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donderdag 30 november 2017

Nature Protocols Contents: Volume 12 Number 12, pp 2447-2659

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Nature Protocols


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December 2017, Volume 12 No 12
In this issue
Protocol Extension

Analyze Large and Small Molecule Inhibitors in a Single Homogeneous Assay

Want to analyze downstream cell signaling events impacted by both large and small molecule inhibitors in a single assay? Learn about a no-wash platform for screening antibodies and small molecule inhibitors, in this example used to characterize chemokine receptor inhibitors. 

Download Application Note

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Identification of RNA-binding domains of RNA-binding proteins in cultured cells on a system-wide scale with RBDmap pp2447 - 2464
Here the authors provide an extension to their earlier RNA interactome capture protocol. This Protocol Extension describes RBDmap[mdash]a method to identify the regions of RNA-binding proteins engaged in native interactions with RNA, in a proteome-wide manner.
Alfredo Castello et al.
Published online: 02 November 2017 | doi:10.1038/nprot.2017.106
Abstract | Full Text | PDF (2,673K)



A high-throughput in vivo screening method in the mouse for identifying regulators of metastatic colonization pp2465 - 2477
In this protocol, the authors present an experimental metastasis assay in which cancer cells are injected into the tail vein of a mouse, and the resulting secondary organ colonization is assessed, primarily in the lung, 10 d later.
Anneliese O Speak et al.
Published online: 02 November 2017 | doi:10.1038/nprot.2017.118
Abstract | Full Text | PDF (2,540K)

Chromatin-state discovery and genome annotation with ChromHMM pp2478 - 2492
This protocol describes how to use ChromHMM, a robust open-source software package that enables the learning of chromatin states, annotates their occurrences across the genome, and facilitates their biological interpretation.
Jason Ernst and Manolis Kellis
Published online: 09 November 2017 | doi:10.1038/nprot.2017.124
Abstract | Full Text | PDF (1,644K)

Compartmentalized partnered replication for the directed evolution of genetic parts and circuits pp2493 - 2512
This protocol describes the procedures for compartmentalized partnered replication (CPR), an emulsion-based directed evolution method for the generation of proteins, genetic elements, and genetic circuits with improved or altered function.
Zhanar Abil et al.
Published online: 09 November 2017 | doi:10.1038/nprot.2017.119
Abstract | Full Text | PDF (1,639K)

Production of knock-in mice in a single generation from embryonic stem cells pp2513 - 2530
This protocol describes the generation of mice entirely derived from genome-edited embryonic stem cells, enabling the production of transgenic mice in a single generation.
Hideki Ukai, Hiroshi Kiyonari and Hiroki R Ueda
Published online: 16 November 2017 | doi:10.1038/nprot.2017.110
Abstract | Full Text | PDF (1,783K)

Multimodal profiling of single-cell morphology, electrophysiology, and gene expression using Patch-seq pp2531 - 2553
This protocol describes how to integrate whole-cell patch-clamp in single neurons from mouse brain tissue slices with single-cell RNA sequencing and morphological recovery.
Cathryn R Cadwell et al.
Published online: 16 November 2017 | doi:10.1038/nprot.2017.120
Abstract | Full Text | PDF (7,514K)

Chemical synthesis of membrane proteins by the removable backbone modification method pp2554 - 2569
This protocol describes how to chemically synthesize membrane proteins through the installation of solubilizing removable backbone modification tags into hydrophobic transmembrane peptides. The implementation of the protocol is demonstrated by the chemical synthesis of phosphorylated M2 (M2-pSer64), a 97-aa proton channel protein from the influenza A virus. The synthesis of M2-pSer64 at milligram scale takes [sim]200 working hours (excluding the time for lyophilizations).
Shan Tang et al.
Published online: 16 November 2017 | doi:10.1038/nprot.2017.129
Abstract | Full Text | PDF (1,381K)

Nature Collection: 2017 Nobel Prize in Chemistry 

Nature Research present this Collection of articles celebrating the 2017 Nobel Prize in Chemistry to Jacques Dubochet, Joachim Frank and Richard Henderson, recognised "for developing cryo-electron microscopy for the high-resolution structure determination of biomolecules in solution". 

Access the collection here >>

Produced with support from 
Thermo Fisher Scientific

Langmuir-Blodgett nanotemplates for protein crystallography pp2570 - 2589
Protein crystallization still presents a challenge for X-ray crystallography. This protocol describes the Langmuir-Blodgett nanotemplate method, in which 2D protein LB nanotemplates trigger formation of 3D protein crystals by hanging-drop vapor diffusion.
Eugenia Pechkova and Claudio Nicolini
Published online: 30 November 2017 | doi:10.1038/nprot.2017.108
Abstract | Full Text | PDF (7,516K)

Visualizing endocytic recycling and trafficking in live neurons by subdiffractional tracking of internalized molecules pp2590 - 2622
This protocol describes a pulse-chase approach to studying activity-dependent internalization of fluorescent ligands into endocytic compartments using subdiffractional single-particle tracking in live hippocampal neurons.
Merja Joensuu et al.
Published online: 30 November 2017 | doi:10.1038/nprot.2017.116
Abstract | Full Text | PDF (5,838K)

Preparation of viable adult ventricular myocardial slices from large and small mammals pp2623 - 2639
This protocol describes how to obtain 100- to 400-[mu]m-thick slices of a living myocardium from rodents, pigs, humans and dogs that retain the native multicellularity, architecture and physiology of the heart.
Samuel A Watson et al.
Published online: 30 November 2017 | doi:10.1038/nprot.2017.139
Abstract | Full Text | PDF (9,418K)

Deriving genotypes from RAD-seq short-read data using Stacks pp2640 - 2659
In this protocol, the authors provide a strategy and set of methods to analyze restriction-site-associated DNA-sequencing (RAD-seq) data using Stacks, enabling the genome-wide discovery and genotyping of SNPs across a range of systems.
Nicolas C Rochette and Julian M Catchen
Published online: 30 November 2017 | doi:10.1038/nprot.2017.123
Abstract | Full Text | PDF (1,503K)

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