MethodsPub Date : 2026-02-01Epub Date: 2025-11-16DOI: 10.1016/j.ymeth.2025.11.006
Jing Jiang , Junlin Xu , Peng Wang , Yuansheng Liu , Yiping Liu
{"title":"Unravelling cell heterogeneity and gene regulation mechanisms in multiple myeloma through single-cell RNA-seq","authors":"Jing Jiang , Junlin Xu , Peng Wang , Yuansheng Liu , Yiping Liu","doi":"10.1016/j.ymeth.2025.11.006","DOIUrl":"10.1016/j.ymeth.2025.11.006","url":null,"abstract":"<div><div>Multiple myeloma (MM) is the second most common blood cancer in the world, yet its genetic pathology is not fully understood and MM cells have highly heterogeneous regulatory mechanisms. Single-cell RNA-Sequencing (scRNA-Seq) technologies provide an unprecedented opportunity to investigate cell heterogeneity and understand regulatory mechanisms at the single-cell level. Four MM scRNA-Seq datasets were retrieved from the public domain containing 597, 172, 477, and 51,840 cells, respectively. First, they were integrated and jointly analyzed to accurately identify 24 MM cell clusters, using a normal hematopoiesis cells atlas as a control. Then we predicted 651 regulons within the 24 MM cell clusters. The identified regulons can substantially improve the elucidation of heterogeneous gene regulation mechanisms across various cell clusters, and hence can serve as a reference for diagnosis in MM.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"246 ","pages":"Pages 1-9"},"PeriodicalIF":4.3,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145536887","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}
MethodsPub Date : 2026-02-01Epub Date: 2025-12-19DOI: 10.1016/j.ymeth.2025.12.010
Jie Zeng , Zhiyu Shao , Siming Wang , Jun Dong , Weiyan Zhou , Haijian Zhao , Tianjiao Zhang , Jiangtao Zhang , Jing Wang , Hao Zheng , Wenxiang Chen , Chuanbao Zhang
{"title":"Establishment and application of a fully automated serum total free sulfhydryl assay based on 2,2′-DTDP","authors":"Jie Zeng , Zhiyu Shao , Siming Wang , Jun Dong , Weiyan Zhou , Haijian Zhao , Tianjiao Zhang , Jiangtao Zhang , Jing Wang , Hao Zheng , Wenxiang Chen , Chuanbao Zhang","doi":"10.1016/j.ymeth.2025.12.010","DOIUrl":"10.1016/j.ymeth.2025.12.010","url":null,"abstract":"<div><h3>Background</h3><div>Serum free thiols (FTs) are sensitive biomarkers of oxidative stress, closely associated with aging and chronic disease risk. Existing DTNB-based detection methods suffer from product instability, affecting analytical reliability. A more stable and high-throughput method is needed.</div></div><div><h3>Methods</h3><div>We developed an automated FT assay using 2,2′-dithiodipyridine (2,2′-DTDP) on a clinical chemistry analyzer. Serum samples reacted with 2,2′-DTDP under optimized conditions, and absorbance at 340 nm was used to quantify FT levels. Method performance, stability, and associations with cardiovascular disease (CVD) risk factors were assessed in 341 healthy individuals.</div></div><div><h3>Results</h3><div>FTs reacted with 2,2′-DTDP to generate 2-TP, a stable product with maximum absorbance at 340 nm. The method demonstrated excellent linearity (0–1200 μmol/L), low imprecision (1.8 %–3.3 %), and reasonable recovery (≥80 %). Serum FTs were stable for at least one year at −70 °C, 12 h at 2–8 °C, and 2 h at room temperature. In the study population, FT levels were positively correlated with serum albumin, a major thiol carrier, and negatively correlated with age, triglyceride, glucose and creatinine, suggesting links to redox status and CVD risks. These associations support the potential of FTs as indicators of systemic oxidative balance and aging-related health decline.</div></div><div><h3>Conclusion</h3><div>This simple and robust 2,2′-DTDP-based method enables accurate, high-throughput measurement of serum FTs. It is well suited for exploring thiol antioxidant function and evaluating age-related and cardiovascular risk in clinical and research settings.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"246 ","pages":"Pages 236-242"},"PeriodicalIF":4.3,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145802876","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}
MethodsPub Date : 2026-02-01Epub Date: 2025-12-15DOI: 10.1016/j.ymeth.2025.12.004
Huijuan Qi , Yujin Yang , Xiangting Hou , Yuanyuan Chen , Shaohua Gong
{"title":"Sensitivity-improving CRISPR-Cas strategies for non-nucleic acid targets detection","authors":"Huijuan Qi , Yujin Yang , Xiangting Hou , Yuanyuan Chen , Shaohua Gong","doi":"10.1016/j.ymeth.2025.12.004","DOIUrl":"10.1016/j.ymeth.2025.12.004","url":null,"abstract":"<div><div>CRISPR-Cas systems have revolutionized non-nucleic acid targets detection across diverse applications. Nevertheless, the relatively low enzymatic turnover rate of activated Cas nucleases during substrate cleavage remains a critical bottleneck, limiting the sensitivity of such detection methods. To address this challenge, numerous innovative strategies have been proposed to enhance the sensitivity of CRISPR-Cas systems, enabling high-sensitive non-nucleic acid targets detection. This review systematically summarizes the sensitivity-enhancing methodologies for non-nucleic acid targets detection using CRISPR-Cas technologies. We first delineate the working mechanisms of various CRISPR-Cas systems and the signal transduction pathways specific to non-nucleic acid targets. Subsequently, we detail diverse sensitivity-improving approaches, including nucleic acid amplification-facilitated strategies, multimolecular labeling techniques, dual-enzyme cascade methods, and multiplex amplification methodologies. Additionally, the current challenges and future perspectives in this field are discussed, aiming to inspire researchers to develop more ingenious solutions and facilitate real-world applications of CRISPR-Cas system for non-nucleic acid targets detection.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"246 ","pages":"Pages 151-173"},"PeriodicalIF":4.3,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145773257","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}
MethodsPub Date : 2026-01-01Epub Date: 2025-11-07DOI: 10.1016/j.ymeth.2025.11.003
Nirmal Das , Subhadip Basu , Punam K. Saha
{"title":"Scale-adjusted distance transform and its applications to segmentation of multimodal images","authors":"Nirmal Das , Subhadip Basu , Punam K. Saha","doi":"10.1016/j.ymeth.2025.11.003","DOIUrl":"10.1016/j.ymeth.2025.11.003","url":null,"abstract":"<div><div>Distance transform (DT) is widely used for structural analysis of multi-dimensional (mainly 2-D and 3-D) objects. Association of DT values with local structure scale, often, adds challenges and limits the scope of applications of DT in relative structural analysis among multiple objects with varying scales. In this paper, we introduce a new notion of scale-adjusted distance transform (SADT), conceptually different from traditional DT, which is independent of object scale and offers DT values of scale varying objects on a uniform scale with the value of ‘1’ at ridges. It has been shown that scale-adjusted distance is a metric function in a continuous Euclidean space, and SADT generates a normalized field that is invariant under translation, rotation, and isotropic scaling. The computational method for digital objects traces gradient flow paths on a conventional DT field and uses the change in velocity along a digital path to detect local ridges, which are then used to generate a scale-adjusted density (SAD) field. Finally, SADT is computed using the SAD value. The results of applying the method on 2-D and 3-D multimodal image datasets are presented. Two real-life applications of SADT are shown: 1) segmentation of conjoined nuclei from 2-D microscopic images, and 2) multi-scale separation of conjoined artery–vein in 3-D pulmonary CT image of a pig lung phantom. SADT outperforms the traditional marker-controlled watershed algorithm in conjoined nuclei segmentation from 2-D images and achieves highly accurate multi-scale artery–vein separation in the pig lung phantom experiment. The performance of SADT is invariant to image dimension and imaging modality. Unlike modern deep learning methods, the proposed fuzzy method is transparent and data modality independent. The source code and sample data are freely available at: <span><span>https://github.com/CMATERJU-BIOINFO/Scale-Adjusted-Distance-Transform</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"245 ","pages":"Pages 55-68"},"PeriodicalIF":4.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145480462","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}
MethodsPub Date : 2026-01-01Epub Date: 2025-08-30DOI: 10.1016/j.ymeth.2025.08.012
Fernando Silva , Gustavo Costa , Francisco Veiga , Vera Moura , Francisca Dias , Fátima Cerqueira , Rui Medeiros , Ana Cláudia Paiva-Santos
{"title":"Rapid in vitro and computer-aided method for assessing synergistic interactions between NSAIDs and analgesics","authors":"Fernando Silva , Gustavo Costa , Francisco Veiga , Vera Moura , Francisca Dias , Fátima Cerqueira , Rui Medeiros , Ana Cláudia Paiva-Santos","doi":"10.1016/j.ymeth.2025.08.012","DOIUrl":"10.1016/j.ymeth.2025.08.012","url":null,"abstract":"<div><div>Pain is a complex phenomenon that plays a significant role in various diseases, influencing both the physical and psychological well-being of individuals. In clinical practice, combining nonsteroidal anti-inflammatory drugs (NSAIDs) with analgesics, such as paracetamol or metamizole, has become a widely adopted strategy to manage pain. Although the synergistic effects of combining NSAIDs with analgesics are well recognized in clinical practice, this approach is primarily based on empirical clinical experience. Our work aims to present a rapid method for evaluating the anti-inflammatory effects of drug combinations through <em>in vitro</em> assays combined with computer-aided data processing and analysis.</div><div>We conducted two simple and rapid <em>in vitro</em> assays, the Griess and DPPH assays, to evaluate the effects of NSAID–analgesic combinations and demonstrate their synergistic interactions, using the free web application SynergyFinder Plus. This computer-aided analysis enabled a quantitative assessment of drug interactions, enhancing the interpretation of the experimental data. Furthermore, to better understand the results obtained from previous experiments, we analysed the anti-inflammatory effects of ketoprofen and dexketoprofen in combination with metamizole and paracetamol through quantitative real-time PCR (qRT-PCR). Our findings reveal synergistic interactions between NSAIDs and analgesics in terms of their anti-inflammatory and antioxidant activities.</div><div>This work could be the first step for the study of the mechanisms behind the synergistic interactions between NSAIDs and analgesics for the treatment of pain, mainly when inflammatory processes are involved. Consequently, this study aims to contribute to the exploration of non-opioid drug combinations, addressing the urgent need for alternative analgesic strategies that minimize opioid use.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"245 ","pages":"Pages 69-82"},"PeriodicalIF":4.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144937936","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}
MethodsPub Date : 2026-01-01Epub Date: 2025-10-28DOI: 10.1016/j.ymeth.2025.10.009
Ahmad Itani , Marta Velaz Martín , Laura Meisch , Phillip Lemke , Tim Scharnweber , Islam M. Khattab , Kersten S. Rabe , Christof M. Niemeyer
{"title":"Materials-Based spatiotemporal analysis of microbial responses to glyphosate in Winogradsky columns","authors":"Ahmad Itani , Marta Velaz Martín , Laura Meisch , Phillip Lemke , Tim Scharnweber , Islam M. Khattab , Kersten S. Rabe , Christof M. Niemeyer","doi":"10.1016/j.ymeth.2025.10.009","DOIUrl":"10.1016/j.ymeth.2025.10.009","url":null,"abstract":"<div><div>Glyphosate, the active ingredient in many broad-spectrum herbicides, is extensively used in agriculture but has come under increasing scrutiny due to its potential impacts on non-target microbial communities. To investigate these effects within a controlled yet ecologically relevant framework, Winogradsky columns, self-contained sediment-based ecosystems, were employed as a model system. A novel, non-destructive sampling approach was introduced using macroporous elastomeric silicone foam (MESIF) integrated in stainless-steel frames to enable spatiotemporal monitoring of benthic microbial communities. These MESIF-loaded frames were vertically embedded in columns filled with lake sediment and subjected to varying experimental conditions, including light exposure and glyphosate treatment. Microbial colonization of the MESIF was assessed via amplicon sequencing at defined time points. Glyphosate-treated columns exhibited delayed microbial stratification and diminished development of characteristic pigmentation associated with functional groups such as iron-oxidizing and sulfate-reducing bacteria. Although within-column alpha diversity remained relatively constant, glyphosate exposure led to distinct shifts in community composition, including an increased abundance of taxa potentially involved in glyphosate degradation. These findings demonstrate the effectiveness of combining Winogradsky columns with MESIF-based sampling for studying environmental stressors and underscore glyphosate’s influence on microbial succession and functional diversity in sediment ecosystems.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"245 ","pages":"Pages 1-12"},"PeriodicalIF":4.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145407820","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}
MethodsPub Date : 2026-01-01Epub Date: 2025-10-16DOI: 10.1016/j.ymeth.2025.10.006
Andreea Iuliana Ftodiev , Georgiana Necula Petrareanu , Mihaela Puiu , Gheorghe Proteasa , Cristian V.A. Munteanu , Roberta Maria Banciu , Ruchika Chauhan , Diana Visinescu , Cristina Purcarea , Pablo Fanjul-Bolado , David Ibañez , Ronen Fogel , Janice Limson , Monica Potara , Anca Florina Bonciu , Simion Astilean , Camelia Bala , Alina Vasilescu
{"title":"Comprehensive analysis of the inhibition of aldehyde dehydrogenase from Flavobacterium PL002 and its coupling with SERS as a path for the selective detection of thiram","authors":"Andreea Iuliana Ftodiev , Georgiana Necula Petrareanu , Mihaela Puiu , Gheorghe Proteasa , Cristian V.A. Munteanu , Roberta Maria Banciu , Ruchika Chauhan , Diana Visinescu , Cristina Purcarea , Pablo Fanjul-Bolado , David Ibañez , Ronen Fogel , Janice Limson , Monica Potara , Anca Florina Bonciu , Simion Astilean , Camelia Bala , Alina Vasilescu","doi":"10.1016/j.ymeth.2025.10.006","DOIUrl":"10.1016/j.ymeth.2025.10.006","url":null,"abstract":"<div><div>The selective detection of dithiocarbamate fungicides in food and agricultural products presents significant analytical challenges. While Surface-enhanced Raman spectroscopy (SERS) has been extensively investigated to address this, detection systems based on enzymatic inhibition remain underexplored. Using thiram as a model dithiocarbamate, the present work explores the potential application of a cold-active aldehyde dehydrogenase from <em>Flavobacterium PL002</em> for the development of specific, inhibition-based analytical methods. A molecular modelling and docking study confirmed that thiram fits into the binding pocket of the enzyme. An irreversible inhibition mechanism was inferred for thiram based on enzymatic kinetics studies. The mechanism was supported by SERS, mass spectrometry measurements and tests with reducing agents. A simple assay for the detection of the fungicide was developed and compared to a SERS-based procedure. The advantages and the practical limitations of the two methods were revealed by studying the detection of thiram from the surface of fungicide-spiked tomatoes. By coupling enzymatic inhibition with SERS, the selectivity for the detection of individual fungicides can be increased, as illustrated by comparing thiram with ziram, a structurally related compound. The study serves as basis for the development of analytical methods for the selective detection of thiram.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"245 ","pages":"Pages 83-98"},"PeriodicalIF":4.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145317960","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":"Carboxyl-PEG modified Fe3O4 nanoparticles as an ultrasensitive SERS substrate for multiplex detection of exogenous hormones related to endometrial cancer","authors":"Biqing Chen, Jiayin Gao, Haizhu Sun, Yinghan Zhao, Yan Liu, Xiaohong Qiu","doi":"10.1016/j.ymeth.2025.11.002","DOIUrl":"10.1016/j.ymeth.2025.11.002","url":null,"abstract":"<div><div>Traditional surface-enhanced Raman scattering (SERS) technology often struggles to achieve high-precision discrimination in the simultaneous detection of multiple exogenous hormones due to complex spectral overlap and matrix interference, limiting its application in trace analyte analysis within complex matrices (e.g., biological samples). This study developed a SERS substrate based on carboxyl-terminal polyethylene glycol (PEG)-modified iron oxide (Fe<sub>3</sub>O<sub>4</sub>) nanoparticles (Fe<sub>3</sub>O<sub>4</sub>@PEG), integrated with artificial intelligence (AI)-driven high-throughput spectral analysis algorithms. This approach successfully enabled ultrasensitive detection and precise discrimination of multiple typical exogenous hormonal drugs, including tamoxifen, drospirenone, cyproterone acetate, medroxyprogesterone acetate, estradiol ester derivatives, and dydrogesterone. By optimizing the surface enhancement effect of Fe<sub>3</sub>O<sub>4</sub>@PEG nanocomposites and employing machine learning models (e.g., convolutional neural networks, CNN) for collaborative analysis, the weak Raman fingerprint features of target hormones in complex mixtures were effectively extracted and classified, achieving a detection limit at the corresponding to 10<sup>−7</sup>–10<sup>−8</sup> mg/mL level. In matrix-spiked serum and urine samples, which mimic complex biological matrices validations, the AI-SERS platform demonstrated exceptional performance in the identification and quantitative analysis of target exogenous hormones. This research provides an intelligent analytical strategy for rapid and highly sensitive detection of multiple trace exogenous hormones in complex matrices.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"245 ","pages":"Pages 35-52"},"PeriodicalIF":4.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145450534","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}
MethodsPub Date : 2026-01-01Epub Date: 2025-10-13DOI: 10.1016/j.ymeth.2025.09.006
Xinfu Liu , Yirui Wu , Yuting Zhou
{"title":"Zero-shot medical image classification via large multimodal models and knowledge graphs-driven processing","authors":"Xinfu Liu , Yirui Wu , Yuting Zhou","doi":"10.1016/j.ymeth.2025.09.006","DOIUrl":"10.1016/j.ymeth.2025.09.006","url":null,"abstract":"<div><div>With the continuous advancement of medical enterprise, intelligent medical technologies supported by natural language processing and knowledge representation have made significant progress. However, with the continuous generation of vast amounts of medical data, the current methods still perform poorly in handling specialized medical data, particularly unlabeled medical diagnostic data. Inspired by the outstanding performance of large language models in various downstream expert tasks in recent years, this article leverages large language models to handle the massive unlabelled medical data, aiming to provide more accurate technical solutions for medical image classification tasks. Specifically, we propose a novel Cross-Modal Knowledge Representation framework (CMKR) to handle vast unlabeled medical data, which utilizes large language models to extract implicit knowledge from medical images, while also extracting explicit textual knowledge with the aid of knowledge graphs. To better utilize the associative information between medical images and textual records, we have designed a cross-modal alignment strategy that enhances knowledge representation capabilities both intra- and inter-modal. We conducted extensive experiments on public datasets, demonstrating that our method outperforms most mainstream approaches.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"245 ","pages":"Pages 25-34"},"PeriodicalIF":4.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145297807","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}