Biosystems最新文献_第5页

Exact burst-size distributions for gene-expression models with complex promoter structure 具有复杂启动子结构的基因表达模型的精确突发大小分布。

IF 2 4区生物学

Biosystems Pub Date : 2024-09-17 DOI: 10.1016/j.biosystems.2024.105337

Liying Zhou , Haowen Chen , Jinqiang Zhang , Jiajun Zhang , Huahai Qiu , Tianshou Zhou

{"title":"Exact burst-size distributions for gene-expression models with complex promoter structure","authors":"Liying Zhou , Haowen Chen , Jinqiang Zhang , Jiajun Zhang , Huahai Qiu , Tianshou Zhou","doi":"10.1016/j.biosystems.2024.105337","DOIUrl":"10.1016/j.biosystems.2024.105337","url":null,"abstract":"<div><div>In prokaryotic and eukaryotic cells, most genes are transcribed in a bursty fashion on one hand and complex gene regulations may lead to complex promoter structure on the other hand. This raises an unsolved issue: how does promoter structure shape transcriptional bursting kinetics characterized by burst size and frequency? Here we analyze stochastic models of gene transcription, which consider complex regulatory mechanisms. Notably, we develop an efficient method to derive exact burst-size distributions. The analytical results show that if the promoter of a gene contains only one active state, the burst size indeed follows a geometric distribution, in agreement with the previous result derived under certain limiting conditions. However, if it contains a multitude of active states, the burst size in general obeys a non-geometric distribution, which is a linearly weighted sum of geometric distributions. This superposition principle reveals the essential feature of bursting kinetics in complex cases of transcriptional regulation although it seems that there has been no direct experimental confirmation. The derived burst-size distributions not only highlight the importance of promoter structure in regulating bursting kinetics, but can be also used in the exact inference of this kinetics based on experimental data.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105337"},"PeriodicalIF":2.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142300082","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

Construction of amino acids reduced alphabets from molecular descriptors for interpretation of N-carbamylase, luciferase and PI3K mutations 根据分子描述符构建氨基酸缩减字母表，用于解释 N-氨基甲酰酶、荧光素酶和 PI3K 突变

IF 2 4区生物学

Biosystems Pub Date : 2024-09-10 DOI: 10.1016/j.biosystems.2024.105331

Tatiana Suárez , Diego F. Montaño , Rosana Suárez

{"title":"Construction of amino acids reduced alphabets from molecular descriptors for interpretation of N-carbamylase, luciferase and PI3K mutations","authors":"Tatiana Suárez , Diego F. Montaño , Rosana Suárez","doi":"10.1016/j.biosystems.2024.105331","DOIUrl":"10.1016/j.biosystems.2024.105331","url":null,"abstract":"<div><p>The classification of amino acids has proven to be a useful tool for understanding the importance of sequence in protein function. The reduced amino acid alphabets are an example of these classifications, which, when built from physicochemical, structural and quantum characteristics of the amino acids, allow it to simplify the representation of the sequences, being useful in the modelling, design and understanding of proteins. So, an objective selection of amino acids properties is important, due classes formed in a reduced alphabet depend on the descriptors used for classification. In this research, based on a careful selection of descriptors for the 20 amino acids, through techniques such as the information content index and hierarchical cluster analysis with ties in proximity, 20,871,586 reduced amino acid alphabets were constructed. This large collection of reduced alphabets was been used to interpret alterations in the function of three proteins: N-carbamylase, Luciferase, and PI3K, caused by amino acid changes in their sequences. For this, the similar and different descriptors linked to these mutations were studied. Properties such as volume, hydrophobicity, charge and autocorrelation can be associated with variations in the behaviour of these proteins, while the frequency in specific secondary structures, the Gibbs free energy and some topological and quantum properties can be considered as the causes of preventing the deactivation of protein function. This work offers the most complete collection of reduced alphabets that promise to be a useful tool for the interpretation of alterations caused by amino acid mutations in the protein sequence.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105331"},"PeriodicalIF":2.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142172669","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

In enzymatic reactions, the reverse reaction reduces product noise 在酶促反应中，逆反应会降低产物噪音

IF 2 4区生物学

Biosystems Pub Date : 2024-09-10 DOI: 10.1016/j.biosystems.2024.105334

Ching-Chu Hsieh , Yung-Chun Lin , Wei-Bo Lin, Che-Chi Shu

引用次数: 0

Analysis of Shannon's entropy to contrast between the Embodied and Neurocentrist hypothesis of conscious experience 分析香农熵，对比意识体验的 "体现 "假说和 "神经中心 "假说。

IF 2 4区生物学

Biosystems Pub Date : 2024-09-05 DOI: 10.1016/j.biosystems.2024.105323

Sergio J. Martínez García , Pablo Padilla Longoria

{"title":"Analysis of Shannon's entropy to contrast between the Embodied and Neurocentrist hypothesis of conscious experience","authors":"Sergio J. Martínez García , Pablo Padilla Longoria","doi":"10.1016/j.biosystems.2024.105323","DOIUrl":"10.1016/j.biosystems.2024.105323","url":null,"abstract":"<div><p>We usually accept that consciousness is in the brain. This statement corresponds to a Neurocentrist view. However, with all the physical and physiological data currently available, a convincing explanation of how consciousness emerges has not been given this topic is aborded by Anil Seth (2021). Because of this, a natural question arises: Is consciousness really in the brain or not? If the answer is no, this corresponds to the Embodied perspective. We cannot discriminate between these two points of view because we cannot identify how the organism processes the information. If we try to measure information processing in the brain, then the Neurocentrist view is unavoidable. For example, the information integration theory of Tononi's research group and the global work area theory developed by Dehaene and Baars, focus solely on the brain without considering aspects of Embodied vision (See Tononi, 2021; Dehaene, 2021). In this article, we propose an index based on Shannon's entropy, capable of identifying the leading processing elements acting: Are they mainly inner or external? In order to validate it, we performed simulations with networks accounting for different amounts of internal and outer layers. Since Shannon's entropy is an abstract measure of the information content, this index is not dependent on the physical network nor the proportion of different layers. Therefore, we validate the index as free of bias. This index is a way to discriminate between Embodied from Neurocentrist hypotheses.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105323"},"PeriodicalIF":2.0,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0303264724002089/pdfft?md5=b544a42da3972658aba1832fc0bd50c7&pid=1-s2.0-S0303264724002089-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142146786","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

In search for evolutionary roots of a mindful cognition: A Darwinian view on sustained intentional awareness 寻找心智认知的进化根源：关于持续有意识的达尔文观点。

IF 2 4区生物学

Biosystems Pub Date : 2024-09-02 DOI: 10.1016/j.biosystems.2024.105321

Emiliano Bruner

{"title":"In search for evolutionary roots of a mindful cognition: A Darwinian view on sustained intentional awareness","authors":"Emiliano Bruner","doi":"10.1016/j.biosystems.2024.105321","DOIUrl":"10.1016/j.biosystems.2024.105321","url":null,"abstract":"<div><p>The attention system underwent important evolutionary changes and specializations in the human genus. In fact, our outstanding social and technological complexity strictly depends on our attentional ability, which is sustained, intentional, and conscious. Attention, intention, and awareness are key features for what can be defined a <em>mindful cognition</em>, and we may wonder whether a specific combination of these cognitive traits may be the result of a natural selective process, or else an accidental by-product of mental complexity. In this article, basic concepts in evolutionary anthropology are reviewed, to consider whether positive, neutral, or negative selective forces might have influenced the evolution of a mindful cognitive ability. At present, all these alternatives are potentially supported by different kinds of evidence. Hybrid hypotheses, considering stabilizing mechanisms or distinct social roles and intra-specific variation, are also likely. An evolutionary approach to the cognitive abilities involved in attention and awareness can reveal potentialities, limitations, and drawbacks of our individual and collective natural behaviors, especially when dealing with the evolution of the human consciousness.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105321"},"PeriodicalIF":2.0,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0303264724002065/pdfft?md5=6142cf91f5ea36f97701fdc162244977&pid=1-s2.0-S0303264724002065-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142134337","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

The genetic code and its p-adic ultrametric modeling 遗传密码及其 p-adic 超参数模型。

IF 2 4区生物学

Biosystems Pub Date : 2024-09-02 DOI: 10.1016/j.biosystems.2024.105322

Branko Dragovich , Nataša Ž. Mišić

引用次数: 0

On the possibility of implementing a quantum entanglement distribution in a biosystem: Microtubules 在生物系统中实现量子纠缠分布的可能性：微管

IF 2 4区生物学

Biosystems Pub Date : 2024-08-28 DOI: 10.1016/j.biosystems.2024.105320

Sergey E. Shirmovsky

引用次数: 0

Advanced technologies and mathematical metacognition: The present and future orientation 先进技术与数学元认知：现在和未来的方向。

IF 2 4区生物学

Biosystems Pub Date : 2024-08-26 DOI: 10.1016/j.biosystems.2024.105312

Alexios Kouzalis , Antonios Antoniou , Nicos Rossides , Rita Panaoura , Priyanka Yadav

{"title":"Advanced technologies and mathematical metacognition: The present and future orientation","authors":"Alexios Kouzalis , Antonios Antoniou , Nicos Rossides , Rita Panaoura , Priyanka Yadav","doi":"10.1016/j.biosystems.2024.105312","DOIUrl":"10.1016/j.biosystems.2024.105312","url":null,"abstract":"<div><p>The intersection of mathematical cognition, metacognition, and advanced technologies presents a frontier with profound implications for human learning and artificial intelligence. This paper traces the historical roots of these concepts from the Pythagoreans and Aristotle to modern cognitive science and explores their relevance to contemporary technological applications. We examine how the Pythagoreans' view of mathematics as fundamental to understanding the universe and Aristotle's contributions to logic and categorization have shaped our current understanding of mathematical cognition and metacognition. The paper investigates the role of Boolean logic in computational processes and its relationship to human logical reasoning, as well as the significance of Bayesian inference and fuzzy logic in modelling uncertainty in human cognition and decision-making. We also explore the emerging field of Chemical Artificial Intelligence and its potential applications. We argue for unifying mathematical metacognition with advanced technologies, including artificial intelligence and robotics, while identifying the multifaceted benefits and challenges of such unification. The present paper examines essential research directions for integrating cognitive sciences and advanced technologies, discussing applications in education, healthcare, and business management. We provide suggestions for developing cognitive robots using specific cognitive tasks and explore the ethical implications of these advancements. Our analysis underscores the need for interdisciplinary collaboration to realize the full potential of this integration while mitigating potential risks.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"245 ","pages":"Article 105312"},"PeriodicalIF":2.0,"publicationDate":"2024-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142057199","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

Corrigendum to “An efficient approach for identifying important biomarkers for biomedical diagnosis” [Biosystems 237 (2024) 105163] 生物医学诊断中重要生物标志物的有效识别方法"[Biosystems 237 (2024) 105163]更正。

IF 2 4区生物学

Biosystems Pub Date : 2024-08-21 DOI: 10.1016/j.biosystems.2024.105286

Jing-Wen Huang , Yan-Hong Chen , Frederick Kin Hing Phoa , Yan-Han Lin , Shau-Ping Lin

引用次数: 0

Why does a cell function? New arguments in favor of quantum effects 细胞为何能发挥作用？支持量子效应的新论点

IF 2 4区生物学

Biosystems Pub Date : 2024-08-20 DOI: 10.1016/j.biosystems.2024.105311

A.V. Melkikh

引用次数: 0