Nature reviews. Methods primers最新文献

{"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":"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}

{"title":"X-ray absorption spectroscopy","authors":"Christopher T. Chantler,&nbsp;Grant Bunker,&nbsp;Paola D’Angelo,&nbsp;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}

{"title":"Extreme ultraviolet lithography","authors":"Dimitrios Kazazis,&nbsp;Jara Garcia Santaclara,&nbsp;Jan van Schoot,&nbsp;Iacopo Mochi,&nbsp;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":"Extreme ultraviolet lithography","authors":"","doi":"10.1038/s43586-024-00372-w","DOIUrl":"10.1038/s43586-024-00372-w","url":null,"abstract":"This PrimeView highlights the future impacts of extreme ultraviolet lithography on semiconductor devices.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-1"},"PeriodicalIF":50.1,"publicationDate":"2024-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s43586-024-00372-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142754208","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":"A data-centric perspective to fair machine learning for healthcare","authors":"Haoran Zhang,&nbsp;Walter Gerych,&nbsp;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}