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Nature Protocols is an interactive online resource for all laboratory protocols relevant to biological and biomedical research. Nature Protocols includes a free-to-access community site, 'Protocols Network', containing protocols that are posted directly o



 



Advances in the field of single-particle cryo-electron microscopy over the last decade

2017-01-05

Single-particle cryo-electron microscopy has enabled the structures of large proteins to be elucidated. This Perspective discusses technological improvements in this technique, focusing particularly on the past decade and likely future developments.



DNA sequencing technologies: 2006–2016

2017-01-05

In this Perspective, Elaine Mardis reviews a decade of DNA sequencing technology, from the introduction of Next-Generation Sequencing to single-molecule sequencing, including future applications that promise to further biological and biomedical research.



Preparation and implementation of optofluidic neural probes for in vivo wireless pharmacology and optogenetics

2017-01-05

This protocol extension describes the fabrication of optofluidic neural probes and implantation for advanced in vivo pharmacology and optogenetics in freely moving rodents.



Applying the INTACT method to purify endosperm nuclei and to generate parental-specific epigenome profiles

2017-01-05

Moreno-Romero et al. describe how to apply the INTACT method to purify endosperm nuclei from Arabidopsis. Purified nuclei can be used for ChIP-seq analysis or bisulfite sequencing.



A complete workflow for high-resolution spectral-stitching nanoelectrospray direct-infusion mass-spectrometry-based metabolomics and lipidomics

2017-01-12

The metabolome or lipidome of different phenotypes can be compared using this protocol. A complete workflow for direct-infusion mass spectrometry using nanoelectrospray ionization and spectral stitching with the Galaxy platform is described.



The ClusPro web server for protein–protein docking

2017-01-12

ClusPro is a web server that performs rigid-body docking of two proteins by sampling billions of conformations. Low-energy docked structures are clustered, and centers of the largest clusters are used as likely models of the complex.



Nonradioactive quantification of autophagic protein degradation with L-azidohomoalanine labeling

2017-01-12

This protocol from Wang et al. describes a pulse–chase method to investigate autophagic protein degradation through click labeling of long-lived proteins. This is a safer alternative to similar classic methods that use radioactive labeling.



Genome-wide transposon screening and quantitative insertion site sequencing for cancer gene discovery in mice

2017-01-12

Friedrich et al. describe their toolkit for transposon-based insertional mutagenesis in mice for discovering cancer genes. Genome-wide transposon insertion sites are identified, mapped and quantified using QiSeq.



Precise and efficient scarless genome editing in stem cells using CORRECT

2017-01-19

CORRECT is a method comprising two variants, re-Guide and re-Cas, that enables efficient and scarless CRISPR/Cas9-based genome editing in hPSCs by introducing blocking mutations that hamper the re-editing of modified loci by Cas9.



Preparation, characterization, and in vitro dosimetry of dispersed, engineered nanomaterials

2017-01-19

This protocol provides details for dispersion and colloidal characterization of suspended engineered nanomaterials, and computational fate and transport modeling to accurately calculate dose metrics for in vitro cellular nanotoxicology experiments.



Spinal cord regeneration in Xenopus laevis

2017-01-19

Detailed guides for the husbandry of Xenopus laevis and protocols for making reproducible spinal cord injury models and subsequent study of neural stem/progenitor cells during regeneration are described.