Nature Protocols Nature Protocols is an interactive online resource for laboratory protocols, providing step-by-step instructions for using and adapting research techniques that users can take straight to the lab bench and apply in their own research. Protocols are commissioned by the editorial team from leading laboratories. They are edited and peer-reviewed to ensure the highest level of quality and reproducibility. All protocols must have been proven to work, having been used to acquire data in published research papers. The focus is on providing practical information that is not available in research papers, such as explaining the critical points in the procedure, anticipated results (what to expect if the experiment has worked) and how to troubleshoot problems. Nature Protocols publishes protocols used to answer outstanding biological and biomedical research questions, including methods grounded in physics and chemistry that can be applied to biological problems. Protocols are added weekly and cover new methods, as well as classic, wellestablished techniques. Protocols are fully searchable online and also available in print on demand. http://feeds.nature.com/nprot/rss/current Nature Publishing Group en © 2024 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. Nature Protocols © 2024 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. permissions@nature.com Nature Protocols https://www.nature.com/uploads/product/nprot/rss.PNG http://feeds.nature.com/nprot/rss/current <![CDATA[Detection of colinear blocks and synteny and evolutionary analyses based on utilization of MCScanX]]> https://www.nature.com/articles/s41596-024-00968-2 Nature Protocols, Published online: 15 March 2024; doi:10.1038/s41596-024-00968-2

Synteny and colinearity are important parameters that delineate the evolution of genomes and gene families. This protocol describes MCScanX, a user-friendly toolkit that facilitates rapid evolutionary analysis of chromosomal structural changes.]]>
Yupeng WangHaibao TangXiyin WangYing SunPaule V. JosephAndrew H. Paterson doi:10.1038/s41596-024-00968-2 Nature Protocols, Published online: 2024-03-15; | doi:10.1038/s41596-024-00968-2 2024-03-15 Nature Protocols 10.1038/s41596-024-00968-2 https://www.nature.com/articles/s41596-024-00968-2
<![CDATA[Transkingdom Network Analysis (TkNA): a systems framework for inferring causal factors underlying host–microbiota and other multi-omic interactions]]> https://www.nature.com/articles/s41596-024-00960-w Nature Protocols, Published online: 12 March 2024; doi:10.1038/s41596-024-00960-w

Transkingdom Network Analysis (TkNA) is a unique analytical framework for inferring causal factors underlying host–microbiota and other multi-omic interactions, by integrating data from multiple cohorts and diverse omics types.]]>
Nolan K. NewmanMatthew S. MacovskyRichard R. RodriguesAmanda M. BruceJacob W. PedersonJyothi PadiadpuJigui ShanJoshua WilliamsSankalp S. PatilAmiran K. DzutsevNatalia ShulzhenkoGiorgio TrinchieriKevin BrownAndrey Morgun doi:10.1038/s41596-024-00960-w Nature Protocols, Published online: 2024-03-12; | doi:10.1038/s41596-024-00960-w 2024-03-12 Nature Protocols 10.1038/s41596-024-00960-w https://www.nature.com/articles/s41596-024-00960-w
<![CDATA[Single-molecule magnetic tweezers to probe the equilibrium dynamics of individual proteins at physiologically relevant forces and timescales]]> https://www.nature.com/articles/s41596-024-00965-5 Nature Protocols, Published online: 11 March 2024; doi:10.1038/s41596-024-00965-5

Ultra-stable magnetic tweezers allow measuring individual protein dynamics in equilibrium under physiologically relevant pulling forces and over timescales of days to weeks, enabling high-precision molecular studies in mechanobiology.]]>
Rafael Tapia-RojoMarc MoraSergi Garcia-Manyes doi:10.1038/s41596-024-00965-5 Nature Protocols, Published online: 2024-03-11; | doi:10.1038/s41596-024-00965-5 2024-03-11 Nature Protocols 10.1038/s41596-024-00965-5 https://www.nature.com/articles/s41596-024-00965-5
<![CDATA[Publisher Correction: Rapid reaction optimization by robust and economical quantitative benchtop <sup>19</sup>F NMR spectroscopy]]> https://www.nature.com/articles/s41596-024-00982-4 Nature Protocols, Published online: 05 March 2024; doi:10.1038/s41596-024-00982-4

Publisher Correction: Rapid reaction optimization by robust and economical quantitative benchtop 19F NMR spectroscopy]]>
19F NMR spectroscopy]]> G. HeinrichM. KondratiukL. J. GooßenM. P. Wiesenfeldt doi:10.1038/s41596-024-00982-4 Nature Protocols, Published online: 2024-03-05; | doi:10.1038/s41596-024-00982-4 2024-03-05 Nature Protocols 10.1038/s41596-024-00982-4 https://www.nature.com/articles/s41596-024-00982-4
<![CDATA[Profiling native pulmonary basement membrane stiffness using atomic force microscopy]]> https://www.nature.com/articles/s41596-024-00955-7 Nature Protocols, Published online: 01 March 2024; doi:10.1038/s41596-024-00955-7

Atomic force microscopy can be used to determine the stiffness of materials. This protocol describes how to measure and quantify the Young’s modulus E of pulmonary mouse and human basement membranes with atomic force microscopy and the Center for Applied Tissue Engineering and Regenerative Medicine processing toolbox.]]>
Bastian HartmannLutz FleischhauerMonica NicolauThomas Hartvig Lindkær JensenFlorin-Andrei TaranHauke Clausen-SchaumannRaphael Reuten doi:10.1038/s41596-024-00955-7 Nature Protocols, Published online: 2024-03-01; | doi:10.1038/s41596-024-00955-7 2024-03-01 Nature Protocols 10.1038/s41596-024-00955-7 https://www.nature.com/articles/s41596-024-00955-7
<![CDATA[Design and fabrication of wearable electronic textiles using twisted fiber-based threads]]> https://www.nature.com/articles/s41596-024-00956-6 Nature Protocols, Published online: 01 March 2024; doi:10.1038/s41596-024-00956-6

We provide a twisting fabrication process for fiber electrodes that can be assembled into electronic threads and then integrated in electronic textile-based wearables.]]>
Kailin ZhangXiang ShiHaibo JiangKaiwen ZengZihao ZhouPeng ZhaiLihua ZhangHuisheng Peng doi:10.1038/s41596-024-00956-6 Nature Protocols, Published online: 2024-03-01; | doi:10.1038/s41596-024-00956-6 2024-03-01 Nature Protocols 10.1038/s41596-024-00956-6 https://www.nature.com/articles/s41596-024-00956-6
<![CDATA[Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets]]> https://www.nature.com/articles/s41596-024-00957-5 Nature Protocols, Published online: 29 February 2024; doi:10.1038/s41596-024-00957-5

A user-friendly approach for segmentation and spatial analysis of large volume electron microscopy datasets with open-source software tools]]>
Andreas MüllerDeborah SchmidtJan Philipp AlbrechtLucas RieckertMaximilian OttoLeticia Elizabeth Galicia GarciaGunar FabigMichele SolimenaMartin Weigert doi:10.1038/s41596-024-00957-5 Nature Protocols, Published online: 2024-02-29; | doi:10.1038/s41596-024-00957-5 2024-02-29 Nature Protocols 10.1038/s41596-024-00957-5 https://www.nature.com/articles/s41596-024-00957-5
<![CDATA[High-throughput fabrication of antimicrobial phage microgels and example applications in food decontamination]]> https://www.nature.com/articles/s41596-024-00964-6 Nature Protocols, Published online: 27 February 2024; doi:10.1038/s41596-024-00964-6

The authors describe how to prepare antimicrobial phage-based microgels, using polystyrene film templates, and detail their use to kill antibiotic-resistant bacteria in food contamination tests as an example application.]]>
Lei TianKyle JacksonLeon HeShadman KhanMathura ThirugnanasampantharMellissa GomezFereshteh BayatTohid F. DidarZeinab Hosseinidoust doi:10.1038/s41596-024-00964-6 Nature Protocols, Published online: 2024-02-27; | doi:10.1038/s41596-024-00964-6 2024-02-27 Nature Protocols 10.1038/s41596-024-00964-6 https://www.nature.com/articles/s41596-024-00964-6