Nature reviews. Methods primers最新文献

{"title":"In vivo microelectrode arrays for neuroscience.","authors":"Nathaniel P Williams, Mihaly Voroslakos, Delin Shi, May Yoon Pwint, Vittorino Lanzio, Hongwei Mao, Pavlo Zolotavin, Euisik Yoon, Thomas Stieglitz, Chong Xie, Timothy D Harris, Andrew B Schwartz, Xinyan Tracy Cui","doi":"10.1038/s43586-025-00399-7","DOIUrl":"10.1038/s43586-025-00399-7","url":null,"abstract":"<p><p>Microelectrode arrays (MEAs) are devices capable of recording extracellular action potentials (spikes) from many neurons simultaneously and with high spatial and temporal resolution. MEAs have emerged as an invaluable tool for understanding how networks of neurons govern complex sensory, motor and decision-making processes. In this Primer, we introduce various in vivo MEA designs and describe their construction, characterization and applications. We describe approaches for effective device implantation and the use of MEA recordings in behavioural experiments. We then discuss strategies for obtaining high-quality and stable electrophysiological recordings, including through mitigating the foreign body reaction. We introduce the reader to spike sorting approaches with a focus on semi-automated sorting of high-channel-count data, as well as to the analysis of sorted spikes and their uses. Finally, we cover future trends and emerging MEA technology designed to expand current capabilities and overcome limitations, with a focus on biomimetic and multifunctional devices. This Primer should provide the reader with a foundation in the fundamental principles of MEA technology for in vivo use.</p>","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":"5 ","pages":""},"PeriodicalIF":56.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12921556/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147273284","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}

{"title":"Ptychography at all wavelengths.","authors":"Ruihai Wang, Qianhao Zhao, Lars Loetgering, Frederick Allars, Zhixuan Hong, Timothy J Pennycook, Roarke Horstmeyer, John Rodenburg, Andrew Maiden, Guoan Zheng","doi":"10.1038/s43586-025-00438-3","DOIUrl":"10.1038/s43586-025-00438-3","url":null,"abstract":"<p><p>Ptychography is a computational imaging technique that operates across multiple wavelength regimes, from electron (picometres) to X-ray (~0.1 nm), extreme ultraviolet (~10 nm), and visible light (micrometres). By reconstructing both amplitude and phase from diffraction patterns, ptychography enables high-resolution, quantitative imaging without conventional limitations imposed by lens-based optics. Ptychography has enabled advances across a range of scales: achieving record-breaking atomic resolution with electron microscopy, becoming an indispensable tool at X-ray synchrotron facilities worldwide, and overcoming the trade-offs between resolution and field-of-view in optical imaging. This Primer provides a unified treatment of ptychography across these wavelength regimes. First, we discuss theoretical foundations, reconstruction algorithms, experimental considerations and wavelength-specific challenges. We then give examples of raw and processed data from various configurations and wavelengths. Next, we highlight key applications of ptychography in life sciences, materials science and industry. We also discuss data standards, open-source software implementations, and best practices for ensuring reproducibility across different wavelength regimes. Finally, we consider limitations and future opportunities for ptychography. Together with accompanying datasets and code implementations, this Primer aims to serve newcomers and experienced practitioners in the field, facilitating broader adoption of ptychography across different disciplines.</p>","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":"5 ","pages":""},"PeriodicalIF":56.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13024499/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147576886","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}

{"title":"Laser capture microdissection.","authors":"Lance A Liotta, Thomas P Conrads, Marissa A Howard, Robyn P Araujo, Emanuel F Petricoin","doi":"10.1038/s43586-025-00453-4","DOIUrl":"10.1038/s43586-025-00453-4","url":null,"abstract":"<p><p>The tissue microenvironment was once viewed as an impossibly complex heterogeneous ecosystem. Today, tools and data analysis methods probe tissues at multiple resolution levels, from subpopulations to individual cells and individual molecules. Laser capture microdissection (LCM) was one of the first technologies enabling spatial molecular interrogation in tissues, enabling the extraction of precise regions of tissue for downstream acquisition and analysis of multiple classes of molecular analytes - including nucleic acids, proteins, metabolites and lipids. By physically isolating targeted cells or tissue compartments under microscopic visualization, LCM preserves spatial context for downstream multiomic profiling. The approach is agnostic to tissue type, molecular target and analytical tool, providing a powerful platform for spatially resolved analysis of tissue heterogeneity, microenvironment interactions and region-specific signatures. The attributes of LCM have drawn a large and diverse community of users who have imaginatively elevated the technology and its applications far beyond the early versions of LCM. In this Primer, we provide examples of how and when to use LCM and discuss its use with other spatial profiling platforms, providing an essential component of large-scale clinical research trials, revealing disease mechanisms and identifying predictors of therapeutic efficacy. Finally, we explore how the next generation of LCM and companion technologies will help to shape the personalized, designer therapies of the future.</p>","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":"5 ","pages":""},"PeriodicalIF":56.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13001730/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147500877","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}

{"title":"Analysis of metagenomic data.","authors":"Shaopeng Liu, Judith S Rodriguez, Viorel Munteanu, Cynthia Ronkowski, Nitesh Kumar Sharma, Mohammed Alser, Francesco Andreace, Ran Blekhman, Dagmara Błaszczyk, Rayan Chikhi, Keith A Crandall, Katja Della Libera, Dallace Francis, Alina Frolova, Abigail Shahar Gancz, Naomi E Huntley, Pooja Jaiswal, Tomasz Kosciolek, Pawel P Łabaj, Wojciech Łabaj, Tu Luan, Christopher Mason, Ahmed M Moustafa, Harihara Subrahmaniam Muralidharan, Onur Mutlu, Nika Mansouri Ghiasi, Ali Rahnavard, Fengzhu Sun, Shuchang Tian, Braden T Tierney, Emily Van Syoc, Riccardo Vicedomini, Joseph P Zackular, Alex Zelikovsky, Kinga Zielińska, Erika Ganda, Emily R Davenport, Mihai Pop, David Koslicki, Serghei Mangul","doi":"10.1038/s43586-024-00376-6","DOIUrl":"10.1038/s43586-024-00376-6","url":null,"abstract":"<p><p>Metagenomics has revolutionized our understanding of microbial communities, offering unprecedented insights into their genetic and functional diversity across Earth's diverse ecosystems. Beyond their roles as environmental constituents, microbiomes act as symbionts, profoundly influencing the health and function of their host organisms. Given the inherent complexity of these communities and the diverse environments where they reside, the components of a metagenomics study must be carefully tailored to yield accurate results that are representative of the populations of interest. This Primer article examines the methodological advancements and current practices that have shaped the field, from initial stages of sample collection and DNA extraction to the advanced bioinformatics tools employed for data analysis, with a particular focus on the profound impact of next-generation sequencing (NGS) on the scale and accuracy of metagenomics studies. We critically assess the challenges and limitations inherent in metagenomics experimentation, available technologies and computational analysis methods. Beyond technical methodologies, we explore the application of metagenomics across various domains, including human health, agriculture and environmental monitoring. Looking ahead, we advocate for the development of more robust computational frameworks and enhanced interdisciplinary collaborations. This Primer serves as a comprehensive guide for advancing the precision and applicability of metagenomic studies, positioning them to address the complexities of microbial ecology and their broader implications for human health and environmental sustainability.</p>","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":"5 ","pages":""},"PeriodicalIF":50.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12276902/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144676787","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}

{"title":"Droplet-based bioprinting.","authors":"Deepak Gupta, Irem Deniz Derman, Changxue Xu, Yong Huang, Ibrahim T Ozbolat","doi":"10.1038/s43586-025-00394-y","DOIUrl":"10.1038/s43586-025-00394-y","url":null,"abstract":"<p><p>Three-dimensional (3D) bioprinting facilitates the automated patterning of biological entities (such as cells and tissue building blocks) with or without scaffolding biomaterials. The technique enables fabrication of highly organized structures that recapitulate the physiological and biological functions of native tissues. Droplet-based bioprinting (DBB) is unique among the existing bioprinting modalities in its ability to handle and manipulate bioprinting at the cellular level, as well as to develop complex 3D constructs in a high-throughput manner. As an evolving bioprinting modality, DBB has greatly advanced our understanding of cell interactions, tissue and organ formation, and human disease. This Primer gives an overview of the methodology of DBB, detailing its various modalities and its associated hardware and software, including the selection of bioinks and substrates, as well as their interactions and compatibility with different DBB sub-modalities. Finally, recent advances and several limitations of DBB are summarized and considerations are discussed for potential improvements to the technology in the future.</p>","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":"5 ","pages":""},"PeriodicalIF":56.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13007925/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147517347","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}

{"title":"Low-intensity focused ultrasound for human neuromodulation","authors":"","doi":"10.1038/s43586-024-00378-4","DOIUrl":"10.1038/s43586-024-00378-4","url":null,"abstract":"This PrimeView highlights the impact of various tissues on the attentuation of low-frequency focused ultrasound signals, affecting the final intensity of signal that reaches the brain.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-1"},"PeriodicalIF":50.1,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s43586-024-00378-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845204","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}

{"title":"Low-intensity focused ultrasound for human neuromodulation","authors":"Wynn Legon,&nbsp;Andrew Strohman","doi":"10.1038/s43586-024-00368-6","DOIUrl":"10.1038/s43586-024-00368-6","url":null,"abstract":"Low-intensity focused ultrasound (LIFU) is a potentially transformative form of human non-invasive neuromodulation that provides millimetre-sized focal volumes combined with adjustable focal lengths that can target small and deep human brain circuitry. This Primer is intended for those looking to conduct LIFU studies in humans and outlines several important considerations, findings and limitations of focused ultrasound for human neuromodulation. The reader is introduced to the transducer&nbsp;and how ultrasound energy propagates into the human brain with considerations and limitations for doing this effectively. The potential effect of parameters and delivery of LIFU is discussed including mechanisms, exposure and safety. Highlights of findings from LIFU applications in healthy and clinical populations, as well as select in vitro and animal work, are provided to help the reader understand the current state of the field and the outlook of LIFU as a scientific and clinical tool. Low-intensity focused ultrasound offers non-invasive neuromodulation, targeting deep brain structures with adjustable parameters. In this Primer, Legon and Strohman discuss mechanisms and safety considerations and highlight findings from clinical applications, emphasizing its potential as a tool in neuroscience and therapeutic interventions.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-27"},"PeriodicalIF":50.1,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845217","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}

{"title":"mRNA m6A detection","authors":"","doi":"10.1038/s43586-024-00374-8","DOIUrl":"10.1038/s43586-024-00374-8","url":null,"abstract":"This PrimeView highlights the interplay between writers, readers and erasers of mRNA methylation proteins and how these are targeted for therapeutic purposes.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-1"},"PeriodicalIF":50.1,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s43586-024-00374-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142821509","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}

{"title":"mRNA m6A detection","authors":"Sharon Moshitch-Moshkovitz,&nbsp;Michal Sevilla-Sharon,&nbsp;Reut Ashwal-Fluss,&nbsp;Efrat Glick-Saar,&nbsp;Gideon Rechavi,&nbsp;Dan Dominissini","doi":"10.1038/s43586-024-00365-9","DOIUrl":"10.1038/s43586-024-00365-9","url":null,"abstract":"N6-methyladenosine (m6A) is the most prevalent internal mRNA modification. Recent research has highlighted its role as a key regulator of gene expression, influencing cellular processes and determining cell fate. Advances in techniques for global mapping of m6A, the discovery of m6A demethylases that enhance its dynamic properties and the identification of reader proteins that interact with m6A have substantially propelled this field forward. This Primer outlines the available tools for detecting and mapping m6A, discusses the strengths and limitations of each method and offers guidance on selecting the most suitable approach. Identifying and detecting m6A lays the groundwork for functional studies that address important biological and medical questions. N6-methyladenosine (m6A) is an mRNA modification influencing gene expression. Advanced methodologies for mapping m6A enhance understanding of its dynamic roles and interactions. In this Primer, Moshitch-Moshkovitz et al. discuss various detection tools and analysis techniques facilitating insights into RNA epitranscriptomics.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-20"},"PeriodicalIF":50.1,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142821512","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}

{"title":"X-ray absorption spectroscopy","authors":"","doi":"10.1038/s43586-024-00375-7","DOIUrl":"10.1038/s43586-024-00375-7","url":null,"abstract":"This PrimeView highlights how to measure X-ray absorption as a function of energy.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-1"},"PeriodicalIF":50.1,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s43586-024-00375-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142789380","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}