Biosystems最新文献_第6页

How evolution makes us age: Introducing the evolvable soma theory of ageing 进化如何让我们衰老：介绍可进化的衰老理论。

IF 2 4区生物学

Biosystems Pub Date : 2024-07-20 DOI: 10.1016/j.biosystems.2024.105271

Alessandro Fontana, Marios Kyriazis

{"title":"How evolution makes us age: Introducing the evolvable soma theory of ageing","authors":"Alessandro Fontana, Marios Kyriazis","doi":"10.1016/j.biosystems.2024.105271","DOIUrl":"10.1016/j.biosystems.2024.105271","url":null,"abstract":"<div><p>At any moment in time, evolution is faced with a formidable challenge: refining the already highly optimised design of biological species, a feat accomplished through all preceding generations. In such a scenario, the impact of random changes (the method employed by evolution) is much more likely to be harmful than advantageous, potentially lowering the reproductive fitness of the affected individuals. Our hypothesis is that ageing is, at least in part, caused by the cumulative effect of all the experiments carried out by evolution to improve a species’ design. These experiments are almost always unsuccessful, as expected given their pseudorandom nature, cause harm to the body and ultimately lead to death. This hypothesis is consistent with the concept of “terminal addition”, by which nature is biased towards adding innovations at the end of development. From the perspective of evolution as an optimisation algorithm, ageing is advantageous as it allows to test innovations during a phase when their impact on fitness is present but less pronounced. Our inference suggests that ageing has a key biological role, as it contributes to the system’s evolvability by exerting a regularisation effect on the fitness landscape of evolution.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141749574","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 Molecular Basis of Differentiation Wave Activity in Embryogenesis 胚胎发生过程中分化波活动的分子基础 Bradly Alicea.

IF 2 4区生物学

Biosystems Pub Date : 2024-07-20 DOI: 10.1016/j.biosystems.2024.105272

Bradly Alicea , Suroush Bastani , Natalie K. Gordon , Susan Crawford-Young , Richard Gordon

{"title":"The Molecular Basis of Differentiation Wave Activity in Embryogenesis","authors":"Bradly Alicea , Suroush Bastani , Natalie K. Gordon , Susan Crawford-Young , Richard Gordon","doi":"10.1016/j.biosystems.2024.105272","DOIUrl":"10.1016/j.biosystems.2024.105272","url":null,"abstract":"<div><p>As development varies greatly across the tree of life, it may seem difficult to suggest a model that proposes a single mechanism for understanding collective cell behaviors and the coordination of tissue formation. Here we propose a mechanism called differentiation waves, which unify many disparate results involving developmental systems from across the tree of life. We demonstrate how a relatively simple model of differentiation proceeds not from function-related molecular mechanisms, but from so-called differentiation waves. A phenotypic model of differentiation waves is introduced, and its relation to molecular mechanisms is proposed. These waves contribute to a differentiation tree, which is an alternate way of viewing cell lineage and local action of the molecular factors. We construct a model of differentiation wave-related molecular mechanisms (genome, epigenome, and proteome) based on bioinformatic data from the nematode <em>Caenorhabditis elegans</em>. To validate this approach across different modes of development, we evaluate protein expression across different types of development by comparing <em>Caenorhabditis elegans</em> with several model organisms: fruit flies (<em>Drosophila melanogaster</em>), yeast (<em>Saccharomyces cerevisiae</em>), and mouse (<em>Mus musculus</em>). Inspired by gene regulatory networks, two Models of Interactive Contributions (fully-connected MICs and ordered MICs) are used to suggest potential genomic contributions to differentiation wave-related proteins. This, in turn, provides a framework for understanding differentiation and development.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141735631","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

A p− adic approach to the TSPO gene TSPO 基因的 p- Adic 方法。

IF 2 4区生物学

Biosystems Pub Date : 2024-07-19 DOI: 10.1016/j.biosystems.2024.105273

Elif Esenoğlu Bilgin , Dilek Pirim , Gökhan Soydan

{"title":"A p− adic approach to the TSPO gene","authors":"Elif Esenoğlu Bilgin , Dilek Pirim , Gökhan Soydan","doi":"10.1016/j.biosystems.2024.105273","DOIUrl":"10.1016/j.biosystems.2024.105273","url":null,"abstract":"<div><p>TSPO protein is known to be involved in various cellular functions and dysregulations of TSPO expression has been found to be associated with pathologies of different human diseases, including cardiovascular disease, cancer, neuroinflammatory, neurodegenerative, neoplastic disorders. However, there are limited studies in the literature on the effects of sequence variations in the <em>TSPO</em> gene on the function of the protein and their relationship with human diseases. Evaluating the pathogenicity of genetic variants is crucial in terms of prioritizing the functional importance and clinical use. Therefore, various <em>in-silico</em> prediction tools have been developed that combine different algorithms to predict the effects of sequence variations on protein functions or gene regulation. In this study, the <span><math><mi>p</mi></math></span>-adic distance approach in modeling the genetic code, proposed and developed by Dragovich and Dragovich, was discussed in order to obtain an alternative to the existing <em>in-silico</em> prediction tools. Dragovichs’ approach is expressed as follows: A 5-adic space of codons is constructed and 5-adic and 2-adic distances between codons are taken into account. As a result, two codons with the smallest value of 5-adic and 2-adic distances are obtained, encoded for the same amino acid and stop signal. This model describes well the degeneration of the genetic code. This study combined the data obtained from <em>in-silico</em> prediction tools and used a bioinformatics approach to determine the functional relevance of coding SNPs in the TSPO. Overall, we evaluate the potential utility of Dragovichs’ approach by comparing it with other existing prediction tools for variant classification and prioritization.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141735629","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

Social satisficing: Multi-agent reinforcement learning with satisﬁcing agents 社会满意：满足型代理的多代理强化学习

IF 2 4区生物学

Biosystems Pub Date : 2024-07-19 DOI: 10.1016/j.biosystems.2024.105276

Daisuke Uragami , Noriaki Sonota , Tatsuji Takahashi

{"title":"Social satisficing: Multi-agent reinforcement learning with satisﬁcing agents","authors":"Daisuke Uragami , Noriaki Sonota , Tatsuji Takahashi","doi":"10.1016/j.biosystems.2024.105276","DOIUrl":"10.1016/j.biosystems.2024.105276","url":null,"abstract":"<div><p>For a reinforcement learning agent to finish trial-and-error in a realistic time duration, it is necessary to limit the scope of exploration during the learning process. However, limiting the exploration scope means limitation in optimality: the agent could fall into a suboptimal solution. This is the nature of local, bottom-up way of learning. An alternative way is to set a goal to be achieved, which is a more global, top-down way. The risk-sensitive satisﬁcing (RS) value function incorporate, as a method of the latter way, the satisficing principle into reinforcement learning and enables agents to quickly converge to exploiting the optimal solution without falling into a suboptimal one, when an appropriate goal (aspiration level) is given. However, how best to determine the aspiration level is still an open problem. This study proposes social satisficing, a framework for multi-agent reinforcement learning which determines the aspiration level through information sharing among multiple agents. In order to verify the effectiveness of this novel method, we conducted simulations in a learning environment with many suboptimal goals (SuboptimaWorld). The results show that the proposed method, which converts the aspiration level at the episodic level into local (state-wise) aspiration levels, possesses a higher learning efficiency than any of the compared methods, and that the novel method has the ability to autonomously adjust exploration scope, while keeping the shared information minimal. This study provides a glimpse into an aspect of human and biological sociality which has been mentioned little in the context of artificial intelligence and machine learning.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0303264724001618/pdfft?md5=1013f746e0723d63b95dde32bc8a58b3&pid=1-s2.0-S0303264724001618-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141735630","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 physics of the urge to have freedom 渴望自由的物理学。

IF 2 4区生物学

Biosystems Pub Date : 2024-07-18 DOI: 10.1016/j.biosystems.2024.105277

Adrian Bejan

引用次数: 0

Circular cut codes in genetic information 遗传信息中的循环切割代码

IF 2 4区生物学

Biosystems Pub Date : 2024-07-04 DOI: 10.1016/j.biosystems.2024.105263

{"title":"Circular cut codes in genetic information","authors":"","doi":"10.1016/j.biosystems.2024.105263","DOIUrl":"10.1016/j.biosystems.2024.105263","url":null,"abstract":"<div><p>In this work we present an analysis of the dinucleotide occurrences in the three codon sites 1–2, 2–3 and 1–3, based on a computation of the codon usage of three large sets of bacterial, archaeal and eukaryotic genes using the same method that identified a maximal <span><math><msup><mrow><mi>C</mi></mrow><mrow><mn>3</mn></mrow></msup></math></span> self-complementary trinucleotide circular code <span><math><mi>X</mi></math></span> in genes of bacteria and eukaryotes in 1996 (Arquès and Michel, 1996). Surprisingly, two dinucleotide circular codes are identified in the codon sites 1–2 and 2–3. Furthermore, these two codes are shifted versions of each other. Moreover, the dinucleotide code in the codon site 1–3 is circular, self-complementary and contained in the projection of <span><math><mi>X</mi></math></span> onto the 1st and 3rd bases, i.e. by cutting the middle base in each codon of <span><math><mi>X</mi></math></span>. We prove several results showing that the circularity and the self-complementarity of trinucleotide codes is induced by the circularity and the self-complementarity of its dinucleotide cut codes. Finally, we present several evolutionary approaches for an emergence of trinucleotide codes from dinucleotide codes.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141545510","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

Cosmos MIND and matter: Is mind in spacetime? COSMOS 心灵与物质：时空中有心灵吗？

IF 2 4区生物学

Biosystems Pub Date : 2024-07-03 DOI: 10.1016/j.biosystems.2024.105262

{"title":"Cosmos MIND and matter: Is mind in spacetime?","authors":"","doi":"10.1016/j.biosystems.2024.105262","DOIUrl":"10.1016/j.biosystems.2024.105262","url":null,"abstract":"<div><p>We attempt in this article to formulate a conceptual and testable framework weaving Cosmos, Mind and Matter into a whole. We build on three recent discoveries, each requiring more evidence: i. The particles of the Standard Model, SU(3) x SU(2) x U(1), are formally capable of collective autocatalysis. This leads us to ask what roles such autocatalysis may have played in Cosmogenesis, and in trying to answer, Why our Laws? Why our Constants? A capacity of the particles of SU(3) x SU(2) x U(1) for collective autocatalysis may be open to experimental test, stunning if confirmed. ii. Reasonable evidence now suggests that matter can expand spacetime. The first issue is to establish this claim at or beyond 5 sigma if that can be done. If true, this process may elucidate Dark Matter, Dark Energy and Inflation and require alteration of Einstein's Field Equations. Cosmology would be transformed. iii. Evidence at 6.49 Sigma suggests that mind can alter the outcome of the two-slit experiment. If widely and independently verified, the foundations of quantum mechanics must be altered. Mind plays a role in the universe. That role may include Cosmic Mind.</p></div><div><h3>Our considerations concern</h3><p>1. Ontologically Real Potentia and the Unmanifest; 2. Nonlocality as Fundamental; 3. Res potentia, Res extensa, and Actualization; 4. Mind and Qualia, Mind is not in Spacetime; 5. Quantum Vacuum = Potentia not in Spacetime = Mind not in Spacetime; 6. Mind can Actualize Potentia; 7. The emergence of the classical world; 8. Co-evolution of evermore complex matter; 9. Why “My Mind”?; 10. Each embodied mind is coupled bilaterally to the Quantum Vacuum that is Cosmic Mind; 11. Responsible Free Will.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0303264724001473/pdfft?md5=f99bce285540a5f70cacd37f359e0364&pid=1-s2.0-S0303264724001473-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141538882","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

Machine-learning-based structural analysis of interactions between antibodies and antigens 基于机器学习的抗体与抗原相互作用结构分析。

IF 2 4区生物学

Biosystems Pub Date : 2024-07-02 DOI: 10.1016/j.biosystems.2024.105264

Grace Zhang , Xiaohan Kuang , Yuhao Zhang , Yunchao Liu , Zhaoqian Su , Tom Zhang , Yinghao Wu

{"title":"Machine-learning-based structural analysis of interactions between antibodies and antigens","authors":"Grace Zhang , Xiaohan Kuang , Yuhao Zhang , Yunchao Liu , Zhaoqian Su , Tom Zhang , Yinghao Wu","doi":"10.1016/j.biosystems.2024.105264","DOIUrl":"10.1016/j.biosystems.2024.105264","url":null,"abstract":"<div><p>Computational analysis of paratope-epitope interactions between antibodies and their corresponding antigens can facilitate our understanding of the molecular mechanism underlying humoral immunity and boost the design of new therapeutics for many diseases. The recent breakthrough in artificial intelligence has made it possible to predict protein-protein interactions and model their structures. Unfortunately, detecting antigen-binding sites associated with a specific antibody is still a challenging problem. To tackle this challenge, we implemented a deep learning model to characterize interaction patterns between antibodies and their corresponding antigens. With high accuracy, our model can distinguish between antibody-antigen complexes and other types of protein-protein complexes. More intriguingly, we can identify antigens from other common protein binding regions with an accuracy of higher than 70% even if we only have the epitope information. This indicates that antigens have distinct features on their surface that antibodies can recognize. Additionally, our model was unable to predict the partnerships between antibodies and their particular antigens. This result suggests that one antigen may be targeted by more than one antibody and that antibodies may bind to previously unidentified proteins. Taken together, our results support the precision of antibody-antigen interactions while also suggesting positive future progress in the prediction of specific pairing.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141535857","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

Quantum-like environment adaptive model for creation of phenotype 创造表型的类量子环境适应模型

IF 2 4区生物学

Biosystems Pub Date : 2024-07-02 DOI: 10.1016/j.biosystems.2024.105261

Andrei Khrennikov , Satoshi Iryama , Irina Basieva , Keiko Sato

{"title":"Quantum-like environment adaptive model for creation of phenotype","authors":"Andrei Khrennikov , Satoshi Iryama , Irina Basieva , Keiko Sato","doi":"10.1016/j.biosystems.2024.105261","DOIUrl":"10.1016/j.biosystems.2024.105261","url":null,"abstract":"<div><p>The textbook conceptualization of phenotype creation, “genotype (G) + environment (E) + genotype & environment interactions (GE) <span><math><mo>↦</mo></math></span> phenotype (Ph)”, is modeled with open quantum systems theory (OQST) or more generally with adaptive dynamics theory (ADT). The <em>model is quantum-like</em>, i.e., it is not about quantum physical processes in biosystems. Generally such modeling is about applications of the quantum formalism and methodology outside of physics. Macroscopic biosystems, in our case genotypes and phenotypes, are treated as information processors which functioning matches the laws of quantum information theory. Phenotypes are the outputs of the <span><math><mi>E</mi></math></span>-adaptation processes described by the quantum master equation, <em>Gorini–Kossakowski–Sudarshan–Lindblad equation</em> (GKSL). Its stationary states correspond to phenotypes. We highlight the class of GKSL dynamics characterized by the camel-like graphs of (von Neumann) entropy: in the process of <span><math><mi>E</mi></math></span>-adaptation phenotype’s state entropy (disorder) first increases and then falls down — a stable and well-ordered phenotype is created. Traits, an organism’s phenotypic characteristics, are modeled within the quantum measurement theory, as generally unsharp observables given by positive operator valued measures (POVMs. This paper is also a review on the methods and mathematical apparatus of quantum information biology.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0303264724001461/pdfft?md5=b3f2474a2025bfa5eb806c2bcb880b6b&pid=1-s2.0-S0303264724001461-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141535858","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

Quantum Brain Dynamics and Virtual Reality 量子大脑动力学与虚拟现实

IF 2 4区生物学

Biosystems Pub Date : 2024-06-25 DOI: 10.1016/j.biosystems.2024.105259

Akihiro Nishiyama , Shigenori Tanaka , Jack A. Tuszynski

引用次数: 0