky

引用次数: 0

Paleo-phyllotaxis: Fucales, bryophytes, lycophytes and monilophytes 古叶生植物：岩藻、苔藓植物、石生植物和单生植物

IF 2 4区生物学

Biosystems Pub Date : 2025-07-17 DOI: 10.1016/j.biosystems.2025.105541

Jean-Paul Walch

引用次数: 0

Titian's mythological paintings: A pictorial personal code 提香的神话绘画：一种绘画的个人密码

IF 2 4区生物学

Biosystems Pub Date : 2025-07-16 DOI: 10.1016/j.biosystems.2025.105543

Valerio Marconi

{"title":"Titian's mythological paintings: A pictorial personal code","authors":"Valerio Marconi","doi":"10.1016/j.biosystems.2025.105543","DOIUrl":"10.1016/j.biosystems.2025.105543","url":null,"abstract":"<div><div>This paper aims to introduce <em>pictorial personal codes</em> that differ from linguistic ones. Since individual norms distinguish personal codes, the concept of norms serves as the starting point for extending their scope beyond language. Indeed, there is a strong case for nonverbal norms within the philosophy of normativity. Gestures and drawings can establish these nonverbal norms. Drawn norms, such as those enforced by traffic signals, are part of a pictorial code in our everyday experiences. However, the application of this code view has been challenged in the field of semiotics, particularly in art and visual semiotics. Conversely, the <em>pictorial turn</em> suggests that cultural history involves a struggle between words and pictures. Pictures differ from words, yet are not purely visual media. This distinction can be traced back to Marcello Barbieri's differentiation between the <em>world of</em> perceptual <em>objects</em> and the <em>world of names</em>. I hypothesize that pictorial personal codes lack an abstract system of rules but still present a set of norms that can be categorized into shared and individual. I exemplify this with a case study of the Venetian painter Tiziano Vecellio (Titian). By integrating research results from art history, I show that Titian transformed his workshop into a modern firm and, as a form of legitimization, defined his original style in terms of tragic painting, specifically a personal approach to painting that connotes a literary genre such as Greek tragedy. I also evaluate the role of a graphic code in Titian's productive system. Finally, I draw certain conclusions regarding the social ontology of the firm, suggesting that Titian's tragic painting illustrates how firms endure, thanks to personal or brand-specific codes, and propose that gestural personal codes, like pictorial ones and unlike linguistic ones, should include unsystematic <em>legisigns</em> and a set of norms that can be divided into shared and individual ones.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"255 ","pages":"Article 105543"},"PeriodicalIF":2.0,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144653612","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

scSAGRN: Inferring gene regulatory networks from single-cell multi-omics using spatial association scSAGRN：利用空间关联推断单细胞多组学的基因调控网络

IF 2 4区生物学

Biosystems Pub Date : 2025-07-07 DOI: 10.1016/j.biosystems.2025.105531

Qing Ren, Mengdi Nan, Yuhan Fu, Xiang Chen, Yibing Ma, Yongle Shi, Jie Gao

{"title":"scSAGRN: Inferring gene regulatory networks from single-cell multi-omics using spatial association","authors":"Qing Ren, Mengdi Nan, Yuhan Fu, Xiang Chen, Yibing Ma, Yongle Shi, Jie Gao","doi":"10.1016/j.biosystems.2025.105531","DOIUrl":"10.1016/j.biosystems.2025.105531","url":null,"abstract":"<div><div>Identifying the regulatory relationships between transcription factors and target genes is fundamental to understanding molecular regulatory mechanisms in biological processes including development and disease occurrence. Therefore, resolving the relationships between cis-regulatory elements and genes using single-cell multi-omics data is important for understanding transcriptional regulation. Here, scSAGRN is proposed as a framework for inferring gene regulatory networks from single-cell multi-omics. scSAGRN incorporates spatial association to compute correlations between gene expression and chromatin openness data, connects distal cis-regulatory elements to genes, infers gene regulatory networks and identifies key transcription factors. The approach is benchmarked using real single-cell datasets, and scSAGRN shows superior performance in TF recovery, peak-gene linkage prediction, and TF-gene linkage prediction compared to existing methods. Meanwhile, in human peripheral blood mononuclear cells dataset, mouse cerebral cortex dataset and mouse embryonic brain cells dataset, scSAGRN demonstrates its capability to infer gene regulatory networks and identify transcription factors. Overall, scSAGRN provides a reference for predicting transcriptional regulatory patterns from single-cell multi-omics data.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"254 ","pages":"Article 105531"},"PeriodicalIF":2.0,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144588274","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

Pandemic preparedness and new model developments for airborne diseases transmitting via aerosols 大流行防备和通过气溶胶传播的空气传播疾病新模式的发展

IF 2 4区生物学

Biosystems Pub Date : 2025-07-07 DOI: 10.1016/j.biosystems.2025.105532

Aleck H. Alexopoulos

{"title":"Pandemic preparedness and new model developments for airborne diseases transmitting via aerosols","authors":"Aleck H. Alexopoulos","doi":"10.1016/j.biosystems.2025.105532","DOIUrl":"10.1016/j.biosystems.2025.105532","url":null,"abstract":"<div><div>Currently most computational models for airborne disease transmission in epidemics and pandemics are based on the Susceptible-Infected-Recovered, SIR, family of models. Although these models are suitable for describing diseases transmitting by direct contact, e.g., face-to-face coughing, they are less suitable for diseases transmitted by aerosols. In this study a general mathematical formulation for aerosol and direct transmission of an airborne infective agent is described. The formulation utilizes a multivariate population balance equation, PBE, framework that considers not just infected individuals but also infected indoor spaces. These PBEs are significantly more complex than SIR models and require simplifications to reduced models suitable for computational simulations. In this study two levels of reduced models are presented including univariate PBEs and compartment population level descriptions. It is shown how the SIR model can be extracted but also how the simplest possible aerosol SIR model, A-SIR, can be determined. The SIR and A-SIR models are compared for different scenarios and are shown to present significantly different dynamics and outcomes. Finally, the PBE approach appears to avoid many of the shortcomings of the SIR models noted in the literature and enables integration with other modeling approaches.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"255 ","pages":"Article 105532"},"PeriodicalIF":2.0,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144596603","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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