Diego Misseroni, Phanisri P. Pratapa, Ke Liu, Biruta Kresling, Yan Chen, Chiara Daraio, Glaucio H. Paulino
{"title":"Origami engineering","authors":"Diego Misseroni, Phanisri P. Pratapa, Ke Liu, Biruta Kresling, Yan Chen, Chiara Daraio, Glaucio H. Paulino","doi":"10.1038/s43586-024-00313-7","DOIUrl":"10.1038/s43586-024-00313-7","url":null,"abstract":"Origami traces its origins to an ancient art form transforming flat thin surfaces into various complex, fabulous 3D objects. Nowadays, such transformation transcends art by offering a conceptual framework for non-destructive and scale-independent abstractions for engineering applications across diverse fields with potential impact in education, science and technology. For instance, a growing number of architected materials and structures are based on origami principles, leading to unique properties that are distinct from those previously found in either natural or engineered systems. To disseminate those concepts, this Primer provides a comprehensive overview of the major principles and elements in origami engineering, including theoretical fundamentals, simulation tools, manufacturing techniques and testing protocols that require non-standard set-ups. We highlight applications involving deployable structures, metamaterials, robotics, medical devices and programmable matter to achieve functions such as vibration control, mechanical computing and shape morphing. We identify challenges for the field, including finite rigidity, panel thickness accommodation, incompatibility with regular mechanical testing devices, manufacturing of non-developable patterns, sensitivity to imperfections and identifying the relevant physics at the scale of interest. We further envision the future of origami engineering aimed at next-generation multifunctional material and structural systems. Origami engineering offers a conceptual framework for non-destructive and scale-independent abstractions for engineering applications. In this Primer, Misseroni et al. provide a comprehensive overview of the major principles and elements in origami engineering, including theoretical fundamentals, simulation tools, manufacturing techniques and testing protocols.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-19"},"PeriodicalIF":50.1,"publicationDate":"2024-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141513002","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}
David S. Roberts, Joseph A. Loo, Yury O. Tsybin, Xiaowen Liu, Si Wu, Julia Chamot-Rooke, Jeffrey N. Agar, Ljiljana Paša-Tolić, Lloyd M. Smith, Ying Ge
{"title":"Top-down proteomics","authors":"David S. Roberts, Joseph A. Loo, Yury O. Tsybin, Xiaowen Liu, Si Wu, Julia Chamot-Rooke, Jeffrey N. Agar, Ljiljana Paša-Tolić, Lloyd M. Smith, Ying Ge","doi":"10.1038/s43586-024-00318-2","DOIUrl":"10.1038/s43586-024-00318-2","url":null,"abstract":"Proteoforms, which arise from post-translational modifications, genetic polymorphisms and RNA splice variants, play a pivotal role as drivers in biology. Understanding proteoforms is essential to unravel the intricacies of biological systems and bridge the gap between genotypes and phenotypes. By analysing whole proteins without digestion, top-down proteomics (TDP) provides a holistic view of the proteome and can decipher protein function, uncover disease mechanisms and advance precision medicine. This Primer explores TDP, including the underlying principles, recent advances and an outlook on the future. The experimental section discusses instrumentation, sample preparation, intact protein separation, tandem mass spectrometry techniques and data collection. The results section looks at how to decipher raw data, visualize intact protein spectra and unravel data analysis. Additionally, proteoform identification, characterization and quantification are summarized, alongside approaches for statistical analysis. Various applications are described, including the human proteoform project and biomedical, biopharmaceutical and clinical sciences. These are complemented by discussions on measurement reproducibility, limitations and a forward-looking perspective that outlines areas where the field can advance, including potential future applications. Proteoforms can be investigated using top-down proteomics, a technique that analyses whole proteins without previous digestion. This Primer introduces top-down proteomics, exploring mass spectrometry experimental methods, sample preparation, data analysis and applications in understanding human disease.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-23"},"PeriodicalIF":0.0,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141315516","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":"Nanozymes for nanohealthcare","authors":"","doi":"10.1038/s43586-024-00324-4","DOIUrl":"10.1038/s43586-024-00324-4","url":null,"abstract":"This PrimeView highlights the different methods for the surface engineering of nanozymes.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-1"},"PeriodicalIF":0.0,"publicationDate":"2024-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s43586-024-00324-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141182307","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}
Yihong Zhang, Gen Wei, Wanling Liu, Tong Li, Yuting Wang, Min Zhou, Yufeng Liu, Xiaoyu Wang, Hui Wei
{"title":"Nanozymes for nanohealthcare","authors":"Yihong Zhang, Gen Wei, Wanling Liu, Tong Li, Yuting Wang, Min Zhou, Yufeng Liu, Xiaoyu Wang, Hui Wei","doi":"10.1038/s43586-024-00315-5","DOIUrl":"10.1038/s43586-024-00315-5","url":null,"abstract":"Nanozymes, nanomaterial-based artificial enzymes, exhibit potential for emulating the catalytic functions inherent in enzymes. Nanozymes have advantages such as low cost, facile synthesis, high stability and adjustable activities. As a promising approach for healthcare, nanozymes have sparked considerable interest, and have been chosen as one of the 2022 Top Ten Emerging Technologies in Chemistry by the International Union of Pure and Applied Chemistry (IUPAC). This Primer provides theranostic insights from the nanozyme toolbox, encompassing the design of nanoparticles, evaluation of activities and applications. We focus on rational strategies to enhance nanozyme activities, emphasizing standardized evaluations across different activities, and outline specific details for their practical applications. The selection of candidates for diagnosis, as well as those for in vivo theranostic applications, is carefully considered based on appropriateness. We also acknowledge current challenges and limitations, presenting future perspectives and positioning nanozymes as an alternative and effective choice in theranostics. This Primer aims to contribute to the understanding and advancement of nanozyme applications in healthcare, offering a comprehensive guide for researchers in this dynamic field. Nanozymes are nanomaterial-based artificial enzymes that can emulate the catalytic functions inherent in enzymes. In this Primer, Zhang et al. discuss the nanozyme toolbox, including their design and modification, characterization, activity evaluation and applications in healthcare.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-22"},"PeriodicalIF":0.0,"publicationDate":"2024-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141182308","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":"Femtosecond stimulated Raman spectroscopy","authors":"","doi":"10.1038/s43586-024-00321-7","DOIUrl":"10.1038/s43586-024-00321-7","url":null,"abstract":"This PrimeView highlights the analysis of the FSRS response, produced using three laser pulses that, in combination, can detail insights into rapid molecular processes at a femtosecond time resolution.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-1"},"PeriodicalIF":0.0,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s43586-024-00321-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141091713","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}
Giovanni Batignani, Carino Ferrante, Giuseppe Fumero, Miles Martinati, Tullio Scopigno
{"title":"Femtosecond stimulated Raman spectroscopy","authors":"Giovanni Batignani, Carino Ferrante, Giuseppe Fumero, Miles Martinati, Tullio Scopigno","doi":"10.1038/s43586-024-00314-6","DOIUrl":"10.1038/s43586-024-00314-6","url":null,"abstract":"First demonstrated in 1994, femtosecond stimulated Raman scattering (FSRS) has gained popularity since the early 2000s as an ultrafast pump–probe vibrational spectroscopy technique with the potential to circumvent the time and energy limitations imposed by the Heisenberg uncertainty principle. This Primer explores whether, why, when and how the temporal precision and frequency resolution of traditional time-resolved spontaneous Raman spectroscopy can be surpassed by its coherent counterpart (FSRS), while still adhering to the uncertainty principle. We delve into the fundamental concepts behind FSRS and its most common experimental implementations, focusing on instrumentation details, measurement techniques, data analysis and modelling. This includes discussions on synthesizing the Raman pump beam, artificial intelligence (AI)-assisted baseline removal methods and analytical expressions for reproducing experimental data and extracting key parameters such as relaxation times and out-of-equilibrium temperature profiles. Recent applications of FSRS from physics, chemistry and biology are showcased, demonstrating how this approach has facilitated cross-disciplinary studies. We also address the technical and conceptual limitations of FSRS to aid in designing optimal experiments based on specific goals. Finally, we explore future directions, including multidimensional extensions to address vibrational couplings and the use of quantum light to untangle temporal and spectral resolution. Femtosecond stimulated Raman scattering (FSRS) is an ultrafast pump–probe spectroscopy method for investigating the vibrational dynamics of molecules. In this Primer, Batignani et al. introduce the fundamental concepts behind FSRS, its current utility and future integrations of artificial intelligence and quantum light.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-21"},"PeriodicalIF":0.0,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141091698","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":"Secondary ion mass spectrometry","authors":"","doi":"10.1038/s43586-024-00319-1","DOIUrl":"10.1038/s43586-024-00319-1","url":null,"abstract":"This PrimeView highlights how different primary ion beams can be used to sample different surface species.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-1"},"PeriodicalIF":0.0,"publicationDate":"2024-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s43586-024-00319-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140895297","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}
Nicholas P. Lockyer, Satoka Aoyagi, John S. Fletcher, Ian S. Gilmore, Paul A. W. van der Heide, Katie L. Moore, Bonnie J. Tyler, Lu-Tao Weng
{"title":"Secondary ion mass spectrometry","authors":"Nicholas P. Lockyer, Satoka Aoyagi, John S. Fletcher, Ian S. Gilmore, Paul A. W. van der Heide, Katie L. Moore, Bonnie J. Tyler, Lu-Tao Weng","doi":"10.1038/s43586-024-00311-9","DOIUrl":"10.1038/s43586-024-00311-9","url":null,"abstract":"Secondary ion mass spectrometry (SIMS) is a technique for chemical analysis and imaging of solid materials, with applications in many areas of science and technology. It involves bombarding a sample surface under high vacuum with energetic primary ions. The ejected secondary ions undergo mass-to-charge ratio (m/z) analysis and are detected. The resulting mass spectrum contains detailed surface chemical information with sub-monolayer sensitivity. Different experimental configurations provide chemically resolved depth distribution and 2D or 3D images. SIMS is complementary to other surface analysis techniques, such as X-ray photoelectron spectroscopy; chemical imaging techniques, for example, vibrational microspectroscopy methods such as Fourier transform infrared spectroscopy and Raman spectroscopy; and other mass spectrometry imaging techniques, including desorption electrospray ionization and matrix-assisted laser desorption ionization. Features of SIMS include high spatial resolution, high depth resolution and broad chemical sensitivity to all elements, isotopes and molecules up to several thousand mass units. This Primer describes the operating principles of SIMS and outlines how the instrument geometry and operational parameters enable different modes of operation and information to be obtained. Applications, including materials science, surface science, electronic devices, geosciences and life sciences, are explored, finishing with an outlook for the technique. Solid samples can be imaged and chemically analysed using secondary ion mass spectrometry. This Primer describes the secondary ion mass spectrometry experimental setup, in which a primary ion beam sputters secondary ions that are analysed and detected by a mass spectrometer, and explores applications in materials, geological and life sciences.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-21"},"PeriodicalIF":0.0,"publicationDate":"2024-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140895320","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}
Rick A. Homan, John D. Lapek, Christina M. Woo, Sherry Niessen, Lyn H. Jones, Christopher G. Parker
{"title":"Photoaffinity labelling with small molecules","authors":"Rick A. Homan, John D. Lapek, Christina M. Woo, Sherry Niessen, Lyn H. Jones, Christopher G. Parker","doi":"10.1038/s43586-024-00308-4","DOIUrl":"10.1038/s43586-024-00308-4","url":null,"abstract":"Small molecules can serve as leads for new therapeutics as well as powerful tools to investigate biological processes. Understanding the interactions of these molecules, particularly in native biological environments, is fundamentally critical to their utility. Photoaffinity labelling (PAL) represents one of the few strategies that enable the direct mapping of interactions of small molecules with proteins. PAL uses latent functional groups that form reactive intermediates only upon exposure to light of specific wavelengths that, subsequently, covalently adduct to proximal biomolecules, allowing for their enrichment and identification. Although the original applications of PAL date to six decades ago, the more recent integration with powerful mass spectrometry-based proteomic methods has profoundly impacted the ability to illuminate molecular interactions on a global scale. In this Primer, we discuss the current state-of-the-art of PAL-based strategies for studying molecular interactions in native systems, with a focus on investigations of small molecule–protein interactions. We cover topics including the basic principles of PAL chemistries, PAL probe design, experimental considerations, data analysis and applications of PAL illustrated by recent examples. Finally, we provide our perspective on persistent challenges and our outlook on the field. Photoaffinity labelling (PAL) enables the direct mapping of interactions of small molecules with proteins. In this Primer, Homan et al. discuss the basic principles and considerations involved in the design and implementation of PAL reagents and methods.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-23"},"PeriodicalIF":0.0,"publicationDate":"2024-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140819055","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}
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