Biosystems最新文献

{"title":"Circular code identified by the codon usage","authors":"Christian J. Michel","doi":"10.1016/j.biosystems.2024.105308","DOIUrl":"10.1016/j.biosystems.2024.105308","url":null,"abstract":"<div><p>Since 1996, circular codes in genes have been identified thanks to the development of 6 statistical approaches: trinucleotide frequencies per frame (Arquès and Michel, 1996), correlation functions per frame (Arquès and Michel, 1997), frame permuted trinucleotide frequencies (Frey and Michel, 2003, 2006), advanced statistical functions at the gene population level (Michel, 2015) and at the gene level (Michel, 2017). All these 3-frame statistical methods analyse the trinucleotide information in the 3 frames of genes: the reading frame and the 2 shifted frames. Notably, codon usage does not allow for the identification of circular codes (Michel, 2020). This has been a long-standing problem since 1996, hindering biologists’ access to circular code theory.</p><p>By considering circular code conditions resulting from code theory, particularly the concept of permutation class, and building upon previous statistical work, a new statistical approach based solely on the codon usage, i.e. a 1-frame statistical method, surprisingly reveals the 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 bacterial genes and in average (bacterial, archaeal, eukaryotic) genes, and almost in archaeal genes. Additionally, a new parameter definition indicates that bacterial and archaeal genes exhibit codon usage dispersion of the same order of magnitude, but significantly higher than that observed in eukaryotic genes. This statistical finding may explain the greater variability of codes in eukaryotic genes compared to bacterial and archaeal genes, an issue that has been open for many years. Finally, biologists can now search for new (variant) circular codes at both the genome level (across all genes in a given genome) and the gene level using only codon usage, without the need for analysing the shifted frames.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"244 ","pages":"Article 105308"},"PeriodicalIF":2.0,"publicationDate":"2024-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142005741","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":"An exploration of ecoacoustics and its applications in conservation ecology","authors":"A. Farina ,&nbsp;B. Krause ,&nbsp;T.C. Mullet","doi":"10.1016/j.biosystems.2024.105296","DOIUrl":"10.1016/j.biosystems.2024.105296","url":null,"abstract":"<div><p>Our planet is facing unprecedented adversity due to the global impacts of climate change and an emerging sixth mass extinction. These impacts are exacerbated by population and industrial growth, where increased resource extraction is required to meet our insatiable demands. Yet, the tangible elements of our lone inhabited planet in the solar system are not the only things disappearing or being modified. The sounds of Earth are being altered in ways that may never be recovered. Indeed, we occupy a noisier world in this age of machines that comes at a great expense in the form of sonic extinctions. It is profoundly apparent, yet not widely recognized, that conservation efforts must consider the importance of the sonic environment (i.e., sonosphere). Although sound has been integral to life for millions of years, our understanding of its ecological role has only just begun. Sounds are one of the most important extensions of the organismic inner world, becoming testimonials of environmental complexity, integration, and relationships between apparently separated parts. From a semiotic perspective, sounds are signals utilized by many organisms to save energy in patrolling, defending, exploring, and navigating their surroundings. Sounds are tools that establish dynamic biological and ecological competencies through refined partitioning in the natural selection process of evolution. Ecoacoustics is a recent scientific discipline that aims to investigate the role of sound in ecological processes. Despite its youth, Ecoacoustics has had rapid theoretical and applied growth, consolidating a diverse array of research on the ecology of sounds across many disciplines. Here, we present how Ecoacoustics plays a significant role in conservation ecology by exploring the discipline's theoretical framework, new descriptors of sonic complexity, and innovative methods for supporting conservation efforts from singular species to entire landscapes across local and global scales. The combination of automated recording units and ecoacoustic indices present a very promising approach to the study of remote areas, rare species, and data rich analyses. While Ecoacoustics scientists continue to explore this new scientific horizon, we encourage others to consider Ecoacoustics in their conservation agendas because of its application to the study and management of terrestrial, marine, and freshwater habitats.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"245 ","pages":"Article 105296"},"PeriodicalIF":2.0,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141996880","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 innate story code","authors":"Erik Goodwyn","doi":"10.1016/j.biosystems.2024.105285","DOIUrl":"10.1016/j.biosystems.2024.105285","url":null,"abstract":"<div><p>Code biology reveals a great many codes beyond the genetic code as integral to biological functioning. Recent scholars have linked the growing field of code biology to analytical psychology, confirming that the encoded information inherited by the human organism is indeed massive and capable of great sophistication. In this discussion, I will expand on this project by showing how developments in embodied cognition reveal a code that links the world of universal emotional responses to common experiences to the world of embodied visuospatial narratives--i.e., the “archetypes” of analytical psychology. Viewed in this manner, archetypes become spontaneous symbolic narratives that symbolize universal emotional responses to typical human environments. Such symbolic narratives aim toward adaptation, and use a universal code that maps such situations to visuospatial narratives, with the adaptor being the human body itself.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"244 ","pages":"Article 105285"},"PeriodicalIF":2.0,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141917988","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":"Evolutionary stability of developmental commitment","authors":"Yuka Shirokawa","doi":"10.1016/j.biosystems.2024.105309","DOIUrl":"10.1016/j.biosystems.2024.105309","url":null,"abstract":"<div><p>Evolution of unicellular to multicellular organisms must resolve conflicts in reproductive interests between individual cells and the group. The social amoeba <em>Dictyostelium discoideum</em> is a soil-living eukaryote with facultative sociality. While cells grow in the presence of nutrients, cells aggregate under starvation to form fruiting bodies containing spores and altruistic stalk cells. Once cells socially committed, they complete formation of fruiting bodies, even if a new source of nutrients becomes available. The persistence of this social commitment raises questions as it inhibits individual cells from swiftly returning to solitary growth. I hypothesize that traits enabling premature de-commitment are hindered from being selected. Recent work has revealed outcomes of the premature de-commitment through forced refeeding; The de-committed cells take an altruistic prestalk-like position due to their reduced cohesiveness through interactions with socially committed cells. I constructed an evolutionary model assuming their division of labor. The results revealed a valley in the fitness landscape that prevented invasion of de-committing mutants, indicating evolutionary stability of the social commitment. The findings provide a general scheme that maintains multicellularity by evolving a specific division of labor, in which less cohesive individuals become altruists.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"244 ","pages":"Article 105309"},"PeriodicalIF":2.0,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141996893","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":"Evolutionary dynamics of cooperation coupled with ecological feedback compensation","authors":"Zi-Xuan Guo ,&nbsp;Tian-Jiao Feng ,&nbsp;Yi Tao ,&nbsp;Rui-Wu Wang ,&nbsp;Xiu-Deng Zheng","doi":"10.1016/j.biosystems.2024.105282","DOIUrl":"10.1016/j.biosystems.2024.105282","url":null,"abstract":"<div><p>A simple theoretical model (or a demonstrative example) was developed to illustrate how the evolution of cooperation can be affected by the density-dependent survival competition, in which we assume that the fertility of an individual depends only on the pairwise interaction between him and other individuals based on Prisoner’s Dilemma game, while its viability is only related to the density-dependent survival competitiveness. Our results show that not only cooperation could be evolutionarily stable if the advantage of cooperators in viability can compensate for the cost they pay for their fertility, but also the long-term stable coexistence of cooperation and defection is possible if none of cooperation and defection is evolutionarily stable. Moreover, for the stochastic evolutionary dynamics in a finite population, our analysis shows that the increase (or decrease) of the survival competitiveness of cooperators (or defectors) should be conductive to the evolutionary emergence of cooperation.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"244 ","pages":"Article 105282"},"PeriodicalIF":2.0,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141989441","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 evolutionary arch of bioenergetics from prebiotic mechanisms to the emergence of a cellular respiratory chain","authors":"Miklós Péter Kalapos ,&nbsp;Lidia de Bari","doi":"10.1016/j.biosystems.2024.105288","DOIUrl":"10.1016/j.biosystems.2024.105288","url":null,"abstract":"<div><p>This article proposes an evolutionary trajectory for the development of biological energy producing systems. Six main stages of energy producing system evolution are described, from early evolutionary pyrite-pulled mechanism through the Last Universal Common Ancestor (LUCA) to contemporary systems. We define the Last Pure Chemical Entity (LPCE) as the last completely non-enzymatic entity. LPCE could have had some life-like properties, but lacked genetic information carriers, thus showed greater instability and environmental dependence than LUCA. A double bubble model is proposed for compartmentalization and cellularization as a prerequisite to both highly efficient protein synthesis and transmembrane ion-gradient. The article finds that although LUCA predominantly functioned anaerobically, it was a non-exclusive anaerobe, and sulfur dominated metabolism preceded phosphate dominated one.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"244 ","pages":"Article 105288"},"PeriodicalIF":2.0,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141917987","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 polyphyletic origins of glycyl-tRNA synthetase and lysyl-tRNA synthetase and their implications","authors":"Massimo Di Giulio","doi":"10.1016/j.biosystems.2024.105287","DOIUrl":"10.1016/j.biosystems.2024.105287","url":null,"abstract":"<div><p>I analyzed the polyphyletic origin of glycyl-tRNA synthetase (GlyRS) and lysyl-tRNA synthetase (LysRS), making plausible the following implications. The fact that the genetic code needed to evolve aminoacyl-tRNA synthetases (ARSs) only very late would be in perfect agreement with a late origin, in the main phyletic lineages, of both GlyRS and LysRS. Indeed, as suggested by the coevolution theory, since the genetic code was structured by biosynthetic relationships between amino acids and as these occurred on tRNA-like molecules which were evidently already loaded with amino acids during its structuring, this made possible a late origin of ARSs. All this corroborates the coevolution theory of the origin of the genetic code to the detriment of theories which would instead predict an early intervention of the action of ARSs in organizing the genetic code. Furthermore, the assembly of the GlyRS and LysRS protein domains in main phyletic lineages is itself at least evidence of the possibility that ancestral genes were assembled using pieces of genetic material that coded these protein domains. This is in accordance with the exon theory of genes which postulates that ancestral exons coded for protein domains or modules that were assembled to form the first genes. This theory is exemplified precisely in the evolution of both GlyRS and LysRS which occurred through the assembly of protein domains in the main phyletic lineages, as analyzed here. Furthermore, this late assembly of protein domains of these proteins into the two main phyletic lineages, i.e. a polyphyletic origin of both GlyRS and LysRS, appears to corroborate the progenote evolutionary stage for both LUCA and at least the first part of the evolutionary stages of the ancestor of bacteria and that of archaea. Indeed, this polyphyletic origin would imply that the genetic code was still evolving because at least two ARSs, i.e. proteins that make the genetic code possible today, were still evolving. This would imply that the evolutionary stages involved were characterized not by cells but by protocells, that is, by progenotes because this is precisely the definition of a progenote. This conclusion would be strengthened by the observation that both GlyRS and LysRS originating in the phyletic lineages leading to bacteria and archaea, would demonstrate that, more generally, proteins were most likely still in rapid and progressive evolution. Namely, a polyphyletic origin of proteins which would qualify at least the initial phase of the evolutionary stage of the ancestor of bacteria and that of archaea as stages belonging to the progenote.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"244 ","pages":"Article 105287"},"PeriodicalIF":2.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141914468","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 chromolinker hypothesis: Are eukaryotic genomes also circular?","authors":"Richard Gordon","doi":"10.1016/j.biosystems.2024.105280","DOIUrl":"10.1016/j.biosystems.2024.105280","url":null,"abstract":"<div><p>Over more than the past century, reports that chromosomes in Eukaryotes are linked have been published. Recently this has been confirmed by micromanipulation. The chromolinkers are DNAse sensitive, as has been previously reported. The arguments for and against chromolinkers have been reviewed, and a call for definitive research made, because if chromolinkers do exist, the whole basis for <del>nuclear DNA</del> genetics may require revision.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"244 ","pages":"Article 105280"},"PeriodicalIF":2.0,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141890845","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":"Reevaluating human-microbiota symbiosis: Strain-level insights and evolutionary perspectives across animal species","authors":"Gabriel Trueba ,&nbsp;Paul Cardenas ,&nbsp;German Romo ,&nbsp;Bernardo Gutierrez","doi":"10.1016/j.biosystems.2024.105283","DOIUrl":"10.1016/j.biosystems.2024.105283","url":null,"abstract":"<div><p>The prevailing consensus in scientific literature underscores the mutualistic bond between the microbiota and the human host, suggesting a finely tuned coevolutionary partnership that enhances the fitness of both parties. This symbiotic relationship has been extensively studied, with certain bacterial attributes being construed as hallmarks of natural selection favoring the benefit of the human host. Some scholars go as far as equating the intricate interplay between humans and their intestinal microbiota to that of endosymbiotic relationships, even conceptualizing microbiota as an integral human organ.</p><p>However, amidst the prevailing narrative of bacterial species being categorized as beneficial or detrimental to human health, a critical oversight often emerges – the inherent functional diversity within bacterial strains. Such reductionist perspectives risk oversimplifying the complex dynamics at play within the microbiome. Recent genomic analysis at the strain level is highly limited, which is surprising given that strain information provides critical data about selective pressures in the intestine. These pressures appear to focus more on the well-being of bacteria rather than human health. Connected to this is the extent to which animals depend on metabolic activity from intestinal bacteria, which varies widely across species. While omnivores like humans exhibit lower dependency, certain herbivores rely entirely on bacterial activity and have developed specialized compartments to house these bacteria.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"244 ","pages":"Article 105283"},"PeriodicalIF":2.0,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141894811","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":"Disproportional fraction of inactive components leads to the variation in metabolic scaling","authors":"Chen Hou","doi":"10.1016/j.biosystems.2024.105284","DOIUrl":"10.1016/j.biosystems.2024.105284","url":null,"abstract":"<div><p>In biological systems, solitary organisms or eusocial groups, the metabolic rate often scales allometrically with systems’ size, when they are inactive, and the scaling becomes nearly isometric when the systems are active. Here I propose a hypothesis attempting to offer a departing point for a general joint understanding of the difference in the scaling powers between inactive and active states. When the system is inactive, there exist inactive components, which consume less energy than the active ones, and the larger the system is, the larger the fraction of the inactive components, which leads to sublinear scaling. When the system is active, most inactive components are activated, which leads to nearly isometric scaling. I hypothesize that the disproportional fraction of the inactive components is caused by the diffusants screening in the complex transportation network. I.e., when metabolites or information diffuses in the system, due to the physical limitation of the network structure and the diffusant’s physical feature, not all the components can equally receive the diffusants so that these components are inactive. Using the mammalian pulmonary system, ant colonies, and other few systems as examples, I discuss how the screening leads to the allometric and isometric metabolic scaling powers in inactive and active states respectively. It is noteworthy that there are a few exceptions, in which the metabolic rate of the system has an isometric scaling relationship with size at rest. I show that these exceptions not only do not disapprove the hypothesis, but actually support it.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"243 ","pages":"Article 105284"},"PeriodicalIF":2.0,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141894810","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}