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Correction: Streaming Long-Read Sequence Alignments for HLA Predictions Using HLAminer 更正:流式长读序列比对HLA预测使用HLAminer
Current protocols Pub Date : 2025-05-05 DOI: 10.1002/cpz1.70144
René L. Warren, Inanc Birol
{"title":"Correction: Streaming Long-Read Sequence Alignments for HLA Predictions Using HLAminer","authors":"René L. Warren,&nbsp;Inanc Birol","doi":"10.1002/cpz1.70144","DOIUrl":"https://doi.org/10.1002/cpz1.70144","url":null,"abstract":"<p><i>Current Protocols</i> is issuing corrections for the following protocol article.</p><p>Warren, R. L., &amp; Birol, I. (2025). Streaming long-read sequence alignments for HLA predictions using HLAminer. <i>Current Protocols</i>, <i>5</i>, e70124. doi: 10.1002/cpz1.70124</p><p>In the above-referenced article:</p><p>In Table 4, line 2, the dataset value has been changed from “NA12878, dataset A” to “NA19240, dataset A”.</p><p>The current version online now includes this correction and may be considered the authoritative version of record.</p>","PeriodicalId":93970,"journal":{"name":"Current protocols","volume":"5 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cpz1.70144","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143909025","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Highly Adaptable Analysis Tools for Mapping Spatial Features of Cellular Aggregates in Tissues 组织中细胞聚集体空间特征映射的高适应性分析工具
Current protocols Pub Date : 2025-05-05 DOI: 10.1002/cpz1.70135
Andrew Sawyer, Nick Weingaertner, Ellis Patrick, Carl G. Feng
{"title":"Highly Adaptable Analysis Tools for Mapping Spatial Features of Cellular Aggregates in Tissues","authors":"Andrew Sawyer,&nbsp;Nick Weingaertner,&nbsp;Ellis Patrick,&nbsp;Carl G. Feng","doi":"10.1002/cpz1.70135","DOIUrl":"https://doi.org/10.1002/cpz1.70135","url":null,"abstract":"<p>Multiplex imaging technologies have developed rapidly over the past decades. The advancement of multiplex imaging has been driven in part by the recognition that the spatial organization of cells can represent important prognostic biomarkers and that simply studying the composition of cells in diseased tissue is often insufficient. There remains a lack of tools that can perform spatial analysis at the level of cellular aggregates (a common histopathological presentation) such as tumors and granulomas, with most analysis packages focusing on smaller regions of interest and potentially missing patterns in the overall lesion structure and cellular distribution. Here, we present protocols to quantitatively describe the cellular structure of entire tissue lesions, built around two novel metrics. The Total Cell Preference Index reports whether a lesion tends to change in density in its central versus peripheral areas and can indicate the extent of necrosis across the entire lesion. The Immune Cell Preference Index then reports whether each immune cell type is located more centrally or peripherally across the entire lesion. The output of both indexes is a single number readout for simple interpretation and visualization, and these indexes can be applied to lesions of any size or shape. This simplifies cross-lesion comparison compared to traditional Euclidian distance–based analysis, which outputs multiple values for each lesion (one for output for each band used in the infiltration analysis). Additionally, this approach can be applied to any slide-scanning multiplexed imaging system, based on either protein or nucleic acid staining. Finally, the approach uses the open-source software QuPath and can be utilized by researchers with a basic understanding of QuPath, with the full analysis able to be applied to pre-generated images within 1 hr. © 2025 The Author(s). Current Protocols published by Wiley Periodicals LLC.</p><p><b>Basic Protocol 1</b>: Image preparation and lesion selection</p><p><b>Basic Protocol 2</b>: Total Cell Preference Index and Immune Cell Preference Index</p>","PeriodicalId":93970,"journal":{"name":"Current protocols","volume":"5 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cpz1.70135","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143904887","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Purification of Low-Complexity Domain Proteins FUS, EWSR1, and Their Fusions 低复杂度结构域蛋白FUS、EWSR1的纯化及其融合
Current protocols Pub Date : 2025-04-26 DOI: 10.1002/cpz1.70136
Jesse J. Altemus, Michelle A. Lay, Valery F. Thompson, Jacob C. Schwartz
{"title":"Purification of Low-Complexity Domain Proteins FUS, EWSR1, and Their Fusions","authors":"Jesse J. Altemus,&nbsp;Michelle A. Lay,&nbsp;Valery F. Thompson,&nbsp;Jacob C. Schwartz","doi":"10.1002/cpz1.70136","DOIUrl":"https://doi.org/10.1002/cpz1.70136","url":null,"abstract":"<p>FET proteins are large multifunctional proteins that have several key roles in biology. The FET family of proteins, including FUS, EWSR1, and TAF15, play critical roles in transcription regulation, RNA processing, and DNA damage repair. These multifunctional RNA- and DNA-binding proteins are ubiquitously expressed and conserved across vertebrate species. They contain low-complexity (LC) domains that allow them to assemble and phase separate but also makes the proteins prone to aggregation. Aberrations in FET proteins, such as point mutations, aggregation, or translocations leading to fusion proteins, have been implicated in several pathologies, including frontotemporal lobar degeneration (FTLD), amyotrophic lateral sclerosis (ALS), and Ewing sarcoma. In vitro study of FET proteins is hampered by their propensity to aggregate, their disordered structure, and their susceptibility to proteolysis, making high-yield production difficult. Here, we present optimized methods for the purification of full-length FUS, EWSR1, and their fusion proteins. These protocols enable researchers to overcome issues related to aggregation and solubility, facilitating biochemical and biophysical studies of these critical yet complex proteins. © 2025 The Author(s). Current Protocols published by Wiley Periodicals LLC.</p><p><b>Basic Protocol</b>: Purification of EWSR1 and FUS proteins</p><p><b>Alternate Protocol</b>: Purification for fusion proteins</p>","PeriodicalId":93970,"journal":{"name":"Current protocols","volume":"5 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cpz1.70136","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143875529","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A Highly Sensitive Tissue-specific qRT-PCR-based Assay for Detection of Melanoma Cells in Tumor-Draining Lymph Nodes 一种高度敏感的组织特异性qrt - pcr检测肿瘤引流淋巴结黑色素瘤细胞的方法
Current protocols Pub Date : 2025-04-26 DOI: 10.1002/cpz1.70139
Kristian M. Hargadon, Travis B. Goodloe III
{"title":"A Highly Sensitive Tissue-specific qRT-PCR-based Assay for Detection of Melanoma Cells in Tumor-Draining Lymph Nodes","authors":"Kristian M. Hargadon,&nbsp;Travis B. Goodloe III","doi":"10.1002/cpz1.70139","DOIUrl":"https://doi.org/10.1002/cpz1.70139","url":null,"abstract":"<p>Melanoma invasion of regional lymph nodes, a critical event in the progression of this disease, is well documented as a poor prognostic factor for patients with melanoma. Assessing lymph node involvement is therefore a routine part of the diagnostic workup for patients presenting with melanoma at a T stage of ≥T2a. In clinical settings, the status and degree of melanoma lymph node involvement is traditionally characterized by histopathological analysis of tissue obtained during a sentinel lymph node biopsy, a labor-intensive and costly approach that requires technically challenging sample preparation and interpretation by a trained pathologist. Alternative approaches that might reduce the financial burden and turnaround time of a sentinel lymph node biopsy workup are therefore desirable. Likewise, the ability to accurately assess lymph node invasion by melanoma in experimental settings is necessary to gain new insights into mechanisms of distant metastasis and tumor-associated immune suppression. With these applications in mind, we recently developed, and describe herein, a tissue-specific qRT-PCR-based protocol for detecting melanoma cells within tumor-draining lymph nodes. Using murine models of lymph-node-invasive and lymph-node-noninvasive melanoma cell lines and a melanin-biosynthesis-pathway-specific <i>Trp2</i> gene expression assay, we validated this method as a highly sensitive strategy for assessing lymph node involvement by melanoma. © 2025 Wiley Periodicals LLC.</p><p><b>Basic Protocol 1</b>: Growth and maintenance of murine melanoma cell cultures</p><p><b>Basic Protocol 2</b>: Extraction and quantification of RNA from murine melanoma cultures</p><p><b>Basic Protocol 3</b>: cDNA synthesis via reverse transcription</p><p><b>Basic Protocol 4</b>: Probe and primer design for TaqMan-based qPCR</p><p><b>Basic Protocol 5</b>: qPCR analysis of tissue-specific <i>Trp2</i> gene expression</p><p><b>Basic Protocol 6</b>: <i>In vitro</i> validation of qRT-PCR <i>Trp2</i> gene expression assay for detection of melanoma cells in murine whole lymph node preparations</p><p><b>Basic Protocol 7</b>: <i>In vivo</i> validation of qRT-PCR <i>Trp2</i> gene expression assay for detection of melanoma cells in murine tumor-draining lymph nodes</p>","PeriodicalId":93970,"journal":{"name":"Current protocols","volume":"5 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143877827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Cryptococcus neoformans Biofilm Formation and Quantification 新型隐球菌生物膜的形成与定量
Current protocols Pub Date : 2025-04-25 DOI: 10.1002/cpz1.70133
Oscar Romero, Davier Gutierrez-Gongora, Jennifer Geddes-McAlister
{"title":"Cryptococcus neoformans Biofilm Formation and Quantification","authors":"Oscar Romero,&nbsp;Davier Gutierrez-Gongora,&nbsp;Jennifer Geddes-McAlister","doi":"10.1002/cpz1.70133","DOIUrl":"https://doi.org/10.1002/cpz1.70133","url":null,"abstract":"<p><i>Cryptococcus neoformans</i> is an opportunistic fungal pathogen that heads the Fungal Priority Pathogen List published by the World Health Organization (WHO) in 2022. This pathogen is a primary cause of death for immunocompromised individuals (e.g., those with HIV/AIDS, the elderly, immunotherapy recipients), causing approximately 118,000 deaths yearly worldwide. <i>C. neoformans</i> relies on virulence factors that include a polysaccharide capsule, melanin, extracellular enzymes, and thermotolerance to initiate and sustain host infection. Additionally, similar to other fungal pathogens (e.g., <i>Candida albicans</i>), <i>C. neoformans</i> may develop a biofilm organization linked to more persistent cryptococcal infections. Cryptococcal biofilms are highlighted in cases of cryptococcal meningitis, in which biofilm-like structures form that are highly resistant to host immune response and to antifungal therapies. In this regard, fungal biofilm formation has become an important area of study as a means to improve our understanding of the mechanisms regulating biofilm formation and infection and to advance the discovery of antibiofilm therapeutics. To assess biofilm properties and compare across treatments, quantification and evaluation of cell viability are important. Herein, we describe a standardized method to establish a cryptococcal biofilm and quantify total biomass and cell viability. © 2025 The Author(s). <i>Current Protocols</i> published by Wiley Periodicals LLC.</p><p><b>Basic Protocol 1</b>: Culturing and biofilm formation</p><p><b>Basic Protocol 2</b>: Biofilm quantification</p><p><b>Alternate Protocol</b>: Biofilm viability assay</p>","PeriodicalId":93970,"journal":{"name":"Current protocols","volume":"5 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cpz1.70133","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143875570","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Enhancing Visual Discrimination Task: Optimized Mouse Motivation in the Touchscreen Paradigm 增强视觉辨别任务:在触屏范式下优化鼠标动机
Current protocols Pub Date : 2025-04-25 DOI: 10.1002/cpz1.70126
Jeremy Jehl, Fabrice Riet, Aline Simonet, Yann Herault
{"title":"Enhancing Visual Discrimination Task: Optimized Mouse Motivation in the Touchscreen Paradigm","authors":"Jeremy Jehl,&nbsp;Fabrice Riet,&nbsp;Aline Simonet,&nbsp;Yann Herault","doi":"10.1002/cpz1.70126","DOIUrl":"https://doi.org/10.1002/cpz1.70126","url":null,"abstract":"<p>Mouse models are essential for understanding gene function, environmental interaction, and brain structure and function. This is reinforced by the ability of mice to perform complex behavioral tasks. Still, their cognitive assessments often rely on aversive paradigms, such as fear conditioning and the Morris water maze. A promising alternative is the automated touchscreen platform, which enables cognitive tests comparable to those used in humans, such as the Cambridge Neuropsychological Test Automated Battery (CANTAB). This approach enhances standardization and reduces stress by employing appetitive reinforcement. Although widely used in non-human primates, touchscreen testing remains underutilized in rodents despite its potential for cross-species cognitive research. Motivation is key to successful touchscreen tasks, often achieved through water restriction, which mice tolerate well. However, water restriction is a stressful condition, combining negative and positive reinforcement. Here, we propose an alternative that uses citric acid (CA) water to avoid classical food privation in the touchscreen paradigm to mitigate mice's stress. By creating a strong contrast with the reward, we increase the reward's positive valence. We used the touchscreen visual discrimination task to assess the effectiveness of CA water in enhancing motivation. Our results show that administering CA water on training days while allowing access to plain water on weekends reduces the learning phase duration without causing significant weight loss in wild-type C57BL/6J mice. In addition, we observed a strong commitment to performing the pattern dissociation task. This approach offers a welfare-friendly alternative for maintaining motivation in touchscreen-based cognitive tasks while minimizing stress. © 2025 Wiley Periodicals LLC.</p><p><b>Basic Protocol</b>: Pattern dissociation paradigm using sour water</p>","PeriodicalId":93970,"journal":{"name":"Current protocols","volume":"5 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143875571","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Leveraging the MethMotif Toolkit to Characterize Context-Specific Features and Roles of Methylation Sensitive Transcription Factors 利用MethMotif工具包表征甲基化敏感转录因子的环境特异性特征和作用
Current protocols Pub Date : 2025-04-25 DOI: 10.1002/cpz1.70129
Matthew Dyer, Gastongay Siu, Denis Thieffry, Touati Benoukraf
{"title":"Leveraging the MethMotif Toolkit to Characterize Context-Specific Features and Roles of Methylation Sensitive Transcription Factors","authors":"Matthew Dyer,&nbsp;Gastongay Siu,&nbsp;Denis Thieffry,&nbsp;Touati Benoukraf","doi":"10.1002/cpz1.70129","DOIUrl":"https://doi.org/10.1002/cpz1.70129","url":null,"abstract":"<p>This article presents a comprehensive guide for using the MethMotif platform, which includes the MethMotif database, the TFregulomeR R package, and a new R library, Forked-TF, designed specifically for analyzing leucine-zipper transcription factors (TFs) that bind DNA as dimers. The MethMotif platform integrates transcription factor binding site (TFBS) motifs with DNA methylation profiles, providing an in-depth analysis of how methylation modulates TF binding across different cell types and conditions. The protocols are organized into three main workflows: (1) Exploration of transcription factor dimerization partners, (2) visualization of methylation-specific TF motifs using TFregulomeR, and (3) characterization of leucine-zipper TF binding patterns with a focus on dimerization. Using the platform's MethMotif database, users can retrieve ChIP-seq and DNA methylation data, intersect TFBS peak regions, and generate TFBS-methylation-informed motif logos. A case study of CEBPB in K562 cells is included to demonstrate the use of the platform, showing how to identify TF dimers, analyze their co-binding behavior, and visualize the impact of DNA methylation on binding specificity. The protocols also provide step-by-step instructions for software installation, data input formats, and interpretation of results, making it accessible to researchers with varying levels of computational expertise. Through these protocols, users can uncover how DNA methylation and TF dimerization influence gene regulatory networks, with a focus on leucine-zipper TFs in a cell-type-specific context. © 2025 The Author(s). Current Protocols published by Wiley Periodicals LLC.</p><p><b>Basic Protocol 1</b>: Exploration of transcription factor dimerization partners</p><p><b>Support Protocol 1</b>: Software installation</p><p><b>Support Protocol 2</b>: Docker installation</p><p><b>Support Protocol 3</b>: Verifying installation</p><p><b>Basic Protocol 2</b>: Visualization of alternative cofactors</p><p><b>Basic Protocol 3</b>: Characterization of bZIP partners/cofactors</p><p><b>Basic Protocol 4</b>: Context-independent and context-dependent analysis</p>","PeriodicalId":93970,"journal":{"name":"Current protocols","volume":"5 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cpz1.70129","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143875573","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Label-Free Quantification of Protein Density in Living Cells 活细胞中蛋白密度的无标记定量
Current protocols Pub Date : 2025-04-24 DOI: 10.1002/cpz1.70130
Robert J. Clements, Ruixin Guo, Jonathan C. Petruccelli, Michael A. Model
{"title":"Label-Free Quantification of Protein Density in Living Cells","authors":"Robert J. Clements,&nbsp;Ruixin Guo,&nbsp;Jonathan C. Petruccelli,&nbsp;Michael A. Model","doi":"10.1002/cpz1.70130","DOIUrl":"https://doi.org/10.1002/cpz1.70130","url":null,"abstract":"<p>Intracellular water content, W, and protein concentration, P, are essential characteristics of living cells. Healthy cells maintain them within a narrow range, but often become dehydrated under severe stress; moreover, persistent loss of water (an increase in P) can lead to apoptotic death. It is very likely that protein concentration affects cellular metabolism and signaling through macromolecular crowding (MC) effects, to which P is directly related, but much remains unknown in this area. Obviously, in order to study the biological roles and regulation of MC in living cells, one needs a method to measure it. Simple and accurate measurements of P in adherent cells can be based on its relationship to refractive index. The latter can be derived from two or more (depending on the algorithm) mutually defocused brightfield images processed by the transport-of-intensity equation (TIE) that must be complemented by a determination of volume. Here, we describe the experimental considerations for both TIE imaging and for a particular method of cell volume measurement, transmission-through-dye (TTD). We also introduce an ImageJ plugin for solving TIE. TIE and TTD are fully compatible with each other as well as with fluorescence. A similar approach can be applied to subcellular organelles; however, in this case, the volume must be determined differently.© 2025 The Author(s). <i>Current Protocols</i> published by Wiley Periodicals LLC.</p><p><b>Basic Protocol 1</b>: Sample preparation for TIE with or without TTD</p><p><b>Basic Protocol 2</b>: Acquisition of TIE and TTD images</p><p><b>Basic Protocol 3</b>: Calibration of TIE</p><p><b>Basic Protocol 4</b>: Measurement of the absorption coefficient of the medium used for TTD</p><p><b>Basic Protocol 5</b>: Image processing using Fiji</p><p><b>Support Protocol 1</b>: Installation and use of TIE plugin</p><p><b>Support Protocol 2</b>: Automation of the double TTD/TIE processing using a Fiji macro</p>","PeriodicalId":93970,"journal":{"name":"Current protocols","volume":"5 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cpz1.70130","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143871532","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Getting Started with Machine Learning for Experimental Biochemists and Other Molecular Scientists 实验生物化学家和其他分子科学家的机器学习入门
Current protocols Pub Date : 2025-04-21 DOI: 10.1002/cpz1.70085
Matthew J. K. Vince, Kristin A. Hughes, Anastasiya Buzuk, Deborah L. Perlstein, Lauren A. Viarengo-Baker, Adrian Whitty
{"title":"Getting Started with Machine Learning for Experimental Biochemists and Other Molecular Scientists","authors":"Matthew J. K. Vince,&nbsp;Kristin A. Hughes,&nbsp;Anastasiya Buzuk,&nbsp;Deborah L. Perlstein,&nbsp;Lauren A. Viarengo-Baker,&nbsp;Adrian Whitty","doi":"10.1002/cpz1.70085","DOIUrl":"https://doi.org/10.1002/cpz1.70085","url":null,"abstract":"<p>Machine learning (ML) is rapidly gaining traction in many areas of experimental molecular science for elucidating relationships and patterns in large or complex data sets. Historically, ML was largely the preserve of those with specialized training in fields such as statistics or cheminformatics. Increasingly, however, ML methodologies are becoming part of the standard toolkit for experimental scientists across a range of disciplines. For scientists without a significant background in computer science or statistics, lowering the barrier of entry to these ML techniques is important to broadening access to these powerful methods. Here we provide detailed, step-by-step protocols for performing four ML methods that are particularly useful for applications in biochemistry, cell biology, and drug discovery: hierarchical clustering, principal component analysis (PCA), partial least squares discriminant analysis (PLSDA), and partial least squares regression (PLSR). The protocols are written for the widely used software MATLAB, but no prior experience with MATLAB is required to use them. We include an explanation of each step, pitched at a level to be understood by investigators without any prior experience with ML, MATLAB, or any kind of coding. We also highlight the scientific issues pertaining to selecting and scaling the data to be analyzed. Throughout, we emphasize the relationship between the scientific question and how to choose data and methods that will allow it to be addressed in a meaningful way. Our aim is to provide a basic introduction that will equip experimental chemical biologists, chemists, and other biomedical scientists with the knowledge required to use ML to aid in the design of experiments, the formulation and data-driven testing of hypotheses, and the analysis of experimental data. © 2025 Wiley Periodicals LLC.</p><p><b>Basic Protocol 1</b>: Clustering</p><p><b>Basic Protocol 2</b>: Principal component analysis</p><p><b>Basic Protocol 3</b>: Partial least squares-discriminant analysis</p><p><b>Basic Protocol 4</b>: Partial least squares regression</p>","PeriodicalId":93970,"journal":{"name":"Current protocols","volume":"5 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143852716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Reverse-Transcriptase Loop-Mediated Isothermal Amplification (RT-LAMP) for Viral Detection — A Case Study 用于病毒检测的反转录酶环路介导等温扩增(RT-LAMP)--案例研究
Current protocols Pub Date : 2025-04-21 DOI: 10.1002/cpz1.70127
Ashley Hassman, Renée Richie Casey, Colby Rouchka, Diego Sunino, Felix Veloz Espinal, Mona Youssef
{"title":"Reverse-Transcriptase Loop-Mediated Isothermal Amplification (RT-LAMP) for Viral Detection — A Case Study","authors":"Ashley Hassman,&nbsp;Renée Richie Casey,&nbsp;Colby Rouchka,&nbsp;Diego Sunino,&nbsp;Felix Veloz Espinal,&nbsp;Mona Youssef","doi":"10.1002/cpz1.70127","DOIUrl":"https://doi.org/10.1002/cpz1.70127","url":null,"abstract":"<p>An assay and protocol framework are provided for utilizing reverse-transcriptase loop-mediated isothermal amplification (RT-LAMP) at the point-of-care for diagnosing and monitoring a hypothetical zoonotic viral outbreak in a resource-limited area. This manuscript utilizes a previously published decision tree algorithm to determine an appropriate molecular diagnostic point-of-care test that can effectively address the outbreak presented in the hypothetical case study. © 2025 Wiley Periodicals LLC.</p>","PeriodicalId":93970,"journal":{"name":"Current protocols","volume":"5 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143852717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","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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