Progress in Biophysics & Molecular Biology最新文献

{"title":"The phoenix flora: Plant survival, succession, and putative adaptation in the post-atomic landscapes of Hiroshima and Nagasaki","authors":"Gian Marco Ludovici ,&nbsp;Paola Amelia Tassi ,&nbsp;Alba Iannotti ,&nbsp;Colomba Russo ,&nbsp;Fausto D'Agostino ,&nbsp;Matilde Neble Segade ,&nbsp;Timothy Alexander Mousseau ,&nbsp;Andrea Malizia","doi":"10.1016/j.pbiomolbio.2026.02.004","DOIUrl":"10.1016/j.pbiomolbio.2026.02.004","url":null,"abstract":"<div><div>The atomic bombings of Hiroshima and Nagasaki in 1945 created a unique environment of acute, high-dose ionizing radiation, contrasting sharply with the chronic low-dose rate exposure in the Chernobyl and Fukushima Exclusion Zones. This stands in stark contrast to the chronic, low-dose rate contamination that defines the Chernobyl and Fukushima Exclusion Zones. While the long-term ecological effects of the latter are well-documented, a systematic synthesis of the floral response to the atomic bombings is lacking. This review integrates historical data with modern radio-ecological principles to analyze plant survival and succession. We document the remarkable recovery of vegetation, from the resprouting of survivor trees, the <em>hibakujumoku</em>, such as <em>Ginkgo biloba</em> trees, to the role of soil seed banks. We propose that this recovery was driven by constitutive resilience, relying on pre-existing traits such as robust DNA repair, antioxidant capacity, and protective morphology, rather than the multi-generational genetic adaptation observed in chronic exposure zones. By framing these events against the backdrop of Chernobyl and Fukushima, this review demonstrates how the nature of the radiological insult dictates fundamentally different ecological and evolutionary outcomes. The flora of Hiroshima and Nagasaki thus serves as a critical case study of extreme instantaneous stress tolerance. We conclude by proposing a future research agenda that employs advanced genomic tools on these living archives to uncover the mechanistic basis of their survival, thereby integrating a pivotal historical case into a holistic understanding of plant persistence in radically altered environments.</div></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"200 ","pages":"Pages 1-5"},"PeriodicalIF":4.5,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146162092","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}

{"title":"Overcoming the warming bottleneck in animal vitrification: Volumetric heating and enabling technologies for reproductive cryobanking","authors":"Jesse Oluwaseun Ayantoye ,&nbsp;Baigao Yang ,&nbsp;Hang Zhang ,&nbsp;Jianhua Dong ,&nbsp;Xiaomeng Zhang ,&nbsp;Haoran Song ,&nbsp;Muhammad Shahzad ,&nbsp;Hubdar Ali Kolachi ,&nbsp;Osamede Henry Osaiyuwu ,&nbsp;Pengcheng Wan ,&nbsp;Hongmei Pan ,&nbsp;Xueming Zhao","doi":"10.1016/j.pbiomolbio.2025.11.003","DOIUrl":"10.1016/j.pbiomolbio.2025.11.003","url":null,"abstract":"<div><div>Reproductive cryopreservation via vitrification is vital for livestock breeding and biodiversity conservation, as it enables ice-free storage of gametes and embryos. However, success increasingly depends on achieving rapid, uniform warming to avoid devitrification: the critical warming rate (CWR) required is often orders of magnitude higher than the critical cooling rate (CCR). Conventional convective thawing (e.g., water baths) produces edge-to-core thermal gradients that can lead to lethal ice formation in larger or more complex samples. Suboptimal warming disrupts cellular ultrastructure, leading to meiotic spindle collapse, mitochondrial depolarization, reactive oxygen species production, DNA damage, and apoptosis. These changes manifest as impaired embryo development and the formation of necrotic tissue cores. Notably, lipid-rich porcine oocytes and embryos are particularly susceptible to recrystallization during slow warming, with higher fragmentation and lower viability than their bovine and ovine counterparts. This review synthesizes thermophysical principles underlying the CWR requirement and biological evidence of the warming bottleneck across animal systems. This thermophysical imbalance means that rewarming, rather than cooling, is the decisive barrier to successful vitrification. We then discuss emerging volumetric rewarming technologies that uniformly deliver energy: magnetic nanoparticle-induced nanowarming, laser-driven photothermal heating, dielectric (radiofrequency/microwave) rewarming, and ultrafast Joule (ohmic) heating. These methods have demonstrably exceeded CWR thresholds in embryos, tissues, and organs, improving cell survival and function. We also highlight enabling tools such as microfluidic cryoprotectant (CPA) handling, automated vitrification platforms, artificial intelligence (AI)-guided protocol optimization, and isochoric (constant-volume) vitrification, which collectively enhance reproducibility and scalability of cryopreservation workflows. In conclusion, integrating volumetric heating modalities with these engineering innovations promises to transform animal cryopreservation: uniformly rapid warming will improve immediate post-thaw viability and preserve biological integrity, enabling routine, large-scale germplasm banking for livestock production and conservation.</div></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"199 ","pages":"Pages 31-45"},"PeriodicalIF":4.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145679604","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}

{"title":"Advances in nanomaterials-assisted drug delivery, diagnosis, and action towards drug-resistant Mycobacterium","authors":"Parikshana Mathur ,&nbsp;Pinky Choudhary ,&nbsp;Rajkuberan Chandrasekaran ,&nbsp;Ragini Singh ,&nbsp;Hemant Kumar Daima","doi":"10.1016/j.pbiomolbio.2025.11.001","DOIUrl":"10.1016/j.pbiomolbio.2025.11.001","url":null,"abstract":"<div><div>Threatening impact of tuberculosis (TB) on public health remains significant even after the global initiatives and emergence of multi-drug resistance (MDR) strains have made the situation complicated. Herein, the exploitation of the same medications for several decades, ineffective drug administration, and insufficient patient follow-up are some of the variables that have fuelled the resistance. As a result, the twenty-first century has seen the greatest number of multi-drug resistance TB cases. Nevertheless, nanotechnology has emerged as a promising tool against drug-resistant <em>Mycobacterium tuberculosis</em>, the bacterium responsible for TB. This seminal review highlights the most important findings from nanomaterials-related research to detect and counter TB. First, a deeper understanding of the essential molecular mechanisms underlying drug-resistance and drug-tolerance in <em>Mycobacterium</em> pathogen is provided along with biofilm formation and intracellular survival mechanisms. It is followed by detailed discussions about innovative nanomaterials-based drug delivery for antituberculosis medications, and different types of nanomaterials for direct antimicrobial actions. Then, nanotechnology-assisted diagnosis techniques and anti-biofilm possibilities for drug-resistant <em>M. tuberculosis</em> are elaborated. Finally, the challenges and perspectives related to nanomaterials-based theranostic for TB drug-resistance and treatment are provided with concluding remarks.</div></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"199 ","pages":"Pages 1-19"},"PeriodicalIF":4.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145566385","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}

{"title":"Electric Cell-Substrate Impedance Sensing (ECIS) for the analysis of shear stress effects on cell monolayers","authors":"Fernando Pesantez Torres ,&nbsp;Michael Detweiler ,&nbsp;Charles R. Keese","doi":"10.1016/j.pbiomolbio.2026.02.002","DOIUrl":"10.1016/j.pbiomolbio.2026.02.002","url":null,"abstract":"<div><div>Shear stress, a stress that acts co-planar with the cross-section of a system, profoundly influences cellular behavior and function. Understanding how cells respond to shear stress is critical for advancing research in vascular biology, tissue engineering, and cancer metastasis. On the other hand, Electric Cell-Substrate Impedance Sensing (ECIS) is a powerful tool for real-time, label-free monitoring of cellular behavior. This review examines the application of combining ECIS and flow systems to study, in real-time, the effects of shear stress on cell monolayers, such as the impact on barrier function. It highlights its advantages, the various experimental setups, and key experimental findings.</div></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"199 ","pages":"Pages 246-254"},"PeriodicalIF":4.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146127501","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}

{"title":"Biomagnetism of oral tissues and external magnetic field interactions with cell membranes, oral microflora, and orthodontic magnetic therapies: A review","authors":"Sisenando Itabaiana Sobrinho ,&nbsp;Luiz Claudio Meira-Belo ,&nbsp;Nelcy Della Santina Mohallem","doi":"10.1016/j.pbiomolbio.2026.01.003","DOIUrl":"10.1016/j.pbiomolbio.2026.01.003","url":null,"abstract":"<div><div>Various rare earth magnets have been successfully applied in clinical orthodontics; however, their interactions with the oral environment remain only partially understood. Various controversies remain regarding magnetic fields (MFs) in cell biophysics owing to the heterogeneity of field parameters (including intensity, exposure time, and waveform) and experimental conditions, with little consensus on the topic. This article aimed to comprehensively review recent findings on biomagnetism in oral tissues, the mechanisms of action of exogenous MFs, the behavior of MF-stimulated cell membranes, the biocompatibility of magnetic materials, and their effects on oral microflora. Additionally, novel concepts regarding orthodontic movement, such as biomagnetism, diamagnetic anisotropy of biological tissues, and bone semiconduction, are discussed. The interplay of these phenomena with external MFs and bone piezoelectricity may provide novel insights into the electromagnetic phenomena involved in orthodontic movements. To date, research on MFs and oral microbiota has yielded inconclusive results. Hence, improving magnetic materials, clarifying the magnetic properties of tissues and their interactions, and considering the use of magnetic materials as complementary therapy in orthodontic movement is crucial for achieving a new level of clinical excellence.</div></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"199 ","pages":"Pages 209-221"},"PeriodicalIF":4.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146047300","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}

{"title":"WATER roles in cells: Biological and biophysical perspectives","authors":"Eugenio Frixione,&nbsp;Lourdes Ruiz-Zamarripa","doi":"10.1016/j.pbiomolbio.2025.12.003","DOIUrl":"10.1016/j.pbiomolbio.2025.12.003","url":null,"abstract":"<div><div>Water, elected as Molecule of the Year by the American Society for Biochemistry and Molecular Biology, is the substance in which life originated on this planet and became then involved in numerous cell functions of all animal and vegetal tissues, up to being the most abundant component of all living systems. Despite its importance, however, the various conditions and roles of water in the protoplasm are mostly absent in current cell biology textbooks and common related reviews, so the subject demands consideration of how it should be now taught to graduate students interested in biochemistry and molecular biology. The present paper offers an overview of how knowledge about water involvement in cell structure and function has evolved from the mid 19th century up to our time, starting with early microscopic inspections of living cells, proceeding next to the emergence of notions about water distribution within them, including its various particular behaviors in the protoplasm and the roles it plays in cell function, plus succinct notes about recent reports of experimental approaches with their results and particular views on the topic for different types of cells.</div></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"199 ","pages":"Pages 162-166"},"PeriodicalIF":4.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145696329","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}

{"title":"Field potential duration and its variability as essential parameters for revealing proarrhythmia: problematic aspects of analysis in cardiomyocytes derived from human pluripotent stem cells","authors":"Martin Král ,&nbsp;Olga Švecová ,&nbsp;Pavel Jurák ,&nbsp;Josef Halámek ,&nbsp;Milena Šimurdová ,&nbsp;Jiří Šimurda ,&nbsp;Markéta Bébarová","doi":"10.1016/j.pbiomolbio.2025.12.004","DOIUrl":"10.1016/j.pbiomolbio.2025.12.004","url":null,"abstract":"<div><div>The microelectrode array (MEA) is an easy, high-throughput method, ideal for obtaining a large amount of data from excitable cells, including cardiomyocytes. However, the analysis can be problematic, especially the analysis of the field potential duration (FPD). Several factors, including the differentiation protocol, culture duration, recording settings, and signal processing, may influence the results. In this paper, we focused on the MEA recording settings, analysis, and evaluation of FPD from cardiomyocytes, especially those derived from human pluripotent stem cells (hPSC). By examining more than 120 original articles using MEA and any cardiac preparation, we detected an inconsistency in the acquisition setting. It is striking that only one-third of the studies provided complete information about filtering of the signal, even though this may substantially influence the shape of the signal and, thus, FPD. The performed analysis emphasizes a thorough inspection of both the ‘raw’ and filtered signals to estimate proper FPD values, as well as a careful determination of the relationship between FPD and cycle length before using any correction formula.</div></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"199 ","pages":"Pages 99-113"},"PeriodicalIF":4.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145745495","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}

{"title":"Energy-driven innovations in computational de novo protein engineering","authors":"Kevser Kübra Kırboğa ,&nbsp;Ecir Uğur Küçüksille","doi":"10.1016/j.pbiomolbio.2026.01.005","DOIUrl":"10.1016/j.pbiomolbio.2026.01.005","url":null,"abstract":"<div><div>Energy models play a crucial role in the advancement of computational de novo protein engineering, enabling the design of novel proteins with tailored functionalities. Proteins serve as the foundation of biochemical processes, making their precise engineering essential for applications in biotechnology, medicine, and synthetic biology. Unlike traditional approaches that focus on modifying existing proteins, de novo engineering introduces entirely new constructs, a paradigm shift driven by energy-based strategies that guide protein folding, stability, and functionality through comprehensive simulations of energy landscapes. Computational techniques such as molecular dynamics (MD), thermodynamic integration, and Monte Carlo sampling are fundamental in evaluating designed proteins' stability and dynamic behavior. Widely used tools such as CHARMM, Amber, and Rosetta leverage advanced energy functions to optimize protein structures, facilitating accurate predictions of folding pathways and binding affinities. Additionally, the integration of machine learning (ML) and deep learning (DL) has significantly improved the speed and precision of energy-based modeling, enhancing the design and optimization process. This review systematically analyzes recent studies, provides quantitative benchmarking of major computational platforms, and presents a decision framework for method selection based on accuracy-cost-throughput trade-offs. By integrating classical force fields, quantum mechanical (QM) approaches, and AI-driven predictions with experimental validation, this work outlines a roadmap for advancing therapeutic and industrial protein design through synergistic physics-based and data-driven strategies.</div></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"199 ","pages":"Pages 176-196"},"PeriodicalIF":4.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146030334","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}

{"title":"Rewiring lipid Metabolism: The central role of CPT1 in metabolic dysfunction","authors":"Dan Ni ,&nbsp;Yuxuan Liu ,&nbsp;Xiaofang Lin ,&nbsp;Manqing Luo ,&nbsp;Chuanhuan Deng ,&nbsp;Jing Li ,&nbsp;Pengfei Liang ,&nbsp;Zhenguo Liu ,&nbsp;Bimei Jiang","doi":"10.1016/j.pbiomolbio.2025.11.002","DOIUrl":"10.1016/j.pbiomolbio.2025.11.002","url":null,"abstract":"<div><div>Carnitine palmitoyltransferase 1 (CPT1) serves as a critical gatekeeper in mitochondrial fatty acid oxidation and plays a central role in systemic energy homeostasis. The CPT1 family comprises three isoforms—CPT1A, CPT1B, and CPT1C—which exhibit distinct tissue distributions and regulatory features, enabling specialized metabolic functions in the liver, heart, skeletal muscle, and brain. CPT1 activity is tightly controlled through multiple mechanisms, including inhibition by malonyl-CoA, epigenetic modifications, and protein–protein interactions, all of which coordinate nutrient sensing and energy adaptation. Dysregulation of CPT1 has been implicated in the development of various metabolic disorders, including obesity, metabolic (dysfunction)-associated fatty liver disease (MAFLD), diabetic cardiomyopathy, and metabolic syndrome. This review summarizes recent advances in understanding the regulatory landscape and pathological roles of CPT1 and further discusses emerging therapeutic strategies. While CPT1-targeted interventions hold promise, challenges such as isoform specificity, off-target effects, and tissue-selective delivery must be addressed to achieve precision metabolic modulation.</div></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"199 ","pages":"Pages 20-30"},"PeriodicalIF":4.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145582827","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}

{"title":"Computational advances in RNA-small molecule binding site prediction","authors":"Lang Yang,&nbsp;Zou Yan,&nbsp;Yanhui Liu,&nbsp;Yuyu Feng","doi":"10.1016/j.pbiomolbio.2026.02.003","DOIUrl":"10.1016/j.pbiomolbio.2026.02.003","url":null,"abstract":"<div><div>RNA-small molecule interactions are fundamental to cellular regulation and have emerged as highly attractive therapeutic targets. Despite their potential, discovering RNA-binding small molecules remains challenging due to RNA's intrinsic structural flexibility, transient and context-dependent binding pockets, and the limited availability of high-resolution complex structures. Computational prediction approaches have evolved from early statistical models relying on handcrafted descriptors to advanced machine and deep learning frameworks that integrate sequence, structural, energetic, and topological information. More recently, large language models have enabled the capture of long-range sequence dependencies and contextual patterns, complementing structure-based encoders for multimodal modeling of RNA-ligand interactions. In this review, we summarize the principles and current state of computational strategies for RNA-ligand binding site prediction, highlighting methodological evolution, multimodal feature integration, and persisting challenges, and we discuss emerging directions toward accurate, generalizable, and interpretable predictions to accelerate rational RNA-targeted drug discovery.</div></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"199 ","pages":"Pages 267-278"},"PeriodicalIF":4.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146138075","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}