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donderdag 12 juli 2018

Nature Protocols Contents: Volume 13 Number 7

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Nature Protocols

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TABLE OF CONTENTS

July 2018 Volume 13, Issue 7

Correspondence
Protocols
Amendments & Corrections
 
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Correspondence

 

Defining distance restraints in HADDOCK    p1503
Alexandre M. J. J. Bonvin, Ezgi Karaca, Panagiotis L. Kastritis & João P. G. L. M. Rodrigues
doi:10.1038/s41596-018-0017-6

Reply to ‘Defining distance restraints in HADDOCK’    pp1503 - 1505
Zsuzsanna Orbán-Németh, Rebecca Beveridge, David M. Hollenstein, Evelyn Rampler, Thomas Stranzl et al.
doi:10.1038/s41596-018-0018-5

Protocols

 

Standardized assays for determining the catalytic activity and kinetics of peroxidase-like nanozymes    pp1506 - 1520
Bing Jiang, Demin Duan, Lizeng Gao, Mengjie Zhou, Kelong Fan et al.
doi:10.1038/s41596-018-0001-1

Nanozymes are nanomaterials that possess intrinsic enzyme-like properties and are increasingly used in various biological applications. This protocol describes standardized assays of the catalytic activity and kinetics of peroxidase-like nanozymes.

 

Surface-wetting characterization using contact-angle measurements    pp1521 - 1538
Tommi Huhtamäki, Xuelin Tian, Juuso T. Korhonen & Robin H. A. Ras
doi:10.1038/s41596-018-0003-z

The wettability of a surface can be determined by measurement of the contact angle between a water droplet and the surface. This protocol describes sessile-drop goniometry for the measurement of advancing and receding contact angles.

 

Nature Protocols
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Evoking and tracking zebrafish eye movement in multiple larvae with ZebEyeTrack    pp1539 - 1568
Florian A. Dehmelt, Adam von Daranyi, Claire Leyden & Aristides B. Arrenberg
doi:10.1038/s41596-018-0002-0

This protocol describes procedures for evoking and tracking zebrafish eye movement, integrating optogenetics and calcium imaging, and analyzing optokinetic data using the customizable, LabVIEW-based software ZebEyeTrack.

 

Programming DNA origami assembly for shape-resolved nanomechanical imaging labels    pp1569 - 1585
Jie Chao, Honglu Zhang, Yikang Xing, Qian Li, Huajie Liu et al.
doi:10.1038/s41596-018-0004-y

This protocol describes the design of DNA origami-based shape IDs and their applications in the identification of single-nucleotide polymorphisms using atomic force microscopy.

 

In vitro generation of mouse polarized embryo-like structures from embryonic and trophoblast stem cells    pp1586 - 1602
Sarah Ellys Harrison, Berna Sozen & Magdalena Zernicka-Goetz
doi:10.1038/s41596-018-0005-x

This protocol describes how to direct the assembly of extra-embryonic trophoblast stem cells and embryonic stem cells to recapitulate post-implantation mouse embryogenesis.

 

High-throughput imaging flow cytometry by optofluidic time-stretch microscopy    pp1603 - 1631
Cheng Lei, Hirofumi Kobayashi, Yi Wu, Ming Li, Akihiro Isozaki et al.
doi:10.1038/s41596-018-0008-7

This protocol describes how to build an optical time-stretch microscope and a cell-focusing microfluidic device for high-throughput (>10,000 cells per s) single-cell imaging by optofluidic time-stretch microscopy.

 

Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography–mass spectrometry    pp1632 - 1661
Philipp Mertins, Lauren C. Tang, Karsten Krug, David J. Clark, Marina A. Gritsenko et al.
doi:10.1038/s41596-018-0006-9

This protocol describes a workflow for multiplexed deep-scale, quantitative proteome and phosphoproteome analysis of tumor tissue samples. The procedure includes step-by-step instructions for all stages, from sample preparation to data analysis.

 

Directed differentiation of human induced pluripotent stem cells into mature kidney podocytes and establishment of a Glomerulus Chip    pp1662 - 1685
Samira Musah, Nikolaos Dimitrakakis, Diogo M. Camacho, George M. Church & Donald E. Ingber
doi:10.1038/s41596-018-0007-8

Ingber and colleagues describe how to generate kidney glomerular podocytes from human pluripotent stem cells and how to engineer a human kidney Glomerulus Chip.

 

Sucrose preference test for measurement of stress-induced anhedonia in mice    pp1686 - 1698
Meng-Ying Liu, Chun-Yu Yin, Li-Juan Zhu, Xian-Hui Zhu, Chu Xu et al.
doi:10.1038/s41596-018-0011-z

This protocol describes how to carry out the sucrose preference test (SPT) in a standardized way to reduce data variability. The SPT is a widely used behavioral assay to monitor depression-related behavior in rodents.

 

Integrated analysis of anatomical and electrophysiological human intracranial data    pp1699 - 1723
Arjen Stolk, Sandon Griffin, Roemer van der Meij, Callum Dewar, Ignacio Saez et al.
doi:10.1038/s41596-018-0009-6

This protocol describes how to computationally process, integrate, visualize, and analyze anatomical and functional data obtained during intracranial electroencephalography (iEEG) of the human brain.

 

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Date: Tuesday, July 31, 2018

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Amendments & Corrections

 

Author Correction: Structural prediction of protein models using distance restraints derived from cross-linking mass spectrometry data    p1724
Zsuzsanna Orbán-Németh, Rebecca Beveridge, David M Hollenstein, Evelyn Rampler, Thomas Stranzl et al.
doi:10.1038/s41596-018-0024-7

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