Nature Protocols Contents: Volume 12 Number 2, pp 209-451

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TABLE OF CONTENTS
February 2017, Volume 12 No 2
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PERSPECTIVES Top Advances in the field of single-particle cryo-electron microscopy over the last decade pp209 - 212 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. Joachim Frank Published online: 05 January 2017 | doi:10.1038/nprot.2017.004 Abstract | Full Text | PDF (1,094K) DNA sequencing technologies: 2006-2016 pp213 - 218 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. Elaine R Mardis Published online: 05 January 2017 | doi:10.1038/nprot.2016.182 Abstract | Full Text | PDF (635K) PROTOCOL EXTENSIONS Top Preparation and implementation of optofluidic neural probes for in vivo wireless pharmacology and optogenetics pp219 - 237 This protocol extension describes the fabrication of optofluidic neural probes and implantation for advanced in vivo pharmacology and optogenetics in freely moving rodents. Jordan G McCall et al. Published online: 05 January 2017 | doi:10.1038/nprot.2016.155 Abstract | Full Text | PDF (4,780K) Applying the INTACT method to purify endosperm nuclei and to generate parental-specific epigenome profiles pp238 - 254 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. Jordi Moreno-Romero, Juan Santos-Gonzalez, Lars Hennig and Claudia Kohler Published online: 05 January 2017 | doi:10.1038/nprot.2016.167 Abstract | Full Text | PDF (1,581K) PROTOCOLS Top A complete workflow for high-resolution spectral-stitching nanoelectrospray direct-infusion mass-spectrometry-based metabolomics and lipidomics pp255 - 273 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. Andrew D Southam et al. Published online: 12 January 2017 | doi:10.1038/nprot.2016.156 Abstract | Full Text | PDF (1,490K) The ClusPro web server for protein-protein docking pp255 - 278 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. Dima Kozakov et al. Published online: 12 January 2017 | doi:10.1038/nprot.2016.169 Abstract | Full Text | PDF (4,988K) Nonradioactive quantification of autophagic protein degradation with L-azidohomoalanine labeling pp279 - 288 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. Jigang Wang et al. Published online: 12 January 2017 | doi:10.1038/nprot.2016.160 Abstract | Full Text | PDF (605K) Genome-wide transposon screening and quantitative insertion site sequencing for cancer gene discovery in mice pp289 - 309 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. Mathias J Friedrich et al. Published online: 12 January 2017 | doi:10.1038/nprot.2016.164 Abstract | Full Text | PDF (1,642K) Precise and efficient scarless genome editing in stem cells using CORRECT pp329 - 354 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. Dylan Kwart, Dominik Paquet, Shaun Teo and Marc Tessier-Lavigne Published online: 19 January 2017 | doi:10.1038/nprot.2016.171 Abstract | Full Text | PDF (2,345K) Preparation, characterization, and in vitro dosimetry of dispersed, engineered nanomaterials pp355 - 371 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. Glen M DeLoid, Joel M Cohen, Georgios Pyrgiotakis and Philip Demokritou Published online: 19 January 2017 | doi:10.1038/nprot.2016.172 Abstract | Full Text | PDF (1,931K) Spinal cord regeneration in Xenopus laevis  pp372 - 389 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. Gabriela Edwards-Faret et al. Published online: 19 January 2017 | doi:10.1038/nprot.2016.177 Abstract | Full Text | PDF (3,722K) Use of the supported membrane tube assay system for real-time analysis of membrane fission reactions pp390 - 400 This protocol describes how to form and use membrane tubes supported on a passivated glass coverslip via hydration of a dry lipid mix in physiological buffer and subsequent flow-induced extrusion of the lipid reservoir into long membrane tubes. Srishti Dar, Sukrut C Kamerkar and Thomas J Pucadyil Published online: 26 January 2017 | doi:10.1038/nprot.2016.173 Abstract | Full Text | PDF (1,598K) Modeling and docking of antibody structures with Rosetta pp401 - 416 Weitzner et al. describe a computational protocol that uses RosettaAntibody to predict antibody structures from sequence data. SnugDock is then used for docking of these structures to protein antigens. Brian D Weitzner et al. Published online: 26 January 2017 | doi:10.1038/nprot.2016.180 Abstract | Full Text | PDF (943K) N-formylation and N-methylation of amines using metal-free N-heterocyclic carbene catalysts and CO2 as carbon source pp417 - 428 This protocol describes the environmentally benign N-formylation and N-methylation of primary and secondary amines using carbon dioxide as the carbon source, hydrosilanes as reductants and N-heterocyclic carbenes as catalysts. Felix D Bobbink, Shoubhik Das and Paul J Dyson Published online: 26 January 2017 | doi:10.1038/nprot.2016.175 Abstract | Full Text | PDF (1,408K) Strain Library Imaging Protocol for high-throughput, automated single-cell microscopy of large bacterial collections arrayed on multiwell plates pp429 - 438 SLIP is a high-throughput, automated microscopy workflow for large strain collections. Bacterial cultures are transferred to large agar pads using replicator pins, and thousands of images are automatically acquired for single-cell quantification. Handuo Shi, Alexandre Colavin, Timothy K Lee and Kerwyn Casey Huang Published online: 26 January 2017 | doi:10.1038/nprot.2016.181 Abstract | Full Text | PDF (1,749K) Conditional reprogramming and long-term expansion of normal and tumor cells from human biospecimens pp439 - 451 This protocol demonstrates how to establish primary epithelial cell cultures in vitro from healthy human tissue and human cancer samples using ROCK inhibitor and irradiated feeder cells. Xuefeng Liu et al. Published online: 26 January 2017 | doi:10.1038/nprot.2016.174 Abstract | Full Text | PDF (3,030K) Nature Protocols JOBS of the week Associate Research Scientist Columbia University Research Resource Director Weill Cornell Medicine Tenure Track Research Faculty Position: Synthetic Biology Automation INRA (French National Institute for Agricultural Research) More Science jobs from Nature Protocols EVENT More science events from

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