Biosystems最新文献

{"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":"240 ","pages":"Article 105230"},"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":"240 ","pages":"Article 105228"},"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":"240 ","pages":"Article 105226"},"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":"240 ","pages":"Article 105227"},"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":"239 ","pages":"Article 105211"},"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":"240 ","pages":"Article 105216"},"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}

{"title":"Theories of the origin of the genetic code: Strong corroboration for the coevolution theory","authors":"Massimo Di Giulio","doi":"10.1016/j.biosystems.2024.105217","DOIUrl":"https://doi.org/10.1016/j.biosystems.2024.105217","url":null,"abstract":"&lt;div&gt;&lt;p&gt;I analyzed all the theories and models of the origin of the genetic code, and over the years, I have considered the main suggestions that could explain this origin. The conclusion of this analysis is that the coevolution theory of the origin of the genetic code is the theory that best captures the majority of observations concerning the organization of the genetic code. In other words, the biosynthetic relationships between amino acids would have heavily influenced the origin of the organization of the genetic code, as supported by the coevolution theory. Instead, the presence in the genetic code of physicochemical properties of amino acids, which have also been linked to the physicochemical properties of anticodons or codons or bases by stereochemical and physicochemical theories, would simply be the result of natural selection. More explicitly, I maintain that these correlations between codons, anticodons or bases and amino acids are in fact the result not of a real correlation between amino acids and codons, for example, but are only the effect of the intervention of natural selection. Specifically, in the genetic code table we expect, for example, that the most similar codons - that is, those that differ by only one base - will have more similar physicochemical properties. Therefore, the 64 codons of the genetic code table ordered in a certain way would also represent an ordering of some of their physicochemical properties. Now, a study aimed at clarifying which physicochemical property of amino acids has influenced the allocation of amino acids in the genetic code has established that the partition energy of amino acids has played a role decisive in this. Indeed, under some conditions, the genetic code was found to be approximately 98% optimized on its columns. In this same work, it was shown that this was most likely the result of the action of natural selection. If natural selection had truly allocated the amino acids in the genetic code in such a way that similar amino acids also have similar codons - this, not through a mechanism of physicochemical interaction between, for example, codons and amino acids - then it might turn out that even different physicochemical properties of codons (or anticodons or bases) show some correlation with the physicochemical properties of amino acids, simply because the partition energy of amino acids is correlated with other physicochemical properties of amino acids. It is very likely that this would inevitably lead to a correlation between codons (or anticodons or bases) and amino acids. In other words, since the codons (anticodons or bases) are ordered in the genetic code, that is to say, some of their physicochemical properties should also be ordered by a similar order, and given that the amino acids would also appear to have been ordered in the genetic code by selection natural, then it should inevitably turn out that there is a correlation between, for example, the hydrophobicity of anticodons","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"239 ","pages":"Article 105217"},"PeriodicalIF":1.6,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140647576","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":"Unsolved morphogenesis problems and the hidden order","authors":"A.V. Melkikh","doi":"10.1016/j.biosystems.2024.105218","DOIUrl":"https://doi.org/10.1016/j.biosystems.2024.105218","url":null,"abstract":"<div><p>In this work, the morphogenesis mechanisms are considered from the complexity perspective. It is shown that both morphogenesis and the functioning of organs should be unstable in the case of short-range interaction potentials. The repeatability of forms during evolution is a strong argument for its directionality. The formation of organs during evolution can occur only in the presence of a priori information about the structure of such an organ. The focus of the discussion is not merely on constraining potential possibilities but on the concept of directed evolution itself. A morphogenesis model was constructed based on nontrivial quantum effects. These interaction effects between biologically important molecules ensure the accurate synthesis of cells, tissues, and organs.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"239 ","pages":"Article 105218"},"PeriodicalIF":1.6,"publicationDate":"2024-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140643651","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 emergence of theoretical biology: Two fundamental works of Ervin Bauer (1890–1938) in English translation","authors":"Miklós Müller ,&nbsp;Abir U. Igamberdiev","doi":"10.1016/j.biosystems.2024.105201","DOIUrl":"10.1016/j.biosystems.2024.105201","url":null,"abstract":"<div><p>Ervin Bauer (1890–1938) outlined the paradigm of theoretical biology from the perspective of biophysics and bioenergetics. His molecular-based biological theory is centered on the principle of sustainable non-equilibrium, which is continuously produced and maintained by all biological systems throughout their life. Ervin Bauer became the victim of Stalin's Great Terror. Here we present two of the fundamental works of Ervin Bauer in English translation: the paper “The definition of living beings on the basis of their thermodynamic properties, and the fundamental biological principles that follow from it” published in Naturwissenschaften (1920) and the excerpts from his magnum opus “Theoretical Biology” (1935). These works became a bibliographical rarity. A complete English translation of “Theoretical Biology” is an important task for the future.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"241 ","pages":"Article 105201"},"PeriodicalIF":1.6,"publicationDate":"2024-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0303264724000868/pdfft?md5=ce464ab908e51009e23d0f13e4d325c0&pid=1-s2.0-S0303264724000868-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140864014","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":"Bio-analog dissipative structures and principles of biological behavior","authors":"Benjamin De Bari ,&nbsp;Dilip K. Kondepudi ,&nbsp;Ashwin Vaidya ,&nbsp;James A. Dixon","doi":"10.1016/j.biosystems.2024.105214","DOIUrl":"https://doi.org/10.1016/j.biosystems.2024.105214","url":null,"abstract":"<div><p>The place of living organisms in the natural world is a nearly perennial question in philosophy and the sciences; how can inanimate matter yield animate beings? A dominant answer for several centuries has been to treat organisms as sophisticated machines, studying them with the mechanistic physics and chemistry that have given rise to technology and complex machines. Since the early 20th century, many scholars have sought instead to naturalize biology through thermodynamics, recognizing the precarious far-from-equilibrium state of organisms. Erwin Bauer was an early progenitor of this perspective with ambitions of “general laws for the movement of living matter”. In addition to taking a thermodynamic perspective, Bauer recognized that organisms are fundamentally <em>behaving</em> systems, and that explaining the physics of life requires explaining the origins of intentionality, adaptability, and self-regulation. Bauer, like some later scholars, seems to advocate for a “new physics”, one that extends beyond mechanics and classical thermodynamic, one that would be inclusive of living systems. In this historical review piece, we explore some of Bauer's ideas and explain how similar concepts have been explored in modern non-equilibrium thermodynamics and dissipative structure theory. Non-living dissipative structures display end-directedness, self-maintenance, and adaptability analogous to organisms. These findings also point to an alternative framework for the life sciences, that treats organisms not as machines but as sophisticated dissipative structures. We evaluate the differences between mechanistic and thermodynamic perspectives on life, and what each theory entails for understanding the behavior of organisms.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"239 ","pages":"Article 105214"},"PeriodicalIF":1.6,"publicationDate":"2024-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140621783","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}