IF 4.2 3区生物学

Methods Pub Date : 2025-02-01 DOI: 10.1016/j.ymeth.2024.12.010

Haitao Fu , Zewen Ding , Wen Wang

引用次数: 0

Novel approaches to biomarker discover 生物标志物发现的新方法

IF 4.2 3区生物学

Methods Pub Date : 2025-02-01 DOI: 10.1016/j.ymeth.2025.01.005

Brian K. McFarlin PhD (Special Issue Editor)

引用次数: 0

Validation of plasmonic-based biosensors for rapid and in depth characterization of monoclonal antibodies directed against rabbit haemorrhagic and foot-and-mouth disease viruses in biological samples 验证基于等离子体的生物传感器在生物样品中快速和深入地表征针对兔出血性和口蹄疫病毒的单克隆抗体。

IF 4.2 3区生物学

Methods Pub Date : 2025-02-01 DOI: 10.1016/j.ymeth.2024.12.003

Chiara Urbinati , Giulia Pezzoni , Patrizia Cavadini , Vittoria Di Giovanni , Lorenzo Capucci , Marco Rusnati

{"title":"Validation of plasmonic-based biosensors for rapid and in depth characterization of monoclonal antibodies directed against rabbit haemorrhagic and foot-and-mouth disease viruses in biological samples","authors":"Chiara Urbinati , Giulia Pezzoni , Patrizia Cavadini , Vittoria Di Giovanni , Lorenzo Capucci , Marco Rusnati","doi":"10.1016/j.ymeth.2024.12.003","DOIUrl":"10.1016/j.ymeth.2024.12.003","url":null,"abstract":"<div><div>ELISA and RT-PCR represent the standard tools for the sensitive identification of viruses in biological samples, but they lack the capacity to finely characterize the binding of viruses or viral antigens to monoclonal antibodies (MAbs). Biosensing technologies are gaining increasing importance as powerful MAb characterization tools in the field of virology. Surface plasmon resonance (SPR) is an optical biosensing technology already used for the in depth characterization of MAbs of diagnostic and therapeutic value. Rabbit haemorrhagic disease virus (RHDV) and foot-and-mouth disease virus (FMDV) are top veterinary issues for which the development of novel methods aimed at the characterization of antiviral MAbs represents a priority with important livestock healthcare and economic implications. With these premises in mind, here we prepared a series of SPR biosensors by immobilizing RHDV2 or its 6S subunit by different strategies that were then used to characterize the binding capacity of a panel of anti-RHDV2 MAbs. From the comparison of the results obtained, the biosensor composed of intact RHDV2 captured with catcher-MAb covalently immobilized to the surface showed the best analytical performances. To evaluate the versatility of the biosensor, the same strategy was then adopted using FMVD in cell extracts. The results obtained are discussed in view of the exploitation of SPR in the rapid and resilient fine characterization of antiviral MAbs for diagnostic or therapeutic purposes in the field of animal virology.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"234 ","pages":"Pages 85-92"},"PeriodicalIF":4.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142799033","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

CHiTA: A scarless high-throughput pipeline for characterization of ribozymes 一种无疤痕的高通量管道用于核酶的表征。

IF 4.2 3区生物学

Methods Pub Date : 2025-02-01 DOI: 10.1016/j.ymeth.2024.12.007

Lauren N. McKinley , Philip C. Bevilacqua

{"title":"CHiTA: A scarless high-throughput pipeline for characterization of ribozymes","authors":"Lauren N. McKinley , Philip C. Bevilacqua","doi":"10.1016/j.ymeth.2024.12.007","DOIUrl":"10.1016/j.ymeth.2024.12.007","url":null,"abstract":"<div><div>Small self-cleaving ribozymes are catalytic RNAs that cleave their phosphodiester backbone rapidly and site-specifically, without the assistance of proteins. Their catalytic properties make them ideal targets for applications in RNA pharmaceuticals and bioengineering. Consequently, computational pipelines that predict or design thousands of self-cleaving ribozyme candidates have been developed. Traditional experimental techniques for verifying the activity of these putative ribozymes, however, are low-throughput and time intensive. High-throughput (HT) pipelines that employ next-generation sequencing (NGS) analyze the activity of these thousands of ribozymes simultaneously. Until recently, the application of these HT pipelines has been limited to studying all single and double mutants of a select representative ribozyme. Unfortunately, this prevents the exploration of candidates having different lengths, circular permutations, and auxiliary stem-loops. Moreover, pipelines that analyze ribozymes <em>en masse</em> often include transcription of non-native flanking sequences that preclude accurate assessment of the intrinsic rate of ribozyme self-cleavage. To overcome these limitations, we developed a HT pipeline, “<em>C</em>leavage <em>Hi</em>gh-<em>T</em>hroughput <em>A</em>ssay (CHiTA)”, which employs NGS and massively parallel oligonucleotide synthesis (MPOS) to characterize ribozyme activity for thousands of candidates in a scarless fashion. Herein, we describe detailed strategies and protocols to implement CHiTA to measure the activity of putative ribozymes from a wide range of ribozyme classes.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"234 ","pages":"Pages 120-130"},"PeriodicalIF":4.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142811777","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

SV-JIM, detailed pairwise structural variant calling using long-reads and genome assemblies SV-JIM，详细的两两结构变异调用使用长读和基因组组装。

IF 4.2 3区生物学

Methods Pub Date : 2025-02-01 DOI: 10.1016/j.ymeth.2024.12.015

Clarence Todd , Lingling Jin , Ian McQuillan

{"title":"SV-JIM, detailed pairwise structural variant calling using long-reads and genome assemblies","authors":"Clarence Todd , Lingling Jin , Ian McQuillan","doi":"10.1016/j.ymeth.2024.12.015","DOIUrl":"10.1016/j.ymeth.2024.12.015","url":null,"abstract":"<div><div>This paper proposes a detailed process for SV calling that permits a data-driven assessment of multiple SV callers that uses both genome assemblies and long-reads. The process is implemented as a software pipeline named Structural Variant − Jaccard Index Measure, or SVJIM, using the Snakemake <span><span>[20]</span></span> workflow management system. Like most state-of-the-art SV callers, SV-JIM detects the presence of variations between pairs of genomes, but it streamlines the numerous SV calling stages into a single process for user convenience and evaluates the multiple SV sets produced using the Jaccard index measure to identify those with the highest consistency among the included SV callers. SV-JIM then produces aggregated SV results based on how many callers supported the reported SVs. For validation, SV-JIM was assessed through three case studies on the Homo sapiens genome and two plant genomes – Brassica nigra and Arabidopsis thaliana. Executing SV-JIM identified a significant amount of inter-caller variance which varied by tens of thousands of results on the larger Brassica nigra and Homo sapiens genomes. Further, aggregating the SV sets helped simplify better retention of the less frequently occurring SV types by requiring a level of minimum support rather than from a specific SV caller combination. Finally, these case studies identified a potential for inflated precision reporting that can occur during evaluation. SV-JIM is available publicly under MIT license at <span><span>https://github.com/USask-BINFO/SV-JIM</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"234 ","pages":"Pages 305-313"},"PeriodicalIF":4.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142997939","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Nanotechnological approaches to improve corticosteroids ocular therapy 改进皮质类固醇眼部疗法的纳米技术方法。

IF 4.2 3区生物学

Methods Pub Date : 2025-02-01 DOI: 10.1016/j.ymeth.2024.12.008

María Lina Formica, Juan Matías Pernochi Scerbo, Hamoudi Ghassan Awde Alfonso, Pablo Tomás Palmieri, Julieta Ribotta, Santiago Daniel Palma

{"title":"Nanotechnological approaches to improve corticosteroids ocular therapy","authors":"María Lina Formica, Juan Matías Pernochi Scerbo, Hamoudi Ghassan Awde Alfonso, Pablo Tomás Palmieri, Julieta Ribotta, Santiago Daniel Palma","doi":"10.1016/j.ymeth.2024.12.008","DOIUrl":"10.1016/j.ymeth.2024.12.008","url":null,"abstract":"<div><div>The administration of corticosteroids is the first-line treatment of the clinical conditions with ocular inflammation. Nonetheless, ocular physiological mechanisms, anatomical barriers and corticosteroid properties prevent it from reaching the target site. Thus, frequent topical administered doses or ocular injections are required, leading to a higher risk of adverse events and poor patient compliance.</div><div>Designing novel drug delivery systems based on nanotechnological tools is a useful approach to overcome disadvantages associated with the ocular delivery of corticosteroids. Nanoparticle-based drug delivery systems represent an alternative to the current dosage forms for the ocular administration of corticosteroids, since due to their particle size and the properties of their materials, they can increase their solubility, improve ocular permeability, control their release and increase bioavailability after their ocular administration. In this way, lipid and polymer-based nanoparticles have been the main strategies developed, giving rise to novel patent applications to protect these innovative drug delivery systems as a product, its preparation or administration method. Additionally, it should be noted that at least 10 clinical trials are being carried out to evaluate the ocular application of different pharmaceutical formulations based on corticosteroid-loaded nanoparticles.</div><div>Through a comprehensive and extensive analysis, this review highlights the impact of nanotechnology applications in ocular inflammation therapy with corticosteroids.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"234 ","pages":"Pages 152-177"},"PeriodicalIF":4.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142826531","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

Inferring multi-slice spatially resolved gene expression from H&E-stained histology images with STMCL 从h&e染色组织学图像推断STMCL的多层空间分辨基因表达。

IF 4.2 3区生物学

Methods Pub Date : 2025-02-01 DOI: 10.1016/j.ymeth.2024.11.016

Zhiceng Shi , Fangfang Zhu , Wenwen Min

{"title":"Inferring multi-slice spatially resolved gene expression from H&E-stained histology images with STMCL","authors":"Zhiceng Shi , Fangfang Zhu , Wenwen Min","doi":"10.1016/j.ymeth.2024.11.016","DOIUrl":"10.1016/j.ymeth.2024.11.016","url":null,"abstract":"<div><div>Spatial transcriptomics has significantly advanced the measurement of spatial gene expression in the field of biology. However, the high cost of ST limits its application in large-scale studies. Using deep learning to predict spatial gene expression from H&E-stained histology images offers a more cost-effective alternative, but existing methods fail to fully leverage the multimodal information provided by Spatial transcriptomics and pathology images. In response, this paper proposes <strong>STMCL</strong>, a novel multimodal contrastive learning framework. STMCL integrates multimodal information, including histology images, gene expression features of spots, and their locations, to accurately infer spatial gene expression profiles. We tested four different types of multi-slice spatial transcriptomics datasets generated by the 10X Genomics platform. The results indicate that STMCL has advantages over baseline methods in predicting spatial gene expression profiles. Furthermore, STMCL is capable of capturing cancer-specific highly expressed genes and preserving gene expression patterns while maintaining the original spatial structure of gene expression. Our code is available at <span><span>https://github.com/wenwenmin/STMCL</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"234 ","pages":"Pages 187-195"},"PeriodicalIF":4.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142926191","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

Microplate fluorescence quenching for high throughput screening of affinity constants – Serum albumins and zearalenones case study 用于高通量筛选亲和常数的微孔板荧光淬灭技术--血清白蛋白和玉米赤霉烯酮案例研究。

IF 4.2 3区生物学

Methods Pub Date : 2025-02-01 DOI: 10.1016/j.ymeth.2024.12.011

Heiðar Már Aðalsteinsson , Lavínia Quartin Pinto , Tatiana Q. Aguiar , José A. Teixeira , Luís Abrunhosa

{"title":"Microplate fluorescence quenching for high throughput screening of affinity constants – Serum albumins and zearalenones case study","authors":"Heiðar Már Aðalsteinsson , Lavínia Quartin Pinto , Tatiana Q. Aguiar , José A. Teixeira , Luís Abrunhosa","doi":"10.1016/j.ymeth.2024.12.011","DOIUrl":"10.1016/j.ymeth.2024.12.011","url":null,"abstract":"<div><div>Measurements of changes in fluorescence signal is one of the most commonly applied methods for studying protein-ligand affinities. These measurements are generally carried out using cuvettes in spectrofluorometers, which can only measure one sample at a time. This makes screening procedures for multiple ligands and proteins extremely laborious, as each protein must be measured with multiple ligand concentrations, and usually in triplicate. Moreover, multiple equations exist to extract the affinity constants and other information from the data, and their underlying assumptions are often disregarded. In this study, the affinities of human, bovine and rat serum albumins for the mycotoxin zearalenone and five of its common derivatives were measured in 96-well microplates, allowing quick measurements of multiple samples using less reagent amounts. In comparison to measurements using a cuvette in a spectrofluorometer, the microplate method was shown to reproduce the affinity constants accurately. The results were discussed in terms of common pitfalls regarding experimental setup and available equations to analyze protein-ligand binding in fluorescence quenching assays. The commonly used Stern-Volmer equation was discussed in detail and the results used to show how inaccurate it is when a fluorescent protein-ligand complex is formed, and when other underlying approximations are ignored.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"234 ","pages":"Pages 253-263"},"PeriodicalIF":4.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142968898","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

Retraction notice to “A methodological framework for rigorous systematic reviews: Tailoring comprehensive analyses to clinicians and healthcare professionals” [Methods 225 (2024) 38–43]

IF 4.2 3区生物学

Methods Pub Date : 2025-02-01 DOI: 10.1016/j.ymeth.2025.01.007

Stefano Mancin , Marco Sguanci , Giuliano Anastasi , Lea Godino , Alessio Lo Cascio , Emanuela Morenghi , Michela Piredda , Maria Grazia De Marinis

引用次数: 0

BCDB: A dual-branch network based on transformer for predicting transcription factor binding sites BCDB：基于 Transformer 的双分支网络，用于预测转录因子结合位点。

IF 4.2 3区生物学

Methods Pub Date : 2025-02-01 DOI: 10.1016/j.ymeth.2024.12.006

Jia He , Yupeng Zhang , Yuhang Liu , Zhigan Zhou , Tianhao Li , Yongqing Zhang , Boqia Xie

{"title":"BCDB: A dual-branch network based on transformer for predicting transcription factor binding sites","authors":"Jia He , Yupeng Zhang , Yuhang Liu , Zhigan Zhou , Tianhao Li , Yongqing Zhang , Boqia Xie","doi":"10.1016/j.ymeth.2024.12.006","DOIUrl":"10.1016/j.ymeth.2024.12.006","url":null,"abstract":"<div><div>Transcription factor binding sites (TFBSs) are critical in regulating gene expression. Precisely locating TFBSs can reveal the mechanisms of action of different transcription factors in gene transcription. Various deep learning methods have been proposed to predict TFBS; however, these models often need help demonstrating ideal performance under limited data conditions. Furthermore, these models typically have complex structures, which makes their decision-making processes difficult to transparentize. Addressing these issues, we have developed a framework named BCDB. This framework integrates multi-scale DNA information and employs a dual-branch output strategy. Integrating DNABERT, convolutional neural networks (CNN), and multi-head attention mechanisms enhances the feature extraction capabilities, significantly improving the accuracy of predictions. This innovative method aims to balance the extraction of global and local information, enhancing predictive performance while utilizing attention mechanisms to provide an intuitive way to explain the model's predictions, thus strengthening the overall interpretability of the model. Prediction results on 165 ChIP-seq datasets show that BCDB significantly outperforms other existing deep learning methods in terms of performance. Additionally, since the BCDB model utilizes transfer learning methods, it can transfer knowledge learned from many unlabeled data to specific cell line prediction tasks, allowing our model to achieve cross-cell line TFBS prediction. The source code for BCDB is available on <span><span>https://github.com/ZhangLab312/BCDB</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"234 ","pages":"Pages 141-151"},"PeriodicalIF":4.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142862849","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

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