Biosystems最新文献_第3页

Ervin Bauer and the foundations of theoretical biology.

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

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

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

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

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

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

Miguel R.O. Panão

{"title":"On the infodynamics of ramifications in constructal design","authors":"Miguel R.O. Panão","doi":"10.1016/j.biosystems.2024.105388","DOIUrl":"10.1016/j.biosystems.2024.105388","url":null,"abstract":"<div><div>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 <em>informature</em>, defined as a measure of the amount of information in indeterminate physical systems, and <em>infotropy</em> – 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 <span><math><mi>Ψ</mi></math></span> expresses the ability of the flow architecture to promote thermofluid performance. By contextualizing the informature with <span><math><mi>Ψ</mi></math></span>, 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.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"248 ","pages":"Article 105388"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142958156","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

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

IF 2 4区生物学

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

Omar Jurado , Marco V. José , Eugenio Frixione

{"title":"Fragile X mental retardation protein modulates translation of proteins with predicted tendencies for liquid-liquid phase separation","authors":"Omar Jurado , Marco V. José , Eugenio Frixione","doi":"10.1016/j.biosystems.2025.105405","DOIUrl":"10.1016/j.biosystems.2025.105405","url":null,"abstract":"<div><div>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 <em>Fmr1</em> 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.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"248 ","pages":"Article 105405"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143076470","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

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

IF 2 4区生物学

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

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

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

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

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

引用次数: 0

Unravelling intrinsically disordered and compositionally biased proteins in the cereal proteomes

IF 2 4区生物学

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

Mouna Choura , Vladimir N. Uversky

{"title":"Unravelling intrinsically disordered and compositionally biased proteins in the cereal proteomes","authors":"Mouna Choura , Vladimir N. Uversky","doi":"10.1016/j.biosystems.2025.105409","DOIUrl":"10.1016/j.biosystems.2025.105409","url":null,"abstract":"<div><div>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.</div><div>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.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"248 ","pages":"Article 105409"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143076473","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

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

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

{"title":"A mechanistic approach to optimize combination antibiotic therapy","authors":"F. Clarelli , P.O. Ankomah , H. Weiss , J.M. Conway , G. Forsdahl , P. Abel zur Wiesch","doi":"10.1016/j.biosystems.2024.105385","DOIUrl":"10.1016/j.biosystems.2024.105385","url":null,"abstract":"<div><div>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.</div><div>We demonstrate the utility of this tool with in vitro <em>Escherichia coli</em> 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.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"248 ","pages":"Article 105385"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142900071","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