Methods最新文献 - Book学术

Rapid cell-free antibody fragment production and binding analysis via fluorescence correlation. 快速无细胞抗体片段产生和荧光相关结合分析。

IF 3.6 3区生物学

Methods Pub Date : 2026-09-04 DOI: 10.1016/j.ymeth.2026.08.007

Shakiba Nikfarjam, Chao Liu, Emma J Laurence, Adam N Laurence, Jennifer L Chlebek, Dante P Ricci, Steven A Hoang-Phou, Isabella M Carrano, Ted A Laurence, Matthew A Coleman

{"title":"Rapid cell-free antibody fragment production and binding analysis via fluorescence correlation.","authors":"Shakiba Nikfarjam, Chao Liu, Emma J Laurence, Adam N Laurence, Jennifer L Chlebek, Dante P Ricci, Steven A Hoang-Phou, Isabella M Carrano, Ted A Laurence, Matthew A Coleman","doi":"10.1016/j.ymeth.2026.08.007","DOIUrl":"https://doi.org/10.1016/j.ymeth.2026.08.007","url":null,"abstract":"<p><p>This study presents a workflow for rapid production and functional characterization of antibody fragments using an E. coli-based cell-free protein synthesis (CFPS) system. We quantified binding interactions by fluorescence correlation spectroscopy (FCS), which enabled determination of dissociation constants (K<sub>D</sub>) between antibodies and the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein. As an initial validation, two conventionally expressed anti-RBD antibodies were analyzed to establish the reliability of the FCS-based binding measurements. To enable efficient cell-free production, strategies were developed to improve the solubility and yield of single-chain variable fragments (scFvs), including implementation of an established two-stage refolding workflow adapted for CFPS-derived proteins. This approach enabled recovery of functional scFvs from insoluble fractions. In addition, Fab fragments were successfully produced and characterized, with binding measurements confirming retention of antigen recognition. Together, these results demonstrate that CFPS can be combined with FCS to enable rapid, solution-phase evaluation of antibody fragment binding without reliance on conventional cell-based expression systems. This integrated platform provides a scalable approach for antibody screening and characterization, with potential applications in therapeutic antibody development and high-throughput discovery.</p>","PeriodicalId":390,"journal":{"name":"Methods","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148890737","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

A formal Bayesian decisional framework for automated cell subset assignment in multiparametric flow cytometry: The LBC-flow approach. 多参数流式细胞术中自动细胞子集分配的正式贝叶斯决策框架：LBC-flow方法。

IF 3.6 3区生物学

Methods Pub Date : 2026-09-02 DOI: 10.1016/j.ymeth.2026.08.011

Francis Lacombe, Benoit Dupont, Gilbert Carron, Marie-Christine Béné

{"title":"A formal Bayesian decisional framework for automated cell subset assignment in multiparametric flow cytometry: The LBC-flow approach.","authors":"Francis Lacombe, Benoit Dupont, Gilbert Carron, Marie-Christine Béné","doi":"10.1016/j.ymeth.2026.08.011","DOIUrl":"https://doi.org/10.1016/j.ymeth.2026.08.011","url":null,"abstract":"<p><p>Multiparametric flow cytometry (MFC) data analyses still largely rely on expert-dependent subjective manual gating strategies. While unsupervised clustering methods have improved data exploitation, no formal probabilistic decisional framework has yet been proposed for the critical subsequent step of cell subset assignment and quantitation. LBC-Flow (patent pending) is a structured naïve Gaussian Bayesian decisional framework built upon FlowSOM clustering. Unlike black-box machine learning approaches, every classification decision is fully interpretable, explicit and mathematically justified by its posterior probability value. A reference model including all cell distribution parameters must be constructed from normal body fluid, enabling the computation of posterior probabilities for each cell. Cells failing to meet predefined acceptance thresholds are flagged as a new specific class of Non-Classifiable Events (NCE). A leukocyte differential panel was used as proof-of-concept on 36 blood samples. Five analytical strategies were compared: manual gating, FlowSOM-only quantification, and three Bayesian classification approaches-(i.e. two discrete based on nodes (BDN) or cells (BDC) and one gaussian based on cells (BCGC)-. Using intraclass correlation coefficient ICC(3,1) and Z score for comparisons, BCGC demonstrated better performance than the other methods particularly for rare subsets. Complete results were delivered for 26 identified leukocyte subpopulations and NCE, in less than 30 s per sample. LBC-Flow is an original formal Bayesian decisional framework, explicitly addressing the gap between unsupervised clustering output and reproducible cell subset assignment and quantitation. Panel-agnostic by design, this approach provides a methodological foundation to be tested with other flow cytometry datasets in clinical or research contexts.</p>","PeriodicalId":390,"journal":{"name":"Methods","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148878862","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

Purification-free chemical conversion-coupled RT-PCR for ultralow-input detection and quantification of a⁶A-labelled RNA. 用于a6a标记RNA的超低输入检测和定量的免纯化化学转化偶联RT-PCR。

IF 3.6 3区生物学

Methods Pub Date : 2026-08-30 DOI: 10.1016/j.ymeth.2026.08.010

Shanshan Jiang, Wenping Li, Xiao Shu

{"title":"Purification-free chemical conversion-coupled RT-PCR for ultralow-input detection and quantification of a<sup>6</sup>A-labelled RNA.","authors":"Shanshan Jiang, Wenping Li, Xiao Shu","doi":"10.1016/j.ymeth.2026.08.010","DOIUrl":"10.1016/j.ymeth.2026.08.010","url":null,"abstract":"<p><p>Nucleoside analogue-based RNA labelling provides powerful approaches for investigating RNA synthesis, turnover, and post-transcriptional regulation. However, conventional detection workflows often require chemical treatment, reagent removal, and repeated RNA purification, which can cause substantial sample loss and limit their application to ultralow-input samples. Here, we present a chemical conversion-coupled RT-PCR method that eliminates post-conversion RNA purification for the detection and quantification of N<sup>6</sup>-allyladenosine (a<sup>6</sup>A)-labelled RNA. Iodine-induced cyclization converts a<sup>6</sup>A into a cyclized adenosine derivative that generates characteristic cDNA mutation signatures during reverse transcription. By eliminating iodine removal, alkaline stabilization, and post-conversion RNA purification, the workflow enables reverse transcription directly from the chemical reaction mixture and reduces handling steps that may otherwise cause sample loss. Optimization of iodine treatment and reverse transcriptase compatibility identified Induro reverse transcriptase as suitable for quantitative analysis because it combined a high mutation rate with the highest estimated read-through efficiency across cyclized a<sup>6</sup>A sites. The method detected a<sup>6</sup>A-labelled RNA from femtogram-level inputs and supported mutation-rate-based quantification across a broad input range. Its applicability was further demonstrated by time-resolved tracking of IVT-generated mRNA carrying different poly(A) tails using ultralow amounts of total RNA. This workflow provides a sensitive platform for the detection and relative quantification of a<sup>6</sup>A-labelled RNA when sample availability is limited.</p>","PeriodicalId":390,"journal":{"name":"Methods","volume":" ","pages":"23-31"},"PeriodicalIF":3.6,"publicationDate":"2026-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148860408","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

Engineering considerations for 3D cell culture and disease modelling on-chip platforms: A review. 三维细胞培养和疾病建模芯片平台的工程考虑：综述。

IF 3.6 3区生物学

Methods Pub Date : 2026-08-29 DOI: 10.1016/j.ymeth.2026.08.009

Oindrila Banik, Tokárová Viola, Bala Chakravarthy Neelapu, Ayyappasamy Sudalaiyadum Perumal, Prasoon Kumar, Earu Banoth

{"title":"Engineering considerations for 3D cell culture and disease modelling on-chip platforms: A review.","authors":"Oindrila Banik, Tokárová Viola, Bala Chakravarthy Neelapu, Ayyappasamy Sudalaiyadum Perumal, Prasoon Kumar, Earu Banoth","doi":"10.1016/j.ymeth.2026.08.009","DOIUrl":"10.1016/j.ymeth.2026.08.009","url":null,"abstract":"<p><p>In the era of miniaturization, the advent of sensors and chips is rapidly increasing for systematic investigation, monitoring and diagnosing unprecedented diseases in preclinical and clinical research. Early-stage detection demands a miniaturized platform/ artificial model in clinical laboratories and healthcare centers. This enables us to investigate and study the physiological processes of the samples and the drug's efficacy on them in a cost-effective and time-efficient manner. The technology of chip systems is rapidly evolving in an attempt to bridge the gaps between preclinical and clinical studies, as well as their wide applications in research laboratories in low-resource settings. Emerging research is focusing on 3D cell culture in microfluidic devices in order to facilitate the uniform distribution of nutrients and in-vitro investigation for assessing various biological processes and phenomena due to limitations in conventional 2D cell culture. It is crucial to understand extensively the significant parameters associated with the development of microfluidic chips for culturing and forming uniform 3D cell masses. The goal of this review is to highlight the various on-chip models that offer precise control over the size of 3D aggregates and their respective microenvironment, making them suitable for drug screening and delivery in therapeutic applications. Additionally, the manuscript discusses the design considerations and feasible microfabrication techniques for generating tumor models, organoids, or organ-on-chips, and the respective computational parameters that govern nutrient flow and permeation, growth conditions, and the microenvironment, cultivating the state-of-the-art microfluidic chips for 3D cell culture.</p>","PeriodicalId":390,"journal":{"name":"Methods","volume":" ","pages":"32-53"},"PeriodicalIF":3.6,"publicationDate":"2026-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148856799","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

Novel methods for the discovery of disease-associated T cell epitopes in autoimmunity 发现自身免疫疾病相关T细胞表位的新方法

IF 4.3 3区生物学

Methods Pub Date : 2026-04-01 Epub Date: 2026-02-11 DOI: 10.1016/j.ymeth.2026.02.004

Eline Mertens , Barbara Willekens , Judith Derdelinckx , Nathalie Cools

{"title":"Novel methods for the discovery of disease-associated T cell epitopes in autoimmunity","authors":"Eline Mertens , Barbara Willekens , Judith Derdelinckx , Nathalie Cools","doi":"10.1016/j.ymeth.2026.02.004","DOIUrl":"10.1016/j.ymeth.2026.02.004","url":null,"abstract":"<div><div>A detailed understanding of the pathology of autoimmune diseases hinges on the identification of self-antigens and epitopes targeted by the immune system. While the characterization of autoantibodies is now well-established, facilitating both mechanistic insights and clinical biomarker applications, the identification of autoreactive T cell epitopes remains considerably more challenging. This complexity is amplified by the presence of autoreactive T cells in healthy individuals, necessitating highly sensitive and specific methods to allow for the detection of subtle differences between the autoreactive T cell population in healthy controls and in patients. Fortunately, T cell epitope discovery is a rapidly advancing field, with new methods continually emerging to improve sensitivity, throughput, and resolution. In this review, we will provide a structured overview of the key methods used to identify T cell epitopes, spanning both foundational techniques thathave been instrumental in the early discovery of self-epitopes involved in autoimmunity as well as recent high throughput approaches that offer enhanced precision and scalability. In the second part, we give an overview of the techniques used in the validation of the role of self-peptides in the autoimmune disorder. We conclude by discussing future directions in the field, emphasizing the critical role of T cell epitope discovery in driving the development of targeted, antigen-specific therapies for autoimmune disorders. This review aims to provide a practical and conceptual framework for T cell epitope discovery in autoimmune diseases, integrating established experimental approaches with emerging computational and high-throughput methodologies to guide informed method selection in contemporary research.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"248 ","pages":"Pages 64-82"},"PeriodicalIF":4.3,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146187063","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

Ultra-sensitive diagnostic platform utilizing gold nanoparticle integrated in a freestanding hydrogel matrix 利用金纳米颗粒集成在独立水凝胶基质中的超灵敏诊断平台。

IF 4.3 3区生物学

Methods Pub Date : 2026-04-01 Epub Date: 2026-02-02 DOI: 10.1016/j.ymeth.2026.02.002

Omar M. Rahman , Shengxi Lan , Andrea M.A. Pizano , Woosuk Chung , Younghun Kim , Dae Kun Hwang

{"title":"Ultra-sensitive diagnostic platform utilizing gold nanoparticle integrated in a freestanding hydrogel matrix","authors":"Omar M. Rahman , Shengxi Lan , Andrea M.A. Pizano , Woosuk Chung , Younghun Kim , Dae Kun Hwang","doi":"10.1016/j.ymeth.2026.02.002","DOIUrl":"10.1016/j.ymeth.2026.02.002","url":null,"abstract":"<div><div>Fluorescence-based analysis for protein detection has been widely adopted; however, they fall short in achieving ultra-sensitive detection because of their inherently low signal-to-noise ratio at sub-picomolar concentrations. To overcome this limitation, signal amplifying materials such as gold nanoparticles (AuNPs) have been integrated into various detection platforms to enhance fluorescence signals. However, fabrication of such AuNP integrated platforms remains complex, often requiring sophisticated fabrication steps, yet none approach the ultra-sensitive detection range of 10<sup>0</sup> fg mL<sup>−1</sup>. In this study, we enabled analysis of captured protein/antibody at 10<sup>0</sup> fg mL<sup>−1</sup> concentrations through fluorescence signals utilizing freestanding gold nanoparticle integrated freestanding hydrogel platforms. The platform is fabricated by integrating AuNPs into the hydrogel matrix using a single-step photolithographic technique. The integrated AuNPs significantly enhanced the fluorescence signals compared to controls. Notably, at fg mL<sup>−1</sup> levels of fluorophore, the AuNP integrated hydrogels produced a robust optical signal in contrast to negligible responses observed in controls. The platform’s versatility was validated using tumor necrosis factor-alpha antibody (TNF-α Ab), achieving detection at 10<sup>0</sup> fg mL<sup>−1</sup>. By synergizing the hydrogels’ porous structure with AuNPs’ signal amplification, this platform successfully achieves fluorescence-based ultra-sensitive protein/antibody detection.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"248 ","pages":"Pages 43-52"},"PeriodicalIF":4.3,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146117321","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

An optimized method for establishing experimental rat periodontitis using “double-ligature” technique 采用“双结扎”技术建立实验性大鼠牙周炎的优化方法。

IF 4.3 3区生物学

Methods Pub Date : 2026-04-01 Epub Date: 2026-02-03 DOI: 10.1016/j.ymeth.2026.01.010

Cheng Hu , Haixia Wang , Yuwei Liao , Xiaoli Hu

{"title":"An optimized method for establishing experimental rat periodontitis using “double-ligature” technique","authors":"Cheng Hu , Haixia Wang , Yuwei Liao , Xiaoli Hu","doi":"10.1016/j.ymeth.2026.01.010","DOIUrl":"10.1016/j.ymeth.2026.01.010","url":null,"abstract":"<div><div>Establishing stable and dependable animal models of experimental periodontitis is critical in advancing our understanding of the etiology, clinical diagnosis, and treatment of periodontitis. However, conventional silk ligation methods for inducing periodontitis in rats have limitations, with silk thread detachment being a major concern. In this study, we established a reliable rat periodontitis model using a novel “double-ligature” technique combining silk sutures with orthodontic wires, augmented by a high-sugar diet. Thirty rats were randomized into five groups: control, wire-only, silk-only, wire+silk, and wire+silk+sugar. After 2 weeks, the wire+silk+sugar group demonstrated significantly elevated clinical indices (sulcus bleeding index, probing depth, plaque index) versus controls (*p* < 0.05), alongside severe alveolar bone resorption quantified by micro-CT. Molecular analyses revealed upregulated inflammatory gene expression (e.g., TNF-α, IL-1β) in double-ligature groups. Histology confirmed extensive immune infiltration and periodontal ligament disruption. The combined approach induced robust periodontitis with 103% greater CEJ-ABC distance versus controls, while TRAP staining revealed 5-fold increased osteoclast activity. By this “double-ligature” technique, the pathogenesis of periodontitis can be studied on the one hand, and the therapeutic effect of biomaterials on the alveolar bone defects caused by periodontitis can be verified on the other hand. This reproducible method overcomes traditional silk ligature limitations (e.g., thread detachment) and provides a foundation for translational periodontitis research.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"248 ","pages":"Pages 20-29"},"PeriodicalIF":4.3,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146123306","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

Disentangling the events that constitute the main phase transition of predominantly neutral lipid bilayers containing anionic lipids by measuring their macroscopic properties 通过测量阴离子脂质的宏观性质，解开构成主要中性脂质双分子层主要相变的事件。

IF 4.3 3区生物学

Methods Pub Date : 2026-04-01 Epub Date: 2026-02-08 DOI: 10.1016/j.ymeth.2026.02.005

Ramona Petko , Ivan Marić , Barbara Pem , Danijela Bakarić

{"title":"Disentangling the events that constitute the main phase transition of predominantly neutral lipid bilayers containing anionic lipids by measuring their macroscopic properties","authors":"Ramona Petko , Ivan Marić , Barbara Pem , Danijela Bakarić","doi":"10.1016/j.ymeth.2026.02.005","DOIUrl":"10.1016/j.ymeth.2026.02.005","url":null,"abstract":"<div><div>The thinning of lipid bilayers during their main phase transition, as the outcome of the weakening of van der Waals interactions between their hydrocarbon chains and the hydration of the polar headgroup region, displays a peak at the specific temperature (<em>T</em><sub>m</sub>). The most common technique used for <em>T</em><sub>m</sub> determination is differential scanning calorimetry (DSC), which provides the required information straightforwardly and rapidly, but it cannot provide any details on the molecular-level events that underlie the main phase transition. To uncouple the impact of hydrogen bonding and (de)protonation in the polar headgroup region on the measured <em>T</em><sub>m</sub>, in this work, we determined the latter of anionic lipid-containing predominantly neutral bilayers (10:90% molar ratio) in Britton-Robinson buffers with pH values 4, 7, and 9 using macroscopic techniques. Specifically, the temperature-dependent UV–Vis spectra combined with the measurement of refractive indices allowed the modeling of the bilayer thickness (<em>d</em>) change during the main phase transition. Significantly, the alteration in the hydrogen bonding pattern affected the change in <em>d</em>, unlike the deprotonation of anionic lipids. A molecular polarizability displayed an abrupt decrease upon the main phase transition, but its magnitude and associated uncertainty level were found to be acceptable only for a lipid mixture in which anionic lipid does not exchange protons with aqueous milieu, i.e., a pH-dependent (de)protonation obscures more precise determination of <em>T</em><sub>m</sub>. Besides the determination of <em>T</em><sub>m</sub> values, this new methodology enabled us to rank the contributions to <em>T</em><sub>m</sub> value: van der Waals interactions > hydrogen bonding > (de)protonation.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"248 ","pages":"Pages 53-63"},"PeriodicalIF":4.3,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146155723","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

DNA-regulated structural engineering of metal nanomaterials: A strategy for advanced optical biosensing dna调控的金属纳米材料结构工程：一种先进的光学生物传感策略

IF 4.3 3区生物学

Methods Pub Date : 2026-04-01 Epub Date: 2026-02-03 DOI: 10.1016/j.ymeth.2026.02.001

Junyao Li , Ling Cai , Peiming Liu , Rui Zhang , Wenrong Cai , Datong Wu , Laidi Xu , Yong Kong

{"title":"DNA-regulated structural engineering of metal nanomaterials: A strategy for advanced optical biosensing","authors":"Junyao Li , Ling Cai , Peiming Liu , Rui Zhang , Wenrong Cai , Datong Wu , Laidi Xu , Yong Kong","doi":"10.1016/j.ymeth.2026.02.001","DOIUrl":"10.1016/j.ymeth.2026.02.001","url":null,"abstract":"<div><div>The development of highly sensitive optical biosensors has emerged as a focal point in chemical research, exerting a profound influence on numerous fields related to the national economy and public welfare. Owing to their dual nanostructural and metallic properties, metal nanomaterials exhibit certain distinctive optical properties. Among them, localized surface plasmon resonance (LSPR), surface-enhanced Raman scattering (SERS), and fluorescence emission are particularly prominent. Therefore, metal nanomaterials possess significant potential to enhance the analytical performance of optical biosensors. Compared to peptides and proteins, DNA demonstrates remarkable superiority in terms of the diversity of length, sequence, backbone structure, and modification groups. Integrating DNA with metal nanomaterials provides a prerequisite for accurately identifying targets and precisely regulating metal nanomaterials. Effectively combining the superior properties of DNA and metal nanomaterials represents a critical scientific challenge in facilitating the development of highly sensitive optical analytical approaches. Exploring novel strategies to regulate the optical properties of metal nanomaterials can provide more opportunities for developing high-performance optical biosensors. In this review, the regulation modes of DNA with metal nanomaterials can be summarized into three parts <em>i.e.</em>: the morphological evolution of DNA-guided metal nanomaterials, the assembly of DNA with metal nanomaterials, and the formation of DNA-templated metal nanomaterials. For each part, typical applications have been displayed based on regulating the optical properties of metal nanomaterials via DNA. Furthermore, perspectives and challenges are also discussed at the end of the review.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"248 ","pages":"Pages 1-19"},"PeriodicalIF":4.3,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146122717","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

From wrinkles to malignancy: small-molecule-mediated stem cell approaches in skin aging 从皱纹到恶性肿瘤：小分子介导的干细胞在皮肤衰老中的应用。

IF 4.3 3区生物学

Methods Pub Date : 2026-04-01 Epub Date: 2026-02-06 DOI: 10.1016/j.ymeth.2026.02.003

Abdullah Alkhammash, Ghallab Alotaibi

{"title":"From wrinkles to malignancy: small-molecule-mediated stem cell approaches in skin aging","authors":"Abdullah Alkhammash, Ghallab Alotaibi","doi":"10.1016/j.ymeth.2026.02.003","DOIUrl":"10.1016/j.ymeth.2026.02.003","url":null,"abstract":"<div><div>Skin aging is driven by the progressive exhaustion of stem cell niches, epigenetic drift, and accumulation of senescent cells, which together promote both aesthetic decline and a pro-tumorigenic microenvironment. This review focuses on the emerging methodological theme of small-molecule-mediated reprogramming as a strategy to restore skin homeostasis. We evaluated the shift from traditional regenerative medicine toward targeted chemical modulation, focusing on the use of small-molecule cocktails to induce partial reprogramming and rejuvenate aged stem cell populations without erasing cellular identity. Central to this theme is the integration of high-throughput virtual screening and AI-driven predictive modeling to identify potent modulators of Wnt, Notch, and TGF-β pathways. We further bridge the gap between preclinical innovation and clinical application by analyzing “serious clinical studies” with proven efficacy, including randomized controlled trials of stem cell-derived secretomes and clinically validated small molecules, such as tretinoin and firming peptides. By contextualizing advanced delivery systems, including microneedles and stimuli-responsive nanoparticles, within this reprogramming framework, we demonstrate how spatially controlled interventions can optimize clinical outcomes. This review provides a unified perspective on how the intersection of computational drug discovery and niche-targeted pharmacology is moving small-molecule skin rejuvenation from theoretical potential to widespread clinical translation.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"248 ","pages":"Pages 30-42"},"PeriodicalIF":4.3,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146140679","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