Biosystems最新文献

{"title":"Coupling of the energetic and purinergic activities of ATP in ischemic and hypoxic disease states","authors":"William D. Ehringer,&nbsp;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}

{"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":"10.1016/j.biosystems.2025.105533","url":null,"abstract":"<div><div>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.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"256 ","pages":"Article 105533"},"PeriodicalIF":1.9,"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}

{"title":"Ecosystem-based reservoir computing. Hypothesis paper","authors":"Alessandro Chiolerio ,&nbsp;Zoran Konkoli ,&nbsp;Andrew Adamatzky","doi":"10.1016/j.biosystems.2025.105525","DOIUrl":"10.1016/j.biosystems.2025.105525","url":null,"abstract":"<div><div>Reservoir computing (RC) has emerged as a powerful computational paradigm, leveraging the intrinsic dynamics of complex systems to process temporal data efficiently. Here we propose to extend RC into ecological domains, where the ecosystems themselves can function as computational reservoirs, exploiting their complexity and extreme degree of interconnectedness. This position paper explores the concept of ecosystem-based reservoir computing (ERC), examining its theoretical foundations, empirical evidence, and potential applications. We argue that ERC not only offers a novel approach to computation, but also provides insights into the computational capabilities inherent in ecological systems and offers a new paradigm for remote sensing applications.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"255 ","pages":"Article 105525"},"PeriodicalIF":2.0,"publicationDate":"2025-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144683549","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":"Paleo-phyllotaxis: Fucales, bryophytes, lycophytes and monilophytes","authors":"Jean-Paul Walch","doi":"10.1016/j.biosystems.2025.105541","DOIUrl":"10.1016/j.biosystems.2025.105541","url":null,"abstract":"<div><div>Fibonacci spiral arrangements have evolved independently in brown algae, bryophytes, in lycophytes and euphyllophytes. “Non-Fibonacci spirals” have been described in <em>Asteroxylon mackiei</em> from the Rhynie chert and on the rhyzomes of lycopsid fossils (stigmaria) as well as several groups of living lycophytes and euphyllophytes. The occurrence of the same phyllotaxis patterns in phylogenetically distant groups and the rare spiral arrangements in early leafy plants are intriguing phenomena. We applied an inhibition model to brown algae and early diverging plants. We show that the same general physico-chemical processes that determine the position of primordia on meristems underlie spiral and whorled phyllotaxis in different lineages from brown algae to angiosperms. If Fibonacci spirals optimize light capture, “non-Fibonacci spirals” are in fact asymmetric whorls. The scales on the rhyzomes of lycopsids, which did not need to optimize their root-like appendage for photosynthesis, have this type of asymmetric whorled arrangement.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"255 ","pages":"Article 105541"},"PeriodicalIF":2.0,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144663316","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":"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}

{"title":"scSAGRN: Inferring gene regulatory networks from single-cell multi-omics using spatial association","authors":"Qing Ren,&nbsp;Mengdi Nan,&nbsp;Yuhan Fu,&nbsp;Xiang Chen,&nbsp;Yibing Ma,&nbsp;Yongle Shi,&nbsp;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}

{"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}

{"title":"Structural reduction of amino acid activating ribozyme KK13","authors":"Kiichi Aizawa ,&nbsp;Yusuke Saga ,&nbsp;Mika Waida ,&nbsp;Hiromi Mutsuro-Aoki ,&nbsp;Takuya Umehara ,&nbsp;Koji Tamura","doi":"10.1016/j.biosystems.2025.105530","DOIUrl":"10.1016/j.biosystems.2025.105530","url":null,"abstract":"<div><div>Protein synthesis requires at least three steps: amino acid activation, amino acid transfer to tRNA, and peptide bond formation. Of these, the energy level of the reaction product in the first step, catalyzed by aminoacyl-tRNA synthetase, is the highest, and this reaction consumes ATP and connects amino acids to AMP via acyl phosphate bonds (formation of aminoacyl-AMP). In this study, we focused on KK13, a ribozyme with a length of 114 nucleotides, which catalyzes the formation of acyl phosphate bonds between the α-phosphate of 5ʹ-terminal triphosphate of the ribozyme and the carboxylate of amino acid with concomitant release of inorganic pyrophosphate. Based on the prediction of the secondary and tertiary structures of KK13, we aimed to reduce the size of the ribozyme, plausible on the primitive Earth, which can activate amino acids. Finally, several mutants were created, and the relationship between their structural and evolutionary features is discussed.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"254 ","pages":"Article 105530"},"PeriodicalIF":2.0,"publicationDate":"2025-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144563169","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":"The origins of ATP synthases, the identity of LUCA, and the progenote","authors":"Massimo Di Giulio","doi":"10.1016/j.biosystems.2025.105528","DOIUrl":"10.1016/j.biosystems.2025.105528","url":null,"abstract":"<div><div>Here, I analyze the origins and evolution of ATP synthases. Observations regarding the early evolution of life would imply that the Last Universal Common Ancestor (LUCA) and its most direct descendants were progenotes. That is to say, the main conclusion would be that around the root of the tree of life the cell stage had not yet been reached. In other words, that cells would have appeared only during the formation of the main phyletic lineages leading to bacteria and archaea. Such implications arise from a conjecture that by linking the evolution of ATP synthases to methanogenesis and the latter to the origin of the genetic code which in turn would be linked to the definition of progenote, would be able to link the evolution of ATP synthases to the definition of progenote.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"254 ","pages":"Article 105528"},"PeriodicalIF":2.0,"publicationDate":"2025-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144580351","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":"An account of a century of ATP research","authors":"Sunil Nath","doi":"10.1016/j.biosystems.2025.105527","DOIUrl":"10.1016/j.biosystems.2025.105527","url":null,"abstract":"<div><div>The synthesis of adenosine triphosphate (ATP), the universal biological energy currency, by oxidative phosphorylation and photophosphorylation catalyzed by the F_OF₁-ATP synthase is the fundamental means of cellular energy generation in animals, plants, and microorganisms. Since the ocean area and the amount of biomass is very large, the formation of ATP and its utilization by the myriad energy-consuming processes in the cell is the principal net chemical reaction taking place on the surface of the earth. This is indeed a most important reaction. How exactly does it occur? Since the development of the famous colorimetric assay for measurement of inorganic phosphate (Pi) in 1925, followed by the discovery of ATP in 1929, an enormous amount of research has been done to understand these intracellular energy-linked processes. I present an account of the major developments on ATP synthesis and hydrolysis in a century of research, and summarize the current state of knowledge. My account focuses on the fields of bioenergetics, muscle contraction and motility in cell life, and covers key aspects of metabolic disease, mitochondrial apoptosis and cell death in relation to ATP and the ATP synthase, and the permeability transition pore. It includes developments at molecular, cellular, and macroscopic levels—ascending into ecology—thanks to the conservative nature of metabolic pathways, with ATP as the universal intermediate in the coupled reactions of biological energy transduction. New, emerging sub-fields on ATP and the Warburg Effect, purinergic signaling, condensates and the role of ATP as a biological hydrotope are discussed briefly, and applications in aging and precision medicine are foreseen. I have divided the subject matter into the following five eras to cover the vast ground. (i)—the beginning era of the 1920s (Section 2), (ii)—an era of trials and trails of the 1930s–1940s (Sections 3.1–3.5), (iii)—an era of population-based biochemistry and enzymology in the 1950s–1980s (Sections 4.1–4.9), (iv)—a high-tech era of the 1990s–2020s of high-resolution structural and single-molecule studies, but also an interdisciplinary era of systems biology that integrates approaches from physics, chemistry, biology, mathematics, and engineering (Sections 5.1–5.15), (v)—future prospects (Section 6). The article works out new explanations—with quantitative equations or physical criteria developed for the first time—that may help resolve longstanding issues in muscle contraction, bioenergetics, and transport. My tryst with ATP during 35-years of research is also described, and the search for a theory with greater numerical accuracy is emphasized. Errors of previous theories are identified and corrected, and apparent contradictions are resolved. The aim is to explain and correctly interpret the cumulative experimental record, check for consistency of theory with experiment, remove the inconsistencies in previous theories, and arrive at","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"256 ","pages":"Article 105527"},"PeriodicalIF":1.9,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144565444","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}