IF 2 4区生物学

Biosystems Pub Date : 2024-11-05 DOI: 10.1016/j.biosystems.2024.105362

Shounan Lu, Yang Wang

引用次数: 0

Human-driven evolution of cultivated plants and the origin of early civilizations: The concept of Neolithic revolution in the works of Nikolai Vavilov. 人类推动的栽培植物进化和早期文明的起源：尼古拉-瓦维洛夫作品中的新石器革命概念。

IF 2 4区生物学

Biosystems Pub Date : 2024-10-30 DOI: 10.1016/j.biosystems.2024.105359

Abir U Igamberdiev

{"title":"Human-driven evolution of cultivated plants and the origin of early civilizations: The concept of Neolithic revolution in the works of Nikolai Vavilov.","authors":"Abir U Igamberdiev","doi":"10.1016/j.biosystems.2024.105359","DOIUrl":"https://doi.org/10.1016/j.biosystems.2024.105359","url":null,"abstract":"<p><p>The concept of centers of origin of cultivated plants (crop biodiversity hotspots) developed by Nikolai Vavilov (1887-1943) is essential for understanding the origin and evolution of human civilization. Vavilov formulated the principles of Neolithic agricultural revolution and substantiated the basic patterns for the emergence of agricultural civilizations. He established that the center of speciation of the plants that have a potential for cultivation determines the origin of primary civilization. Humans actively performed the selection of plants with valuable properties, which led to the formation of new cultivated species and varieties, while the starting point for such unconsciously human-directed evolution was the presence of potentially useful traits due to the increased genetic diversity in the center of origin. The spreading of agriculturally important cultivars from the center of their origin led to the propagation of beneficial farming technologies over large areas. The establishment of human civilization resulted from the dynamic quasi-symbiotic relationship between humans and domesticated plants and animals, which human-driven evolution became an essential factor for the transformation and dynamics of human societies. In the addendum, we present archive materials on the cooperation of Nikolai Vavilov with the historians and ethnologists from the editorial board of the journal \"Novy Vostok\" (\"Nouvel Orient\"). These materials include his letters to Professor Ilya Borozdin.</p>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142565068","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

Complex dynamic behavioral transitions in auditory neurons induced by chaotic activity 听觉神经元在混沌活动诱导下的复杂动态行为转换

IF 2 4区生物学

Biosystems Pub Date : 2024-10-22 DOI: 10.1016/j.biosystems.2024.105358

Guodong Huang, Shu Zhou, Rui Zhu, Yunhai Wang, Yuan Chai

{"title":"Complex dynamic behavioral transitions in auditory neurons induced by chaotic activity","authors":"Guodong Huang, Shu Zhou, Rui Zhu, Yunhai Wang, Yuan Chai","doi":"10.1016/j.biosystems.2024.105358","DOIUrl":"10.1016/j.biosystems.2024.105358","url":null,"abstract":"<div><div>Chaotic sequences are widely used in secure communication due to their high randomness. Chaotic resonance (CR) refers to the resonant response of a system to weak signals induced by chaotic activity, but its practical application remains limited. This study designs a simplified FitzHugh-Nagumo (FHN) auditory neuron model by simulating the physiological activities of auditory neurons and considering the combined stimulation of chaotic activity and sound signals. It is found that the neuron dynamics depend on both external sound stimuli and chaotic current intensity. Chaotic currents induce spikes in the neuron output sequence through CR, and the spikes become more frequent with increasing current intensity, eventually leading to a chaotic state regardless of the initial state. However, the sensitivity of the initial value of this chaotic sequence shifts to the chaotic current excitation system. The injection of chaotic currents can reduce the system's average Hamiltonian energy under certain conditions. By measuring the complexity of the generated sequences, we find that the addition of chaotic currents can enhance the complexity of the original sequences, and the enhancement ability increases with the intensity. This provides a new approach to enhance the complexity of original chaotic sequences. Moreover, different chaotic currents can induce different chaotic sequences with varying abilities to enhance the complexity of the original sequences. We hope our work can contribute to secure communication.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142512370","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

Is there a bias in the codon frequency corresponding to homo-repeats found in human proteins? 人类蛋白质中的同源重复密码子频率是否存在偏差？

IF 2 4区生物学

Biosystems Pub Date : 2024-10-21 DOI: 10.1016/j.biosystems.2024.105357

Nikita V. Dovidchenko , Mikhail Yu. Lobanov , Oxana V. Galzitskaya

{"title":"Is there a bias in the codon frequency corresponding to homo-repeats found in human proteins?","authors":"Nikita V. Dovidchenko , Mikhail Yu. Lobanov , Oxana V. Galzitskaya","doi":"10.1016/j.biosystems.2024.105357","DOIUrl":"10.1016/j.biosystems.2024.105357","url":null,"abstract":"<div><div>It is well known that there is a codon usage bias in genomes, that is, some codons are observed more often than others. Codons implicated in the homo-repeats regions in human proteins are no exception. In this work, we analyzed the codon usage bias for all amino acid residues in homo-repeats larger than 4 in 3753 human proteins from 20447 protein sequences from the canonically reviewed human proteome. We have discovered that almost all homo-repeats in the human proteome, most of which encode Ala, Glu, Gly, Leu, Pro, and Ser (∼80% of all homo-repeats), have a codon usage bias, i.e. are mainly encoded by one codon. Moreover, there is a strong shift in homo-repeats in favor of the content of GC rich codons. Homo-repeats with Ala, Glu, Gly, Leu, Pro, and Ser predominate in the PDB, which has both ordered and disordered status. Examining the distribution of splicing sites, we found that about 15% of homo-repeats either contain or are located within 10 nucleotides of the splicing site, and Glu and Leu predominate in these homo-repeats. Our data is important for future study of the functions of homo-repeats, protein-protein interactions, and evolutionary fitness.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142512371","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

Dynamics of two feed forward genetic motifs in the presence of molecular noise 存在分子噪音时两种前馈遗传模式的动力学。

IF 2 4区生物学

Biosystems Pub Date : 2024-10-20 DOI: 10.1016/j.biosystems.2024.105352

Cooper Doe, David Brown, Hanqing Li

引用次数: 0

Intrinsic structural disorder on proteins is involved in the interactome evolution 蛋白质的内在结构紊乱参与了相互作用组的进化。

IF 2 4区生物学

Biosystems Pub Date : 2024-10-20 DOI: 10.1016/j.biosystems.2024.105351

Diego M. Bustos

引用次数: 0

Reality and imagination intertwined: A sensorimotor paradox interpretation 现实与想象交织：感官运动悖论解读》。

IF 2 4区生物学

Biosystems Pub Date : 2024-10-19 DOI: 10.1016/j.biosystems.2024.105350

Clémence Ortega Douville

{"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":null,"pages":null},"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}

引用次数: 0

Universal dynamical function behind all genetic codes: P-adic attractor dynamical model 所有遗传密码背后的通用动力学函数P-adic 吸引子动力学模型

IF 2 4区生物学

Biosystems Pub Date : 2024-10-18 DOI: 10.1016/j.biosystems.2024.105353

Ekaterina Yurova Axelsson, Andrei Khrennikov

{"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":null,"pages":null},"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}

引用次数: 0

Living cognition and the nature of organisms 生命认知与生物的本质。

IF 2 4区生物学

Biosystems Pub Date : 2024-10-18 DOI: 10.1016/j.biosystems.2024.105356

Breno B. Just , Sávio Torres de Farias

{"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":null,"pages":null},"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}

引用次数: 0

Techno-ethical concerns related to genetic sequencing reports 与基因测序报告有关的技术伦理问题。

IF 2 4区生物学

Biosystems Pub Date : 2024-10-17 DOI: 10.1016/j.biosystems.2024.105354

Zeki Topcu , Sevil Zencir , Matthis Krischel , Heiner Fangerau

{"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":null,"pages":null},"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}

引用次数: 0

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