Biosystems最新文献

英文中文

Ervin Bauer and the foundations of theoretical biology.

IF 2 4区生物学 Q2 BIOLOGY

Biosystems

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

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

Ervin Bauer (1890-1938) outlined the paradigm of theoretical biology in his monograph "Fundamental principles of biology as a 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.

埃尔文-鲍尔（1890-1938 年）在其专著《生物学作为一门纯自然科学的基本原理及其在生理学和病理学中的应用》（1920 年）中概述了理论生物学的范式，并在其《理论生物学》（1935 年）一书中进一步发展了这些思想。在这些著作中，他从生物物理学和生物能学的角度确定了理论生物学的基础，提出了所有生物系统终生持续保持的可持续非平衡态原理，并对细胞分化、适应和进化提出了独到的见解。1938 年，埃尔文-鲍尔和妻子斯蒂法尼亚成为斯大林大恐怖的受害者。1920 年》一书于 1920 年以德文出版。该书概述了鲍尔概念的主要原则。鲍尔的巨著《理论生物学》（1935 年）以俄文出版，1967 年以匈牙利文再版（与 1920 年的专著一起），并多次以俄文再版。俄文版出版后，又立即出版了两章的德文译本。该书的英译本只出版了少量节选。在此，我们介绍这两本书的完整英译本。这两本书包含许多重要观点，这些观点在今天仍具有现实意义，并对进一步发展现代生命基础、生物物质结构和进化概念具有巨大潜力。

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引用次数: 0

Thermodynamic for biological development: A hypothesis

IF 2 4区生物学 Q2 BIOLOGY

Biosystems

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

Qinyi Zhao

This paper proposes a thermodynamic model of biological development. Several key thoughts are presented: 1) in view of thermodynamics, biological development processes irreversibly; 2) in view of thermodynamics and molecular biology, positive autoregulation, or self-regulation, of transcription factors is the only way to ensure irreversibility of a thermodynamic process of biology; 3) change in the autoregulation of transcription factors can irreversibly result in alterations in the physiological state) a physiological state is a system of signaling networks; 5) a cell and its physiological state can be identified by the pattern of its transcription factors. 6) from points aforementioned, we can analyze some thermodynamic properties of biological development by knowledge of molecular biology and biochemistry. The possible mechanisms of plant vernalization are also proposed.

引用次数: 0

Synechism 2.0: Contours of a new theory of continuity in bioengineering

IF 2 4区生物学 Q2 BIOLOGY

Biosystems

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

Ahti-Veikko Pietarinen , Vera Shumilina

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.

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引用次数: 0

Anti-wetting wing surface characteristics of a water bug, Diplonychus annulatus

IF 2 4区生物学 Q2 BIOLOGY

Biosystems

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

Shubham Sharma , R. Uma Shaanker , Anand Kumar Subramaniyan

Diplonychus annulatus (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.

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引用次数: 0

On the infodynamics of ramifications in constructal design 论建筑设计分枝的信息动力学。

IF 2 4区生物学 Q2 BIOLOGY

Biosystems

Pub Date : 2025-02-01 DOI: 10.1016/j.biosystems.2024.105388

Miguel R.O. Panão

Infodynamics is the study of how information behaves and changes within a system during its development. This study investigates the insights that informational analysis can provide regarding the ramifications predicted by constructal design. First, infodynamic neologisms informature, defined as a measure of the amount of information in indeterminate physical systems, and infotropy – contextualized informature representing the degree of transformation of indeterminate physical systems – are introduced. Flow architectures can be designed using either symmetric or asymmetric branching. The infodynamic analysis of symmetric branching revealed diminishing returns in information content, demonstrating that informature serves as a measure of diversity. These findings align with the principle of “few large and many small, but not too many,” which is consistent with higher thermofluid performance. The Performance Scaled Svelteness

Ψ

expresses the ability of the flow architecture to promote thermofluid performance. By contextualizing the informature with

Ψ

, a performance infotropy that quantifies the degree of transformation associated with the link between thermofluid performance and diversity in the ramified flow structure is obtained. A predicted growth and decay effect with increasing branching levels leads to a local maximum, highlighting that the evolutionary direction of the ramifications is inversely proportional to the scale of the environment in which the flow structure develops. Assuming an evolutionary trend toward maximum infodynamic complexity, a pattern of asymmetric ramifications emerges, similar to the sap distribution in leaves or branching of trees.

信息动力学研究的是信息在系统开发过程中的行为和变化。本研究探讨了信息分析对结构设计预测的后果所能提供的见解。首先，介绍了信息动态新词“信息”和“信息熵”，前者被定义为不确定物理系统中信息量的度量，后者是表示不确定物理系统转换程度的上下文化信息。流架构可以使用对称或非对称分支来设计。对称分支的信息动态分析揭示了信息内容的收益递减，表明信息可以作为多样性的度量。这些发现符合“少大多小”的原则，这与更高的热流体性能是一致的。性能缩放曲线Ψ表达了流动结构促进热流体性能的能力。通过将这些信息与Ψ联系起来，可以获得一个性能信息熵，该信息熵量化了与分支流结构中热流体性能和多样性之间的联系相关的转换程度。随着分支水平的增加，预测的生长和衰减效应导致局部最大值，突出表明分支的进化方向与流结构发展的环境规模成反比。假设进化趋势趋向于最大的信息动态复杂性，就会出现一种不对称分支的模式，类似于树叶或树枝上的汁液分布。

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引用次数: 0

Fragile X mental retardation protein modulates translation of proteins with predicted tendencies for liquid-liquid phase separation

IF 2 4区生物学 Q2 BIOLOGY

Biosystems

Pub Date : 2025-02-01 DOI: 10.1016/j.biosystems.2025.105405

Omar Jurado , Marco V. José , Eugenio Frixione

The Fragile X Mental Retardation Protein (FMRP) is an RNA-binding protein and a key regulator of translation in neurons, hence crucial for neural development and plasticity. FMRP loss, resulting from mutations in the Fmr1 gene, leads to Fragile X Syndrome (FXS) and Autism Spectrum Disorder (ASD), the most common inherited intellectual disabilities. Ribosome profiling in neurons consistently reveals that FMRP-knockout (FK) significantly down-regulates the translation of numerous lengthy genes, many of which are FMRP-binding targets and associated with ASD. Despite these findings, the functional explanation for FMRP's translation regulation of large neuronal proteins remains elusive. Our present study compiles data from published ribosome profiling studies, to identify genes with significantly decreased translation in FK neurons. Using bioinformatic analysis and machine-learning sequence-based tools, PSPredictor and FuzDrop, we found that the proteins encoded by these genes are predicted to be enriched in intrinsically disordered regions and are prone to liquid-liquid phase separation. These findings suggest that FMRP modulates the translation of proteins involved in the formation of biomolecular condensates. Our results can have significant implications for understanding the molecular mechanisms of FXS and ASD, adding complexity to FMRP's regulatory functions, thus offering avenues for further exploration and targeted therapeutic interventions in intellectual disability disorders.

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引用次数: 0

The regulatory network that controls lymphopoiesis 控制淋巴生成的调节网络。

IF 2 4区生物学 Q2 BIOLOGY

Biosystems

Pub Date : 2025-02-01 DOI: 10.1016/j.biosystems.2025.105399

Luis Mendoza, Ricardo Vázquez-Ramírez, Juan Manuel Tzompantzi-de-Ita

Lymphopoiesis is the generation of the T, B and NK cell lineages from a common lymphoid-biased haematopoietic stem cell. The experimental study of this process has generated a large amount of cellular and molecular data. As a result, there is a considerable number of mathematical and computational models regarding different aspects of lymphopoiesis. We hereby present a regulatory network consisting of 95 nodes and 202 regulatory interactions among them. The network is studied as a qualitative dynamical system, which has as stationary states the molecular patterns reported for CLP, pre-B, B naive, PC, pNK, iNK, NK, DP, CD8 naive, CTL, CD4 naive, Th1, Th2, Th17 and Treg cells. Also, we show that the system is able to respond to specific stimuli to reproduce the ontogeny of the T, B and NK cell lineages.

淋巴生成是从一个共同的淋巴偏向性造血干细胞中产生T、B和NK细胞谱系。这一过程的实验研究已经产生了大量的细胞和分子数据。因此，有相当数量的数学和计算模型关于淋巴系统的不同方面。我们在此提出了一个由95个节点和202个节点之间的监管交互组成的监管网络。该网络作为一个定性的动力系统进行研究，该系统具有固定状态的CLP、pre-B、B幼稚、PC、pNK、iNK、NK、DP、CD8幼稚、CTL、CD4幼稚、Th1、Th2、Th17和Treg细胞的分子模式。此外，我们表明该系统能够对特定刺激作出反应，以再现T、B和NK细胞系的个体发生。

引用次数: 0

Hopf bifurcation in the shadow of extinction: Collaborating with epidemic dynamics through lethal mutations and declining ancestor infections

IF 2 4区生物学 Q2 BIOLOGY

Biosystems

Pub Date : 2025-02-01 DOI: 10.1016/j.biosystems.2025.105406

Ali Demirci, Ayse Peker-Dobie, Cihangir Ozemir, Semra Ahmetolan

This study delves into the intricate realm of controlling Hopf and degenerate Hopf bifurcations within a Susceptible–Infectious–Susceptible model. Employing Braga’s control theory as our cornerstone, we embark on an exploration of the model’s dynamics, particularly focusing on an equilibrium point under the influence of control inputs. Our specific aim is to induce limit cycles associated with Hopf bifurcations of co-dimension 1 and 2. Through the integration of controllability principles, we endeavor to unravel the underlying mechanisms governing the manipulation of parameters to shape the occurrence and attributes of these periodic fluctuations. By examining how the behavior of infectious diseases changes in response to various control parameters, our study aims to provide a practical example of their application.

引用次数: 0

Unravelling intrinsically disordered and compositionally biased proteins in the cereal proteomes

IF 2 4区生物学 Q2 BIOLOGY

Biosystems

Pub Date : 2025-02-01 DOI: 10.1016/j.biosystems.2025.105409

Mouna Choura , Vladimir N. Uversky

Intrinsically disordered proteins (IDPs) play key biological functions despite lacking predetermined 3D structures. They are often compositionally biased and characterized by specific amino acid compositions. Here, we investigated protein intrinsic disorder in rice, wheat, barley, maize, sorghum, oat and rye proteomes. Then, we studied the distribution of compositionally biased proteins (CBs) in these species. The data showed that the contents of compositional biased proteins (CB), the average protein sizes, and biased sequence sizes were similar in the studied proteomes. Furthermore, the CB proteins were enriched in intrinsic disorder and IDPs were characterized by noticeable composition biases. In addition, the polar and the charged residues were the most abundant among the types of the biased residues. Gene Ontology analysis revealed that CB proteins in the studied species are mainly involved in binding, catalytic activity, and transcription regulation.

Altogether, our findings indicated that there is a noticeable conservation of intrinsically disordered and CB proteins in cereals. The evolutionary conservation of these features implies that cereals may use common cellular and regulatory mechanisms to adapt to various environmental constraints.

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引用次数: 0

A mechanistic approach to optimize combination antibiotic therapy 一种优化抗生素联合治疗的机制方法。

IF 2 4区生物学 Q2 BIOLOGY

Biosystems

Pub Date : 2025-02-01 DOI: 10.1016/j.biosystems.2024.105385

F. Clarelli , P.O. Ankomah , H. Weiss , J.M. Conway , G. Forsdahl , P. Abel zur Wiesch

Antimicrobial resistance is one of the most significant healthcare challenges of our times. Multidrug or combination therapies are sometimes required to treat severe infections; for example, the current protocols to treat pulmonary tuberculosis combine several antibiotics. However, combination therapy is usually based on lengthy empirical trials, and it is difficult to predict its efficacy. We propose a new tool to identify antibiotic synergy or antagonism and optimize combination therapies. Our model explicitly incorporates the mechanisms of individual drug action and estimates their combined effect using a mechanistic approach. By quantifying the impact on growth and death of a bacterial population, we can identify optimal combinations of multiple drugs. Our approach also allows for the investigation of the drugs’ actions and the testing of theoretical hypotheses.

We demonstrate the utility of this tool with in vitro Escherichia coli data using a combination of ampicillin and ciprofloxacin. In contrast to previous interpretations, our model finds a slight synergy between the antibiotics. Our mechanistic model allows investigating possible causes of the synergy.

抗菌素耐药性是我们这个时代最重大的医疗保健挑战之一。有时需要多种药物或联合治疗来治疗严重感染；例如，目前治疗肺结核的方案结合了几种抗生素。然而，联合治疗通常是基于长期的经验试验，很难预测其疗效。我们提出了一个新的工具，以确定抗生素协同或拮抗和优化联合治疗。我们的模型明确地结合了单个药物作用的机制，并使用机制方法估计它们的综合效应。通过量化对细菌种群生长和死亡的影响，我们可以确定多种药物的最佳组合。我们的方法也允许研究药物的作用和理论假设的测试。我们用氨苄西林和环丙沙星联合使用的体外大肠杆菌数据证明了该工具的实用性。与之前的解释相反，我们的模型发现抗生素之间有轻微的协同作用。我们的机制模型允许调查协同作用的可能原因。

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