Biosystems最新文献

{"title":"What do stimulated beta cells have in common with cancer cells?","authors":"Marko Marhl","doi":"10.1016/j.biosystems.2024.105257","DOIUrl":"10.1016/j.biosystems.2024.105257","url":null,"abstract":"<div><p>This study investigates the metabolic parallels between stimulated pancreatic beta cells and cancer cells, focusing on glucose and glutamine metabolism. Addressing the significant public health challenges of Type 2 Diabetes (T2D) and cancer, we aim to deepen our understanding of the mechanisms driving insulin secretion and cellular proliferation. Our analysis of anaplerotic cycles and the role of NADPH in biosynthesis elucidates their vital functions in both processes. Additionally, we point out that both cell types share an antioxidative response mediated by the Nrf2 signaling pathway, glutathione synthesis, and UCP2 upregulation. Notably, UCP2 facilitates the transfer of C4 metabolites, enhancing reductive TCA cycle metabolism. Furthermore, we observe that hypoxic responses are transient in beta cells post-stimulation but persistent in cancer cells. By synthesizing these insights, the research may suggest novel therapeutic targets for T2D, highlighting the shared metabolic strategies of stimulated beta cells and cancer cells. This comparative analysis not only illuminates the metabolic complexity of these conditions but also emphasizes the crucial role of metabolic pathways in cell function and survival, offering fresh perspectives for tackling T2D and cancer challenges.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"242 ","pages":"Article 105257"},"PeriodicalIF":1.6,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0303264724001424/pdfft?md5=1e8f035d2de7eb7bed67fc9a6954be77&pid=1-s2.0-S0303264724001424-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141321845","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}

{"title":"Determining cellular lineage directed networks in hematopoiesis using single-cell transcriptomic data and volatility-constrained correlation","authors":"Tomoshiro Ochiai ,&nbsp;Jose C. Nacher","doi":"10.1016/j.biosystems.2024.105248","DOIUrl":"10.1016/j.biosystems.2024.105248","url":null,"abstract":"<div><p>Single-cell transcriptome sequencing (scRNA-seq) has revolutionized our understanding of cellular processes by enabling the analysis of expression profiles at an individual cell level. This technology has shown promise in uncovering new cell types, gene functions, cell differentiation, and trajectory inference through the study of various biological processes, such as hematopoiesis. Recent scRNA-seq analysis of mouse bone marrow cells has provided a network model of hematopoietic lineage. However, all data analyses have predicted undirected network maps for the associated cell trajectories. Moreover, the debate regarding the origin of basophil cells still persists. In this work, we apply the Volatility Constrained (VC) correlation method to predict not only the network structure but also the causality or directionality between the cell types present in the hematopoietic process. Our findings suggest a dual origin of basophils, from both granulocyte/macrophage and erythrocyte progenitors, the latter being a trajectory less explored in previous research. The proposed approach and predictions may assist in developing a complete hematopoietic process map, impacting our understanding of hematopoiesis and providing a robust directional network framework for further biomedical research.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"242 ","pages":"Article 105248"},"PeriodicalIF":2.0,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141318914","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}

{"title":"Thermodynamic model for memory","authors":"Qinyi Zhao","doi":"10.1016/j.biosystems.2024.105247","DOIUrl":"10.1016/j.biosystems.2024.105247","url":null,"abstract":"<div><p>A thermodynamic model for memory formation is proposed. Key points include: 1) Any thought or consciousness corresponds to a thermodynamic system of nerve cells. 2) The system concept of nerve cells can only be described by thermodynamics of condensed matter. 3) The memory structure is logically associated with the system structure or the normal structure of biology. 4) The development of our thoughts is processed irreversibly, and numerous states or thoughts can be generated. 5) Memory formation results from the reorganization and change of cellular structures (or memory structures), which are related to nerve cell skeleton and membrane. Their alteration can change the excitability of nerve cells and the pathway of neural impulse conduction. 6) Amnesia results from the loss of thermodynamic stability of the memory structure, which can be achieved by different ways. Some related phenomena and facts are discussed. The analysis shows that thermodynamics can account for the basic properties of memory.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"242 ","pages":"Article 105247"},"PeriodicalIF":1.6,"publicationDate":"2024-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141312164","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}

{"title":"Effective identification and differential analysis of anticancer peptides","authors":"Lichao Zhang ,&nbsp;Xueli Hu ,&nbsp;Kang Xiao ,&nbsp;Liang Kong","doi":"10.1016/j.biosystems.2024.105246","DOIUrl":"10.1016/j.biosystems.2024.105246","url":null,"abstract":"<div><p>Anticancer peptides (ACPs) have recently emerged as promising cancer therapeutics due to their selectivity and lower toxicity. However, the number of experimentally validated ACPs is limited, and identifying ACPs from large-scale sequence data is time-consuming and expensive. Therefore, it is critical to develop and improve upon existing computational models for identifying ACPs. In this study, a computational method named ACP_DA was proposed based on peptide residue composition and physiochemical properties information. To curtail overfitting and reduce computational costs, a sequential forward selection method was utilized to construct the optimal feature groups. Subsequently, the feature vectors were fed into light gradient boosting machine classifier for model construction. It was observed by an independent set test that ACP_DA achieved the highest Matthew's correlation coefficient of 0.63 and accuracy of 0.8129, displaying at least a 2% enhancement compared to state-of-the-art methods. The satisfactory results demonstrate the effectiveness of ACP_DA as a powerful tool for identifying ACPs, with the potential to significantly contribute to the development and optimization of promising therapies. The data and resource codes are available at <span>https://github.com/Zlclab/ACP_DA</span><svg><path></path></svg>.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"241 ","pages":"Article 105246"},"PeriodicalIF":1.6,"publicationDate":"2024-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141288899","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}

{"title":"Aggregate Boid behavior to aid in artificial autopoietic organization","authors":"Steven Lawrence,&nbsp;Chrystopher L. Nehaniv","doi":"10.1016/j.biosystems.2024.105245","DOIUrl":"10.1016/j.biosystems.2024.105245","url":null,"abstract":"<div><p>Analyzing carbon-based life on earth can lead to biased inferences on the nature of life as might exist in elsewhere in the universe in alternative forms, therefore, scientists have looked into either abstracting life into constituent systems it is comprised of, or logics of life, or lists of essential criteria, or essential dynamic patterning that characterizes the living. A system-level characterization that is and referred to as a general pattern of minimal life is <em>autopoiesis</em> (Varela et al., 1974) including production, maintenance and replacement of required constituents for setting up and maintaining an internal environment with self/other separation that regulates and is constitutive of processes that produce the environment and components for processes that comprise this ongoing activity of self-production in ‘recursively’, i.e., in a manner that allows the organizational pattern to continually reconstitute the conditions, components and processes required for its own perpetuation. This seminal concept of an autopoiesis is instantiated in life as we know it, but might also be instantiated in different media and in unforeseen ways. Other researchers have argued life is more than autopoiesis and that it is a co-emergent property of autopoiesis and cognition. Life produces many emergent properties such as synchronization and patterns as seen in flocks and herds of different animal species. The mechanics of this synchrony displayed in flocks and herd animals has been extracted by Craig Reynolds into a generative model referred to as “Boids”. With these concepts in mind, we address the following research question: How can the synchronous maneuvers and aggregate behavior of Boids contribute to constitutive subsystems in realizing an autopoietic system? Can such a system exhibit minimal cognition? This work attempts to answer these questions with a bottom-up approach to constructing an artificial life system. We exhibit a computational model of autopoiesis and a minimal level of cognition in the sense of M. Bitbol and P. Luigi Luisi, whereby an autopoietic entity engages in active assimilation of external components as part of its activity of self-production.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"242 ","pages":"Article 105245"},"PeriodicalIF":1.6,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0303264724001308/pdfft?md5=c05922d2f995dec110768bea2047e4cc&pid=1-s2.0-S0303264724001308-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141238779","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}

{"title":"The effect of avian eggshell membrane structure on microbial penetration: A simulation study","authors":"Seungwoo Sim ,&nbsp;Cheol-Min Park ,&nbsp;Sang-Hee Lee ,&nbsp;Haeun Cho ,&nbsp;Youngheum Ji ,&nbsp;Heeso Noh ,&nbsp;Sang-im Lee","doi":"10.1016/j.biosystems.2024.105234","DOIUrl":"10.1016/j.biosystems.2024.105234","url":null,"abstract":"<div><p>Avian eggshells exhibit excellent antimicrobial properties. In this study, we conducted simulation experiments to explore the defense mechanisms of eggshell membranes with regards to their physical features. We developed a mathematical model for the movement of microorganisms and estimated their penetration ratio into eggshell membranes based on several factors, including membrane thickness, microbial size, directional drift, and attachment probability to membrane fibers. These results not only suggest that an eggshell membrane with multiple layers and low porosity indicates high antimicrobial performance, but also imply that the fibrous network structure of the membrane might contribute to effective defense. Our simulation results aligned with experimental findings, specifically in measuring the penetration time of <em>Escherichia coli</em> through the eggshell membrane. We briefly discuss the significance and limitations of this pilot study, as well as the potential for these results, to serve as a foundation for the development of antimicrobial materials.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"240 ","pages":"Article 105234"},"PeriodicalIF":1.6,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140960125","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}

{"title":"A memory access gate controlled by dynamic contexts","authors":"Andrés Pomi ,&nbsp;Juan Lin ,&nbsp;Eduardo Mizraji","doi":"10.1016/j.biosystems.2024.105232","DOIUrl":"10.1016/j.biosystems.2024.105232","url":null,"abstract":"<div><p>Temporary difficulties in accessing the contents of memories are a common experience in everyday life, for example, when we try to recognize a known person in an unusual context. In addition, recent experiments seem to indicate that retrograde amnesia in the early stages of Alzheimer's disease is due to disorders in accessing memories that were installed normally. These facts suggest the existence of an intermediate step between the stimulus arrival and the associative recognition. In this work, a multimodular neurocomputational model is presented postulating the existence of a neural gate that controls the access of the stimulus with its context to the consolidated memory. If recognition is not achieved, a random search is initiated in a contextual network aroused by the initial context. The search continues until the appropriate context that allows for recognition is found or until the process is turned off because the initial stimulus is no longer maintained in the working memory. The model is based on vector patterns of neural activity and context-dependent matrix memories. Simple Markov chain simulations are presented to exemplify possible search scenarios in the contextual network. Finally, we discuss some of the characteristics of the model and the phenomenon under study.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"241 ","pages":"Article 105232"},"PeriodicalIF":1.6,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140959980","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}

{"title":"A multi-objective optimisation approach for the linear modelling of cerebral autoregulation system","authors":"Felipe-Andrés Bello-Robles ,&nbsp;Manuel Villalobos-Cid ,&nbsp;Max Chacón ,&nbsp;Mario Inostroza-Ponta","doi":"10.1016/j.biosystems.2024.105231","DOIUrl":"10.1016/j.biosystems.2024.105231","url":null,"abstract":"<div><h3>Objective:</h3><p>Dynamic cerebral autoregulation (dCA) has been addressed through different approaches for discriminating between normal and impaired conditions based on spontaneous fluctuations in arterial blood pressure (ABP) and cerebral blood flow (CF). This work presents a novel multi-objective optimisation (MO) approach for finding good configurations of a cerebrovascular resistance-compliance model.</p></div><div><h3>Methods:</h3><p>Data from twenty-nine subjects under normo and hypercapnic (5% CO<span><math><msub><mrow></mrow><mrow><mn>2</mn></mrow></msub></math></span> in air) conditions was used. Cerebrovascular resistance and vessel compliance models with ABP as input and CF velocity as output were fitted using a MO approach, considering fitting Pearson’s correlation and error.</p></div><div><h3>Results:</h3><p>MO approach finds better model configurations than the single-objective (SO) approach, especially for hypercapnic conditions. In addition, the Pareto-optimal front from the multi-objective approach enables new information on dCA, reflecting a higher contribution of myogenic mechanism for explaining dCA impairment.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"241 ","pages":"Article 105231"},"PeriodicalIF":1.6,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140960065","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}

{"title":"From the principle of sustainable non-equilibrium to sustainable development","authors":"Dmitry Ermakov ,&nbsp;Alexander Ermakov","doi":"10.1016/j.biosystems.2024.105233","DOIUrl":"10.1016/j.biosystems.2024.105233","url":null,"abstract":"<div><p>Ervin Bauer was Hungarian and Soviet scientist, who had a short, but bright and talented life. In 1935, working at the Institute of Experimental Medicine in the USSR, he published the book «Theoretical Biology», in which he proposed an idea of a special “non-equilibrium” state of living systems and the existence of internal machineries in the organism that work against thermodynamic equilibrium and increase the organism's capacity for work. Currently, this idea is called “the principle of sustainable non-equilibrium” or “Bauer's principle”. During the repressions of the 1930s in the USSR, Bauer was executed, the book « Theoretical Biology» was banned. Currently, his works are poorly known, especially outside the post-socialist region. We believe that his ideas could help in rethinking not only the biochemistry and bioenergetics of cells and tissues of living organisms, but also biogeochemical and civilizational processes on a planetary scale.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"241 ","pages":"Article 105233"},"PeriodicalIF":1.6,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140960070","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}

{"title":"Ambush strategy enhances organisms’ performance in rock–paper–scissors games","authors":"R. Barbalho ,&nbsp;S. Rodrigues ,&nbsp;M. Tenorio ,&nbsp;J. Menezes","doi":"10.1016/j.biosystems.2024.105229","DOIUrl":"10.1016/j.biosystems.2024.105229","url":null,"abstract":"<div><p>We study a five-species cyclic system wherein individuals of one species strategically adapt their movements to enhance their performance in the spatial rock–paper–scissors game. Environmental cues enable the awareness of the presence of organisms targeted for elimination in the cyclic game. If the local density of target organisms is sufficiently high, individuals move towards concentrated areas for direct attack; otherwise, they employ an ambush tactic, maximising the chances of success by targeting regions likely to be dominated by opponents. Running stochastic simulations, we discover that the ambush strategy enhances the likelihood of individual success compared to direct attacks alone, leading to uneven spatial patterns characterised by spiral waves. We compute the autocorrelation function and measure how the ambush tactic unbalances the organisms’ spatial organisation by calculating the characteristic length scale of typical spatial domains of each species. We demonstrate that the threshold for local species density influences the ambush strategy’s effectiveness, while the neighbourhood perception range significantly impacts decision-making accuracy. The outcomes show that long-range perception improves performance by over 60%, although there is potential interference in decision-making under high attack triggers. Understanding how organisms’ adaptation their environment enhances their performance may be helpful not only for ecologists, but also for data scientists, aiming to improve artificial intelligence systems.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"240 ","pages":"Article 105229"},"PeriodicalIF":1.6,"publicationDate":"2024-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S030326472400114X/pdfft?md5=5f6b332bb69ad36727fc6bcdac1ae8b9&pid=1-s2.0-S030326472400114X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140917413","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}