Biosystems最新文献_第10页

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 : 2025-06-01 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":"<div><div>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 German. It outlines the main principles of Bauer's concept. Bauer's <em>magnum opus</em> “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.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"252 ","pages":"Article 105424"},"PeriodicalIF":2.0,"publicationDate":"2025-06-01","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

Theoretical biology 理论生物学。

IF 2 4区生物学

Biosystems Pub Date : 2025-06-01 DOI: 10.1016/j.biosystems.2025.105426

Ervin Bauer

引用次数: 0

Fundamental principles of biology as 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 : 2025-06-01 DOI: 10.1016/j.biosystems.2025.105425

Ervin Bauer

引用次数: 0

Thermodynamics of Nath’s 2-ion model for ATP synthesis ATP合成的Nath 2离子模型热力学。

IF 2 4区生物学

Biosystems Pub Date : 2025-05-30 DOI: 10.1016/j.biosystems.2025.105505

Lee D. Hansen , Sunil Nath

引用次数: 0

Formation flight design via Constructal Law 基于构造法的编队飞行设计。

IF 2 4区生物学

Biosystems Pub Date : 2025-05-27 DOI: 10.1016/j.biosystems.2025.105482

Samuel A. Savitt

引用次数: 0

Mechanism and biological significance of erythrocyte homoaggregation (rouleaux formation): temperature-dependent entropic liberation of water from cells and macromolecules 红细胞同质聚集（rouleaux形成）的机制和生物学意义：温度依赖的水从细胞和大分子的熵释放

IF 2 4区生物学

Biosystems Pub Date : 2025-05-27 DOI: 10.1016/j.biosystems.2025.105504

Donald R. Forsdyke

{"title":"Mechanism and biological significance of erythrocyte homoaggregation (rouleaux formation): temperature-dependent entropic liberation of water from cells and macromolecules","authors":"Donald R. Forsdyke","doi":"10.1016/j.biosystems.2025.105504","DOIUrl":"10.1016/j.biosystems.2025.105504","url":null,"abstract":"<div><div>In the pre-antibiotic era, infections were usually more frequent and serious than today. Robin Fåhraeus (1888–1958) examined the erythrocyte sedimentation rate (ESR) test for infections, which was normally carried out in vitro with freshly drawn blood. His extensive studies on the mechanism and physiological significance of the enhanced sedimentation of erythrocyte aggregates (rouleaux) in disease included in vivo simulation. This led him to propose an explanation for the finding of long white strips (“fibrin coagula”) within the blood vessels of those who had died from infections. The surge of serious infections in pandemic times has likely kindled a reemergence. He further speculated that (i) the weak aggregation of red blood cells (RBCs) followed the liberation of water molecules from their surfaces, and (ii) the importance of their aggregation, which was induced by changes in serum proteins (not necessarily antibodies), extended beyond the clinic. In modern times these changes have led to immunologically significant entropic interpretations of infection-associated aggregations, whether cellular (e.g., RBC) or molecular (i.e., macromolecular polymerizations). Thus, rouleaux formation displays a process at the cellular level that can proceed in parallel at a less visible macromolecular level. It has been proposed that, when intracellular, aggregations would discriminate between self and not-self proteins in the crowded cytosol. Favoured by an associated pyrexia, this could lead, by mechanisms to be determined, to the preferential loading of peptides from proteins deemed “foreign” for presentation as major histocompatibility complexes (MHCs) to specific clones of immune cells.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"254 ","pages":"Article 105504"},"PeriodicalIF":2.0,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144166201","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 Bayesian approach to investigating presumed retinal micro(nano)plastics 一种贝叶斯方法来研究假定的视网膜微（纳米）塑料

IF 2 4区生物学

Biosystems Pub Date : 2025-05-25 DOI: 10.1016/j.biosystems.2025.105502

Tan Aik Kah

{"title":"A Bayesian approach to investigating presumed retinal micro(nano)plastics","authors":"Tan Aik Kah","doi":"10.1016/j.biosystems.2025.105502","DOIUrl":"10.1016/j.biosystems.2025.105502","url":null,"abstract":"<div><div>The human retina, a highly vascularized, metabolically active, and immunologically privileged neural tissue, stands in contrast to the ubiquity of micro(nano)plastics (MNPs), which have been reported in every other organ system. Despite this, the presence of MNPs in the retina remains undocumented, a critical gap given their potential to contribute to local inflammation, microvascular occlusion, or act as cofactors in diseases such as diabetic retinopathy, age-related macular degeneration, or uveitis. Furthermore, the diverse physicochemical properties of MNPs – including their varying sizes, shapes, colors, and optical characteristics – raise the intriguing possibility that their presence within the retina could mimic commonly observed ophthalmic features. I hypothesize that certain features—previously attributed to other causes—such as tiny discrete foci in fundus photography and hyperreflective retinal foci in optical coherence tomography, may actually contain MNPs. This hypothesis carries significant biological implications not only for ophthalmology but also for environmental toxicology and public health. To formally evaluate its plausibility, I constructed a Bayesian model incorporating initial skepticism and considering varying likelihoods of observed evidence under both null and alternative assumptions. The model demonstrates that even with an extremely low prior probability, the reproducibility and discernible patterns of certain imaging findings can justify a significantly increased posterior belief, thus warranting further scientific inquiry. This work offers a probabilistic framework to re-evaluate retinal anomalies and encourages empirical investigation in environmental ophthalmology, without definitively proving MNP presence. The development of retinal imaging techniques for the specific detection of MNPs could provide a valuable tool for environmental toxicology, preventive medicine, and public health by offering a non-invasive biomarker for systemic MNPs exposure.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"253 ","pages":"Article 105502"},"PeriodicalIF":2.0,"publicationDate":"2025-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144155181","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

Impacts of a high-glucose diet or starvation on microRNA-transcription factor networks in Caenorhabditis elegans through Boolean mathematical modeling 通过布尔数学模型研究高糖饮食或饥饿对秀丽隐杆线虫microrna -转录因子网络的影响

IF 2 4区生物学

Biosystems Pub Date : 2025-05-25 DOI: 10.1016/j.biosystems.2025.105503

Roberto Carlos Martinez-Padilla , Luis Mendoza , Juan Miranda-Rios

{"title":"Impacts of a high-glucose diet or starvation on microRNA-transcription factor networks in Caenorhabditis elegans through Boolean mathematical modeling","authors":"Roberto Carlos Martinez-Padilla , Luis Mendoza , Juan Miranda-Rios","doi":"10.1016/j.biosystems.2025.105503","DOIUrl":"10.1016/j.biosystems.2025.105503","url":null,"abstract":"<div><div>We analyzed the expression of the genes of <em>Caenorhabditis elegans</em> that are components of the Insulin/Insulin-like growth factor (IIS) and Target of Rapamycin (TOR) signaling pathways, and the microRNAs that regulate their expression. These genes are involved in longevity and their expression is differentially regulated under starvation conditions and high-glucose diets. We inferred the regulatory network from experimental data and analyzed its dynamics using Boolean networks. The regulatory network contains 26 nodes and 60 regulatory interactions. Upon examining their dynamic behavior, we discovered the presence of six fixed-point attractors. Two attractors align with the physiological response of a normal diet and another two align with gene expression associated with starvation conditions. In the starvation conditions, pro-longevity genes were found to be active, which explains the positive effect observed when the worms are grown in these conditions. One of the attractors is consistent with the gene expression found when worms are grown in high-glucose diets. In this case, anti-longevity genes were expressed, as found in the literature. Interestingly, we found another attractor in the high-glucose diet in which pro-longevity genes were observed, suggesting that under some circumstances a high-glucose diet can have a positive effect on lifespan. We also performed simulations of knock-out (KO) experiments of critical components of the network, such as LET-7, DAF-2, DAF-16, SKN-1, HLH-30, PHA-4, and DAF-15 (a component of the TORC1 complex) and our results were similar to the reported experimental evidence.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"255 ","pages":"Article 105503"},"PeriodicalIF":2.0,"publicationDate":"2025-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144163496","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

Domains of laws yet domains of No Law: Energy and work, responsible free will choice, and doing 法律的领域和无法律的领域：能量和工作，负责任的自由意志选择和行动。

IF 2 4区生物学

Biosystems Pub Date : 2025-05-24 DOI: 10.1016/j.biosystems.2025.105501

Sudip Patra , Stuart A. Kauffman

引用次数: 0

A survey of the methodological process of modeling, inference, and evaluation of gene regulatory networks using scRNA-Seq data 使用scRNA-Seq数据建模、推断和评估基因调控网络的方法学过程的调查

IF 2 4区生物学

Biosystems Pub Date : 2025-05-21 DOI: 10.1016/j.biosystems.2025.105464

José Eduardo H. da Silva, Heder S. Bernardino, Itamar L. de Oliveira, José J. Camata

{"title":"A survey of the methodological process of modeling, inference, and evaluation of gene regulatory networks using scRNA-Seq data","authors":"José Eduardo H. da Silva, Heder S. Bernardino, Itamar L. de Oliveira, José J. Camata","doi":"10.1016/j.biosystems.2025.105464","DOIUrl":"10.1016/j.biosystems.2025.105464","url":null,"abstract":"<div><div>The advent of scRNA-Seq sequencing technology has provided unprecedented resolutions in the analysis of gene regulatory networks (GRNs) at the single-cell level. However, new technical and methodological challenges also emerged. Factors such as the large number of zeros reported in expression levels, the biological variation due to the stochastic nature of gene expression, environmental niche, and effects created by the cell cycle make it difficult to correctly interpret the data obtained in the sequencing stage. On the other hand, the development of methods for the inference of GRNs, specifically using scRNA-Seq technology, proved to be of similar quality to random predictors. The lack of adequate pre-processing of gene expression data, including selection steps for subsets of genes of interest, smoothing, and discretization of gene expression, in addition to the different ways of modeling networks and network motifs, are factors that affect the performance of inference approaches. Finally, the lack of knowledge about the ground-truth network and the non-standardization of appropriate metrics to measure the quality of inferred networks make the process of comparing performance between algorithms a major problem, given the unbalanced nature of the data and the interpretation bias caused by the chosen metric. This article brings these issues to light, aiming to show how these factors influence both the inference process and the performance evaluation of inferred networks, through comparative computational experiments and provides suggestions for a more robust methodological process for researchers dealing with inference of GRNs.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"253 ","pages":"Article 105464"},"PeriodicalIF":2.0,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144108150","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