Biosystems最新文献_第3页

Quantifying pleiotropy through directed signaling networks: A synchronous Boolean network approach and in-silico pleiotropic scoring 通过定向信令网络量化多效性：一种同步布尔网络方法和计算机多效性评分。

IF 2 4区生物学

Biosystems Pub Date : 2025-02-21 DOI: 10.1016/j.biosystems.2025.105416

Muhammad Mazhar Fareed , Sergey Shityakov

{"title":"Quantifying pleiotropy through directed signaling networks: A synchronous Boolean network approach and in-silico pleiotropic scoring","authors":"Muhammad Mazhar Fareed , Sergey Shityakov","doi":"10.1016/j.biosystems.2025.105416","DOIUrl":"10.1016/j.biosystems.2025.105416","url":null,"abstract":"<div><div>Pleiotropy refers to a gene's ability to influence multiple phenotypes or traits. In the context of human genetic diseases, pleiotropy manifests as different pathological effects resulting from mutations in the same gene. This phenomenon plays a crucial role in understanding gene–gene interactions in system-level biological diseases. Previous studies have largely focused on pleiotropy within undirected molecular correlation networks, leaving a gap in examining pleiotropy induced by directed signaling networks, which can better explain dynamic gene–gene interactions. In this study, we utilized a synchronous Boolean network model to explore pleiotropic dynamics induced by various mutations in large-scale networks. We introduced an in-silico Pleiotropic Score (sPS) to quantify the impact of gene mutations and validated the model against observational pleiotropy data from the Human Phenotype Ontology (HPO). Our results indicate a significant correlation between sPS and network structural characteristics, including degree centrality and feedback loop involvement. The highest correlation was observed between closeness centrality and sPS (0.6), suggesting that genes more central in the network exhibit higher pleiotropic potential. Furthermore, genes involved in feedback loops demonstrated higher sPS values (p < 0.0001), supporting the role of feedback loops in amplifying pleiotropic behavior. Our model provides a novel approach for quantifying pleiotropy through directed network dynamics, complementing traditional observational methods.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"250 ","pages":"Article 105416"},"PeriodicalIF":2.0,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143484382","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

Theoretical Biology. 理论生物学。

IF 2 4区生物学

Biosystems Pub Date : 2025-02-21 DOI: 10.1016/j.biosystems.2025.105426

Ervin Bauer, Abir U Igamberdiev, Miklós Müller, Gábor Elek, George E Mikhailovsky

引用次数: 0

An algorithm for the transformation of the Petri net models of biological signaling networks into influence graphs 生物信号网络Petri网模型转化为影响图的一种算法。

IF 2 4区生物学

Biosystems Pub Date : 2025-02-20 DOI: 10.1016/j.biosystems.2025.105415

Simon Gamache-Poirier , Alexia Souvane , William Leclerc , Catherine Villeneuve , Simon V. Hardy

引用次数: 0

Surface code model for Fibonacci helical pathways of the Orch OR microtubule Orch OR微管斐波那契螺旋路径的表面代码模型

IF 2 4区生物学

Biosystems Pub Date : 2025-02-18 DOI: 10.1016/j.biosystems.2025.105414

Seungju An , Byung-Soo Choi

{"title":"Surface code model for Fibonacci helical pathways of the Orch OR microtubule","authors":"Seungju An , Byung-Soo Choi","doi":"10.1016/j.biosystems.2025.105414","DOIUrl":"10.1016/j.biosystems.2025.105414","url":null,"abstract":"<div><div>The Objective Reduction (<em>OR</em>) theory suggested by Sir Roger Penrose presented a novel perspective on the measurement problem of quantum mechanics and consciousness. Subsequently, based on the assertion of anesthesiologist Dr. Hameroff, the theory proposed that the phenomenon of <em>OR</em> could also manifest in microtubules within neurons. This would, serve as the trigger for consciousness, thereby forming the basis of Orchestrated <em>OR</em> (<em>Orch OR</em>). The peculiarity of this theory lies in the claim that tubulin and its higher neuronal information structures are not simply additive, rather, they are formed in a topological manner. Specifically, higher information structure of tubulin, helical pathways are presumed to form an intersecting pattern in both left-handed and right-handed directions, following a repeating Fibonacci series (3, 5, 8, 13, …), and are interconnected with each other. There have been attempts to examine these unique characteristics. However, experimenting upon these quantum characteristics in the microtubule appears to be plagued by certain limitations. Therefore, this study proposed a surface code model to implement this biological model on a quantum computer, focusing on its quantum properties. To the best of our knowledge, this is the first study to attempt this. The study emphasizes that interpreting asymmetric Fibonacci helical pathways as logical qubits can stabilize surface code. In addition, we analyzed the conditions required for experimenting with this model based on the development of current quantum computer. Although the experimental feasibility of this study is dependents on future quantum computer development, it provides significant insights into <em>Orch OR</em> research by offering a novel perspective.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"249 ","pages":"Article 105414"},"PeriodicalIF":2.0,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143464361","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

Fundamental principles of biology as a pure natural science and their applications in physiology and pathology. 生物学作为一门纯粹的自然科学的基本原理及其在生理学和病理学中的应用。

IF 2 4区生物学

Biosystems Pub Date : 2025-02-18 DOI: 10.1016/j.biosystems.2025.105425

Erwin Bauer, Miklós Müller, Abir U Igamberdiev, Gábor Elek, George E Mikhailovsky

引用次数: 0

Quantum effects in ion transport: A thermodynamic resource theory approach 离子输运中的量子效应：一种热力学资源理论方法

IF 2 4区生物学

Biosystems Pub Date : 2025-02-17 DOI: 10.1016/j.biosystems.2025.105412

Amin Mohammadi, Afshin Shafiee

{"title":"Quantum effects in ion transport: A thermodynamic resource theory approach","authors":"Amin Mohammadi, Afshin Shafiee","doi":"10.1016/j.biosystems.2025.105412","DOIUrl":"10.1016/j.biosystems.2025.105412","url":null,"abstract":"<div><div>In recent years, understanding thermodynamics in the quantum regime has garnered significant attention, driven by advances in nanoscale physics and experimental techniques. In parallel, growing evidence supports the importance of quantum effects in various biological processes, making them increasingly relevant to quantum thermodynamics. In this study, we apply resource theory formulations of thermodynamics to investigate the role of quantum properties in ion transport across cell membranes. Within this framework, quantum properties are treated as resources under generalized thermodynamic constraints in the quantum regime. Specifically, our findings reveal that non-Markovianity, which reflects memory effects in ion transport dynamics, is a key quantum resource that enhances the yield and efficiency of the ion transport process. In contrast, quantum coherence, manifested as the superposition of energy states in ion-transport proteins, reduces these metrics but plays a crucial role in distinguishing between ion channels and ion pumps—two distinct types of ion-transport proteins in cell membranes. Finally, we demonstrate that introducing an additional coherent system allows coherence to facilitate the transformation of an ion pump into an ion channel.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"249 ","pages":"Article 105412"},"PeriodicalIF":2.0,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143429177","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

Ervin Bauer and the foundations of theoretical biology. 欧文·鲍尔和理论生物学的基础。

IF 2 4区生物学

Biosystems Pub Date : 2025-02-12 DOI: 10.1016/j.biosystems.2025.105424

Abir U Igamberdiev, Miklós Müller, Gábor Elek, George E Mikhailovsky

{"title":"Ervin Bauer and the foundations of theoretical biology.","authors":"Abir U Igamberdiev, Miklós Müller, Gábor Elek, George E Mikhailovsky","doi":"10.1016/j.biosystems.2025.105424","DOIUrl":"10.1016/j.biosystems.2025.105424","url":null,"abstract":"<p><p>Ervin Bauer (1890-1938) outlined the paradigm of theoretical biology in his monograph \"Fundamental Principles of Biology as Pure Natural Science and their Applications in Physiology and Pathology\" (1920) and further developed these ideas in his book \"Theoretical Biology\" (1935). In these works, he defined the foundations of theoretical biology from the perspective of biophysics and bioenergetics, formulated the principle of a sustainable non-equilibrium state, which is continuously maintained by all biological systems throughout their life, and developed original views on cell differentiation, adaptation, and evolution. In 1938, Ervin Bauer and his wife Stefánia became the victims of Stalin's Great Terror. The book of 1920 was published in 1920 in German. It outlines the main principles of Bauer's concept. Bauer's magnum opus \"Theoretical Biology\" (1935) was published in Russian and republished in 1967 in Hungarian (together with the monograph of 1920) and several times in Russian. Immediately after the Russian edition appeared, two chapters were also published in German translation. Only small excerpts of the book were published in English translation. Here we present a complete English translation of both books. The books contain many important ideas that remain actual today and have great potential for further development in modern concepts of the foundations of life, the structure of living matter, and evolution.</p>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":" ","pages":"105424"},"PeriodicalIF":2.0,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143426571","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

Thermodynamic for biological development: A hypothesis 生物发育的热力学：一个假说。

IF 2 4区生物学

Biosystems Pub Date : 2025-02-08 DOI: 10.1016/j.biosystems.2025.105413

Qinyi Zhao

引用次数: 0

Synechism 2.0: Contours of a new theory of continuity in bioengineering 协同2.0：生物工程中连续性新理论的轮廓。

IF 2 4区生物学

Biosystems Pub Date : 2025-02-07 DOI: 10.1016/j.biosystems.2025.105410

Ahti-Veikko Pietarinen , Vera Shumilina

{"title":"Synechism 2.0: Contours of a new theory of continuity in bioengineering","authors":"Ahti-Veikko Pietarinen , Vera Shumilina","doi":"10.1016/j.biosystems.2025.105410","DOIUrl":"10.1016/j.biosystems.2025.105410","url":null,"abstract":"<div><div>The methodological principle of synechism, the all-pervading continuity first proposed by Charles Peirce in 1892, is reinvigorated in the present paper to prompt a comprehensive reevaluation of the integrated concepts of life, machines, agency, and intelligence. The evidence comes from the intersections of synthetic bioengineering, developmental biology, and cognitive and computational sciences. As a regulative principle, synechism, “that continuity governs the whole domain of experience in every element of it”, has been shown to infiltrate fundamental issues of contemporary biology, including cognition in different substrates, embodied agency, collectives (swarm and nested), intelligence on multiple scales, and developmental bioelectricity in morphogenesis. In the present paper, we make explicit modern biology's turn to this fundamental feature of science in its rejection of conceptual binaries, preference for collectives over individuals, quantitative over qualitative, and multiscale applicability of the emerging hypotheses about the integration of the first principles of the diversity of life. Specifically, synechism presents itself as the bedrock for research encompassing biological machines, chimaeras, organoids, and Xenobots. We then review a synechistic framework that embeds functionalist, information-theoretic, pragmaticist and inferentialist approaches to springboard to continuum-driven biosystemic behaviour.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"250 ","pages":"Article 105410"},"PeriodicalIF":2.0,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143383685","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Anti-wetting wing surface characteristics of a water bug, Diplonychus annulatus 水蝽环翅双爪龙翅面抗湿特性。

IF 2 4区生物学

Biosystems Pub Date : 2025-02-01 DOI: 10.1016/j.biosystems.2025.105402

Shubham Sharma , R. Uma Shaanker , Anand Kumar Subramaniyan

{"title":"Anti-wetting wing surface characteristics of a water bug, Diplonychus annulatus","authors":"Shubham Sharma , R. Uma Shaanker , Anand Kumar Subramaniyan","doi":"10.1016/j.biosystems.2025.105402","DOIUrl":"10.1016/j.biosystems.2025.105402","url":null,"abstract":"<div><div><em>Diplonychus annulatus</em> (family Belostomatidae and order Hemipetra) is an aquatic water bug, adapted to ponds and wetlands. Commonly referred to as toe-biters or electric-light bugs, both the nymph and the adults prey on other invertebrates in the water. In search of both food and mates, the adults frequently fly between water bodies, leading to an amphibious lifestyle. It is likely that because of such a lifestyle, they have evolved structures on their wings that enable them to be dry and be able to fly. In this paper, we report the anti-wetting property of the fore and hind wings. We show that wings, have intricately designed hierarchical structures of setae, microtrichia, and a “micro-architectured well” interspersed with club-like projections. The wings were extremely superhydrophobic with water contact angle ranging between 160° to 170°. FTIR analysis of the wings indicated the presence of hydrophobic groups. Thus, due to both, the intricate surface features as well as possibly the low surface energy due to the hydrophobic groups on the wings, the water bug can maintain a high degree of dryness in its wings. We discuss these findings in the context of how wing adaptations contribute to the insect's ability to thrive in its amphibious lifestyle.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"248 ","pages":"Article 105402"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143025673","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