Biosystems最新文献_第2页

A workflow for the hybrid modelling and simulation of multi-timescale biological systems 多时间尺度生物系统混合建模与仿真工作流程。

IF 2 4区生物学

Biosystems Pub Date : 2024-11-22 DOI: 10.1016/j.biosystems.2024.105365

Mostafa Herajy , Fei Liu , Monika Heiner

引用次数: 0

The existence of the two domains of life, Bacteria and Archaea, would in itself imply that LUCA and the ancestors of these domains were progenotes 细菌和古细菌这两个生命领域的存在本身就意味着 LUCA 和这些领域的祖先是原生生物。

IF 2 4区生物学

Biosystems Pub Date : 2024-11-21 DOI: 10.1016/j.biosystems.2024.105375

Massimo Di Giulio

{"title":"The existence of the two domains of life, Bacteria and Archaea, would in itself imply that LUCA and the ancestors of these domains were progenotes","authors":"Massimo Di Giulio","doi":"10.1016/j.biosystems.2024.105375","DOIUrl":"10.1016/j.biosystems.2024.105375","url":null,"abstract":"<div><div>The length of the deepest branches of the tree of life would tend to support the hypothesis that the distance of the branch that separates the sequences of archaea from those of bacteria, i.e. the interdomain one, is longer than the intradomain ones, i.e. those that separate the sequences of archaea and those of bacteria within them. Why should interdomain distance be larger than intradomain distances? The fact that the rate of amino acid substitutions was slowed as the domains of life appeared would seem to imply an evolutionary transition. The slowdown in the speed of evolution that occurred during the formation of the two domains of life would be the consequence of the progenote- > cell evolutionary transition. Indeed, the evolutionary stage of the progenote being characterized by an accelerated tempo and mode of evolution might explain the considerable interdomain distance because the accumulation of many amino acid substitutions on this branch would indicate the progenote stage that is also characterized by a high rate of amino acid substitutions. Furthermore, the fact that intradomain distances are smaller than interdomain distances would corroborate the hypothesis of the achievement of cellularity at the appearance of the main phyletic lineages. Indeed, the cell stage, unlike the progenotic one, definitively establishes the relationship between the genotype and phenotype, lowering the rate of evolution. Therefore, the arguments presented lead to the conclusion that LUCA was a progenote.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"247 ","pages":"Article 105375"},"PeriodicalIF":2.0,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142693809","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

Benchmark for quantitative characterization of circadian clock cycles 昼夜节律时钟周期定量表征的基准。

IF 2 4区生物学

Biosystems Pub Date : 2024-11-17 DOI: 10.1016/j.biosystems.2024.105363

Odile Burckard , Michèle Teboul , Franck Delaunay , Madalena Chaves

{"title":"Benchmark for quantitative characterization of circadian clock cycles","authors":"Odile Burckard , Michèle Teboul , Franck Delaunay , Madalena Chaves","doi":"10.1016/j.biosystems.2024.105363","DOIUrl":"10.1016/j.biosystems.2024.105363","url":null,"abstract":"<div><div>Understanding circadian clock mechanisms is fundamental in order to counteract the harmful effects of clock malfunctioning and associated diseases. Biochemical, genetic and systems biology approaches have provided invaluable information on the mechanisms of the circadian clock, from which many mathematical models have been developed to understand the dynamics and quantitative properties of the circadian oscillator. To better analyze and compare quantitatively all these circadian cycles, we propose a method based on a previously proposed circadian cycle segmentation into stages. We notably identify a sequence of eight stages that characterize the progress of the circadian cycle. Next, we apply our approach to an experimental dataset and to five different models, all built with ordinary differential equations. Our method permits to assess the agreement of mathematical model cycles with biological properties or to detect some inconsistencies. As another application of our method, we provide insights on how this segmentation into stages can help to analyze the effect of a clock gene loss of function on the dynamic of a genetic oscillator. The strength of our method is to provide a benchmark for characterization, comparison and improvement of new mathematical models of circadian oscillators in a wide variety of model systems.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"247 ","pages":"Article 105363"},"PeriodicalIF":2.0,"publicationDate":"2024-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142649571","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

Sensing, feeling and sentience in unicellular organisms and living cells 单细胞生物和活细胞的感知、感觉和知觉。

IF 2 4区生物学

Biosystems Pub Date : 2024-11-17 DOI: 10.1016/j.biosystems.2024.105374

F. Baluška , W.B. Miller , P. Slijepcevic , A.S. Reber

引用次数: 0

Senescence, change, and competition: When the desire to pick one model harms our understanding 衰老、变化和竞争：当选择一种模式的欲望损害了我们的理解力时。

IF 2 4区生物学

Biosystems Pub Date : 2024-11-12 DOI: 10.1016/j.biosystems.2024.105364

André C.R. Martins

{"title":"Senescence, change, and competition: When the desire to pick one model harms our understanding","authors":"André C.R. Martins","doi":"10.1016/j.biosystems.2024.105364","DOIUrl":"10.1016/j.biosystems.2024.105364","url":null,"abstract":"<div><div>The question of why we age is a fundamental one. It is about who we are, and it also might have critical practical aspects as we try to find ways to age slower. Or to not age at all. Different reasons point at distinct strategies for the research of anti-aging drugs. While the main reason why biological systems work as they do is evolution, for quite a while, it was believed that aging required another explanation. Aging seems to harm individuals so much that even if it has group benefits, those benefits were unlikely to be enough. That has led many scientists to propose non-evolutionary explanations as to why we age. But those theories seem to fail at explaining all the data on how species age. Here, I will show that the insistence of finding the one idea that explains it all might be at the root of the difficulty of getting a full picture. By exploring an evolutionary model of aging where locality and temporal changes are fundamental aspects of the problem, I will show that environmental change causes the barrier for group advantages to become much weaker. That weakening might help small group advantages to add up to the point they could make an adaptive difference. To answer why we age, we might have to abandon asking which models are correct. The full answer might come from considering how much each hypothesis behind each existing model, evolutionary and non-evolutionary ones, contributes to the real world’s solution.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"247 ","pages":"Article 105364"},"PeriodicalIF":2.0,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142632119","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

The Neurobehavioral State hypothesis 神经行为状态假说。

IF 2 4区生物学

Biosystems Pub Date : 2024-11-08 DOI: 10.1016/j.biosystems.2024.105361

Luis Fernando Ontiveros-Araiza

{"title":"The Neurobehavioral State hypothesis","authors":"Luis Fernando Ontiveros-Araiza","doi":"10.1016/j.biosystems.2024.105361","DOIUrl":"10.1016/j.biosystems.2024.105361","url":null,"abstract":"<div><div>Since the early attempts to understand the brain made by Greek philosophers more than 2000 years ago, one of the main questions in neuroscience has been how the brain perceives all the stimuli in the environment and uses this information to implement a response. Recent hypotheses of the neural code rely on the existence of an ideal observer, whether on specific areas of the cerebral cortex or distributed network composed of cortical and subcortical elements. The Neurobehavioral State hypothesis stipulates that neurons are in a quasi-stable state due to the dynamic interaction of their molecular components. This increases their computational capabilities and electrophysiological behavior further than a binary active/inactive state. Together, neuronal populations across the brain learn to identify and associate internal and external stimuli with actions and emotions. Furthermore, such associations can be stored through the regulation of neuronal components as new quasi-stable states. Using this framework, behavior arises as the result of the dynamic interaction between internal and external stimuli together with previously established quasi-stable states that delineate the behavioral response. Finally, the Neurobehavioral State hypothesis is firmly grounded on present evidence of the complex dynamics within the brain, from the molecular to the network level, and avoids the need for a central observer by proposing the brain configures itself through experience-driven associations.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"247 ","pages":"Article 105361"},"PeriodicalIF":2.0,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142632070","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

Exploring the spatial effects influencing the EGFR/ERK pathway dynamics with machine learning surrogate models 利用机器学习代用模型探索影响表皮生长因子受体/表皮生长受体激酶通路动态的空间效应。

IF 2 4区生物学

Biosystems Pub Date : 2024-11-07 DOI: 10.1016/j.biosystems.2024.105360

Juan A. Garcia, Anass Bouchnita

{"title":"Exploring the spatial effects influencing the EGFR/ERK pathway dynamics with machine learning surrogate models","authors":"Juan A. Garcia, Anass Bouchnita","doi":"10.1016/j.biosystems.2024.105360","DOIUrl":"10.1016/j.biosystems.2024.105360","url":null,"abstract":"<div><div>The fate of cells is regulated by biochemical reactions taking place inside of them, known as intracellular pathways. Cells display a variety of characteristics related to their shape, structure and contained fluid, which influences the diffusion of proteins and their interactions. To gain insights into the spatial effects shaping intracellular regulation, we apply machine learning (ML) to explore a previously developed spatial model of the epidermal growth factor receptor (EGFR) signaling. The model describes the reactions between molecular species inside of cells following the transient activation of EGF receptors. To train our ML models, we conduct 10,000 numerical simulations in parallel where we calculate the cumulative activation of molecules and transcription factors under various conditions such as different diffusion speeds, inactivation rates, and cell structures. We take advantage of the low computational cost of ML algorithms to investigate the effects of cell and nucleus sizes, the diffusion speed of proteins, and the inactivation rate of the Ras molecules on the activation strength of transcription factors. Our results suggest that the predictions by both neural networks and random forests yielded minimal mean square error (MSEs), while linear generalized models displayed a significantly larger MSE. The exploration of the surrogate models has shown that smaller cell and nucleus radii as well, larger diffusion coefficients, and reduced inactivation rates increase the activation of transcription factors. These results are confirmed by numerical simulations. Our ML algorithms can be readily incorporated within multiscale models of tumor growth to embed the spatial effects regulating intracellular pathways, enabling the use of complex cell models within multiscale models while reducing the computational cost.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"247 ","pages":"Article 105360"},"PeriodicalIF":2.0,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142632109","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

Adjustment of link weights based on tolerance promotes cooperation in spatial prisoner's dilemma game 根据容忍度调整链接权重，促进空间囚徒困境博弈中的合作。

IF 2 4区生物学

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

Shounan Lu , Yang Wang

{"title":"Adjustment of link weights based on tolerance promotes cooperation in spatial prisoner's dilemma game","authors":"Shounan Lu , Yang Wang","doi":"10.1016/j.biosystems.2024.105362","DOIUrl":"10.1016/j.biosystems.2024.105362","url":null,"abstract":"<div><div>Understanding and explaining cooperative behavior in human society has become an open question. In this paper, we propose a dynamic adjustment of pair relationships in a spatial prisoner's dilemma game. Unlike previous studies that individuals dynamically adjust the intensity of interaction with their opponents at each step, this work consider tolerance, in which the intensity of interaction is adjusted when the time of successive defections by an individual exceeds a tolerance threshold <em>T</em>. We find that although the proposed mechanism can significantly improve cooperation compared to traditional versions, a higher tolerance for continuous defection behavior is not conducive to the evolution of cooperation. Furthermore, an environmental adaptor that dynamically adjusts the paired relationship with the opponent at all times is beneficial for the evolution of cooperation. And the higher the degree of adjustment in the paired relationship, the lower the probability of continuous exploitation by defector. We hope that our work can provide some insights into explaining the existence and maintenance of cooperation.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105362"},"PeriodicalIF":2.0,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142606475","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

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":"10.1016/j.biosystems.2024.105359","url":null,"abstract":"<div><div>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 the 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.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"247 ","pages":"Article 105359"},"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":"OA","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":"246 ","pages":"Article 105358"},"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