Pub Date : 2024-10-20DOI: 10.1016/j.biosystems.2024.105352
Cooper Doe, David Brown, Hanqing Li
Understanding the function of common motifs in gene regulatory networks is an important goal of systems biology. Feed forward loops (FFLs) are an example of such a motif. In FFLs, a gene (X) regulates another gene (Z) both directly and via an intermediary gene (Y). Previous theoretical studies have suggested several possible functions for FFLs, based on their transient responses to changes in input signals (using deterministic models) and their fluctuations around steady state (using stochastic models). In this paper we study stochastic models of the two most common FFLs, “coherent type 1” and “incoherent type 1”. We incorporate molecular noise by treating DNA binding, transcription, translation, and decay as stochastic processes. By comparing the dynamics of these loops with models of alternative networks (in which X does not regulate Y), we explore how FFLs act to process information in the presence of noise. This work highlights the importance of incorporating realistic molecular noise in studying both the transient and steady-state behavior of gene regulatory networks.
{"title":"Dynamics of two feed forward genetic motifs in the presence of molecular noise","authors":"Cooper Doe, David Brown, Hanqing Li","doi":"10.1016/j.biosystems.2024.105352","DOIUrl":"10.1016/j.biosystems.2024.105352","url":null,"abstract":"<div><div>Understanding the function of common motifs in gene regulatory networks is an important goal of systems biology. Feed forward loops (FFLs) are an example of such a motif. In FFLs, a gene (X) regulates another gene (Z) both directly and via an intermediary gene (Y). Previous theoretical studies have suggested several possible functions for FFLs, based on their transient responses to changes in input signals (using deterministic models) and their fluctuations around steady state (using stochastic models). In this paper we study stochastic models of the two most common FFLs, “coherent type 1” and “incoherent type 1”. We incorporate molecular noise by treating DNA binding, transcription, translation, and decay as stochastic processes. By comparing the dynamics of these loops with models of alternative networks (in which X does not regulate Y), we explore how FFLs act to process information in the presence of noise. This work highlights the importance of incorporating realistic molecular noise in studying both the transient and steady-state behavior of gene regulatory networks.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105352"},"PeriodicalIF":2.0,"publicationDate":"2024-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142479897","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}
Pub Date : 2024-10-20DOI: 10.1016/j.biosystems.2024.105351
Diego M. Bustos
New mathematical tools help understand cell functions, adaptability, and evolvability to discover hidden variables to predict phenotypes that could be tested in the future in wet labs. Different models have been successfully used to discover the properties of the protein-protein interaction networks or interactomes. I found that in the hyperbolic Popularity-Similarity model, cellular proteins with the highest contents of structural intrinsic disorder cluster together in many different eukaryotic interactomes and this is not the case for the prokaryotic E. coli, where proteins with high degree of intrinsic disorder are scarce. I also found that the normalized theta variable from the Popularity-Similarity model for orthologues proteins correlate to the complexity of the organisms in analysis.
{"title":"Intrinsic structural disorder on proteins is involved in the interactome evolution","authors":"Diego M. Bustos","doi":"10.1016/j.biosystems.2024.105351","DOIUrl":"10.1016/j.biosystems.2024.105351","url":null,"abstract":"<div><div>New mathematical tools help understand cell functions, adaptability, and evolvability to discover hidden variables to predict phenotypes that could be tested in the future in wet labs. Different models have been successfully used to discover the properties of the protein-protein interaction networks or interactomes. I found that in the hyperbolic Popularity-Similarity model, cellular proteins with the highest contents of structural intrinsic disorder cluster together in many different eukaryotic interactomes and this is not the case for the prokaryotic <em>E. coli,</em> where proteins with high degree of intrinsic disorder are scarce. I also found that the normalized theta variable from the Popularity-Similarity model for orthologues proteins correlate to the complexity of the organisms in analysis.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105351"},"PeriodicalIF":2.0,"publicationDate":"2024-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142479898","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}
Pub Date : 2024-10-19DOI: 10.1016/j.biosystems.2024.105350
Clémence Ortega Douville
As a hypothesis on the origins of mind and language, the evolutionary theory of the sensorimotor paradox suggests that capacities for imagination, self-representation and abstraction would operate from a dissociation in what is known as the forward model. In some studies, sensory perception is understood as a system of prediction and confirmation (feedforward and feedback processes) that would share common yet distinct and overlapping neural networks with mental imagery. The latter would then mostly operate through internal feedback processes. The hypothesis of our theory is that dissociation and parallelism between those processes would make it less likely for imaginary prediction to match and simultaneously coincide with any sensory feedback, contradicting the stimulus/response pattern. The gap between the two and the effort required to maintain this gap, born from the development of bipedal stance and a radical change to our relation to our own hands, would be the very structural foundation to our capacity to elaborate abstract thoughts, by partially blocking and inhibiting motor action. Mental imagery would structurally be dissociated from perception, though maintaining an intricated relation of interdependence. Moreover, the content of the images would be subordinate to their function as emotional regulators, prioritising consistency with some global, conditional and socially learnt body-image. As a higher-level and proto-aesthetic function, we can speculate that the action and instrumentalisation of dissociating imagination from perception would become the actual prediction and their coordination, the expected feedback.
{"title":"Reality and imagination intertwined: A sensorimotor paradox interpretation","authors":"Clémence Ortega Douville","doi":"10.1016/j.biosystems.2024.105350","DOIUrl":"10.1016/j.biosystems.2024.105350","url":null,"abstract":"<div><div>As a hypothesis on the origins of mind and language, the evolutionary theory of the sensorimotor paradox suggests that capacities for imagination, self-representation and abstraction would operate from a dissociation in what is known as the forward model. In some studies, sensory perception is understood as a system of prediction and confirmation (feedforward and feedback processes) that would share common yet distinct and overlapping neural networks with mental imagery. The latter would then mostly operate through internal feedback processes. The hypothesis of our theory is that dissociation and parallelism between those processes would make it less likely for imaginary prediction to match and simultaneously coincide with any sensory feedback, contradicting the stimulus/response pattern. The gap between the two and the effort required to maintain this gap, born from the development of bipedal stance and a radical change to our relation to our own hands, would be the very structural foundation to our capacity to elaborate abstract thoughts, by partially blocking and inhibiting motor action. Mental imagery would structurally be dissociated from perception, though maintaining an intricated relation of interdependence. Moreover, the content of the images would be subordinate to their function as emotional regulators, prioritising consistency with some global, conditional and socially learnt body-image. As a higher-level and proto-aesthetic function, we can speculate that the action and instrumentalisation of dissociating imagination from perception would become the actual prediction and their coordination, the expected feedback.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105350"},"PeriodicalIF":2.0,"publicationDate":"2024-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142479900","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}
Pub Date : 2024-10-18DOI: 10.1016/j.biosystems.2024.105353
Ekaterina Yurova Axelsson, Andrei Khrennikov
The genetic code is a map which gives the correspondence between codons in DNA and amino acids. In the attractor dynamical model (ADM), genetic codes can be described as the sets of the cyclic attractors of discrete dynamical systems - the iterations of functions acting in the ring of 2-adic integers This ring arises from representation of nucleotides by binary vectors and hence codons by triples of binary vectors. We construct a Universal Function such that the dynamical functions for all known genetic codes can be obtained from by simple transformations on the set of codon cycles - the “Addition” and “Division” operations. ADM can be employed for study of phylogenetic dynamics of genetic codes. One can speculate that the “common ancestor genetic code” was caused by We remark that this function has 24 cyclic attractors which distribution coincides with the distribution for the hypothetical pre-LUCA code. This coupling of the Universal Function with the pre-LUCA code assigns the genetic codes evolution perspective to ADM. All genetic codes are generated from through the special chains of the “Addition” and “Division” operations. The challenging problem is to assign the biological meaning to these mathematical operations.
遗传密码是 DNA 密码子与氨基酸之间的对应关系图。在吸引子动力学模型（ADM）中，遗传密码可以描述为离散动力系统的循环吸引子集--作用于二元整数环 Z2 的函数迭代。二进制向量表示核苷酸，二进制向量的三元组表示密码子，从而产生了这个环。我们构建了一个通用函数 B，通过对密码子循环集的简单变换--"加法 "和 "除法 "运算--可以从 B 得到所有已知遗传密码的动力学函数。ADM 可用于研究遗传密码的系统发育动力学。我们可以推测，"共同祖先遗传密码 "是由 B 引起的。我们注意到，该函数有 24 个循环吸引子，其分布与假定的前 LUCA 密码的分布相吻合。通用函数与前 LUCA 代码的这种耦合将遗传密码进化的视角赋予了 ADM。所有遗传密码都是通过 "加法 "和 "除法 "运算的特殊链从 B 生成的。如何为这些数学运算赋予生物学意义是一个具有挑战性的问题。
{"title":"Universal dynamical function behind all genetic codes: P-adic attractor dynamical model","authors":"Ekaterina Yurova Axelsson, Andrei Khrennikov","doi":"10.1016/j.biosystems.2024.105353","DOIUrl":"10.1016/j.biosystems.2024.105353","url":null,"abstract":"<div><div>The genetic code is a map which gives the correspondence between codons in DNA and amino acids. In the attractor dynamical model (ADM), genetic codes can be described as the sets of the cyclic attractors of discrete dynamical systems - the iterations of functions acting in the ring of 2-adic integers <span><math><mrow><msub><mrow><mi>Z</mi></mrow><mrow><mn>2</mn></mrow></msub><mo>.</mo></mrow></math></span> This ring arises from representation of nucleotides by binary vectors and hence codons by triples of binary vectors. We construct a Universal Function <span><math><mi>B</mi></math></span> such that the dynamical functions for all known genetic codes can be obtained from <span><math><mi>B</mi></math></span> by simple transformations on the set of codon cycles - the “Addition” and “Division” operations. ADM can be employed for study of phylogenetic dynamics of genetic codes. One can speculate that the “common ancestor genetic code” was caused by <span><math><mrow><mi>B</mi><mo>.</mo></mrow></math></span> We remark that this function has 24 cyclic attractors which distribution coincides with the distribution for the hypothetical pre-LUCA code. This coupling of the Universal Function with the pre-LUCA code assigns the genetic codes evolution perspective to ADM. All genetic codes are generated from <span><math><mi>B</mi></math></span> through the special chains of the “Addition” and “Division” operations. The challenging problem is to assign the biological meaning to these mathematical operations.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105353"},"PeriodicalIF":2.0,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142479902","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}
Pub Date : 2024-10-18DOI: 10.1016/j.biosystems.2024.105356
Breno B. Just , Sávio Torres de Farias
There is no consensus about what cognition is. Different perspectives conceptualize it in different ways. In the same vein, there is no agreement about which systems are truly cognitive. This begs the question, what makes a process or a system cognitive? One of the most conspicuous features of cognition is that it is a set of processes. Cognition, in the end, is a collection of processes such as perception, memory, learning, decision-making, problem-solving, goal-directedness, attention, anticipation, communication, and maybe emotion. There is a debate about what they mean, and which systems possess these processes. One aspect of this problem concerns the level at which cognition and the single processes are conceptualized. To make this scenario clear, evolutionary and self-maintenance arguments are taken. Given the evolutive landscape, one sees processes shared by all organisms and their derivations in specific taxa. No matter which side of the complexity spectrum one favors, the similarities of the simple processes with the complex ones cannot be ignored, and the differences of some complex processes with their simple versions cannot be blurred. A final cognitive framework must make sense of both sides of the spectrum, their differences and similarities. Here, we discuss from an evolutionary perspective the basic elements shared by all living beings and whether these may be necessary and sufficient for understanding the cognitive process. Following these considerations, cognition can be expanded to every living being. Cognition is the set of informational and dynamic processes an organism must interact with and grasp aspects of its world. Understood at their most basic level, perception, memory, learning, problem-solving, decision-making, action, and other cognitive processes are basic features of biological functioning.
{"title":"Living cognition and the nature of organisms","authors":"Breno B. Just , Sávio Torres de Farias","doi":"10.1016/j.biosystems.2024.105356","DOIUrl":"10.1016/j.biosystems.2024.105356","url":null,"abstract":"<div><div>There is no consensus about what cognition is. Different perspectives conceptualize it in different ways. In the same vein, there is no agreement about which systems are truly cognitive. This begs the question, what makes a process or a system cognitive? One of the most conspicuous features of cognition is that it is a set of processes. Cognition, in the end, is a collection of processes such as perception, memory, learning, decision-making, problem-solving, goal-directedness, attention, anticipation, communication, and maybe emotion. There is a debate about what they mean, and which systems possess these processes. One aspect of this problem concerns the level at which cognition and the single processes are conceptualized. To make this scenario clear, evolutionary and self-maintenance arguments are taken. Given the evolutive landscape, one sees processes shared by all organisms and their derivations in specific taxa. No matter which side of the complexity spectrum one favors, the similarities of the simple processes with the complex ones cannot be ignored, and the differences of some complex processes with their simple versions cannot be blurred. A final cognitive framework must make sense of both sides of the spectrum, their differences and similarities. Here, we discuss from an evolutionary perspective the basic elements shared by all living beings and whether these may be necessary and sufficient for understanding the cognitive process. Following these considerations, cognition can be expanded to every living being. Cognition is the set of informational and dynamic processes an organism must interact with and grasp aspects of its world. Understood at their most basic level, perception, memory, learning, problem-solving, decision-making, action, and other cognitive processes are basic features of biological functioning.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105356"},"PeriodicalIF":2.0,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142479903","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}
Recombinant DNA technologies of the current era, most of which are comparable to past works of science fiction, have had diverse and significant impacts on social life. Among them, genetic sequencing deserves particular attention. The widespread use of genetic testing has raised numerous concerns regarding autonomy, confidentiality and privacy. In this context, the proliferation of ‘gene for X’ reports influences debates about the potentially beneficial or detrimental uses of genetics. While several studies have reported concerns related to the collection, storage and use of genetic data, few have considered the technical shortcomings that can affect the reliability of interpretation of sequencing data. In this essay, we will cover some of the current practices of genetic testing and safety aspects of DNA data. To evaluate the reliability of DNA data we will raise the question whether an ‘overestimation’ of researchers' results might reflect an ‘underestimation’ of our genetic make-up in terms of the limitations of the parameters necessary for the correct interpretation of genomic DNA. Following that question we will highlight the responsibility of researchers for proper science communication to avoid misleading information about genetic sequencing data.
当今时代的 DNA 重组技术（其中大部分堪比过去的科幻小说）对社会生活产生了多种多样的重大影响。其中，基因测序尤其值得关注。基因检测的广泛使用引起了人们对自主权、保密性和隐私权的诸多关注。在这种情况下，"X 基因 "报告的激增影响了关于基因的潜在有益或有害用途的辩论。虽然有几项研究报告了与基因数据的收集、储存和使用有关的问题，但很少有人考虑到可能影响测序数据解读可靠性的技术缺陷。在本文中，我们将介绍目前基因检测的一些做法和 DNA 数据的安全问题。为了评估 DNA 数据的可靠性，我们将提出这样一个问题：研究人员对结果的 "高估 "是否反映了我们对基因构成的 "低估"，即正确解读基因组 DNA 所需的参数的局限性。在这个问题之后，我们将强调研究人员有责任进行正确的科学交流，以避免基因测序数据信息的误导性。
{"title":"Techno-ethical concerns related to genetic sequencing reports","authors":"Zeki Topcu , Sevil Zencir , Matthis Krischel , Heiner Fangerau","doi":"10.1016/j.biosystems.2024.105354","DOIUrl":"10.1016/j.biosystems.2024.105354","url":null,"abstract":"<div><div>Recombinant DNA technologies of the current era, most of which are comparable to past works of science fiction, have had diverse and significant impacts on social life. Among them, genetic sequencing deserves particular attention. The widespread use of genetic testing has raised numerous concerns regarding autonomy, confidentiality and privacy. In this context, the proliferation of ‘gene for X’ reports influences debates about the potentially beneficial or detrimental uses of genetics. While several studies have reported concerns related to the collection, storage and use of genetic data, few have considered the technical shortcomings that can affect the reliability of interpretation of sequencing data. In this essay, we will cover some of the current practices of genetic testing and safety aspects of DNA data. To evaluate the reliability of DNA data we will raise the question whether an ‘overestimation’ of researchers' results might reflect an ‘underestimation’ of our genetic make-up in terms of the limitations of the parameters necessary for the correct interpretation of genomic DNA. Following that question we will highlight the responsibility of researchers for proper science communication to avoid misleading information about genetic sequencing data.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105354"},"PeriodicalIF":2.0,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142479901","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}
Pub Date : 2024-10-17DOI: 10.1016/j.biosystems.2024.105355
Nikola Štambuk , Elena Fimmel , Paško Konjevoda , Krunoslav Brčić-Kostić , Antonija Gračanin , Hadi Saleh
Ancestral relationships among biological species are often represented and analyzed by means of phylogenetic trees. Substitution and distance matrices are two main types of matrices that are used in phylogeny analyses. Substitution matrices describe a frequency change of amino acids in nucleotide or protein sequence over time, while distance matrices estimate phylogeny using a matrix of pairwise distances based on a particular code or analytical concept. Recent investigation by Elena Fimmel and coworkers (Life 11:1338, 2021) showed that: 1. the robustness of a genetic code against point mutations can be described using the conductance measure, and 2. all possible point mutations of the genetic code can be represented as a weighted graph with weights that correspond to the probabilities of these mutations. In this article, we constructed and tested three novel distance matrices based on conductance measure, that take into account the point mutation robustness of the Standard Genetic Code (SGC). These distance matrices are based on maximum (CMAX), average (CAVG), and minimum (CMIN) conductance-optimized distances between codons coding for individual amino acids. The performance of those distance matrices was tested on a dataset of RecA proteins in Bacteria, Archaea (RadA homolog) and Eukarya (Rad51 homolog). RecA protein and its functional homologs were selected for this investigation since they are essential for the repair and maintenance of DNA, and consequently well conserved and present in all domains of life. PAM250 and BLOSUM62 matrices were usually used as a standard for distance matrix testing. PAM250 and BLOSUM62 substitution matrices specified accurately three biological domains of life according to Carl Woese and George Fox (Proc Natl Acad Sci U S A 74:5088, 1977). An identical result was obtained using three novel distance matrices (CMIN, CMAX, CAVG). This result supports the applicability of novel distance matrices based on the conductance method and suggests that further investigations based on this approach are justified.
生物物种之间的始祖关系通常通过系统发生树来表示和分析。取代矩阵和距离矩阵是系统发生分析中使用的两种主要矩阵。替代矩阵描述的是核苷酸或蛋白质序列中氨基酸随着时间推移而发生的频率变化，而距离矩阵则根据特定的代码或分析概念，利用成对距离矩阵来估计系统发生。Elena Fimmel 及其同事的最新研究（Life 11:1338, 2021）表明：1：1.遗传密码对点突变的稳健性可以用电导测量来描述；2.遗传密码所有可能的点突变都可以用加权图来表示，加权图的权重与这些突变的概率相对应。在本文中，我们构建并测试了三个基于电导测量的新型距离矩阵，它们考虑到了标准遗传密码（SGC）的点突变鲁棒性。这些距离矩阵基于编码单个氨基酸的密码子之间的最大（CMAX）、平均（CAVG）和最小（CMIN）电导优化距离。这些距离矩阵的性能在细菌、古生菌（RadA 同源物）和真核生物（Rad51 同源物）的 RecA 蛋白数据集上进行了测试。本次研究选择了 RecA 蛋白及其功能同源物，因为它们对 DNA 的修复和维护至关重要，因此在所有生命领域中都得到了很好的保护。PAM250 和 BLOSUM62 矩阵通常用作距离矩阵测试的标准。根据 Carl Woese 和 George Fox 的研究（Proc Natl Acad Sci U S A 74:5088，1977 年），PAM250 和 BLOSUM62 取代矩阵准确地指定了生命的三个生物领域。使用三个新的距离矩阵（CMIN、CMAX、CAVG）也得到了相同的结果。这一结果证明了基于电导法的新型距离矩阵的适用性，并表明基于这种方法的进一步研究是合理的。
{"title":"Novel amino acid distance matrices based on conductance measure","authors":"Nikola Štambuk , Elena Fimmel , Paško Konjevoda , Krunoslav Brčić-Kostić , Antonija Gračanin , Hadi Saleh","doi":"10.1016/j.biosystems.2024.105355","DOIUrl":"10.1016/j.biosystems.2024.105355","url":null,"abstract":"<div><div>Ancestral relationships among biological species are often represented and analyzed by means of phylogenetic trees. Substitution and distance matrices are two main types of matrices that are used in phylogeny analyses. Substitution matrices describe a frequency change of amino acids in nucleotide or protein sequence over time, while distance matrices estimate phylogeny using a matrix of pairwise distances based on a particular code or analytical concept. Recent investigation by Elena Fimmel and coworkers (Life 11:1338, 2021) showed that: 1. the robustness of a genetic code against point mutations can be described using the conductance measure, and 2. all possible point mutations of the genetic code can be represented as a weighted graph with weights that correspond to the probabilities of these mutations. In this article, we constructed and tested three novel distance matrices based on conductance measure, that take into account the point mutation robustness of the Standard Genetic Code (SGC). These distance matrices are based on maximum (CMAX), average (CAVG), and minimum (CMIN) conductance-optimized distances between codons coding for individual amino acids. The performance of those distance matrices was tested on a dataset of RecA proteins in <em>Bacteria</em>, <em>Archaea</em> (RadA homolog) and <em>Eukarya</em> (Rad51 homolog). RecA protein and its functional homologs were selected for this investigation since they are essential for the repair and maintenance of DNA, and consequently well conserved and present in all domains of life. PAM250 and BLOSUM62 matrices were usually used as a standard for distance matrix testing. PAM250 and BLOSUM62 substitution matrices specified accurately three biological domains of life according to Carl Woese and George Fox (Proc Natl Acad Sci U S A 74:5088, 1977). An identical result was obtained using three novel distance matrices (CMIN, CMAX, CAVG). This result supports the applicability of novel distance matrices based on the conductance method and suggests that further investigations based on this approach are justified.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105355"},"PeriodicalIF":2.0,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142479899","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}
Pub Date : 2024-10-10DOI: 10.1016/j.biosystems.2024.105349
Sergey V. Petoukhov
This article is devoted to the problem of genetically coding of inherited cyclic structures in biological bodies, whose life activity is based on a great inherited set of mutually coordinated cyclic processes. The author puts forward and arguments the idea that the genetic coding system is capable of encoding inherited cyclic processes because it itself is a system of cyclic codes connected with Boolean algebra of logic. In other words, the physiological processes in question are cyclical because they are genetically encoded by cyclic codes. In support of this idea, the author presents a set of his results on the connection of the genetic coding system with cyclic Gray codes, which are one of many known types of cyclic codes. This opens up the possibility of using for modeling inherited cyclic biostructures those algebraic and logical theories and constructions that are associated with Gray codes and have long been used in engineering technologies: Karnaugh maps, Hilbert curve, Hadamard matrices, Walsh functions, dyadic analysis, etc. The author believes that when studying the origin, evolution and function of the genetic code, it is necessary to take into account the ability of the genetic system to encode many mutually related cyclic processes.
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Pub Date : 2024-10-09DOI: 10.1016/j.biosystems.2024.105342
A. Samoletov, B. Vasiev
Biological entities are inherently dynamic. As such, various ecological disciplines use mathematical models to describe temporal evolution. Typically, growth curves are modelled as sigmoids, with the evolution modelled by ordinary differential equations. Among the various sigmoid models, the logistic, Gompertz and Richards equations are well-established and widely used for the purpose of fitting growth data in the fields of biology and ecology. The present paper puts forth a mathematical framework for the statistical analysis of population growth models. The analysis is based on a mathematical model of the population–environment relationship, the theoretical foundations of which are discussed in detail. By applying this theory, stochastic evolutionary equations are obtained, for which the logistic, Gompertz, Richards and Birch equations represent a limiting case. To substantiate the models of population growth dynamics, the results of numerical simulations are presented. It is demonstrated that a variety of population growth models can be addressed in a comparable manner. It is suggested that the discussed mathematical framework for statistical interpretation of the joint population–environment evolution represents a promising avenue for further research.
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Pub Date : 2024-09-28DOI: 10.1016/j.biosystems.2024.105345
Sávio Torres de Farias , Ana Karoline Nunes-Alves , Marco José
The transition from RNA as the informational molecule of primordial biological systems to the DNA genomes of modern organisms represents one of the greatest evolutionary transitions in the history of life. One way to understand this transition is to comprehend the origin of the enzymes responsible for the metabolism of nucleic acid polymers. In the present work, we reconstructed the ancestral sequence of RNA-dependent DNA polymerase (RdDp) and modeled its structure. The data demonstrate that, in terms of primary sequence, the ancestral sequences exhibit characteristic elements of RdDp; however, structurally, they are more similar to RNA-dependent RNA polymerase (RdRp). The presented data suggest that RdDp may have originated through modifications and neofunctionalization from an RdRp-like ancestor.
从原始生物系统的信息分子 RNA 到现代生物的 DNA 基因组，是生命史上最伟大的进化转变之一。理解这一转变的方法之一是了解负责核酸聚合物新陈代谢的酶的起源。在本研究中，我们重建了依赖 RNA 的 DNA 聚合酶（RdDp）的祖先序列，并对其结构进行了建模。数据表明，在主序列方面，祖先序列表现出 RdDp 的特征元素；但在结构上，它们与 RNA 依赖性 RNA 聚合酶（RdRp）更为相似。所提供的数据表明，RdDp 可能是通过修改和新功能化从类似 RdRp 的祖先起源的。
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