Biosystems最新文献

英文中文

Novel amino acid distance matrices based on conductance measure 基于电导测量的新型氨基酸距离矩阵

IF 2 4区生物学 Q2 BIOLOGY

Biosystems

Pub Date : 2024-10-17 DOI: 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。

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引用次数: 0

Genetic code, the problem of coding biological cycles, and cyclic Gray codes 遗传密码、生物循环编码问题和循环格雷码

IF 2 4区生物学 Q2 BIOLOGY

Biosystems

Pub Date : 2024-10-10 DOI: 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.

本文专门讨论生物体中遗传循环结构的基因编码问题，生物体的生命活动是建立在一套巨大的相互协调的遗传循环过程基础之上的。作者提出并论证了这样一个观点：遗传编码系统之所以能够对遗传循环过程进行编码，是因为它本身就是一个与布尔逻辑代数相连的循环编码系统。换句话说，有关的生理过程是循环的，因为它们是由循环码遗传编码的。为了支持这一观点，作者介绍了他在遗传编码系统与循环格雷码之间的联系方面取得的一系列成果。这为使用与格雷码相关的代数和逻辑理论及构造来模拟遗传循环生物结构提供了可能性，而这些理论和构造早已用于工程技术领域：卡尔诺图、希尔伯特曲线、哈达玛矩阵、沃尔什函数、二元分析等。作者认为，在研究遗传密码的起源、演变和功能时，有必要考虑到遗传系统对许多相互关联的循环过程进行编码的能力。

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引用次数: 0

A mathematical framework for the statistical interpretation of biological growth models 生物生长模型统计解释的数学框架。

IF 2 4区生物学 Q2 BIOLOGY

Biosystems

Pub Date : 2024-10-09 DOI: 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.

生物实体本身就是动态的。因此，各种生态学科都使用数学模型来描述时间演化。通常情况下，生长曲线被建模为西格玛模型，其演化由常微分方程模拟。在各种 sigmoid 模型中，Logistic 方程、Gompertz 方程和 Richards 方程已被广泛应用于生物学和生态学领域的生长数据拟合。本文提出了人口增长模型统计分析的数学框架。分析以种群与环境关系的数学模型为基础，并详细讨论了该模型的理论基础。通过应用这一理论，可以得到随机演化方程，其中逻辑方程、贡珀茨方程、理查兹方程和桦树方程代表了极限情况。为了证实人口增长动力学模型，介绍了数值模拟的结果。结果表明，各种人口增长模型都能以类似的方式加以解决。我们认为，所讨论的对种群-环境联合演化进行统计解释的数学框架是一个很有前途的进一步研究途径。

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引用次数: 0

From RNA to DNA: Emergence of reverse transcriptases from an ancestral RNA-dependent RNA polymerase 从 RNA 到 DNA：从依赖 RNA 的原始 RNA 聚合酶到逆转录酶的出现。

IF 2 4区生物学 Q2 BIOLOGY

Biosystems

Pub Date : 2024-09-28 DOI: 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。

引用次数: 0

Reflexive neural circuits and the origin of language and music codes 反射神经回路与语言和音乐代码的起源。

IF 2 4区生物学 Q2 BIOLOGY

Biosystems

Pub Date : 2024-09-28 DOI: 10.1016/j.biosystems.2024.105346

Abir U. Igamberdiev

Conscious activity is grounded in the reflexive self-awareness in sense perception, through which the codes signifying sensual perceptive events operate and constrain human behavior. These codes grow via the creative generation of hypertextual statements. We apply the model of Vladimir Lefebvre (Lefebvre, V.A., 1987, J. Soc. Biol. Struct. 10, 129–175) to reveal the underlying structures on which the perception and creative development of language and music codes are based. According to this model, the reflexive structure of conscious subject is grounded in three thermodynamic cycles united by the control of the basic functional cycle by the second one, and resulting in the internal action that it turn is perceived by the third cycle evaluating this action. In this arrangement, the generative language structures are formed and the frequencies of sounds that form musical phrases and patterns are selected. We discuss the participation of certain neural brain structures and the establishment of reflexive neural circuits in the ad hoc transformation of perceptive signals, and show the similarities between the processes of perception and of biological self-maintenance and morphogenesis. We trace the peculiarities of the temporal encoding of emotions in music and musical creativity, as well as the principles of sharing musical information between the performing and the perceiving individuals.

意识活动以感官知觉中的反射性自我意识为基础，通过感官知觉事件的代码运作和约束人类行为。这些代码通过创造性地生成超文本语句而发展。我们运用弗拉基米尔-勒菲弗（Vladimir Lefebvre, V.A.，1987 年，《社会生物结构》杂志，10, 129-175）的模型来揭示语言和音乐代码的感知和创造性发展所基于的基本结构。根据这一模型，有意识主体的反射结构建立在三个热力学循环的基础上，通过第二个循环对基本功能循环的控制而结合在一起，并产生内部动作，而这一动作又被评估这一动作的第三个循环所感知。在这种安排下，生成语言结构得以形成，构成乐句和模式的声音频率得以选择。我们讨论了某些大脑神经结构的参与以及反射神经回路在感知信号临时转换过程中的建立，并展示了感知过程与生物自我维护和形态发生过程之间的相似之处。我们追溯了音乐和音乐创作中情感时间编码的特殊性，以及表演者和感知者之间共享音乐信息的原则。

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引用次数: 0

William Bateson, black slavery, eugenics and speciation: The relative roles of politics and science 威廉-贝特森、黑人奴隶制、优生学和物种繁衍：政治与科学的相对作用。

IF 2 4区生物学 Q2 BIOLOGY

Biosystems

Pub Date : 2024-09-28 DOI: 10.1016/j.biosystems.2024.105348

Donald R. Forsdyke

The peace of the world is challenged by societal confrontations that can often be labeled “racial” or “ethnic.” Emblematic of this is discrimination based on skin colour. William Bateson's background suggests sympathy with the black emancipation movement. Yet the movement's success is attributed more to battles between political figures than between scientists with contending views on the biology of racial differences. However, in the long term, Bateson's contributions to slavery and eugenic issues may be seen as no less important than those of politicians. Mendel's discovery of what we now know as “genes” languished until seized upon by Bateson in 1900. For six exhausting years he struggled to win scientific acceptance of these biological character-determining units. Later, he pressed the Mendelian message home to the general public, opposing simplistic applications of Mendelian principles to human affairs, and arguing that minor genic differences that distinguished “races” – e.g. skin colour – do not initiate new species. Bateson praised the “physiological selection” speciation hypothesis of Darwin's young research associate, George Romanes. This enthusiasm was rekindled by Robert Lock and formulated in modern terms with C. R. Crowther. Thus, the spark that initiates a divergence into two species can be non-genic. This normal form of hybrid sterility, based on genome-wide DNA sequence differences, operates on, but has not succeeded in dividing, the human species. It should not be labeled “idiopathic,” and be clearly distinguished both from pathological sterility and undiagnosed sterilities that may prove to be pathological. We are one reproductively isolated population, the human species.

世界的和平受到了社会对抗的挑战，这些对抗往往被冠以 "种族 "或 "民族 "的标签。其中的代表就是基于肤色的歧视。威廉-贝特森的背景表明他同情黑人解放运动。然而，这场运动的成功更多地归功于政治人物之间的争斗，而不是对种族差异的生物学观点有争议的科学家之间的争斗。然而，从长远来看，贝特森对奴隶制和优生问题的贡献可能并不亚于政治家的贡献。孟德尔发现了我们现在所知的 "基因"，但这一发现一直被束之高阁，直到 1900 年被贝特森发现。在长达六年的艰苦奋斗中，他努力争取科学界接受这些决定生物特征的单位。后来，他向公众宣传孟德尔学说，反对将孟德尔原理简单地应用于人类事务，并认为区分 "种族 "的微小基因差异（如肤色）并不能创造新物种。贝特森赞扬了达尔文的年轻研究助手乔治-罗曼尼斯（George Romanes）提出的 "生理选择 "物种形成假说。罗伯特-洛克（Robert Lock）重新点燃了这种热情，C-R-克劳瑟（C. R. Crowther）则用现代术语对其进行了表述。因此，引发两个物种分化的火花可能是非基因性的。这种基于全基因组 DNA 序列差异的正常形式的杂交不育在人类物种中发生，但并未成功分裂。它不应被称为 "特发性不育"，而应与病理不育和可能被证明为病理的未诊断不育明确区分开来。我们人类是一个在生殖上孤立的群体。

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引用次数: 0

Avian influenza A H5N1 hemagglutinin protein models have distinct structural patterns re-occurring across the 1959–2023 strains 禽流感甲型 H5N1 血凝素蛋白模型在 1959-2023 株中重复出现不同的结构模式。

IF 2 4区生物学 Q2 BIOLOGY

Biosystems

Pub Date : 2024-09-28 DOI: 10.1016/j.biosystems.2024.105347

Marni E. Cueno, Noriaki Kamio, Kenichi Imai

Influenza A H5N1 hemagglutinin (HA) plays a crucial role in viral pathogenesis and changes in the HA receptor binding domain (RBD) have been attributed to alterations in viral pathogenesis. Mutations often occur within the HA which in-turn results in HA structural changes that consequently contribute to protein evolution. However, the possible occurrence of mutations that results to reversion of the HA protein (going back to an ancestral protein conformation) which in-turn creates distinct HA structural patterns across the 1959–2023 H5N1 viral evolution has never been investigated. Here, we generated and verified the quality of the HA models, identified similar HA structural patterns, and elucidated the possible variations in HA RBD structural dynamics. Our results show that there are 7 distinct structural patterns occurring among the 1959–2023 H5N1 HA models which suggests that reversion of the HA protein putatively occurs during viral evolution. Similarly, we found that the HA RBD structural dynamics vary among the 7 distinct structural patterns possibly affecting viral pathogenesis.

甲型流感 H5N1 血凝素（HA）在病毒致病过程中起着至关重要的作用，HA 受体结合域（RBD）的变化被认为是病毒致病过程发生改变的原因。HA内部经常发生突变，从而导致HA结构发生变化，进而促进蛋白质的进化。然而，在 1959-2023 年的 H5N1 病毒进化过程中，可能发生的突变导致 HA 蛋白的还原（回到祖先的蛋白构象），进而产生不同的 HA 结构模式，这种情况从未被研究过。在此，我们生成并验证了 HA 模型的质量，确定了相似的 HA 结构模式，并阐明了 HA RBD 结构动态中可能存在的变化。我们的结果表明，1959-2023 年的 H5N1 HA 模型有 7 种不同的结构模式，这表明在病毒进化过程中，HA 蛋白可能发生了还原。同样，我们发现在这 7 种不同的结构模式中，HA RBD 结构动态也各不相同，这可能会影响病毒的致病机理。

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引用次数: 0

A novel hypothesis about mechanism of thalidomide action on pattern formation 沙利度胺对模式形成作用机制的新假设

IF 2 4区生物学 Q2 BIOLOGY

Biosystems

Pub Date : 2024-09-26 DOI: 10.1016/j.biosystems.2024.105344

Denis Touroutine , Nadya Morozova

Morphogenesis, the complex process governing the formation of functional living structures, is regulated by a multitude of molecular mechanisms at various levels. While research in recent decades has shed light on many pathways involved in morphogenesis, none singularly accounts for the precise geometric shapes of organisms and their components in space. To bridge this conceptual gap between specific molecular mechanisms and the creation of definitive morphological forms, we have proposed the "epigenetic code hypothesis" in our previous work. In this framework, "epigenetic" means any inheritable cellular information beyond the genetic code that regulates cell fate alongside genetic information. In this study, we conduct a comprehensive analysis of thalidomide's teratogenic effects through the lens of our proposed "epigenetic code" theory, revealing significant indirect support for our hypothesis. We also explore the structural and functional parallels between thalidomide and auxin.

形态发生是控制生物功能结构形成的复杂过程，受不同层次的多种分子机制调控。虽然近几十年来的研究已经揭示了形态发生的多种途径，但没有一种途径能单独解释生物体及其组成部分在空间中的精确几何形状。为了弥合特定分子机制与确定形态的形成之间的概念差距，我们在之前的工作中提出了 "表观遗传密码假说"。在这一框架中，"表观遗传 "指的是遗传密码之外的任何可遗传的细胞信息，这些信息与遗传信息一起调控着细胞的命运。在本研究中，我们通过我们提出的 "表观遗传密码 "理论，对沙利度胺的致畸效应进行了全面分析，结果显示我们的假说得到了重要的间接支持。我们还探讨了沙利度胺与辅酶在结构和功能上的相似之处。

引用次数: 0

Intelligence: Natural, artificial, or what? 智能：自然智能、人工智能还是什么？

IF 2 4区生物学 Q2 BIOLOGY

Biosystems

Pub Date : 2024-09-26 DOI: 10.1016/j.biosystems.2024.105343

Ron Cottam, Roger Vounckx

We consider the competing attributes of natural intelligence (NI) and artificial intelligence (AI). Attention is paid to conceptual, theoretical, stylistic and structural aspects of both, and non-human intelligence. Intelligence is related to information processing and current views of physical structuring. Means of distinguishing between NI and AI are noted, and neural and digital structures are described. Pribram's bi-computational neural networks are introduced, and high-level Pribram computation is discussed. We describe the hierarchical Aquarium scheme, along with an AI implementation, and conclude with a proposition for future quantum-based artificial intelligence.

我们考虑了自然智能（NI）和人工智能（AI）的竞争属性。我们关注自然智能和非人类智能的概念、理论、风格和结构方面。智能与信息处理和当前的物理结构观点有关。指出了区分非人类智能和人工智能的方法，并描述了神经和数字结构。介绍了普里布拉姆的双计算神经网络，并讨论了高级普里布拉姆计算。我们描述了分层水瓶计划以及人工智能的实现，最后提出了未来基于量子的人工智能的命题。

引用次数: 0

A control measure for epidemic spread based on the susceptible–infectious–susceptible (SIS) model 基于易感-传染-易感（SIS）模型的流行病传播控制措施。

IF 2 4区生物学 Q2 BIOLOGY

Biosystems

Pub Date : 2024-09-25 DOI: 10.1016/j.biosystems.2024.105341

Jin-Xuan Yang, Haiyan Wang, Xin Li, Ying Tan, Yongjuan Ma, Min Zeng

When an epidemic occurs in a network, finding the important links and cutting them off is an effective measure for preventing the spread of the epidemic. Traditional methods that remove important links easily lead to a disconnected network, inevitably incurring high costs arising from quarantining individuals or communities in a real-world network. In this study, we combine the clustering coefficient and the eigenvector to identify the important links using the susceptible–infectious–susceptible (SIS) model. The results show that our approach can improve the epidemic threshold while maintaining the connectivity of the network to control the spread of the epidemic. Experiments on multiple real-world and synthetic networks of varying sizes, demonstrate the effectiveness and scalability of our approach.

当网络中发生流行病时，找到并切断重要链接是防止流行病传播的有效措施。传统的去除重要链接的方法容易导致网络断开，在现实世界的网络中，隔离个体或群体不可避免地会产生高昂的成本。在本研究中，我们结合聚类系数和特征向量，利用易感-传染-易感（SIS）模型来识别重要链接。结果表明，我们的方法可以提高流行病阈值，同时保持网络的连通性，从而控制流行病的传播。在多个真实世界和不同规模的合成网络上进行的实验证明了我们方法的有效性和可扩展性。

引用次数: 0

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