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Biological Systems as Physical Data Processors: Evolution as a Case of Embodied Computing 作为物理数据处理器的生物系统：作为具身计算案例的进化
IF 3.3 3区 生物学
BioEssays Pub Date : 2026-10-09 DOI: 10.1002/bies.70196
Víctor de Lorenzo
{"title":"Biological Systems as Physical Data Processors: Evolution as a Case of Embodied Computing","authors":"Víctor de Lorenzo","doi":"10.1002/bies.70196","DOIUrl":"https://doi.org/10.1002/bies.70196","url":null,"abstract":"<p>The prevailing view of biological evolution is not unlike bricolage/pastiche/tinkering—in sharp contrast with rational engineering. Yet, different paths often lead to solutions that coincide or converge whether they emerge from naturally-occurring evolution or rationally designed. Such a conjunction—often presented as an anecdote—reveals the ability of biological systems to explore solution spaces and gravitate toward information-rich attractors, which can be found through different routes. This scenario evokes one of embodied computing, a non-conventional type of data processing in which the solution to a problem is not delivered through numerical calculations but through its implementation in a material object. Once left to undergo a physical process the object manages a large number of parameters for reaching a multi objective optimum through thermodynamically-driven processes. The course of information is thus a physical flow and the outcome is a physical currency. The consequences of this notion for bioengineering are remarkable.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"48 10","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.70196","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149146708","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Interplay Between Motor Proteins and Microtubule Stability: Involvement of Tubulin PTMs and MAPs 运动蛋白与微管稳定性之间的相互作用：微管蛋白PTMs和map的参与
IF 3.3 3区 生物学
BioEssays Pub Date : 2026-10-09 DOI: 10.1002/bies.70192
Pelin Zobaroğlu-Özer, Gamze Bora-Akoğlu
{"title":"Interplay Between Motor Proteins and Microtubule Stability: Involvement of Tubulin PTMs and MAPs","authors":"Pelin Zobaroğlu-Özer,&nbsp;Gamze Bora-Akoğlu","doi":"10.1002/bies.70192","DOIUrl":"https://doi.org/10.1002/bies.70192","url":null,"abstract":"<div>\u0000 \u0000 <p>Microtubules and motor proteins are components of a cytoskeleton that influence each other to maintain cellular functions. Microtubules act as tracks for motor protein-driven intracellular transport of organelles, vesicles, and macromolecules; therefore, their structural organization and stability are important. Kinesin and dynein motor proteins function not only as cargo transporters but also as contributors to the regulation of microtubule organization, stability, and interactions. The interaction of motor proteins and microtubules is essential for cellular homeostasis, and dysregulations can affect motility-dependent cellular processes such as intracellular trafficking and cell division. In this review, we summarize current knowledge on the relationship between motor proteins and factors associated with microtubule stability, particularly tubulin post-translational modifications and microtubule-associated proteins and discuss how alterations in these processes associate with disease.</p>\u0000 </div>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"48 10","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149146361","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 Partition Code: How RNA Modifications Set the Address of Transcripts Among Membraneless Compartments 分区代码：RNA修饰如何在无膜区室中设置转录本的地址
IF 3.3 3区 生物学
BioEssays Pub Date : 2026-10-09 DOI: 10.1002/bies.70194
Hidenori Tani
{"title":"The Partition Code: How RNA Modifications Set the Address of Transcripts Among Membraneless Compartments","authors":"Hidenori Tani","doi":"10.1002/bies.70194","DOIUrl":"https://doi.org/10.1002/bies.70194","url":null,"abstract":"<div>\u0000 \u0000 <p>Where a transcript goes among a cell's membraneless compartments—stress granules, P-bodies, paraspeckles, nuclear speckles—is an addressable, rewritable property that this article proposes chemical modifications of RNA help write. The code's output depends on the transcript's role: for client messenger RNAs, an apparent partition coefficient (K<sub>part</sub>), its enrichment in a condensate; for the rare long noncoding RNAs acting as architectural scaffolds, the saturation concentration that decides whether the compartment forms at all. This client/scaffold asymmetry is the framework's central proposal, its scaffold arm as yet untested. Only m6A has cellular partitioning evidence; A-to-I editing sets nuclear address by a related route, and the remaining marks are candidates or structure-based predictions. The value is a variable and a falsifiable test: perturb a mark at fixed sequence and state, and ask whether the address moves. It reframes scattered epitranscriptomic and condensate biology as one control problem.</p>\u0000 </div>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"48 10","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149146727","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Metabolic Structure: A Paradigm Revisited in Light of the Fundamental Parameters of Living Systems 代谢结构：在生命系统基本参数的光下重新审视的范式
IF 3.3 3区 生物学
BioEssays Pub Date : 2026-10-09 DOI: 10.1002/bies.70193
Jacques Fantini
{"title":"Metabolic Structure: A Paradigm Revisited in Light of the Fundamental Parameters of Living Systems","authors":"Jacques Fantini","doi":"10.1002/bies.70193","DOIUrl":"https://doi.org/10.1002/bies.70193","url":null,"abstract":"<p>The concept of ‘metabolic structure’, which considers metabolism as a stable, genetically encoded architecture with enzymes occupying fixed control positions, is indispensable but incomplete, and it obscures metabolism's true nature. I propose redefining metabolism as a dynamic field of emergent biochemical fluxes, governed by six fundamental parameters: time, water, entropy, quantum effects, space, and electrostatic potential, shaping the thermodynamic trajectories of living matter. Metabolic control analysis already supports this view: flux control coefficients are state- and time-dependent coordinates within a thermodynamic field, not intrinsic enzyme properties. This perspective manifests across scales: electrostatics govern fructose 1,6-bisphosphate cleavage in aldolase; hepatic zonation shows spatial reorganization through a single parameter; glucose deprivation quantitatively redirects intestinal cancer cell metabolism from glycolytic to oxidative flux, driving differentiation into an enterocyte-like state; post-meal walking redirects glucose flux from storage to oxidation without pharmacological intervention; inherited metabolic diseases can sometimes be managed without correcting the causal mutation. These examples converge into a new framework: metabolism possesses not only a sophisticated architecture but also states that shape its fluxes. And states, unlike static structures, can be reconfigured.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"48 10","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.70193","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149146360","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Crosstalk in Silence: PIWIL/piRNA in ncRNA Hubs for Immune Gene Regulation and Epigenetic Antiviral Defense 沉默中的串扰：免疫基因调控和表观遗传抗病毒防御的ncRNA枢纽PIWIL/piRNA
IF 3.3 3区 生物学
BioEssays Pub Date : 2026-10-09 DOI: 10.1002/bies.70188
Athira Ramesh, Rupa Roy, Jayamuruga Pandian Arunachalam, Subbulakshmi Chidambaram
{"title":"Crosstalk in Silence: PIWIL/piRNA in ncRNA Hubs for Immune Gene Regulation and Epigenetic Antiviral Defense","authors":"Athira Ramesh,&nbsp;Rupa Roy,&nbsp;Jayamuruga Pandian Arunachalam,&nbsp;Subbulakshmi Chidambaram","doi":"10.1002/bies.70188","DOIUrl":"https://doi.org/10.1002/bies.70188","url":null,"abstract":"<div>\u0000 \u0000 <p>Recent studies indicate that PIWI (P-element-induced WImpy testis) like proteins and their cognate PIWI-interacting RNAs (piRNAs), initially identified in germline cells for protecting genomic stability by transposon silencing, also exert multiple regulatory functions in somatic and immune systems. Additionally, PIWIL/piRNA pathways are linked to innate antiviral defense and immune signaling pathway regulation. This review systematically compiles the reports on the immunological functions of noncoding RNAs (ncRNAs) and delineates the potential molecular processes and functional characteristics of PIWIL/piRNA pathways. We propose that PIWIL/piRNAs function as a molecular link between adaptive and reproductive immunity and maintain barrier integrity in immune-privileged settings. Predictive bioinformatic analysis further revealed specific piRNAs that could interact with long noncoding RNAs (lncRNAs) and miRNAs to regulate immune response components within the TLR and JAK/STAT pathways, highlighting their potential role in antiviral and immunomodulatory signaling networks. We conclude by discussing the emerging opportunities to integrate ncRNA-mediated regulatory mechanisms into personalized medicine and targeted therapies while addressing the key hurdles in clinical application.</p>\u0000 </div>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"48 10","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149146425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Correction to “Rethinking One Health: Microbial Foundations for Ecological Governance” 更正“重新思考一个健康：生态治理的微生物基础”。
IF 3.3 3区 生物学
BioEssays Pub Date : 2026-10-08 DOI: 10.1002/bies.70176
{"title":"Correction to “Rethinking One Health: Microbial Foundations for Ecological Governance”","authors":"","doi":"10.1002/bies.70176","DOIUrl":"10.1002/bies.70176","url":null,"abstract":"<p>A. Fernandez Diaz, F. Keck, M. K. Melby, V.-K. Nguyen, and L.-P. Haraoui, “Rethinking One Health: Microbial Foundations for Ecological Governance,” Bioessays 48 (2026): 202400807, https://doi.org/10.1002/ardp.202400807.</p><p>In the article published as Bioessays 2026; 48; 202400807, https://doi.org/10.1002/ardp.202400807.</p><p>The correction needed involves adding Louis-Patrick Haraoui as a second corresponding author to the article in the author list on the first page, and adding the following correspondence email for him:</p><p><span>[email protected]</span></p><p>We apologize for this error.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"48 10","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.70176","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149135310","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Protein-Ratio Rheostats: Integrating Stoichiometry, Abundance, and Binding Affinity in Cellular Function 蛋白质比率变阻器：整合细胞功能中的化学计量学、丰度和结合亲和力。
IF 3.3 3区 生物学
BioEssays Pub Date : 2026-10-08 DOI: 10.1002/bies.70195
Subbaya Subramanian, Reena V. Kartha
{"title":"Protein-Ratio Rheostats: Integrating Stoichiometry, Abundance, and Binding Affinity in Cellular Function","authors":"Subbaya Subramanian,&nbsp;Reena V. Kartha","doi":"10.1002/bies.70195","DOIUrl":"10.1002/bies.70195","url":null,"abstract":"<p>Cellular function is frequently interpreted in terms of gene presence, protein abundance, and dose–response relationships. Yet interacting proteins operate within binding and assembly regimes in which relative abundance can alter which molecular complexes predominate. We propose a protein-ratio rheostat framework in which functional output depends jointly on component ratios, absolute concentrations relative to binding affinities, interaction stoichiometry, and in multivalent systems, valency and cooperativity. The same protein ratio can therefore generate different molecular and functional states under different concentration or affinity regimes. We develop testable predictions of this framework, illustrate its application to competitive protein interactions and biomolecular condensates, and outline experimental strategies for identifying composition-sensitive behavior within defined abundance and affinity regimes.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"48 10","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.70195","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149135338","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Molecular Control of Replication Fork Speed: dNTP Availability, Phosphorylation, PARylation, and UFMylation 分子控制的复制叉速度：dNTP可用性，磷酸化，PARylation，和UFMylation。
IF 3.3 3区 生物学
BioEssays Pub Date : 2026-10-07 DOI: 10.1002/bies.70185
Zheng Li, Akira Shinohara, Yisui Xia, Xingzhi Xu, Shunichi Takeda
{"title":"Molecular Control of Replication Fork Speed: dNTP Availability, Phosphorylation, PARylation, and UFMylation","authors":"Zheng Li,&nbsp;Akira Shinohara,&nbsp;Yisui Xia,&nbsp;Xingzhi Xu,&nbsp;Shunichi Takeda","doi":"10.1002/bies.70185","DOIUrl":"10.1002/bies.70185","url":null,"abstract":"<div>\u0000 \u0000 <p>The regulation of replication fork (RF) speed is essential for faithful genome duplication and the maintenance of genome stability, and its dysregulation contributes to carcinogenesis and developmental disorders. Although many anticancer therapies perturb DNA replication, the molecular mechanisms by which RF speed is controlled remain incompletely understood. A major limitation has been the frequent omission of direct measurements of cellular deoxynucleotide triphosphate (dNTP) pools, despite their strong and immediate influence on DNA polymerase kinetics. In this review, we first summarize how dNTP availability constrains RF progression under physiological and stress conditions. We then discuss how anticancer agents targeting DNA replication modulate RF speed through phosphorylation-dependent signaling pathways. Finally, we examine emerging roles of PARylation and UFMylation as rapid, replisome-centered regulatory mechanisms that fine-tune fork progression and stability, and we highlight their clinical implications, including a mechanistic link between aberrant replisome regulation and microcephalic primordial dwarfism.</p>\u0000 </div>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"48 10","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149104501","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Kinetic Control of Condensate Function: How the Formation Dynamics of APBs Influence ALT Cancer Telomere Length Heterogeneity 凝聚功能的动力学控制：apb的形成动力学如何影响ALT癌端粒长度异质性。
IF 3.3 3区 生物学
BioEssays Pub Date : 2026-09-30 DOI: 10.1002/bies.70187
Huaiying Zhang
{"title":"Kinetic Control of Condensate Function: How the Formation Dynamics of APBs Influence ALT Cancer Telomere Length Heterogeneity","authors":"Huaiying Zhang","doi":"10.1002/bies.70187","DOIUrl":"10.1002/bies.70187","url":null,"abstract":"<p>Telomerase-free cancer cells use a recombination-based alternative lengthening of telomeres (ALT) pathway to maintain telomere length. ALT cancer cells exhibit extreme heterogeneity in telomere length, which requires the formation of a specialized nuclear condensate, the ALT telomere-associated PML bodies (APBs). Recent findings on APB assembly reveal that APBs form through two mechanistically and kinetically distinct pathways. These pathways modulate the strength of ALT activity. In this essay, I discuss how APB formation dynamics may contribute to telomere-length variability in ALT cells and consider the broader implications of these findings for other chromatin-associated nuclear condensates.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"48 10","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13625942/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149079909","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Controlling Meiotic Double-Strand Break Formation in Mice: A Web of Multivalent Protein–Protein Interactions 控制小鼠减数分裂双链断裂的形成：一个多价蛋白相互作用的网络。
IF 3.3 3区 生物学
BioEssays Pub Date : 2026-09-30 DOI: 10.1002/bies.70190
Jiaqi Xu, Scott Keeney
{"title":"Controlling Meiotic Double-Strand Break Formation in Mice: A Web of Multivalent Protein–Protein Interactions","authors":"Jiaqi Xu,&nbsp;Scott Keeney","doi":"10.1002/bies.70190","DOIUrl":"10.1002/bies.70190","url":null,"abstract":"<div>\u0000 \u0000 <p>A complex network of protein interactions promotes the cooperative assembly of biomolecular condensates that control the formation of meiotic DNA double-strand breaks (DSBs). In many species, programmed DSBs made by SPO11 are required for the faithful pairing and segregation of homologous chromosomes during meiosis I. DSBs must be tightly regulated to support their intended function but also to minimize the risk of genomic damage from mutation or defective DSB repair. Multiple chromosome axis-associated proteins are important for the control of meiotic DSB formation and recombination, but the underlying mechanisms of those proteins remain poorly understood. Here, we present a current view of how these proteins work together in mice, based on recent advances in the characterization of their function and structure.</p>\u0000 </div>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"48 10","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149079917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
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