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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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July 2018 Volume 13, Issue 7

Amendments & Corrections
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Defining distance restraints in HADDOCK    p1503
Alexandre M. J. J. Bonvin, Ezgi Karaca, Panagiotis L. Kastritis & João P. G. L. M. Rodrigues

Reply to ‘Defining distance restraints in HADDOCK’    pp1503 - 1505
Zsuzsanna Orbán-Németh, Rebecca Beveridge, David M. Hollenstein, Evelyn Rampler, Thomas Stranzl et al.



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.

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

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

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.

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

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.

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.

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

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.

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.

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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Nature Research Custom Media presents a webcast on: Optical Trapping of Ion Coulomb Crystals

Date: Tuesday, July 31, 2018

Join our webcast to understand the trapping of neutral and charged atoms and how to exploit optically trapped ions to investigate quantum-phase transitions.

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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.

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