Biosystems最新文献

{"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}

{"title":"Cholesterol-ester prevents lipoprotein core from solidifying: Molecular dynamics simulation","authors":"Olga S. Knyazeva ,&nbsp;Anton A. Oreshkin ,&nbsp;Sofia I. Kisil ,&nbsp;Ekaterina A. Samarina ,&nbsp;Kristina N. Mikheeva ,&nbsp;Alexey A. Tsukanov ,&nbsp;Irina V. Gosteva ,&nbsp;Eugene A. Grachev","doi":"10.1016/j.biosystems.2024.105390","DOIUrl":"10.1016/j.biosystems.2024.105390","url":null,"abstract":"<div><div>As an important part of lipid metabolism the liver produces large particles called very low density lipoproteins, filled mostly with triglyceride and cholesterol esters mixture. A large percentage of the mixture composition components has a melting point above physiological temperature. Thus solid cluster formation or phase transition could be expected. Though various single-component triglyceride systems are well researched both experimentally and by various simulation techniques, to our best knowledge, tripalmitin/cholesteryl-palmitate binary mixture was not yet studied. We study tripalmitin single component system, as well as 20%–80% and 50%–50% binary mixtures of cholesteryl-palmitate and tripalmitin using molecular dynamics approach. All systems are studied at the pressure of 1 atm and the physiological temperature of 310 K, which is below the melting points of both tripalmitin and cholesteryl-palmitate. Our results show that at the time of 1000 ns, there is still no phase transition, but there is a noticeable tendency to intermolecular organizing and early signs of clustering. We check fatty acid arrangements of tripalmitin molecules in both single component system and binary mixtures with two different percentages of cholesteryl-palmitate mixed in. Our results show that the more cholesteryl-palmitate molecules are in the mixture the smaller number of tripalmitin molecules transitions to ’a fork/chair’ configuration during the same calculation time. Calculated angle distributions between fatty acid chains of tripalmitin molecules confirm that. Thus, our simulation results suggest slowing down or interfering effect of cholesteryl-palmitate on the crystallizing process of the binary mixture.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"248 ","pages":"Article 105390"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142957153","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 concepts of code biology","authors":"Marcello Barbieri","doi":"10.1016/j.biosystems.2025.105400","DOIUrl":"10.1016/j.biosystems.2025.105400","url":null,"abstract":"<div><div>Today there are two dominant paradigms in Biology: the idea that ‘<em>Life is Chemistry</em>’ and the idea that ‘<em>Life is Chemistry plus Information</em>’. There is also a third paradigm, the idea that ‘<em>Life is Chemistry, Information and Meaning</em>’ but today this is a minority view, despite the fact that meaning is produced by codes and there is ample experimental evidence that hundreds of codes exist in living systems. This is because that evidence has not yet reached the university books, but what exists in nature is bound to exist, one day, also in our books and at that point the codes will become an integral part of biology. This paper is a brief description of the key concepts of that third paradigm that has become known as <em>Code Biology</em>.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"248 ","pages":"Article 105400"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143015645","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":"Nuclear quantum effects explain chemiosmosis: The power of the proton","authors":"Chika Edward Uzoigwe","doi":"10.1016/j.biosystems.2025.105407","DOIUrl":"10.1016/j.biosystems.2025.105407","url":null,"abstract":"<div><div>ATP is a universal bio-currency, with chemiosmosis the metabolic mint by which currency is printed. Chemiosmosis leverages a membrane potential and ion gradient, typically a proton gradient, to generate ATP. The current chemiosmotic hypothesis is both cannon and dogma. However, there are obstacles to the unqualified and uncritical acceptance of this model. Intriguingly the proton is sufficiently small to exhibit quantum phenomena of wave-particle duality, often thought the exclusive prerogative of smaller subcellular particles. Evidence shows that chemiosmosis is by necessity critically dependent upon these nuclear quantum effects (NQE) of hydrogen, most notably as a proton. It is well established scientific orthodoxy that protons in water and hydrogen atoms of water molecules exhibit quantum phenomena. The effect is amplified by the hydrogen bonding and juxta-membrane location of protons in mitochondria and chloroplasts. NQE explains the otherwise inexplicable features of chemiosmosis, including the paucity of protons, the rate of proton movement and ATP genesis in otherwise subliminal proton motive forces and thus functionality of alkaliphiles. It also accounts for the efficiencies of chemiosmosis reported at greater than 100% in certain contexts, which violates the second law of thermodynamics under the paradigm of classical physics.</div><div>Mitochondria may have evolved to exploit quantum biology with notable features such as dimeric ATP synthases adumbrating the first double-slip experiment with the protons. The dramatic global deceleration of mitochondrial chemiosmosis and all cellular function following proton substitution with its heavier isotopes, deuterium and tritium: “deuteruction”, is testimony to the primacy of nuclear quantum effects in this Quantum Chemiosmosis. Indeed the speed of evolution itself and its inexorable route to homeothermy may be due to the power of nuclear quantum effects of the smallest nucleus, the proton. The atom that is almost nothing was selected to bring about the most important processes and complex manifestations of life.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"251 ","pages":"Article 105407"},"PeriodicalIF":2.0,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143076472","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}