Biosystems最新文献

{"title":"A memory access gate controlled by dynamic contexts","authors":"Andrés Pomi ,&nbsp;Juan Lin ,&nbsp;Eduardo Mizraji","doi":"10.1016/j.biosystems.2024.105232","DOIUrl":"10.1016/j.biosystems.2024.105232","url":null,"abstract":"<div><p>Temporary difficulties in accessing the contents of memories are a common experience in everyday life, for example, when we try to recognize a known person in an unusual context. In addition, recent experiments seem to indicate that retrograde amnesia in the early stages of Alzheimer's disease is due to disorders in accessing memories that were installed normally. These facts suggest the existence of an intermediate step between the stimulus arrival and the associative recognition. In this work, a multimodular neurocomputational model is presented postulating the existence of a neural gate that controls the access of the stimulus with its context to the consolidated memory. If recognition is not achieved, a random search is initiated in a contextual network aroused by the initial context. The search continues until the appropriate context that allows for recognition is found or until the process is turned off because the initial stimulus is no longer maintained in the working memory. The model is based on vector patterns of neural activity and context-dependent matrix memories. Simple Markov chain simulations are presented to exemplify possible search scenarios in the contextual network. Finally, we discuss some of the characteristics of the model and the phenomenon under study.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140959980","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}

{"title":"A multi-objective optimisation approach for the linear modelling of cerebral autoregulation system","authors":"Felipe-Andrés Bello-Robles ,&nbsp;Manuel Villalobos-Cid ,&nbsp;Max Chacón ,&nbsp;Mario Inostroza-Ponta","doi":"10.1016/j.biosystems.2024.105231","DOIUrl":"10.1016/j.biosystems.2024.105231","url":null,"abstract":"<div><h3>Objective:</h3><p>Dynamic cerebral autoregulation (dCA) has been addressed through different approaches for discriminating between normal and impaired conditions based on spontaneous fluctuations in arterial blood pressure (ABP) and cerebral blood flow (CF). This work presents a novel multi-objective optimisation (MO) approach for finding good configurations of a cerebrovascular resistance-compliance model.</p></div><div><h3>Methods:</h3><p>Data from twenty-nine subjects under normo and hypercapnic (5% CO<span><math><msub><mrow></mrow><mrow><mn>2</mn></mrow></msub></math></span> in air) conditions was used. Cerebrovascular resistance and vessel compliance models with ABP as input and CF velocity as output were fitted using a MO approach, considering fitting Pearson’s correlation and error.</p></div><div><h3>Results:</h3><p>MO approach finds better model configurations than the single-objective (SO) approach, especially for hypercapnic conditions. In addition, the Pareto-optimal front from the multi-objective approach enables new information on dCA, reflecting a higher contribution of myogenic mechanism for explaining dCA impairment.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140960065","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}

{"title":"From the principle of sustainable non-equilibrium to sustainable development","authors":"Dmitry Ermakov ,&nbsp;Alexander Ermakov","doi":"10.1016/j.biosystems.2024.105233","DOIUrl":"10.1016/j.biosystems.2024.105233","url":null,"abstract":"<div><p>Ervin Bauer was Hungarian and Soviet scientist, who had a short, but bright and talented life. In 1935, working at the Institute of Experimental Medicine in the USSR, he published the book «Theoretical Biology», in which he proposed an idea of a special “non-equilibrium” state of living systems and the existence of internal machineries in the organism that work against thermodynamic equilibrium and increase the organism's capacity for work. Currently, this idea is called “the principle of sustainable non-equilibrium” or “Bauer's principle”. During the repressions of the 1930s in the USSR, Bauer was executed, the book « Theoretical Biology» was banned. Currently, his works are poorly known, especially outside the post-socialist region. We believe that his ideas could help in rethinking not only the biochemistry and bioenergetics of cells and tissues of living organisms, but also biogeochemical and civilizational processes on a planetary scale.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140960070","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}

{"title":"Ambush strategy enhances organisms’ performance in rock–paper–scissors games","authors":"R. Barbalho ,&nbsp;S. Rodrigues ,&nbsp;M. Tenorio ,&nbsp;J. Menezes","doi":"10.1016/j.biosystems.2024.105229","DOIUrl":"10.1016/j.biosystems.2024.105229","url":null,"abstract":"<div><p>We study a five-species cyclic system wherein individuals of one species strategically adapt their movements to enhance their performance in the spatial rock–paper–scissors game. Environmental cues enable the awareness of the presence of organisms targeted for elimination in the cyclic game. If the local density of target organisms is sufficiently high, individuals move towards concentrated areas for direct attack; otherwise, they employ an ambush tactic, maximising the chances of success by targeting regions likely to be dominated by opponents. Running stochastic simulations, we discover that the ambush strategy enhances the likelihood of individual success compared to direct attacks alone, leading to uneven spatial patterns characterised by spiral waves. We compute the autocorrelation function and measure how the ambush tactic unbalances the organisms’ spatial organisation by calculating the characteristic length scale of typical spatial domains of each species. We demonstrate that the threshold for local species density influences the ambush strategy’s effectiveness, while the neighbourhood perception range significantly impacts decision-making accuracy. The outcomes show that long-range perception improves performance by over 60%, although there is potential interference in decision-making under high attack triggers. Understanding how organisms’ adaptation their environment enhances their performance may be helpful not only for ecologists, but also for data scientists, aiming to improve artificial intelligence systems.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S030326472400114X/pdfft?md5=5f6b332bb69ad36727fc6bcdac1ae8b9&pid=1-s2.0-S030326472400114X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140917413","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}

{"title":"Generation of genetic codes with 2-adic codon algebra and adaptive dynamics","authors":"Ekaterina Yurova Axelsson,&nbsp;Andrei Khrennikov","doi":"10.1016/j.biosystems.2024.105230","DOIUrl":"10.1016/j.biosystems.2024.105230","url":null,"abstract":"<div><p>This is a brief review on modeling genetic codes with the aid of 2-adic dynamical systems. In this model amino acids are encoded by the attractors of such dynamical systems. Each genetic code is coupled to the special class of 2-adic dynamics. We consider the discrete dynamical systems, These are the iterations of a function <span><math><mrow><mi>F</mi><mo>:</mo><msub><mrow><mi>Z</mi></mrow><mrow><mn>2</mn></mrow></msub><mo>→</mo><msub><mrow><mi>Z</mi></mrow><mrow><mn>2</mn></mrow></msub><mo>,</mo></mrow></math></span> where <span><math><msub><mrow><mi>Z</mi></mrow><mrow><mn>2</mn></mrow></msub></math></span> is the ring of 2-adic numbers (2-adic tree). A genetic code is characterized by the set of attractors of a function belonging to the code generating functional class. The main mathematical problem is to reduce degeneration of dynamic representation and select the optimal generating function. Here optimality can be treated in many ways. One possibility is to consider the Lipschitz functions playing the crucial role in general theory of iterations. Then we minimize the Lip-constant. The main issue is to find the proper biological interpretation of code-functions. One can speculate that the evolution of the genetic codes can be described in information space of the nucleotide-strings endowed with ultrametric (treelike) geometry. A code-function is a fitness function; the solutions of the genetic code optimization problem are attractors of the code-function. We illustrate this approach by generation of the standard nuclear and (vertebrate) mitochondrial genetics codes.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0303264724001151/pdfft?md5=54861df65cbb214fef55ccb2b43b6c43&pid=1-s2.0-S0303264724001151-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140917415","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}

{"title":"Thermodynamic analysis of energy coupling by determination of the Onsager phenomenological coefficients for a 3×3 system of coupled chemical reactions and transport in ATP synthesis and its mechanistic implications","authors":"Sunil Nath","doi":"10.1016/j.biosystems.2024.105228","DOIUrl":"10.1016/j.biosystems.2024.105228","url":null,"abstract":"<div><p>The nonequilibrium coupled processes of oxidation and ATP synthesis in the fundamental process of oxidative phosphorylation (OXPHOS) are of vital importance in biosystems. These coupled chemical reaction and transport bioenergetic processes using the OXPHOS pathway meet &gt;90% of the ATP demand in aerobic systems. On the basis of experimentally determined thermodynamic OXPHOS flux-force relationships and biochemical data for the ternary system of oxidation, ion transport, and ATP synthesis, the Onsager phenomenological coefficients have been computed, including an estimate of error. A new biothermokinetic theory of energy coupling has been formulated and on its basis the thermodynamic parameters, such as the overall degree of coupling, <span><math><mrow><mi>q</mi></mrow></math></span> and the phenomenological stoichiometry, <span><math><mrow><mi>Z</mi></mrow></math></span> of the coupled system have been evaluated. The amount of ATP produced per oxygen consumed, i.e. the actual, operating P/O ratio in the biosystem, the thermodynamic efficiency of the coupled reactions, <span><math><mrow><mi>η</mi></mrow></math></span>, and the Gibbs free energy dissipation, <span><math><mrow><mi>Φ</mi></mrow></math></span> have been calculated and shown to be in agreement with experimental data. At the concentration gradients of ADP and ATP prevailing under state 3 physiological conditions of OXPHOS that yield <span><math><mrow><msub><mi>V</mi><mi>max</mi></msub></mrow></math></span> rates of ATP synthesis, a <em>maximum</em> in <span><math><mrow><mi>Φ</mi></mrow></math></span> of <span><math><mrow><mo>∼</mo><mn>0.5</mn><mspace></mspace><mi>J</mi><mspace></mspace><msup><mrow><mo>(</mo><mrow><mi>h</mi><mspace></mspace><mi>m</mi><mi>g</mi><mspace></mspace><mi>p</mi><mi>r</mi><mi>o</mi><mi>t</mi><mi>e</mi><mi>i</mi><mi>n</mi></mrow><mo>)</mo></mrow><mrow><mo>−</mo><mn>1</mn></mrow></msup></mrow></math></span>, corresponding to a thermodynamic efficiency of <span><math><mrow><mo>∼</mo><mn>60</mn><mo>%</mo></mrow></math></span> for oxidation on succinate, has been obtained. Novel mechanistic insights arising from the above have been discussed. This is the first report of a 3 × 3 system of coupled chemical reactions with transport in a biological context in which the phenomenological coefficients have been evaluated from experimental data.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140913349","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}

{"title":"The cell as a semiotic system that realizes closure to efficient causation: The semiotic (M, R) system","authors":"Federico Vega","doi":"10.1016/j.biosystems.2024.105226","DOIUrl":"10.1016/j.biosystems.2024.105226","url":null,"abstract":"<div><p>Robert Rosen defines organisms as material systems closed to efficient causation, and proposes the replicative (M, R) system as a model for them. Recently, we presented a cell model that realizes Rosen's formal model, based on Hofmeyr's analysis of the functional organization of cell biochemistry and on Rosen's construction of the replication function. In this article we propose a cell model that, starting from the same biochemical processes, replaces the replication function with a set of semiotic relations between some of the elements that participate in cellular processes. The result is a cell model that constitutes a semiotic system that realizes closure to efficient causation: a semiotic (M, R) system. We compare the models of closure that correspond to the replicative (M, R) system and the semiotic (M, R) system. Additionally, we discuss the role that the genetic code and protein synthesis play in the semiotic closure to efficient causation. Finally, we outline the method to extend this analysis to more complex organisms.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0303264724001114/pdfft?md5=203cbe36862ef2c7c85080ce1d342c84&pid=1-s2.0-S0303264724001114-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140899912","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}

{"title":"Temporal multiscale modeling of biochemical regulatory networks: Calcium-regulated hepatocyte lipid and glucose metabolism","authors":"Arina V. Martyshina,&nbsp;Anna G. Sirotkina,&nbsp;Irina V. Gosteva","doi":"10.1016/j.biosystems.2024.105227","DOIUrl":"https://doi.org/10.1016/j.biosystems.2024.105227","url":null,"abstract":"<div><p>Hepatocyte lipid and glucose metabolism is regulated not only by major hormones like insulin and glucagon but also by many other factors, including calcium ions. Recently, mitochondria-associated membrane (MAM) dysfunction combined with incorrect IP₃-receptor regulation has been shown to result in abnormal calcium signaling in hepatocytes. This dysfunction could further lead to hepatic metabolism pathology. However, the exact contribution of MAM dysfunction, incorrect IP₃-receptor regulation and insulin resistance to the calcium-insulin-glucagon interplay is not understood yet. In this work, we analyze the role of abnormal calcium signaling and insulin dysfunction in hepatocytes by proposing a model of hepatocyte metabolic regulatory network with a detailed focus on the model construction details besides the biological aspect. In this work, we analyze the role of abnormal calcium signaling and insulin dysfunction in hepatocytes by proposing a model of hepatocyte metabolic regulatory network. We focus on the model construction details, model validation, and predictions. We describe the dynamic regulation of signaling processes by sigmoid Hill function. In particular, we study the effect of both the Hill function slope and the distance between Hill function extremes on metabolic processes in hepatocytes as a model of nonspecific insulin dysfunction. We also address the significant time difference between characteristic time of glucose hepatic processing and a typical calcium oscillation period in hepatocytes. Our modeling results show that calcium signaling dysfunction results in an abnormal increase in postprandial glucose levels, an abnormal glucose decrease in fasting, and a decreased amount of stored glycogen. An insulin dysfunction of glucose phosphorylation, glucose dephosphorylation, and glycogen breakdown also cause a noticeable effect. We also get some insight into the so-called hepatic insulin resistance paradox, confirming the hypothesis regarding indirect insulin action on hepatocytes via dysfunctional adipocyte lipolysis.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140878633","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}

{"title":"Editorial: Systems bioinformatics for medicine","authors":"Yoshiyuki Asai,&nbsp;Masahiko Nakatsui,&nbsp;Hiroshi Matsuno","doi":"10.1016/j.biosystems.2024.105211","DOIUrl":"10.1016/j.biosystems.2024.105211","url":null,"abstract":"","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140616197","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}

{"title":"Buckling forces and the wavy folds between pleural epithelial cells","authors":"Joseph Sutlive ,&nbsp;Betty S. Liu ,&nbsp;Stacey A. Kwan ,&nbsp;Jennifer M. Pan ,&nbsp;Kun Gou ,&nbsp;Rongguang Xu ,&nbsp;Ali B. Ali ,&nbsp;Hassan A. Khalil ,&nbsp;Maximilian Ackermann ,&nbsp;Zi Chen ,&nbsp;Steven J. Mentzer","doi":"10.1016/j.biosystems.2024.105216","DOIUrl":"10.1016/j.biosystems.2024.105216","url":null,"abstract":"<div><p>Cell shapes in tissues are affected by the biophysical interaction between cells. Tissue forces can influence specific cell features such as cell geometry and cell surface area. Here, we examined the 2-dimensional shape, size, and perimeter of pleural epithelial cells at various lung volumes. We demonstrated a 1.53-fold increase in 2-dimensional cell surface area and a 1.43-fold increase in cell perimeter at total lung capacity compared to residual lung volume. Consistent with previous results, close inspection of the pleura demonstrated wavy folds between pleural epithelial cells at all lung volumes. To investigate a potential explanation for the wavy folds, we developed a physical simulacrum suggested by D'Arcy Thompson in <em>On Growth and Form</em>. The simulacrum suggested that the wavy folds were the result of redundant cell membranes unable to contract. To test this hypothesis, we developed a numerical simulation to evaluate the impact of an increase in 2-dimensional cell surface area and cell perimeter on the shape of the cell-cell interface. Our simulation demonstrated that an increase in cell perimeter, rather than an increase in 2-dimensional cell surface area, had the most direct impact on the presence of wavy folds. We conclude that wavy folds between pleural epithelial cells reflects buckling forces arising from the excess cell perimeter necessary to accommodate visceral organ expansion.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140868740","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}