Biosystems最新文献

{"title":"Is there a relationship between embryonic bioelectric currents and differentiation waves?","authors":"Richard Gordon","doi":"10.1016/j.biosystems.2025.105483","DOIUrl":"https://doi.org/10.1016/j.biosystems.2025.105483","url":null,"abstract":"<p><p>Differentiation waves usually spread in embryonic epithelia until they reach boundaries whose stopping power has been unexplained. Bioelectricity in embryos has two ranges: cell-to-cell and long-range. It is postulated here that the long-range component somehow alters gap junctions and/or intermediate filaments, creating the boundaries for the trajectories of differentiation waves. A combined EIT (Electric Impedance Tomography)/visual microscope is proposed to investigate this proposed correlation.</p>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":" ","pages":"105483"},"PeriodicalIF":2.0,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144081826","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 Nath-Luxuriæ principles: Unified thermodynamic framework for molecular assembly and non-ergodicity via ATP synthesis/hydrolysis example","authors":"P. Venegas-Aravena ,&nbsp;E.G. Cordaro","doi":"10.1016/j.biosystems.2025.105481","DOIUrl":"10.1016/j.biosystems.2025.105481","url":null,"abstract":"<div><div>Nath's principle posits that the maximization of free energy dissipation (<span><math><mrow><mi>Φ</mi></mrow></math></span>) under specific constraints facilitates the function and assembly of complex organic molecules under specific constraints, challenging the classical view that increased dissipation leads to disorder. To ground this principle in thermodynamics, this study establishes a connection between Nath's principle and a principle applicable beyond biological systems: the Principium Luxuri<em>æ</em>. The latter describes how multiscale systems dissipate energy in response to external forces. The conceptual equivalence of both principles is demonstrated, supporting Nath's unified theory of ATP synthesis/hydrolysis and the existence of non-equilibrium mechanisms for cellular energy dissipation, conservation, and storage. This connection is reinforced by a mathematical relationship demonstrating a negative correlation between <span><math><mrow><mi>Φ</mi></mrow></math></span> and the thermodynamic fractal dimension (<span><math><mrow><mi>D</mi></mrow></math></span>), a parameter quantifying multiscale dissipation in the Principium Luxuri<em>æ</em>. Furthermore, a relationship is established between the equations governing homeostasis and free energy. Given that the multiscale description is predicated on constraints imposed by external forces, which limit possible molecular configurations, the non-ergodic nature of biological systems described by Nath's principle is validated. A comparative analysis is conducted, contrasting these Nath-Luxuri<em>æ</em> principles with Prigogine's work (which describes ergodic systems) in their application to the thermodynamic evolution of biological systems and the constraints present on Earth for the formation of life. It is suggested that the Nath-Luxuri<em>æ</em> principles may significantly enhance the probability of assembling complex molecules necessary for life.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"253 ","pages":"Article 105481"},"PeriodicalIF":2.0,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144081754","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":"Flowing boundaries in autopoietic systems and microniche construction.","authors":"Matěj Jureček, Jana Švorcová","doi":"10.1016/j.biosystems.2025.105477","DOIUrl":"https://doi.org/10.1016/j.biosystems.2025.105477","url":null,"abstract":"<p><p>Organismal boundaries might seem like a straightforward and unproblematic organismal feature to study. They serve as fundamental demarcation lines that differentiate life from its environment, define identity, and maintain the functionality of organisms. But do they amount to an actual demarcation of organismal self? In this paper, we examine the philosophical and biological underpinnings of these boundaries, explore the essentialist and non-essentialist perspectives, and categorise organismal boundaries into three types: life-defining, physical, and those based on structural coupling. We shall argue largely against excessive reliance on physical boundaries, point to the inconsistencies and limitations of such thinking with the help of some formal approaches to boundaries (e.g., Markov blankets or theories such as (M, R) systems or the theory of autopoiesis), and try to harmonise the approaches by introducing a concept of boundary based on structural coupling. Autopoietic systems, such as cells, are structurally coupled to their environment, meaning their structures and those of their environment constantly influence each other. Organisms exhibit varying levels of the coupling capacity, of extending beyond their membranes to modify environments on scales ranging from molecular to planetary. Unicellular organisms, colonies, and multicellular entities construct niches that shape their survival and evolution. Building on the niche construction theory, we introduce the concept of microniches to describe various controlled spaces within organisms whose status of 'internal' is not always straightforward from the host perspective (e.g., intercellular spaces, digestive systems, or xylem). In the next step, we explain how these microniches are a direct result of structural coupling and how this concept can explain what is or is not part of a biological entity. We conclude with a discussion of Kantian organic wholes, starting with the cell in its entirety enclosed by a membrane and moving on to higher-order structures such as multicellular organisms or colonies, which differ in how they are established. Organic wholes of various levels are defined by informational boundaries and shared evolutionary norms that enable cohesion, cooperation, and distinction from the external environment across diverse biological and cultural systems. By integrating various philosophical and biological perspectives, we want to deepen our understanding of how life defines and sustains its boundaries and challenge certain established forms of thinking about organismal boundaries, which often rely on the physical or spatial approach.</p>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":" ","pages":"105477"},"PeriodicalIF":2.0,"publicationDate":"2025-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144055013","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":"Coacervates meet the RNP-world: liquid-liquid phase separation and the emergence of biological compartmentalization","authors":"Francisco Prosdocimi ,&nbsp;Savio Torres de Farias","doi":"10.1016/j.biosystems.2025.105480","DOIUrl":"10.1016/j.biosystems.2025.105480","url":null,"abstract":"<div><div>Understanding the emergence of biological compartmentalization in the context of the primordial soup is essential for unraveling the origin of life on Earth. This study revisits the classical coacervate theory, examining its historical development, supporting evidence, and major criticisms. Building upon Alexandr Oparin's foundational ideas, we propose an updated perspective in which the first biological compartments emerged through the formation of ribonucleoprotein (RNP) condensates—complexes of intrinsically disordered peptides and RNAs—via liquid-liquid phase separation (LLPS). Drawing on contemporary insights into how LLPS mediates intracellular organization, we argue that such membraneless RNP-based aggregates could have facilitated biochemical reactions in the aqueous environments of early Earth. By reinterpreting Oparin's coacervates through the lens of modern molecular biology, this study offers a renewed framework for understanding the origin of biological compartmentalization within the RNP-world hypothesis.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"252 ","pages":"Article 105480"},"PeriodicalIF":2.0,"publicationDate":"2025-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143904014","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":"A call for research on the basis for polygonal pleomorphism in archaea","authors":"Richard Gordon","doi":"10.1016/j.biosystems.2025.105478","DOIUrl":"10.1016/j.biosystems.2025.105478","url":null,"abstract":"<div><div>Morphogenesis is a major unsolved problem. It is usually tackled in the embryogenesis of multicellular organisms, but rarely leans on studies of single-cell organisms. But the latter often have fascinating, puzzling shapes, whose understanding may be key to multicellular embryogenesis, wound healing, and regeneration. Here, I call for new directions in studying what may have been the first shaped, single-celled organisms, the Domain of Archaea, which might have been LUCA (Last Universal Common Ancestor), the first organisms at the origin of life. While their shaping is usually attributed to the “crystallinity” of the S-layer, this may have the liquidity of a bubble raft.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"252 ","pages":"Article 105478"},"PeriodicalIF":2.0,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143902294","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":"Stationary periodic patterns in a model of growing population of motile bacteria","authors":"Valentina Bucur,&nbsp;Bakhtier Vasiev","doi":"10.1016/j.biosystems.2025.105465","DOIUrl":"10.1016/j.biosystems.2025.105465","url":null,"abstract":"<div><div>Biological pattern formation is one of the most intriguing phenomena in nature. Simple examples include travelling waves and stationary periodic patterns, which arise in various biological processes, including morphogenesis and population dynamics. The emergence of such patterns in populations of motile microorganisms, such as <em>Dictyostelium discoideum</em> and <em>E. coli</em>, has been demonstrated in numerous experimental studies. The conditions required for different types of pattern formation are commonly explored in mathematical studies of dynamical systems incorporating diffusion and advection terms. In this work, we introduce a prototype model for a growing population of motile bacteria that move in response to a chemical signal. We conduct a linear analysis of this model to determine the conditions for the formation of stationary periodic patterns, followed by a nonlinear (Fourier) analysis to characterise their properties, such as amplitude and wavelength. Our analytical findings are further validated through numerical simulations.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"252 ","pages":"Article 105465"},"PeriodicalIF":2.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143904015","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":"Statistical algorithms for the analysis of deleterious genetic mutations","authors":"Laurent Serlet,&nbsp;Andrzej Stos,&nbsp;Fabrice Kwiatkowski","doi":"10.1016/j.biosystems.2025.105463","DOIUrl":"10.1016/j.biosystems.2025.105463","url":null,"abstract":"<div><div>We present algorithms for model selection and parameter estimation concerning deleterious genetic mutations. Three models are considered: single gene mutation, double cross-effect mutations or no genetic cause. Each of these models include unknown parameters that must be estimated simultaneously. Available data are phenotypes along family pedigrees but no genotypic data. We compare classical fit methods based on statistical summaries of the data and a neural network approach. We show the performance of our algorithms on simulated datasets of reasonable size. We also consider real data concerning breast/ovarian cancer.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"252 ","pages":"Article 105463"},"PeriodicalIF":2.0,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143904016","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":"Effects of CikA and SasA co-regulation on cyanobacterial circadian clock","authors":"Ying Li,&nbsp;Yao Xu","doi":"10.1016/j.biosystems.2025.105468","DOIUrl":"10.1016/j.biosystems.2025.105468","url":null,"abstract":"<div><div>Cyanobacterial circadian clock is made up of three proteins, KaiA, KaiB and KaiC. KaiA binds to the A-loop to actives the autophosphorylation of KaiC, while KaiB sequesters KaiA from the A-loop to weaken the activity of KaiA. Thus a circadian oscillator of KaiC phosphorylation generates. Recent experiments have found that CikA and SasA both play crucial roles in cyanobacterial circadian clock. They participate in the output pathway and regulate the activity of transcription factors of the core oscillator. However, the specific impact of the regulation of CikA and SasA on the system is still far from clear. To address these questions, we develop an extended mathematical model for cyanobacterial circadian clock including CikA and SasA regulation. The numerical simulation results indicate that CikA and SasA have opposite effects on the system, and the two complement each other to maintain the balance of the system. Specifically, as the concentration of SasA increases, the period and amplitude increase, and the period sensitivity to parameters, phase shift caused by dark pulses and entrainment ability are all decrease. The regulation of CikA has the opposite impact on the above aspects. Based on these results, we can adjust certain indicators of the system by adjusting the concentration of CikA or SasA. The research method in this article can provide ideas for studying the effects of other proteins on the circadian clock. The findings supplement biological studies and provide a theoretical reference for biological research. It helps us gain a deeper understanding of the dynamic mechanism of cyanobacteria circadian clock.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"252 ","pages":"Article 105468"},"PeriodicalIF":2.0,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143937267","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":"Chemical oscillatory reactions with proteinoids","authors":"Shunsuke Ito","doi":"10.1016/j.biosystems.2025.105469","DOIUrl":"10.1016/j.biosystems.2025.105469","url":null,"abstract":"<div><div>This study aimed to investigate the potential of proteinoids to act as substrates for chemical oscillatory reactions. Proteinoids are thermally polymerized polymers of multiple amino acids, and their unique physicochemical properties make them suitable substrates in chemical vibration reactions. To this end, experiments were carried out using the Belousov–Zhabotinsky (BZ) and Briggs–Rauscher (BR) reactions as models, with the proteinoids acting as substrates and the resulting cyclic color changes and redox potential fluctuations being observed. The results demonstrated that specific proteinoids (PV, AEV and APV) exhibited oscillatory behavior in the BZ reaction, with PV exhibiting the highest degree of oscillation and activation energies similar to those of the conventional BZ reaction. In contrast, the BR reaction exhibited cyclic behavior exclusively when DCP was employed as a substrate, suggesting that the molecular structure of the proteinoid exerts a profound influence on its substrate properties. Notably, no oscillatory reactions were observed in the amino acid mixture utilized as a control experiment, underscoring the distinctive nature of proteinoids as unique macromolecules capable of triggering chemical oscillatory reactions. These findings indicate that proteinoids may serve as promising models for investigating the origin and early evolution of life. This research broadens the scope for exploring dynamic molecular systems using proteinoids, offering new avenues for research in life sciences and chemistry.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"252 ","pages":"Article 105469"},"PeriodicalIF":2.0,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143906953","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":"Exploring cooperation evolution in biological and social systems through donation and moral sentiment","authors":"Jianyu Pu,&nbsp;Jiqin Li","doi":"10.1016/j.biosystems.2025.105462","DOIUrl":"10.1016/j.biosystems.2025.105462","url":null,"abstract":"<div><div>This study explores how donation mechanisms and moral sentiment influence the evolution of cooperation in biological and social systems. Using an evolutionary game theory framework, we model a spatial system where individuals can either cooperate or defect, examining how resource transfers from wealthier to poorer individuals shape cooperative dynamics. We introduce a moral sentiment parameter that grants cooperators intrinsic psychological benefits, offsetting the cost of donation and enhancing their overall fitness. Our findings reveal that moderate donation levels significantly stabilize cooperation, particularly in environments with strong incentives to defect. Moreover, moral sentiment bolsters cooperative strategies by making donation more sustainable. The interplay between donation and moral sentiment produces a nonlinear effect, where their combined influence promotes cooperation more effectively than either factor alone. Additionally, we analyze the spatial spread of cooperation, showing that moral sentiment plays a crucial role in maintaining and expanding cooperative behavior across a network. These insights contribute to a deeper understanding of how social and moral factors shape cooperation, with implications for both natural and human communities.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"252 ","pages":"Article 105462"},"PeriodicalIF":2.0,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143887565","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}