Biosystems最新文献

{"title":"On the infodynamics of ramifications in constructal design","authors":"Miguel R.O. Panão","doi":"10.1016/j.biosystems.2024.105388","DOIUrl":"10.1016/j.biosystems.2024.105388","url":null,"abstract":"<div><div>Infodynamics is the study of how information behaves and changes within a system during its development. This study investigates the insights that informational analysis can provide regarding the ramifications predicted by constructal design. First, infodynamic neologisms <em>informature</em>, defined as a measure of the amount of information in indeterminate physical systems, and <em>infotropy</em> – contextualized informature representing the degree of transformation of indeterminate physical systems – are introduced. Flow architectures can be designed using either symmetric or asymmetric branching. The infodynamic analysis of symmetric branching revealed diminishing returns in information content, demonstrating that informature serves as a measure of diversity. These findings align with the principle of “few large and many small, but not too many,” which is consistent with higher thermofluid performance. The Performance Scaled Svelteness <span><math><mi>Ψ</mi></math></span> expresses the ability of the flow architecture to promote thermofluid performance. By contextualizing the informature with <span><math><mi>Ψ</mi></math></span>, a performance infotropy that quantifies the degree of transformation associated with the link between thermofluid performance and diversity in the ramified flow structure is obtained. A predicted growth and decay effect with increasing branching levels leads to a local maximum, highlighting that the evolutionary direction of the ramifications is inversely proportional to the scale of the environment in which the flow structure develops. Assuming an evolutionary trend toward maximum infodynamic complexity, a pattern of asymmetric ramifications emerges, similar to the sap distribution in leaves or branching of trees.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"248 ","pages":"Article 105388"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142958156","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":"Fragile X mental retardation protein modulates translation of proteins with predicted tendencies for liquid-liquid phase separation","authors":"Omar Jurado ,&nbsp;Marco V. José ,&nbsp;Eugenio Frixione","doi":"10.1016/j.biosystems.2025.105405","DOIUrl":"10.1016/j.biosystems.2025.105405","url":null,"abstract":"<div><div>The Fragile X Mental Retardation Protein (FMRP) is an RNA-binding protein and a key regulator of translation in neurons, hence crucial for neural development and plasticity. FMRP loss, resulting from mutations in the <em>Fmr1</em> gene, leads to Fragile X Syndrome (FXS) and Autism Spectrum Disorder (ASD), the most common inherited intellectual disabilities. Ribosome profiling in neurons consistently reveals that FMRP-knockout (FK) significantly down-regulates the translation of numerous lengthy genes, many of which are FMRP-binding targets and associated with ASD. Despite these findings, the functional explanation for FMRP's translation regulation of large neuronal proteins remains elusive. Our present study compiles data from published ribosome profiling studies, to identify genes with significantly decreased translation in FK neurons. Using bioinformatic analysis and machine-learning sequence-based tools, PSPredictor and FuzDrop, we found that the proteins encoded by these genes are predicted to be enriched in intrinsically disordered regions and are prone to liquid-liquid phase separation. These findings suggest that FMRP modulates the translation of proteins involved in the formation of biomolecular condensates. Our results can have significant implications for understanding the molecular mechanisms of FXS and ASD, adding complexity to FMRP's regulatory functions, thus offering avenues for further exploration and targeted therapeutic interventions in intellectual disability disorders.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"248 ","pages":"Article 105405"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143076470","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":"The regulatory network that controls lymphopoiesis","authors":"Luis Mendoza,&nbsp;Ricardo Vázquez-Ramírez,&nbsp;Juan Manuel Tzompantzi-de-Ita","doi":"10.1016/j.biosystems.2025.105399","DOIUrl":"10.1016/j.biosystems.2025.105399","url":null,"abstract":"<div><div>Lymphopoiesis is the generation of the T, B and NK cell lineages from a common lymphoid-biased haematopoietic stem cell. The experimental study of this process has generated a large amount of cellular and molecular data. As a result, there is a considerable number of mathematical and computational models regarding different aspects of lymphopoiesis. We hereby present a regulatory network consisting of 95 nodes and 202 regulatory interactions among them. The network is studied as a qualitative dynamical system, which has as stationary states the molecular patterns reported for CLP, pre-B, B naive, PC, pNK, iNK, NK, DP, CD8 naive, CTL, CD4 naive, Th1, Th2, Th17 and Treg cells. Also, we show that the system is able to respond to specific stimuli to reproduce the ontogeny of the T, B and NK cell lineages.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"248 ","pages":"Article 105399"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143015567","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":"Hopf bifurcation in the shadow of extinction: Collaborating with epidemic dynamics through lethal mutations and declining ancestor infections","authors":"Ali Demirci,&nbsp;Ayse Peker-Dobie,&nbsp;Cihangir Ozemir,&nbsp;Semra Ahmetolan","doi":"10.1016/j.biosystems.2025.105406","DOIUrl":"10.1016/j.biosystems.2025.105406","url":null,"abstract":"<div><div>This study delves into the intricate realm of controlling Hopf and degenerate Hopf bifurcations within a Susceptible–Infectious–Susceptible model. Employing Braga’s control theory as our cornerstone, we embark on an exploration of the model’s dynamics, particularly focusing on an equilibrium point under the influence of control inputs. Our specific aim is to induce limit cycles associated with Hopf bifurcations of co-dimension 1 and 2. Through the integration of controllability principles, we endeavor to unravel the underlying mechanisms governing the manipulation of parameters to shape the occurrence and attributes of these periodic fluctuations. By examining how the behavior of infectious diseases changes in response to various control parameters, our study aims to provide a practical example of their application.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"248 ","pages":"Article 105406"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143372469","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":"Unravelling intrinsically disordered and compositionally biased proteins in the cereal proteomes","authors":"Mouna Choura ,&nbsp;Vladimir N. Uversky","doi":"10.1016/j.biosystems.2025.105409","DOIUrl":"10.1016/j.biosystems.2025.105409","url":null,"abstract":"<div><div>Intrinsically disordered proteins (IDPs) play key biological functions despite lacking predetermined 3D structures. They are often compositionally biased and characterized by specific amino acid compositions. Here, we investigated protein intrinsic disorder in rice, wheat, barley, maize, sorghum, oat and rye proteomes. Then, we studied the distribution of compositionally biased proteins (CBs) in these species. The data showed that the contents of compositional biased proteins (CB), the average protein sizes, and biased sequence sizes were similar in the studied proteomes. Furthermore, the CB proteins were enriched in intrinsic disorder and IDPs were characterized by noticeable composition biases. In addition, the polar and the charged residues were the most abundant among the types of the biased residues. Gene Ontology analysis revealed that CB proteins in the studied species are mainly involved in binding, catalytic activity, and transcription regulation.</div><div>Altogether, our findings indicated that there is a noticeable conservation of intrinsically disordered and CB proteins in cereals. The evolutionary conservation of these features implies that cereals may use common cellular and regulatory mechanisms to adapt to various environmental constraints.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"248 ","pages":"Article 105409"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143076473","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 mechanistic approach to optimize combination antibiotic therapy","authors":"F. Clarelli ,&nbsp;P.O. Ankomah ,&nbsp;H. Weiss ,&nbsp;J.M. Conway ,&nbsp;G. Forsdahl ,&nbsp;P. Abel zur Wiesch","doi":"10.1016/j.biosystems.2024.105385","DOIUrl":"10.1016/j.biosystems.2024.105385","url":null,"abstract":"<div><div>Antimicrobial resistance is one of the most significant healthcare challenges of our times. Multidrug or combination therapies are sometimes required to treat severe infections; for example, the current protocols to treat pulmonary tuberculosis combine several antibiotics. However, combination therapy is usually based on lengthy empirical trials, and it is difficult to predict its efficacy. We propose a new tool to identify antibiotic synergy or antagonism and optimize combination therapies. Our model explicitly incorporates the mechanisms of individual drug action and estimates their combined effect using a mechanistic approach. By quantifying the impact on growth and death of a bacterial population, we can identify optimal combinations of multiple drugs. Our approach also allows for the investigation of the drugs’ actions and the testing of theoretical hypotheses.</div><div>We demonstrate the utility of this tool with in vitro <em>Escherichia coli</em> data using a combination of ampicillin and ciprofloxacin. In contrast to previous interpretations, our model finds a slight synergy between the antibiotics. Our mechanistic model allows investigating possible causes of the synergy.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"248 ","pages":"Article 105385"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142900071","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":"Stages and causes of the evolution of language and consciousness: A theoretical reconstruction","authors":"Nikolai S. Rozov","doi":"10.1016/j.biosystems.2024.105389","DOIUrl":"10.1016/j.biosystems.2024.105389","url":null,"abstract":"<div><div>This article presents a refinement of theoretical explanations of the main stages of linguistic and cognitive evolution in anthropogenesis. The concepts of language, consciousness, self-consciousness, the self, the unconscious, the subconscious, and the relation between free will and determinism remain at the center of active and complex debates in philosophy and neuroscience. A basic theoretical apparatus comprising the central concepts of \"concern\" and \"providing structure\" (an extension of the biological concept of \"adaptation\") develops the paradigm of the extended evolutionary synthesis. Challenge-threats and challenge-opportunities are invariably associated with concerns pertaining to sustenance, safety, sexuality, parenthood, status, and emotional support. The consolidation of successful behavioral tries (tries), in response to these challenges occurs through the formation of a variety of providing structures including practices, abilities, and attitudes. These structures are formed through mechanisms of interactive rituals and internalization. These novel practices facilitate the transformation of both techno-natural environmental niches and group niches. The emergence of new structures gives rise to new challenges and concerns, which in turn necessitate undertaking of new tries. In the context of African multiregionalism, hominin groups and populations that experienced favorable periods of demographic growth, active migration, genetic, technological, and skill exchange also underwent significant demographic disasters. During the most unfavorable bottleneck periods only the most advanced groups, populations and species survived. The achieved potential for these abilities was consolidated as complexes of innate assignments in gene pools through the Baldwin effect and the multilevel selection. This logic provides an explanation for the main stages of language and speech complication (from holophrases and articulation to complex syntax), as well as the emergence of new abilities of consciousness (from the expansion of attention field to self-consciousness and the \"I\"-structure).</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"248 ","pages":"Article 105389"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142923801","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":"Neural networks through the lens of evolutionary dynamics","authors":"Dan C. Baciu","doi":"10.1016/j.biosystems.2024.105386","DOIUrl":"10.1016/j.biosystems.2024.105386","url":null,"abstract":"<div><div>This article revisits Artificial Neural Networks (NNs) through the lens of Evolutionary Dynamics. The two most important features of NNs are shown to reflect the two most general processes of Evolutionary Dynamics. This overlap may serve as a new and powerful connection between NNs and Evolutionary Dynamics, which encompasses a body of knowledge that has been built over multiple centuries and has been expanded to inspire applications across a vast range of disciplines. Consequently, NNs should also be applicable across the same range of disciplines—that is, much more broadly than initially envisioned. The article concludes by opening questions about NN dynamics, based on the new connection to Evolutionary Dynamics.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"248 ","pages":"Article 105386"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142928752","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":"Corrigendum to “The concepts of code biology” [Biosyst. 248 (2025) 105400 1–6]","authors":"Marcello Barbieri","doi":"10.1016/j.biosystems.2025.105403","DOIUrl":"10.1016/j.biosystems.2025.105403","url":null,"abstract":"","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"248 ","pages":"Article 105403"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143076469","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":"The non-canonical nucleotides and prebiotic evolution","authors":"Alexey S. Ruzov ,&nbsp;Alexander S. Ermakov","doi":"10.1016/j.biosystems.2025.105411","DOIUrl":"10.1016/j.biosystems.2025.105411","url":null,"abstract":"<div><div>The mystery of the origin of life has been puzzling mankind for several millenia. Starting from the second half of the 20^th century, when the crucial role of nucleic acids in biological heredity became apparent, the emphasis in the field has shifted to the explanation of the origin of nucleic acids and the mechanisms of copying of macromolecules. In the 1960s, the hypothesis of the RNA World was proposed, according to which the first stages of the origin of life on Earth were associated with the appearance of self-replicating complexes based on RNA, that were akin to RNA-enzymes that catalyze critical for life chemical reactions. Currently, it has been shown that different forms of RNA include not only canonical (adenine, uracil, guanine, cytosine), but also about 170 non-canonical nucleotides. In this review, we discuss potential roles of these non-canonical nucleotides in the processes of molecular prebiotic evolution, such as the emergence of canonical RNA nucleotides and catalytic RNAs, as well as the origin of template synthesis of RNA and proteins.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"248 ","pages":"Article 105411"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143123994","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}