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":"https://doi.org/10.1016/j.biosystems.2025.105503","url":null,"abstract":"<p><p>We analyzed the expression of the genes of Caenorhabditis elegans 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.</p>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":" ","pages":"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

Problematic issues of ATP synthesis in vivo 体内ATP合成的问题。

IF 2 4区生物学

Biosystems Pub Date : 2025-05-19 DOI: 10.1016/j.biosystems.2025.105493

Viktor V. Ivanishchev

{"title":"Problematic issues of ATP synthesis in vivo","authors":"Viktor V. Ivanishchev","doi":"10.1016/j.biosystems.2025.105493","DOIUrl":"10.1016/j.biosystems.2025.105493","url":null,"abstract":"<div><div>The work is devoted to description of processes that provide fundamental conditions for ATP synthesis <em>in vivo</em>. The work presents information on the basis of which a general fundamental picture of formation of electrochemical gradient on the mitochondrial (or chloroplast) membrane and its use for ATP-synthase operation is described. An attempt was made to explain the order of appearance of electrical and chemical gradients, as well as the feedback between electrical and chemical components of the driving force in mitochondria and chloroplasts based on Nath's two-ion theory. The results of the analysis allowed us to conclude that a series of sequential events (which are separated in time and space) is necessary for ATP synthesis <em>in vivo</em>, namely: formation of electrical potential, formation of chemical potential, their use for ATP synthase operation. The electrical component is formed due to light energy (chloroplast) or metabolite-associated processes (mitochondria) by pumping of H<sup>+</sup> by the electron transport chain. Formation of chemical gradients occur only upon collapse of the electrical gradient by counterion translocation. As a result of their interaction, a driving force (plus change in the conformation of membrane components) is formed on the membrane, which makes ATP-synthase work. The reasons for significant differences in the values of the chemical and electrical components of the gradient on the membranes of mitochondria and chloroplasts are shown (explained). Analysis of the active transport of metabolites from the mitochondria allows us to conclude that it is possible to “break” the concentration flow of Krebs cycle metabolites into mitochondria <em>in vivo</em>, which can be maintained by cytoplasmic malate.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"254 ","pages":"Article 105493"},"PeriodicalIF":2.0,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144121441","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

Origin of homochirality in peptides: The first milestone at the origin of life 多肽中同手性的起源：生命起源的第一个里程碑

IF 2 4区生物学

Biosystems Pub Date : 2025-05-19 DOI: 10.1016/j.biosystems.2025.105479

Søren Toxvaerd

{"title":"Origin of homochirality in peptides: The first milestone at the origin of life","authors":"Søren Toxvaerd","doi":"10.1016/j.biosystems.2025.105479","DOIUrl":"10.1016/j.biosystems.2025.105479","url":null,"abstract":"<div><div>Living organisms have some common structures, chemical reactions and molecular structures. The organisms consist of cells with cell division, they have homochirality of protein and carbohydrate units, metabolism, and genetics, and they are mortal. The molecular structures and chemical reactions underlying these features are common to all, from the simplest bacteria to human beings. The origin of life is evolutionary with the emergence of a network of spontaneous biochemical reactions, and the evolution has taken place over a very long time. The evolution contains, however, some “landmarks” and bottlenecks, which in a revolutionary manner directed the evolution, and the article establishes an order of some of these events. Recent articles show that peptides in living organisms are long-time unstable with loss of their secondary homochiral conformations and with D-amino acids. Based on these observations and an extensive scientific literature on Abiogenesis, we argue that the first milestone in the prebiotic evolution is at the emergence of homochiral peptides in an aqueous solution with a high concentration of amino acids and a lower water activity than in the cytosol in living organisms. The homochiral peptides in cytosol are unstable, and the long-time aging of peptides in the cytosol causes mortality of living organisms. The metabolism and genetics are established in an environment with homochiral peptides in the Earth’s crust for <span><math><mo>≈</mo></math></span> 4 Gyr ago at a lower water activity than in the cytosol in living organisms. Finally, the cells with cell division are established in the Hot Springs environment at the interface between the crust and the Hadean Ocean.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"253 ","pages":"Article 105479"},"PeriodicalIF":2.0,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144108168","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

Investigation of the transition between the unfolded and folded states of the protein molecules by using statistical mechanical methods 用统计力学方法研究蛋白质分子的折叠态和未折叠态之间的跃迁。

IF 2 4区生物学

Biosystems Pub Date : 2025-05-16 DOI: 10.1016/j.biosystems.2025.105492

Gorkem Oylumluoglu

{"title":"Investigation of the transition between the unfolded and folded states of the protein molecules by using statistical mechanical methods","authors":"Gorkem Oylumluoglu","doi":"10.1016/j.biosystems.2025.105492","DOIUrl":"10.1016/j.biosystems.2025.105492","url":null,"abstract":"<div><div>A theoretical investigation is presented into the transition between the unfolded and folded states of protein molecules in aqueous environments using a statistical mechanical framework. The model constructs a canonical ensemble in which protein molecules are treated as electric dipoles interacting with an effective electrostatic field that simulates hydration effects. The canonical partition function is derived by integrating over dipole orientations and is analytically related to thermodynamic quantities such as free energy, internal energy, enthalpy, and heat capacity. To incorporate the influence of the chemical environment, the model extends to a grand canonical ensemble by introducing pH-dependent behavior through the concept of proton fugacity. The impact of pH on enthalpic stability is analyzed across multiple temperature conditions. All theoretical expressions are fitted to experimental calorimetric data reported for lysozyme within the pH range of 0–6. The results demonstrate that the folded state is thermodynamically favorable under acidic conditions, characterized by negative enthalpy changes and reduced heat capacity. In contrast, the unfolded state becomes dominant at higher pH levels. This approach successfully captures the enthalpic features of folding transitions and provides valuable insights into the cooperative effects of hydration on protein stability.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"254 ","pages":"Article 105492"},"PeriodicalIF":2.0,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144095671","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

Is there a relationship between embryonic bioelectric currents and differentiation waves? 胚胎生物电流与分化波有关系吗？

IF 2 4区生物学

Biosystems Pub Date : 2025-05-14 DOI: 10.1016/j.biosystems.2025.105483

Richard Gordon

引用次数: 0

The Nath-Luxuriæ principles: Unified thermodynamic framework for molecular assembly and non-ergodicity via ATP synthesis/hydrolysis example nath - luxury原理：通过ATP合成/水解的分子组装和非遍历性的统一热力学框架。

IF 2 4区生物学

Biosystems Pub Date : 2025-05-13 DOI: 10.1016/j.biosystems.2025.105481

P. Venegas-Aravena , E.G. Cordaro

{"title":"The Nath-Luxuriæ principles: Unified thermodynamic framework for molecular assembly and non-ergodicity via ATP synthesis/hydrolysis example","authors":"P. Venegas-Aravena , 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}

引用次数: 0

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