Acta Biotheoretica最新文献

{"title":"Von Uexküll's Umwelt Concept Revived : E. Yong, 2022. An immense world. How animal senses reveal the hidden realms around us. Bodley Head, London, 449 pp; ISBN 978-1-847-92609-8.","authors":"Rob Hengeveld","doi":"10.1007/s10441-024-09487-9","DOIUrl":"https://doi.org/10.1007/s10441-024-09487-9","url":null,"abstract":"","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"72 4","pages":"14"},"PeriodicalIF":1.4,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142666842","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 Fine-Grain to Coarse-Grain Modeling: Estimating Kinetic Parameters of DNA Molecules.","authors":"Jeremy Curuksu","doi":"10.1007/s10441-024-09489-7","DOIUrl":"https://doi.org/10.1007/s10441-024-09489-7","url":null,"abstract":"<p><p>Coarse-grain models are essential to understand the biological function of DNA molecules because the length and time scales of the sequence-dependent physical properties of DNA are often beyond the reach of experimental and all-atom computational methods. Simulating coarse-grain models of DNA, e.g. using Langevin dynamics, requires the parametrization of both potential and kinetic energy functions. Many studies have shown that the flexibility (i.e., potential energy) of a DNA molecule depends on its sequence. In contrast, little is known about the sequence-dependence of DNA mass parameters required to model its kinetic energy. In this paper, an algebraic expression is derived for the kinetic energy as a function of linear and angular velocities of each DNA base parameterized by its mass, center of mass, and rotational inertia tensor. The parameters of this function are then approximated from a set of fine-grain molecular dynamics simulations representing all combinations of the four DNA base pairs AT, TA, GC, and CG, in different sequence contexts. Compatibility conditions associated with the assumption of each base being modeled as a rigid body were verified to be good approximations. The kinetic parameters were found to be significantly different between the four G, C, A, and T bases, and to not be dependent on the sequence context. This suggests that the effective kinetic parameters of a DNA base may depend only on the base itself, not on its neighbors.</p>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"72 4","pages":"15"},"PeriodicalIF":1.4,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142666831","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":"Targeted Hypermutation as a Survival Strategy: A Theoretical Approach","authors":"Seymour Garte","doi":"10.1007/s10441-023-09471-9","DOIUrl":"10.1007/s10441-023-09471-9","url":null,"abstract":"<div><p>Targeted hypermutation has proven to be a useful survival strategy for bacteria under severe stress and is also used by multicellular organisms in specific instances such as the mammalian immune system. This might appear surprising, given the generally observed deleterious effects of poor replication fidelity/high mutation rate. A previous theoretical model designed to explore the role of replication fidelity in the origin of life was applied to a simulated hypermutation scenario. The results confirmed that the same model is useful for analyzing hypermutation and can predict the effects of the same parameters (survival probability, replication fidelity, mutation effect, and others) on the survival of cellular populations undergoing hypermutation as a result of severe stress.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"71 4","pages":""},"PeriodicalIF":1.3,"publicationDate":"2023-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10158697","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":"Assessment of the Global Variance Effective Size of Subdivided Populations, and Its Relation to Other Effective Sizes","authors":"Ola Hössjer,&nbsp;Linda Laikre,&nbsp;Nils Ryman","doi":"10.1007/s10441-023-09470-w","DOIUrl":"10.1007/s10441-023-09470-w","url":null,"abstract":"<div><p>The variance effective population size (<span>(N_{eV})</span>) is frequently used to quantify the expected rate at which a population’s allele frequencies change over time. The purpose of this paper is to find expressions for the global <span>(N_{eV})</span> of a spatially structured population that are of interest for conservation of species. Since <span>(N_{eV})</span> depends on allele frequency change, we start by dividing the cause of allele frequency change into genetic drift within subpopulations (<i>I</i>) and a second component mainly due to migration between subpopulations (<i>II</i>). We investigate in detail how these two components depend on the way in which subpopulations are weighted as well as their dependence on parameters of the model such a migration rates, and local effective and census sizes. It is shown that under certain conditions the impact of <i>II</i> is eliminated, and <span>(N_{eV})</span> of the metapopulation is maximized, when subpopulations are weighted proportionally to their long term reproductive contributions. This maximal <span>(N_{eV})</span> is the sought for global effective size, since it approximates the gene diversity effective size <span>(N_{eGD})</span>, a quantifier of the rate of loss of genetic diversity that is relevant for conservation of species and populations. We also propose two novel versions of <span>(N_{eV})</span>, one of which (the backward version of <span>(N_{eV})</span>) is most stable, exists for most populations, and is closer to <span>(N_{eGD})</span> than the classical notion of <span>(N_{eV})</span>. Expressions for the optimal length of the time interval for measuring genetic change are developed, that make it possible to estimate any version of <span>(N_{eV})</span> with maximal accuracy.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"71 3","pages":""},"PeriodicalIF":1.3,"publicationDate":"2023-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10441-023-09470-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10101207","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":"Social Pressure from a Core Group can Cause Self-Sustained Oscillations in an Epidemic Model","authors":"A. P. Baccili Jr.,&nbsp;L. H. A. Monteiro","doi":"10.1007/s10441-023-09469-3","DOIUrl":"10.1007/s10441-023-09469-3","url":null,"abstract":"<div><p>Let the individuals of a population be divided into two groups with different personal habits. The core group is associated with health risk behaviors; the non-core group avoids unhealthy activities. Assume that the infected individuals of the core group can spread a contagious disease to the whole population. Also, assume that cure does not confer immunity. Here, an epidemiological model written as a set of ordinary differential equations is proposed to investigate the infection propagation in this population. In the model, migrations between these two groups are allowed; however, the transitions from the non-core group into the core group prevail. These migrations can be either spontaneous or stimulated by social pressure. It is analytically shown that, in the scenario of spontaneous migration, the disease is either naturally eradicated or chronically persists at a constant level. In the scenario of stimulated migration, in addition to eradication and constant persistence, self-sustained oscillations in the number of sick individuals can also be found. These analytical results are illustrated by numerical simulations and discussed from a public health perspective.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"71 3","pages":""},"PeriodicalIF":1.3,"publicationDate":"2023-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9738939","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 Role of Information in Evolutionary Biology","authors":"Thomas E. Dickins","doi":"10.1007/s10441-023-09468-4","DOIUrl":"10.1007/s10441-023-09468-4","url":null,"abstract":"<div><p>The Modern Synthesis has received criticism for its purported gene-centrism. That criticism relies on a concept of the gene as a unit of instructional information. In this paper I discuss information concepts and endorse one, developed from Floridi, that sees information as a functional relationship between data and context. I use this concept to inspect developmental criticisms of the Modern Synthesis and argue that the instructional gene arose as an idealization practice when evolutionary biologists made comment on development. However, a closer inspection of key claims shows that at least some associated with the Modern Synthesis were in fact adopting the data led definition I favour and made clear arguments for the role of developmental processes beyond genetic input. There was no instructional gene.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"71 3","pages":""},"PeriodicalIF":1.3,"publicationDate":"2023-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10441-023-09468-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10099986","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":"Sulfur is in the Air: Cyanolichen Marriages and Pollution","authors":"Dilantha Gunawardana,&nbsp;Rasika P. Wanigatunge,&nbsp;Jayani J. Wewalwela,&nbsp;Meththika Vithanage,&nbsp;Chandrani Wijeyaratne","doi":"10.1007/s10441-023-09465-7","DOIUrl":"10.1007/s10441-023-09465-7","url":null,"abstract":"<div><p>Cyanolichens are symbiotic organisms involving cyanobacteria and fungi (bipartite) or with the addition of an algal partner (tripartite). Cyanolichens are known for their heightened susceptibility to environmental pollution. We focus here on the impacts on cyanolichens due to rising air pollution; we are especially interested in the role of sulfur dioxide on cyanolichen biology. Cyanolichens due to air pollution including sulfur dioxide exposure, show symptomatic changes including degradation of chlorophyll, lipid membrane peroxidation, decrease in ATP production, changes in respiration rate, and alteration of endogenous auxins and ethylene production, although symptoms are known to vary with species and genotype. Sulfur dioxide has been shown to be damaging to photosynthesis but is relatively benign on nitrogen fixation which proposes as a hypothesis that the algal partner may be more in harm’s way than the cyanobiont. In fact, the <i>Nostoc</i> cyanobiont of sulfur dioxide-susceptible <i>Lobaria pulmonaria</i> carries a magnified set of sulfur (alkane sulfonate) metabolism genes capable of alkane sulfonate transport and assimilation, which were only unraveled by genome sequencing, a technology unavailable in the 1950–2000 epoch, where most physiology- based studies were performed. There is worldwide a growing corpus of evidence that sulfur has an important role to play in biological symbioses including rhizobia-legumes, mycorrhizae-roots and cyanobacteria-host plants. Furthermore, the fungal and algal partners of <i>L. pulmonaria</i> appear not to have the sulfonate transporter genes again providing the roles of ambient-sulfur (alkanesulfonate metabolism etc.) mediated functions primarily to the cyanobacterial partner. In conclusion, we have addressed here the role of the atmospheric pollutant sulfur dioxide to tripartite cyanolichen viability and suggest that the weaker link is likely to be the photosynthetic algal (chlorophyte) partner and not the nitrogen-fixing cyanobiont.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"71 3","pages":""},"PeriodicalIF":1.3,"publicationDate":"2023-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10441-023-09465-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9425069","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":"The Membrane Potential Has a Primary Key Equation","authors":"Hirohisa Tamagawa,&nbsp;Toi Nakahata,&nbsp;Ren Sugimori,&nbsp;Bernard Delalande,&nbsp;Titus Mulembo","doi":"10.1007/s10441-023-09467-5","DOIUrl":"10.1007/s10441-023-09467-5","url":null,"abstract":"<div><p>It is common to say that the origin of the membrane potential is attributed to transmembrane ion transport, but it is theoretically possible to explain its generation by the mechanism of ion adsorption. It has been previously suggested that the ion adsorption mechanism even leads to potential formulae identical to the famous Nernst equation or the Goldman-Hodgkin-Katz equation. Our further analysis, presented in this paper, indicates that the potential formula based on the ion adsorption mechanism leads to an equation that is a function of the surface charge density of the material and the surface potential of the material. Furthermore, we have confirmed that the equation holds in all the different experimental systems that we have studied. This equation appears to be a key equation that governs the characteristics of the membrane potential in all systems.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"71 3","pages":""},"PeriodicalIF":1.3,"publicationDate":"2023-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9793720","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":"Mathematical Model of Synaptic Long-Term Potentiation as a Bistability in a Chain of Biochemical Reactions with a Positive Feedback","authors":"Pranas Katauskis,&nbsp;Feliksas Ivanauskas,&nbsp;Aidas Alaburda","doi":"10.1007/s10441-023-09466-6","DOIUrl":"10.1007/s10441-023-09466-6","url":null,"abstract":"<div><p>Nitric oxide (NO) is involved in synaptic long-term potentiation (LTP) by multiple signaling pathways. Here, we show that LTP of synaptic transmission can be explained as a feature of signal transduction—bistable behavior in a chain of biochemical reactions with positive feedback, formed by diffusion of NO to the presynaptic site and facilitating the release of glutamate (Glu). The dynamics of Glu, calcium (Ca²⁺) and NO is described by a system of nonlinear reaction–diffusion equations with modified Michaelis–Menten (MM) kinetics. Numerical investigation reveals that the chain of biochemical reactions analyzed can exhibit a bistable behavior under physiological conditions when production of Glu is described by MM kinetics and decay of NO is modeled by means of two enzymatic pathways with different kinetic properties. Our finding extends understanding of the role of NO in LTP: a short high-intensity stimulus is “memorized” as a long-lasting elevation of NO concentration. The conclusions obtained by analysis of the chain of biochemical reactions describing LTP can be generalized to other chains of interactions or for creating the logical elements for biological computers.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"71 3","pages":""},"PeriodicalIF":1.3,"publicationDate":"2023-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10441-023-09466-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9425066","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":"From Minerals to Simplest Living Matter: Life Origination Hydrate Theory","authors":"Elena A. Kadyshevich,&nbsp;Victor E. Ostrovskii","doi":"10.1007/s10441-023-09463-9","DOIUrl":"10.1007/s10441-023-09463-9","url":null,"abstract":"<div><p>Long since, people tried to solve the mystery of the way that led to the appearance and propagation of living entities. However, no harmonious understanding of this mystery existed, because neither the scientifically grounded source minerals nor the ambient conditions were proposed and because it was groundlessly taken that the process of living matter origination is endothermal. The Life Origination Hydrate Theory (LOH-Theory) first suggests the chemical way capable of leading from the specified abundant natural minerals to origination of multitudes of multitudes of simplest living entities and gives an original explanation for the phenomena of chirality and racemization delay. The LOH-Theory covers the period up to origination of the genetic code. The LOH-Theory is grounded on the following three discoveries based on the available information and on the results of our experimental works performed using original instrumentation and computer simulations. (1) There is the only one triad of natural minerals applicable for exothermal thermodynamically possible chemical syntheses of simplest living-matter components. (2) N-base, ribose, and phosphdiester radicals and nucleic acids as whole are size-compatible with structural gas-hydrate cavities. (3) The gas-hydrate structure arises around amido-groups in cooled undisturbed systems consisting of water and highly-concentrated functional polymers with amido-groups.The natural conditions and historic periods favorable for simplest living matter origination are revealed. The LOH-Theory is supported by results of observations, biophysical and biochemical experiments, and wide application of original three-dimensional and two-dimensional computer simulations of biochemical structures within gas-hydrate matrix. The instrumentation and procedures for experimental verification of the LOH-Theory are suggested. If future experiments are successful, they, possibly, could be the first step on the way to industrial synthesis of food from minerals, i.e., to execution of the work that is performed by plants.</p><h3>Graphical Abstract</h3><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"71 2","pages":""},"PeriodicalIF":1.3,"publicationDate":"2023-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10441-023-09463-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9562279","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}