{"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}
Sharon Moshitch-Moshkovitz, Michal Sevilla-Sharon, Reut Ashwal-Fluss, Efrat Glick-Saar, Gideon Rechavi, Dan Dominissini
{"title":"mRNA m6A detection","authors":"Sharon Moshitch-Moshkovitz, Michal Sevilla-Sharon, Reut Ashwal-Fluss, Efrat Glick-Saar, Gideon Rechavi, 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}
Christopher T. Chantler, Grant Bunker, Paola D’Angelo, Sofia Diaz-Moreno
{"title":"X-ray absorption spectroscopy","authors":"Christopher T. Chantler, Grant Bunker, Paola D’Angelo, Sofia Diaz-Moreno","doi":"10.1038/s43586-024-00366-8","DOIUrl":"10.1038/s43586-024-00366-8","url":null,"abstract":"X-ray absorption spectroscopy (XAS) is an established experimental technique for studying the electronic and local geometric structures of materials. As a short-range order structural probe, it can be applied to all states of matter: crystalline or amorphous solids, liquids and gases. The method is element selective and highly sensitive, with little compromise required to integrate complex sample environment set-ups. These characteristics make the technique suitable for applications in a range of scientific disciplines, from chemistry and catalysis to environmental science, materials science, physics, biology, medicine and cultural heritage. An XAS spectrum is obtained by measuring the modulation of the sample absorption coefficient as a function of the incident X-ray beam energy. Data are usually collected in transmission detection mode, although fluorescence and electron yield detection modes are often used. The XAS spectrum is divided into two regimes: X-ray absorption near-edge structure and extended X-ray absorption fine structure. In this Primer, an overview of XAS fundamentals is given, together with a description of the experimental set-ups, sample requirements, data analysis and possible applications. X-ray absorption spectroscopy is an element-specific and orbital-specific technique that can probe local atomic and electronic structures, without the need for long-range order. This Primer discusses the background principles, experimental methods and data analysis processes used in X-ray absorption spectroscopy to derive oxidation states, coordination and bond lengths of solids, liquids and gases.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-25"},"PeriodicalIF":50.1,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142789402","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}
Dimitrios Kazazis, Jara Garcia Santaclara, Jan van Schoot, Iacopo Mochi, Yasin Ekinci
{"title":"Extreme ultraviolet lithography","authors":"Dimitrios Kazazis, Jara Garcia Santaclara, Jan van Schoot, Iacopo Mochi, Yasin Ekinci","doi":"10.1038/s43586-024-00361-z","DOIUrl":"10.1038/s43586-024-00361-z","url":null,"abstract":"Extreme ultraviolet lithography (EUVL) was recently adopted by the semiconductor industry as the leading-edge lithography technique for continued miniaturization of semiconductor devices in line with Moore’s law. EUVL has emerged as a critical technique, taking advantage of shorter wavelengths to achieve nanoscale feature sizes with higher precision and lower defect rates than previous lithography methods. This Primer comprehensively explores the technical evolution from deep ultraviolet to extreme ultraviolet (EUV) lithography, highlighting innovative approaches in source technology, resist materials and optical systems developed to meet the stringent requirements of high-volume manufacturing. Beginning with an overview of the fundamental principles of photolithography, the main components and functionalities of EUV scanners are described. It also covers exposure tools that support research and early development phases. Key topics — such as image formation, photoresist platforms and pattern transfer — are explained with an emphasis on improving resolution and throughput. Additionally, persistent challenges are addressed, such as stochastic effects and resist sensitivity, with insights provided into future directions for EUVL, including high-numerical aperture systems and novel resist platforms. This Primer aims to present a detailed review of current EUVL capabilities and project the future developments and evolution of EUVL in semiconductor manufacturing. Extreme ultraviolet (EUV) lithography is used to fabricate features with nanometre-scale resolution. This Primer explores how EUV lithography can be applied to manufacture semiconductor devices, explaining lithographic tools, photoresists and potential future developments.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-15"},"PeriodicalIF":50.1,"publicationDate":"2024-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142754223","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":"A data-centric perspective to fair machine learning for healthcare","authors":"Haoran Zhang, Walter Gerych, Marzyeh Ghassemi","doi":"10.1038/s43586-024-00371-x","DOIUrl":"10.1038/s43586-024-00371-x","url":null,"abstract":"Machine learning models are increasingly being deployed in real-world clinical settings and have shown promise in patient diagnosis, treatment and outcome tasks. However, such models have also been shown to exhibit biases towards specific demographic groups, leading to inequitable outcomes for under-represented or historically marginalized communities.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-2"},"PeriodicalIF":50.1,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142754206","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":"Uniform manifold approximation and projection","authors":"John Healy, Leland McInnes","doi":"10.1038/s43586-024-00363-x","DOIUrl":"10.1038/s43586-024-00363-x","url":null,"abstract":"Uniform manifold approximation and projection is a nonlinear dimension reduction method often used for visualizing data and as pre-processing for further machine-learning tasks such as clustering. In this Primer, we provide an introduction to the uniform manifold approximation and projection algorithm, the intuitions behind how it works, how best to apply it on data and how to interpret and understand results. Uniform manifold approximation and projection is a dimensionality reduction technique used to visualize and understand high-dimensional data. In this Primer, Healy and McInnes outline the use of the uniform manifold approximation and projection algorithm and its application to diverse data.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-15"},"PeriodicalIF":50.1,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142679982","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":"Uniform manifold approximation and projection","authors":"","doi":"10.1038/s43586-024-00369-5","DOIUrl":"10.1038/s43586-024-00369-5","url":null,"abstract":"This PrimeView highlights the utility of uniform manifold approximation and projection in dimension reduction for data visualization, hypothesis generation and highlighting patterns in complex data.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-1"},"PeriodicalIF":50.1,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s43586-024-00369-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142679932","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":"Fluorescence lifetime imaging microscopy","authors":"","doi":"10.1038/s43586-024-00367-7","DOIUrl":"10.1038/s43586-024-00367-7","url":null,"abstract":"This PrimeView highlights the challenges and opportunities in using fluorescence lifetime imaging microscopy (FLIM), including strategies for improving acquisition speeds and dead-times.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-1"},"PeriodicalIF":50.1,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s43586-024-00367-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142596168","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}
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