Nature reviews. Methods primers最新文献_第2页

Uniform manifold approximation and projection 均匀流形近似和投影

IF 50.1

Nature reviews. Methods primers Pub Date : 2024-11-21 DOI: 10.1038/s43586-024-00369-5

引用次数: 0

Fluorescence lifetime imaging microscopy 荧光寿命成像显微镜

IF 50.1

Nature reviews. Methods primers Pub Date : 2024-11-07 DOI: 10.1038/s43586-024-00367-7

引用次数: 0

Fluorescence lifetime imaging microscopy 荧光寿命成像显微镜

IF 50.1

Nature reviews. Methods primers Pub Date : 2024-11-07 DOI: 10.1038/s43586-024-00358-8

Belen Torrado, Bruno Pannunzio, Leonel Malacrida, Michelle A. Digman

{"title":"Fluorescence lifetime imaging microscopy","authors":"Belen Torrado, Bruno Pannunzio, Leonel Malacrida, Michelle A. Digman","doi":"10.1038/s43586-024-00358-8","DOIUrl":"10.1038/s43586-024-00358-8","url":null,"abstract":"Fluorescence lifetime imaging microscopy (FLIM) is a powerful technique offering profound insights into a broad spectrum of biological processes such as metabolic imaging, protein–protein interactions and live-cell intracellular dynamics. The future of FLIM appears promising, with continuous technological advancements for time-resolved measurements pushing the boundaries for spatiotemporal information. However, the growth of the FLIM community has been slower, owing to the requirement for specialized training and technology. This Primer aims to address this gap by providing a comprehensive overview of FLIM principles, methods and analysis. We discuss various methods for measuring fluorescence lifetimes, including time-tagging and phase-modulation shift methods, along with their implementations and setup variations. Additionally, we explore different avenues for data analysis, with a specific focus on the phasor approach and its crucial considerations. Furthermore, we present a range of applications demonstrating versatility and usability of FLIM. Limitations and optimization strategies are also discussed, covering methodological constraints, equipment limitations and potential errors, along with their solutions. By sharing our expertise, we aim to expand FLIM to broader audiences while reinforcing concepts within the FLIM community. This Primer seeks to inspire bioimaging researchers to fully embrace FLIM, thereby advancing our understanding of complex biological systems. Fluorescence lifetime imaging microscopy can offer insights into biological processes such as metabolic imaging, protein–protein interactions and live-cell intracellular dynamics. In this Primer, Torrado et al. discuss methods for measuring fluorescence lifetimes, including time-tagging and phase-modulation shift methods, along with fluorescence lifetime imaging microscopy setup variations.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-23"},"PeriodicalIF":50.1,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142596173","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

Artificial metalloenzymes 人工金属酶

IF 50.1

Nature reviews. Methods primers Pub Date : 2024-11-01 DOI: 10.1038/s43586-024-00364-w

引用次数: 0

Artificial metalloenzymes 人工金属酶

IF 50.1

Nature reviews. Methods primers Pub Date : 2024-11-01 DOI: 10.1038/s43586-024-00356-w

Tobias Vornholt, Florian Leiss-Maier, Woo Jae Jeong, Cathleen Zeymer, Woon Ju Song, Gerard Roelfes, Thomas R. Ward

{"title":"Artificial metalloenzymes","authors":"Tobias Vornholt, Florian Leiss-Maier, Woo Jae Jeong, Cathleen Zeymer, Woon Ju Song, Gerard Roelfes, Thomas R. Ward","doi":"10.1038/s43586-024-00356-w","DOIUrl":"10.1038/s43586-024-00356-w","url":null,"abstract":"The development of artificial metalloenzymes (ArMs) aims to expand the capabilities of enzymatic catalysis, most notably towards new reaction mechanisms. Frequently, ArMs harness metal cofactors that are not naturally found in enzymes and embed these in specifically selected or designed protein scaffolds. ArMs have been developed for a wide range of natural and non-natural reactions, underscoring their potential to revolutionize fields such as biocatalysis or metabolic engineering. At the same time, replicating the catalytic prowess of natural enzymes is a highly challenging task, and several limitations need to be overcome to make ArM catalysis widely applicable. In this Primer, we introduce the state of the art in designing and engineering ArMs, describing best practices and important examples and achievements. Moreover, we consider potential applications of ArMs, as well as outstanding challenges, and discuss how these may be addressed in the coming years. Artificial metalloenzymes harness metal cofactors that are not naturally found in enzymes and embed these in specifically selected or designed protein scaffolds. In this Primer, Vornholt et al. describe the best practices for designing and engineering artificial metalloenzymes.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-17"},"PeriodicalIF":50.1,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142565984","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

Image-based 3D genomics through chromatin tracing 通过染色质追踪进行基于图像的三维基因组学研究

IF 50.1

Nature reviews. Methods primers Pub Date : 2024-10-24 DOI: 10.1038/s43586-024-00354-y

Tianqi Yang, Siyuan Wang

{"title":"Image-based 3D genomics through chromatin tracing","authors":"Tianqi Yang, Siyuan Wang","doi":"10.1038/s43586-024-00354-y","DOIUrl":"10.1038/s43586-024-00354-y","url":null,"abstract":"Correct organization of higher-order genome folding is essential for the regulation of gene expression, DNA replication and other genomic functions. Technological advances in high-throughput sequencing-based methods have allowed for systematic profiling of the fundamental architectural features of chromatin organization at the genome level. However, how chromatin is folded in 3D space at single-cell and single-chromosome-copy resolution in intact cells and tissues has been a long-standing question owing to a lack of appropriate methodology. Recent advances in chromatin labelling, imaging and automated fluidics technologies have led to the development of chromatin tracing, enabling direct mapping of the 3D chromatin folding trajectory in situ at the single-cell and single-molecule level. Within nearly a decade of its development, chromatin tracing has been applied at different genomic scales and to a spectrum of cell types and model organisms, improving our understanding of the structures, mechanisms and functions of chromatin organization in various biological and medical areas. In this Primer, we introduce the experimental principles, data analysis procedures and current applications of chromatin tracing. We describe how chromatin tracing can be combined with multimodal imaging and genetic screening technologies and provide a perspective on the limitations of current chromatin tracing approaches and the direction of technological developments for filling major gaps in discoveries. Chromatin tracing involves the direct mapping of 3D chromatin folding in situ, and can be applied at a number of genomic scales and to a wide range of cell types and model organisms. In this Primer, Yang & Wang discuss the design of chromatin tracing experiments, data analysis procedures and how chromatin tracing can be combined with multi-modal imaging.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-21"},"PeriodicalIF":50.1,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142519167","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

Image-based 3D genomics through chromatin tracing 通过染色质追踪进行基于图像的三维基因组学研究

IF 50.1

Nature reviews. Methods primers Pub Date : 2024-10-24 DOI: 10.1038/s43586-024-00362-y

引用次数: 0

Non-viral vectors for chimeric antigen receptor immunotherapy 用于嵌合抗原受体免疫疗法的非病毒载体

IF 50.1

Nature reviews. Methods primers Pub Date : 2024-10-10 DOI: 10.1038/s43586-024-00348-w

U. Sandy Tretbar, Joel G. Rurik, Even H. Rustad, Duran Sürün, Ulrike Köhl, Johanna Olweus, Frank Buchholz, Zoltán Ivics, Stephan Fricke, Ulrich Blache

{"title":"Non-viral vectors for chimeric antigen receptor immunotherapy","authors":"U. Sandy Tretbar, Joel G. Rurik, Even H. Rustad, Duran Sürün, Ulrike Köhl, Johanna Olweus, Frank Buchholz, Zoltán Ivics, Stephan Fricke, Ulrich Blache","doi":"10.1038/s43586-024-00348-w","DOIUrl":"10.1038/s43586-024-00348-w","url":null,"abstract":"Chimeric antigen receptor (CAR) T cell therapy has demonstrated remarkable efficacy in haematological malignancies. However, although viral vector-based methods are effective for CAR T cell manufacturing, they present significant biological, logistical and financial challenges. Non-viral vectors — such as mRNA, transposon and precision genome editors — offer a promising alternative, addressing issues of scalability and cost. mRNA and precision genome-editing technologies hold promise in facilitating the implementation of safe in vivo gene delivery for CAR T cell therapy. In this Primer, we discuss recent advancements in non-viral vectors for CAR immunotherapy, focusing on methodologies, clinical results, opportunities and limitations. We discuss permanent and transient gene engineering technologies, highlighting their ability to efficiently deliver genetic material and perform multiple genetic edits in target effector cells, such as T lymphocytes. We briefly describe delivery methods and preclinical development of ex vivo and in vivo T cell engineering using non-viral vectors. Additionally, we outline key considerations for clinical translation, such as reproducibility and good manufacturing practice. Through a comprehensive review of current literature and clinical trials, we underscore the potential of non-viral vectors to further optimize CAR immunotherapies, paving the way for more advanced and accessible cell-based treatments. Non-viral vectors offer scalable, cost-effective alternatives for chimeric antigen receptor T cell therapy. In this Primer, Tretbar et al. highlight advances in the use of non-viral approaches, gene delivery methods, clinical outcomes and key considerations for translating these technologies into practice.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-19"},"PeriodicalIF":50.1,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142435961","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

Non-viral vectors for chimeric antigen receptor immunotherapy 用于嵌合抗原受体免疫疗法的非病毒载体

IF 50.1

Nature reviews. Methods primers Pub Date : 2024-10-10 DOI: 10.1038/s43586-024-00360-0

引用次数: 0

Systematic review and meta-analysis of preclinical studies 临床前研究的系统回顾和荟萃分析

IF 50.1

Nature reviews. Methods primers Pub Date : 2024-10-03 DOI: 10.1038/s43586-024-00359-7

引用次数: 0