Nature Reviews Methods Primers

Journal: Nature Reviews Methods Primers

Abbreviation

Nat. Rev. Methods Primers

Publisher

Nature

ISSN

2662-8449

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Publications 1 - 10 of 16

Light-based vat-polymerization bioprinting
Levato, Riccardo; Dudaryeva, Oksana; Garciamendez-Mijares, Carlos Ezio; et al. (2023)
Nature Reviews Methods Primers
Light-based vat-polymerization bioprinting enables computer-aided patterning of 3D cell-laden structures in a point-by-point, layer-by-layer or volumetric manner, using vat (vats) filled with photoactivatable bioresin (bioresins). This collection of technologies — divided by their modes of operation into stereolithography, digital light processing and volumetric additive manufacturing — has been extensively developed over the past few decades, leading to broad applications in biomedicine. In this Primer, we illustrate the methodology of light-based vat-polymerization 3D bioprinting from the perspectives of hardware, software and bioresin selections. We follow with discussions on methodological variations of these technologies, including their latest advancements, as well as elaborating on key assessments utilized towards ensuring qualities of the bioprinting procedures and products. We conclude by providing insights into future directions of light-based vat-polymerization methods.
Radiocarbon dating
Hajdas, Irka; Ascough, Philippa; Garnett, Mark H.; et al. (2021)
Nature Reviews Methods Primers
Radiocarbon dating uses the decay of a radioactive isotope of carbon (14C) to measure time and date objects containing carbon-bearing material. With a half-life of 5,700 ± 30 years, detection of 14C is a useful tool for determining the age of a specimen formed over the past 55,000 years. In this Primer, we outline key advances in 14C measurement and instrument capacity, as well as optimal sample selection and preparation. We discuss data processing, carbon reservoir age correction, calibration and statistical analyses. We then outline examples of radiocarbon dating across a range of applications, from anthropology and palaeoclimatology to forensics and medical science. Reproducibility and minimum reporting standards are discussed along with potential issues related to accuracy and sensitivity. Finally, we look forwards to the adoption of radiocarbon dating in various fields of research thanks to continued instrument improvement.
Droplet-based microfluidics
Moragues, Thomas; Arguijo, Diana; Beneyton, Thomas; et al. (2023)
Nature Reviews Methods Primers
Droplet-based microfluidic systems generate, manipulate and control sub-microlitre droplets enclosed within an immiscible carrier fluid. Owing to a number of remarkable features, such as the ability to precisely control the chemical and biological payload of each droplet and to produce thousands of droplets per second, this technology is transforming how chemists and biologists perform high-throughput or massively parallel experiments. In this Primer, we initially introduce and describe the basic features of droplet-based microfluidic systems and key issues that should be considered when developing new chemical and biological workflows. We provide a critical evaluation of how droplet-based microfluidic systems should be manufactured and the importance of integrating appropriate detection technologies to probe the small analytical volumes that are representatives of the technology set. We then discuss issues related to data collection and management, providing guidelines on how large data sets should be processed and manipulated. Furthermore, we showcase some of the most successful and important applications of droplet-based systems in the biological and chemical sciences and consider issues that currently hinder progress in both technology development and application. Finally, we provide some opinion on future directions for the technology set and where its greatest impact will be felt in the coming years.
Engineered hydrogels for mechanobiology
Blache, Ulrich; Ford, Eden M.; Ha, Byunghang; et al. (2022)
Nature Reviews Methods Primers
Cells’ local mechanical environment can be as important in guiding cellular responses as many well-characterized biochemical cues. Hydrogels that mimic the native extracellular matrix can provide these mechanical cues to encapsulated cells, allowing for the study of their impact on cellular behaviours. Moreover, by harnessing cellular responses to mechanical cues, hydrogels can be used to create tissues in vitro for regenerative medicine applications and for disease modelling. This Primer outlines the importance and challenges of creating hydrogels that mimic the mechanical and biological properties of the native extracellular matrix. The design of hydrogels for mechanobiology studies is discussed, including the appropriate choice of cross-linking chemistry and strategies to tailor hydrogel mechanical cues. Techniques for characterizing hydrogels are explained, highlighting methods used to analyse cell behaviour. Example applications in regenerative medicine and for studying fundamental mechanobiological processes are provided, along with a discussion of the limitations of hydrogels as mimetics of the native extracellular matrix. The Primer ends with an outlook for the field, focusing on emerging technologies that will enable new insights into mechanobiology and its role in tissue homeostasis and disease.
Scanning probe microscopy
Bian, Ke; Gerber, Christoph; Heinrich, Andreas J.; et al. (2021)
Nature Reviews Methods Primers
Scanning probe microscopy (SPM), a key invention in nanoscience, has by now been extended to a wide spectrum of basic and applied fields. Its application to basic science led to a paradigm shift in the understanding and perception of matter at its nanoscopic and even atomic levels. SPM uses a sharp tip to physically raster-scan samples and locally collect information from the surface. Various signals can be directly detected by SPM in real space with atomic or nanoscale resolution, which provides insights into the structural, electronic, vibrational, optical, magnetic, (bio)chemical and mechanical properties. This Primer introduces the key aspects and general features of SPM and SPM set-up and variations, with particular focus on scanning tunnelling microscopy and atomic force microscopy. We outline how to conduct SPM experiments, as well as data analysis of SPM imaging, spectroscopy and manipulation. Recent applications of SPM to physics, chemistry, materials science and biology are then highlighted, with representative examples. We outline issues with reproducibility, and standards on open data are discussed. This Primer also raises awareness of the ongoing challenges and possible ways to overcome these difficulties, followed by an outlook of future possible directions.
3D extrusion bioprinting
Shrike Zhang, Yu; Haghiashtiani, Ghazaleh; Hübscher, Tania; et al. (2021)
Nature Reviews Methods Primers
Three-dimensional (3D) bioprinting strategies use computer-aided processes to enable automated simultaneous spatial patterning of cells and/or biomaterials. These technologies are suitable for a broad range of biomedical applications owing to their capability to produce structurally sophisticated and functionally relevant tissue constructs. Extrusion-based 3D bioprinting strategies were among the first modalities developed and are now arguably the most widely used for producing 3D tissue constructs. These technologies have rapidly evolved over the past two decades, providing a powerful tool set for the biofabrication of tissues that can facilitate translational efforts in the field. In this Primer, we describe the methodology of 3D extrusion bioprinting, focusing on the selection of hardware, software and bioinks. We expand upon recent advances in 3D extrusion bioprinting by illustrating the key variations that promote its biofabrication abilities. Finally, we provide an outlook on possible future refinements of the technology.
Optimal transport for single-cell and spatial omics
Bunne, Charlotte; Schiebinger, Geoffrey; Krause, Andreas; et al. (2024)
Nature Reviews Methods Primers
High-throughput single-cell profiling provides an unprecedented ability to uncover the molecular states of millions of cells. These technologies are, however, destructive to cells and tissues, raising practical challenges when aiming to track dynamic biological processes. As the same cell cannot be observed at multiple time points, as it changes in time and space in response to a stimulus or perturbation, these large-scale measurements only produce unaligned data sets. In this Primer, we show how such challenges can be effectively addressed using the unifying framework of optimal transport theory and tackled using the many algorithms that have been proposed for the range of scenarios of key interest in computational biology. We further review recent advances integrating optimal transport and deep learning that allow forecasting heterogeneous cellular dynamics and behaviour, crucial in particular for pressing problems in personalized medicine.
Holotomography
Kim, Geon; Hugonnet, Herve; Kim, Kyoohyun; et al. (2024)
Nature Reviews Methods Primers
Holotomography (HT) represents a 3D, label-free optical imaging methodology that leverages refractive index as an inherent quantitative contrast for imaging. This technique has recently seen notable advancements, creating novel opportunities for the comprehensive visualization and analysis of living cells and their subcellular organelles. It has manifested wide-ranging applications spanning cell biology, biophysics, microbiology and biotechnology, substantiating its vast potential. In this Primer, we elucidate the foundational physical principles underpinning HT, detailing its experimental implementations and providing case studies of representative research employing this methodology. We also venture into interdisciplinary territories, exploring how HT harmonizes with emergent technologies, such as regenerative medicine, 3D biology and organoid-based drug discovery and screening. Looking ahead, we engage in a prospective analysis of potential future trajectories for HT, discussing innovation-focused initiatives that may further elevate this field. We also propose possible future applications of HT, identifying opportunities for its integration into diverse realms of scientific research and technological development.
Force spectroscopy of single cells using atomic force microscopy
Viljoen, Albertus; Mathelié-Guinlet, Marion; Ray, Ankita; et al. (2021)
Nature Reviews Methods Primers
Physical forces and mechanical properties have critical roles in cellular function, physiology and disease. Over the past decade, atomic force microscopy (AFM) techniques have enabled substantial advances in our understanding of the tight relationship between force, mechanics and function in living cells and contributed to the growth of mechanobiology. In this Primer, we provide a comprehensive overview of the use of AFM-based force spectroscopy (AFM-FS) to study the strength and dynamics of cell adhesion from the cellular to the single-molecule level, spatially map cell surface receptors and quantify how cells dynamically regulate their mechanical and adhesive properties. We first introduce the importance of force and mechanics in cell biology and the general principles of AFM-FS methods. We describe procedures for sample and AFM probe preparations, the various AFM-FS modalities currently available and their respective advantages and limitations. We also provide details and recommendations for best usage practices, and discuss data analysis, statistics and reproducibility. We then exemplify the potential of AFM-FS in cellular and molecular biology with a series of recent successful applications focusing on viruses, bacteria, yeasts and mammalian cells. Finally, we speculate on the grand challenges in the area for the next decade.
Analysis of metagenomic data
Liu, Shaopeng; Rodriguez, Judith S.; Munteanu, Viorel; et al. (2025)
Nature Reviews Methods Primers
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 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 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.

Publications 1 - 10 of 16

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