Biosystems最新文献

{"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}

{"title":"Towards a Possible Definition of Consciousness","authors":"Marko Vitas","doi":"10.1016/j.biosystems.2025.105526","DOIUrl":"10.1016/j.biosystems.2025.105526","url":null,"abstract":"<div><div>There is no consensus about what cognition and its emergent form, consciousness, are. Yet this article proposes a new definition of consciousness. As many researchers, philosophers and other thinkers believe that life means cognising, this new definition of consciousness stems from a generalisation of the existing definition of life which postulates that <em>Life is a far from equilibrium self-maintaining chemical system capable of processing, transforming, and accumulating information acquired from the environment</em>. The new definition includes the thermodynamical aspect as a far from equilibrium system and considers the flow of information from the environment to a conscious system. The new definition of consciousness presented herein is formulated in a minimal manner; simultaneously, it is general enough to cover all emergent forms of cognition, <em>e.g.</em> thinking and rationality. The newly formulated definition states that <em>Consciousness is an emergent property of a far from equilibrium system of quantum particles sustained by an autopoietic system and capable of processing, transforming, and accumulating information acquired from the environment.</em> The newly proposed definition of consciousness may be of interest to cognitive and computer sciences – and even to the development of artificial intelligence. Furthermore, it presents a possible solution to Chalmers’ hard problem of consciousness. This article discusses a possible generalisation by introducing quantum particles to the definition of life stated herein, refining it into a broader concept: <em>Life is a far from equilibrium self-maintaining system of quantum particles capable of processing, transforming, and accumulating information acquired from the environment</em>.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"254 ","pages":"Article 105526"},"PeriodicalIF":2.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144556716","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":"Detailed analysis of the quantum relaxation features in the cell microtubules: Markovian and non-Markovian dynamics","authors":"V.A. Saenko ,&nbsp;S.Eh. Shirmovsky ,&nbsp;D.V. Shulga","doi":"10.1016/j.biosystems.2025.105520","DOIUrl":"10.1016/j.biosystems.2025.105520","url":null,"abstract":"<div><div>In the present work, the quantum relaxation processes in the microtubule dipole system are studied. The study is conducted in the Markovian and non-Markovian models. The research is based on the numerical simulation of the nonlinear system of differential equations. The detailed derivation of the non-Markovian analytical expressions has been made. The nonlinear character of the quantum relaxation processes has been established. It is shown that the quantum dynamics of the dipole moments has a different - ambivalent nature and depends on the critical values of the environmental factors such as: microtubule length, microtubule anisotropy, temperature. It is established that the dynamics in the non-Markovian model differs markedly from the Markovian one at a small temperature and at small relaxation time values.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"254 ","pages":"Article 105520"},"PeriodicalIF":2.0,"publicationDate":"2025-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144545880","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}