Methods最新文献 - Book学术

Multi-pathway feature-level interpretability in MHC-i antigen presentation via concept-based modeling. 基于概念建模的MHC-i抗原呈递中的多途径特征水平可解释性。

IF 4.3 3区生物学

Methods Pub Date : 2026-05-06 DOI: 10.1016/j.ymeth.2026.05.005

Piyush Borole, Denise Boulanger, Ajitha Rajan

{"title":"Multi-pathway feature-level interpretability in MHC-i antigen presentation via concept-based modeling.","authors":"Piyush Borole, Denise Boulanger, Ajitha Rajan","doi":"10.1016/j.ymeth.2026.05.005","DOIUrl":"https://doi.org/10.1016/j.ymeth.2026.05.005","url":null,"abstract":"<p><p>Accurate prediction of MHC-I antigen presentation is central to neoantigen discovery and immunotherapy development. Although recent deep-learning based predictors achieve high accuracy, most operate as black-box models, which limits interpretability, and consequently trustworthiness of these predictors. We present MHCCBM, a gray-box framework that decomposes antigen presentation into a set of pathway-level intermediate concepts. Each step, i.e. proteasomal cleavage, TAP transport, peptide-MHC binding affinity, and chaperone dependency is treated as an independent predictive module, allowing different computational or experimental estimators to be substituted without altering the overall model. This architecture naturally supports representational multimodality, permitting the integration of sequence-based, structure-informed, or empirical predictors. In our reference implementation, ESM-2-derived models estimate peptide processing and chaperone dependency, while peptide-MHC binding affinity is predicted using MHCflurry. The concept outputs are combined using logistic regression. Our accuracy is comparable to that of state-of-the-art accuracy while providing MHC-I pathway level interpretability consistent with known cellular mechanisms.</p>","PeriodicalId":390,"journal":{"name":"Methods","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147855672","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

TEAMSTER: End-to-end pipeline for generation, processing, and automated quantitative image analysis of 3D tumour spheroids for nanobiology. TEAMSTER：端到端的管道，用于纳米生物学3D肿瘤球体的生成、处理和自动定量图像分析。

IF 4.3 3区生物学

Methods Pub Date : 2026-05-06 DOI: 10.1016/j.ymeth.2026.04.015

Linda Barbieri, Andrea Banfi, Stefania Garbujo, Lucia Salvioni, Chiara Baioni, Giulia Tomaino, Maria Rita Chelazzi, Luisa Fiandra, Miriam Colombo, Davide Prosperi, Metello Innocenti

{"title":"TEAMSTER: End-to-end pipeline for generation, processing, and automated quantitative image analysis of 3D tumour spheroids for nanobiology.","authors":"Linda Barbieri, Andrea Banfi, Stefania Garbujo, Lucia Salvioni, Chiara Baioni, Giulia Tomaino, Maria Rita Chelazzi, Luisa Fiandra, Miriam Colombo, Davide Prosperi, Metello Innocenti","doi":"10.1016/j.ymeth.2026.04.015","DOIUrl":"https://doi.org/10.1016/j.ymeth.2026.04.015","url":null,"abstract":"<p><p>Three-dimensional (3D) tumour spheroids are widely used as physiologically relevant in vitro models to study tumour biology, therapeutic responses, and the distribution of drugs and nanomaterials. However, experimental workflows for spheroid-based studies remain highly heterogeneous, with limited standardization across spheroid generation, processing, and quantitative analysis, hindering reproducibility and accessibility. Here, we present TEAMSTER, an integrated, end-to-end pipeline for the generation, cryosectioning, immunostaining, and quantitative image analysis of tumour spheroids. The workflow combines optimized protocols for reproducible spheroid formation that minimize variability, a liquid nitrogen-free, colour-coded OCT embedding strategy improving spheroid localization during cryosectioning, standardized fixation and staining procedures compatible with multiplex fluorescence imaging, and a semi-automated, GUI-based CellProfiler pipeline enabling unbiased quantitative analysis without coding skills, machine learning, or dedicated computing hardware. TEAMSTER is experimentally validated in two distinct tumour spheroid models treated with fluorescently labelled nanoconjugates. Quantitative performance metrics for spheroid preparation (intraplate and interplate coefficients of variation) and image segmentation benchmarking (Dice and IoU coefficients) support the robustness of single-cell-resolved measurements across cryosectioned spheroid models and imaging conditions. By prioritizing experimental robustness, standardization, and usability, TEAMSTER provides a practical methodological resource for reproducible quantitative spheroid-based studies in cancer biology and nanomedicine.</p>","PeriodicalId":390,"journal":{"name":"Methods","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147855697","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

Identification of black carbon in placental tissue using scanning electron microscopy and energy dispersive X-ray fluorescence. 用扫描电子显微镜和能量色散x射线荧光鉴别胎盘组织中的黑碳。

IF 4.3 3区生物学

Methods Pub Date : 2026-05-05 DOI: 10.1016/j.ymeth.2026.05.002

Garvita Parikh, Pratik Chhapia, Prasenjit Maity, Bhoomika Patel

{"title":"Identification of black carbon in placental tissue using scanning electron microscopy and energy dispersive X-ray fluorescence.","authors":"Garvita Parikh, Pratik Chhapia, Prasenjit Maity, Bhoomika Patel","doi":"10.1016/j.ymeth.2026.05.002","DOIUrl":"https://doi.org/10.1016/j.ymeth.2026.05.002","url":null,"abstract":"<p><p>Currently, there are very few standardized and developed analysis methods for detecting the deposition of black carbon (BC) in human tissues, and they have certain limitations. A non-destructive and robust method has been developed for identifying BC deposits in soft biological tissue using placental tissue matrix as a case study. Placental tissues were obtained from 50 pregnant women in their third trimester. The method employs a correlative workflow, utilizing a scanning electron microscope (SEM) for high-resolution morphological screening of suspected BC particulates and energy-dispersive X-ray fluorescence (EDXRF) for specific elemental confirmation. The method's specificity was first tested in a preliminary experiment conducted by externally embedding charcoal in two placental tissues, which confirmed its ability to distinguish the exogenous BC particles from the native biological matrix based on definitive elemental analysis. Subsequently, this method was applied to 48 original placental tissues without external embedding of charcoal. The deposition of BC was identified on the surface of placental tissue, specifically at the foetal side of the placenta. This correlative SEM-EDXRF method provides a robust and effective framework for identifying exogenous BC in biological tissues, as demonstrated by the clear distinction between the elemental signatures of BC particles and the native biological matrix. The method has limitations in terms of quantification.</p>","PeriodicalId":390,"journal":{"name":"Methods","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147831952","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 high-content imaging workflow to screen for molecules that reduce cellular uptake of α-synuclein preformed fibrils. 筛选减少细胞摄取α-突触核蛋白预形成原纤维的分子的高含量成像工作流程。

IF 4.3 3区生物学

Methods Pub Date : 2026-05-05 DOI: 10.1016/j.ymeth.2026.05.001

Wolfgang E Reintsch, Andrea I Krahn, Chanshuai Han, Emmanuelle Nguyen-Renou, Carol X-Q Chen, Wen Luo, Irina Shlaifer, Tom Pfeifer, Edward A Fon, Thomas M Durcan

{"title":"A high-content imaging workflow to screen for molecules that reduce cellular uptake of α-synuclein preformed fibrils.","authors":"Wolfgang E Reintsch, Andrea I Krahn, Chanshuai Han, Emmanuelle Nguyen-Renou, Carol X-Q Chen, Wen Luo, Irina Shlaifer, Tom Pfeifer, Edward A Fon, Thomas M Durcan","doi":"10.1016/j.ymeth.2026.05.001","DOIUrl":"https://doi.org/10.1016/j.ymeth.2026.05.001","url":null,"abstract":"<p><p>A classical pathological hallmark of many neurodegenerative diseases is the formation of protein-rich aggregates and inclusions. In Parkinson's disease (PD), α-synuclein (α-syn) constitutes a major protein component of pathological inclusions, termed Lewy bodies. These α-syn aggregates are hypothesized to spread throughout the nervous system by cell-to-cell transmission acting as templates to amplify aggregate formation. In vitro generated α-syn aggregates, commonly called preformed fibrils (PFFs), have been used to investigate a number of aspects related to α-syn mediated pathology across different model systems. Here we describe a semi-automated assay to screen for small molecules that interfere with the cellular uptake and accumulation of PFFs. The assay uses dopaminergic progenitor cells (DPCs), derived from human induced pluripotent stem cells (hiPSCs). In an initial screen, we tested 1520 small molecules and identified several molecules that strongly reduce intracellular PFF load in DPCs. From these hits, candidate compounds were validated in dopaminergic neurons (DNs) to demonstrate the utility of the assay. This assay provides a robust, scalable and adaptable tool to screen for molecules that affect PFF uptake in hiPSC-derived cell models. Within the scope of this screen, it led to the identification of a set of compounds with diverse annotated targets that effectively reduce the accumulation of α-syn aggregates in DPCs and DNs.</p>","PeriodicalId":390,"journal":{"name":"Methods","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147831955","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

Burn depth assessment by photoacoustic imaging: A review. 光声成像评价烧伤深度的研究进展。

IF 4.3 3区生物学

Methods Pub Date : 2026-04-30 DOI: 10.1016/j.ymeth.2026.04.014

Jiachen Zhou, Siqi Liang, Jeong Hyeon Park, Anh Nguyen, Myeongsu Seong

引用次数: 0

Biochemical approaches to G protein-coupled receptors dimerization. G蛋白偶联受体二聚化的生化方法。

IF 4.3 3区生物学

Methods Pub Date : 2026-04-25 DOI: 10.1016/j.ymeth.2026.04.012

Michał K Jastrzębski, Artur Wnorowski, Kamil Wojnicki, Ayesha Asim, Agnieszka A Kaczor

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

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

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