Acta Biotheoretica最新文献_第8页

Factors in Protobiomonomer Selection for the Origin of the Standard Genetic Code 标准遗传密码起源的原生物单体选择因素

IF 1.3 4区生物学

Acta Biotheoretica Pub Date : 2021-07-20 DOI: 10.1007/s10441-021-09420-4

Alexander I. Saralov

{"title":"Factors in Protobiomonomer Selection for the Origin of the Standard Genetic Code","authors":"Alexander I. Saralov","doi":"10.1007/s10441-021-09420-4","DOIUrl":"10.1007/s10441-021-09420-4","url":null,"abstract":"<div>Natural selection of specific protobiomonomers during abiogenic development of the prototype genetic code is hindered by the diversity of structural, spatial, and rotational isomers that have identical elemental composition and molecular mass (M), but can vary significantly in their physicochemical characteristics, such as the melting temperature Tm, the Tm:M ratio, and the solubility in water, due to different positions of atoms in the molecule. These parameters differ between cis- and trans-isomers of dicarboxylic acids, spatial monosaccharide isomers, and structural isomers of α-, β-, and γ-amino acids. The stable planar heterocyclic molecules of the major nucleobases comprise four (C, H, N, O) or three (C, H, N) elements and contain a single –C=C bond and two nitrogen atoms in each heterocycle involved in C–N and C=N bonds. They exist as isomeric resonance hybrids of single and double bonds and as a mixture of tautomer forms due to the presence of –C=O and/or –NH2 side groups. They are thermostable, insoluble in water, and exhibit solid-state stability, which is of central importance for DNA molecules as carriers of genetic information. In M–Tm diagrams, proteinogenic amino acids and the corresponding codons are distributed fairly regularly relative to the distinct clusters of purine and pyrimidine bases, reflecting the correspondence between codons and amino acids that was established in different periods of genetic code development. The body of data on the evolution of the genetic code system indicates that the elemental composition and molecular structure of protobiomonomers, and their M, Tm, photostability, and aqueous solubility determined their selection in the emergence of the standard genetic code.</div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2021-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10441-021-09420-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39201496","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

What is Causal Specificity About, and What is it Good for in Philosophy of Biology? 因果专一性是什么，对生物学哲学有什么好处?

IF 1.3 4区生物学

Acta Biotheoretica Pub Date : 2021-07-12 DOI: 10.1007/s10441-021-09419-x

María Ferreira Ruiz

引用次数: 0

A Human-Bovine Schistosomiasis Mathematical Model with Treatment and Mollusciciding 人牛血吸虫病的数学模型与治疗和杀螺

IF 1.3 4区生物学

Acta Biotheoretica Pub Date : 2021-06-30 DOI: 10.1007/s10441-021-09416-0

Solomon Kadaleka, Shirley Abelman, Jean M. Tchuenche

{"title":"A Human-Bovine Schistosomiasis Mathematical Model with Treatment and Mollusciciding","authors":"Solomon Kadaleka, Shirley Abelman, Jean M. Tchuenche","doi":"10.1007/s10441-021-09416-0","DOIUrl":"10.1007/s10441-021-09416-0","url":null,"abstract":"<div>To mitigate the spread of schistosomiasis, a deterministic human-bovine mathematical model of its transmission dynamics accounting for contaminated water reservoirs, including treatment of bovines and humans and mollusciciding is formulated and theoretically analyzed. The disease-free equilibrium is locally and globally asymptotically stable whenever the basic reproduction number (R_0<1), while global stability of the endemic equilibrium is investigated by constructing a suitable Lyapunov function. To support the analytical results, parameter values from published literature are used for numerical simulations and where applicable, uncertainty analysis on the non-dimensional system parameters is performed using the Latin Hypercube Sampling and Partial Rank Correlation Coefficient techniques. Sensitivity analysis to determine the relative importance of model parameters to disease transmission shows that the environment-related parameters namely, (varepsilon _s) (snails shedding rate of cercariae), (p_s) (probability that cercariae shed by snails survive), c (fraction of the contaminated environment sprayed by molluscicides) and (mu _c) (mortality rate of cercariae) are the most significant to mitigate the spread of schistosomiasis. Mollusciciding, which directly impacts the contaminated environment as a single control strategy is more effective compared to treatment. However, concurrently applying mollusciciding and treatment will yield a better outcome.</div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2021-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10441-021-09416-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39122894","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

How Do Trees Grow in Girth? Controversy on the Role of Cellular Events in the Vascular Cambium 树木的周长是如何增长的?关于维管形成层中细胞事件作用的争论

IF 1.3 4区生物学

Acta Biotheoretica Pub Date : 2021-06-21 DOI: 10.1007/s10441-021-09418-y

Anna Wilczek-Ponce, Wiesław Włoch, Muhammad Iqbal

{"title":"How Do Trees Grow in Girth? Controversy on the Role of Cellular Events in the Vascular Cambium","authors":"Anna Wilczek-Ponce, Wiesław Włoch, Muhammad Iqbal","doi":"10.1007/s10441-021-09418-y","DOIUrl":"10.1007/s10441-021-09418-y","url":null,"abstract":"<div>Radial growth has long been a subject of interest in tree biology research. Recent studies have brought a significant change in the understanding of some basic processes characteristic to the vascular cambium, a meristem that produces secondary vascular tissues (phloem and xylem) in woody plants. A new hypothesis regarding the mechanism of intrusive growth of the cambial initials, which has been ratified by studies of the arrangement of cambial cells, negates the influence of this apical cell growth on the expansion of the cambial circumference. Instead, it suggests that the tip of the elongating cambial initial intrudes between the tangential (periclinal) walls, rather than the radial (anticlinal) walls, of the initial(s) and its(their) derivative(s) lying ahead of the elongating cell tip. The new concept also explains the hitherto obscure mechanism of the cell event called ‘elimination of initials’. This article evaluates these new concepts of the cambial cell dynamics and offers a new interpretation for some curious events occurring in the cambial meristem in relation to the radial growth in woody plants.</div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2021-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10441-021-09418-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39251752","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}

引用次数: 6

The Effect of Mitochondrial DNA Half-Life on Deletion Mutation Proliferation in Long Lived Cells 线粒体DNA半衰期对长寿细胞中缺失突变增殖的影响

IF 1.3 4区生物学

Acta Biotheoretica Pub Date : 2021-06-15 DOI: 10.1007/s10441-021-09417-z

Alan G. Holt, Adrian M. Davies

{"title":"The Effect of Mitochondrial DNA Half-Life on Deletion Mutation Proliferation in Long Lived Cells","authors":"Alan G. Holt, Adrian M. Davies","doi":"10.1007/s10441-021-09417-z","DOIUrl":"10.1007/s10441-021-09417-z","url":null,"abstract":"<div>The proliferation of mitochondrial DNA (mtDNA) with deletion mutations has been linked to aging and age related neurodegenerative conditions. In this study we model the effect of mtDNA half-life on mtDNA competition and selection. It has been proposed that mutation deletions ((text {mtDNA}_{del})) have a replicative advantage over wild-type ((text {mtDNA}_{wild})) and that this is detrimental to the host cell, especially in post-mitotic cells. An individual cell can be viewed as forming a closed ecosystem containing a large population of independently replicating mtDNA. Within this enclosed environment a selfishly replicating (text {mtDNA}_{del}) would compete with the (text {mtDNA}_{wild}) for space and resources to the detriment of the host cell. In this paper, we use a computer simulation to model cell survival in an environment where (text {mtDNA}_{wild}) compete with (text {mtDNA}_{del}) such that the cell expires upon (text {mtDNA}_{wild}) extinction. We focus on the survival time for long lived post-mitotic cells, such as neurons. We confirm previous observations that (text {mtDNA}_{del}) do have a replicative advantage over (text {mtDNA}_{wild}). As expected, cell survival times diminished with increased mutation probabilities, however, the relationship between survival time and mutation rate was non-linear, that is, a ten-fold increase in mutation probability only halved the survival time. The results of our model also showed that a modest increase in half-life had a profound affect on extending cell survival time, thereby, mitigating the replicative advantage of (text {mtDNA}_{del}). Given the relevance of mitochondrial dysfunction to various neurodegenerative conditions, we propose that therapies to increase mtDNA half-life could significantly delay their onset.</div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2021-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10441-021-09417-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39234655","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: 6

Correction to: Biology and Pragmatism: The Organism-Environment Bond 更正:生物学与实用主义:生物与环境的结合

IF 1.3 4区生物学

Acta Biotheoretica Pub Date : 2021-06-01 DOI: 10.1007/s10441-021-09414-2

David Depew

引用次数: 0

Memory in Ion Channel Kinetics 离子通道动力学中的记忆

IF 1.3 4区生物学

Acta Biotheoretica Pub Date : 2021-05-27 DOI: 10.1007/s10441-021-09415-1

M. P. Silva, C. G. Rodrigues, W. A. Varanda, R. A. Nogueira

{"title":"Memory in Ion Channel Kinetics","authors":"M. P. Silva, C. G. Rodrigues, W. A. Varanda, R. A. Nogueira","doi":"10.1007/s10441-021-09415-1","DOIUrl":"10.1007/s10441-021-09415-1","url":null,"abstract":"<div>Ion channels are transport proteins present in the lipid bilayers of biological membranes. They are involved in many physiological processes, such as the generation of nerve impulses, hormonal secretion, and heartbeat. Conformational changes in the ion channel-forming protein allow the opening or closing of pores to control the ionic flux through the cell membranes. The opening and closing of the ion channel have been classically treated as a random kinetic process, known as a Markov process. Here the time the channel remains in a given state is assumed to be independent of the condition it had in the previous state. More recently, however, several studies have shown that this process is not random but a deterministic one, where both the open and closed dwell-times and the ionic current flowing through the channel are history-dependent. This property is called long memory or long-range correlation. However, there is still much controversy regarding how this memory originates, which region of the channel is responsible for this property, and which models could best reproduce the memory effect. In this article, we provide a review of what is, where it is, its possible origin, and the mathematical methods used to analyze the long-term memory present in the kinetic process of ion channels.</div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2021-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10441-021-09415-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39022954","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: 7

On Predation–Commensalism Processes as Models of Bi-stability and Constructive Role of Systemic Extinctions 捕食-共生过程作为系统灭绝双稳定性和建设性作用的模型

IF 1.3 4区生物学

Acta Biotheoretica Pub Date : 2021-05-13 DOI: 10.1007/s10441-021-09413-3

E. Sanchez-Palencia, J.-P. Françoise

引用次数: 2

Phylogenetic Inference and the Misplaced Premise of Substitution Rates 系统发育推断与取代率的错置前提

IF 1.3 4区生物学

Acta Biotheoretica Pub Date : 2021-05-06 DOI: 10.1007/s10441-021-09412-4

Kirk Fitzhugh

{"title":"Phylogenetic Inference and the Misplaced Premise of Substitution Rates","authors":"Kirk Fitzhugh","doi":"10.1007/s10441-021-09412-4","DOIUrl":"10.1007/s10441-021-09412-4","url":null,"abstract":"<div>Three competing ‘methods’ have been endorsed for inferring phylogenetic hypotheses: parsimony, likelihood, and Bayesianism. The latter two have been claimed superior because they take into account rates of sequence substitution. Can rates of substitution be justified on its own accord in inferences of explanatory hypotheses? Answering this question requires addressing four issues: (1) the aim of scientific inquiry, (2) the nature of why-questions, (3) explanatory hypotheses as answers to why-questions, and (4) acknowledging that neither parsimony, likelihood, nor Bayesianism are inferential actions leading to explanatory hypotheses. The aim of scientific inquiry is to acquire causal understanding of effects. Observation statements of organismal characters lead to implicit or explicit why-questions. Those questions, conveyed in data matrices, assume the truth of observation statements, which is contrary to subsequently invoking substitution rates within inferences to phylogenetic hypotheses. Inferences of explanatory hypotheses are abductive in form, such that some version of an evolutionary theory(ies) is/are included or implied. If rates of sequence evolution are to be considered, it must be done prior to, rather than within abduction, which requires renaming those putatively-shared nucleotides subject to substitution rates. There are, however, no epistemic grounds for renaming characters to accommodate rates, calling into question the legitimacy of causally accounting for sequence data.</div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2021-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10441-021-09412-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38955494","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: 1

A Mathematical Model of the Tuberculosis Epidemic 结核病流行的数学模型

IF 1.3 4区生物学

Acta Biotheoretica Pub Date : 2021-04-20 DOI: 10.1007/s10441-020-09406-8

Ally Yeketi Ayinla, Wan Ainun Mior Othman, Musa Rabiu

{"title":"A Mathematical Model of the Tuberculosis Epidemic","authors":"Ally Yeketi Ayinla, Wan Ainun Mior Othman, Musa Rabiu","doi":"10.1007/s10441-020-09406-8","DOIUrl":"10.1007/s10441-020-09406-8","url":null,"abstract":"<div>Tuberculosis has continued to retain its title as “the captain among these men of death”. This is evident as it is the leading cause of death globally from a single infectious agent. TB as it is fondly called has become a major threat to the achievement of the sustainable development goals (SDG) and hence require inputs from different research disciplines. This work presents a mathematical model of tuberculosis. A compartmental model of seven classes was used in the model formulation comprising of the susceptible S, vaccinated V, exposed E, undiagnosed infectious I1, diagnosed infectious I2, treated T and recovered R. The stability analysis of the model was established as well as the condition for the model to undergo backward bifurcation. With the existence of backward bifurcation, keeping the basic reproduction number less than unity (({R_{0}}<1)) is no more sufficient to keep TB out of the community. Hence, it is shown by the analysis that vaccination program, diagnosis and treatment helps to control the TB dynamics. In furtherance to that, it is shown that preference should be given to diagnosis over treatment as diagnosis precedes treatment. It is as well shown that at lower vaccination rate (0–20%), TB would still be endemic in the population. As such, high vaccination rate is required to send TB out of the community.</div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2021-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10441-020-09406-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38891053","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: 7