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vrijdag 14 september 2018

Nature Protocols Contents: Volume 13 Number 9

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Nature Protocols
TABLE OF CONTENTS

September 2018 Volume 13, Issue 9

Protocols
 
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Protocols

 

High-throughput and high-sensitivity phosphoproteomics with the EasyPhos platform    pp1897 - 1916
Sean J. Humphrey, Ozge Karayel, David E. James & Matthias Mann
doi:10.1038/s41596-018-0014-9

This protocol describes the EasyPhos platform, a high-throughput and user-friendly workflow for reliable identification of phosphopeptides from small amounts (<200 μg) of sample.

 

A three-dimensional engineered heterogeneous tumor model for assessing cellular environment and response    pp1917 - 1957
Darren Rodenhizer, Teresa Dean, Bin Xu, Dan Cojocari & Alison P. McGuigan
doi:10.1038/s41596-018-0022-9

This protocol describes TRACER, a 3D cell culture system that enables the assembly of heterogeneous model tumors or tissues that easily disassemble for rapid analysis of different cell populations from particular microenvironments.

 

PhIP-Seq characterization of serum antibodies using oligonucleotide-encoded peptidomes    pp1958 - 1978
Divya Mohan, Daniel L. Wansley, Brandon M. Sie, Muhammad S. Noon, Alan N. Baer et al.
doi:10.1038/s41596-018-0025-6

Phage immunoprecipitation sequencing (PhIP-Seq) is a method for analyzing antibody-repertoire binding specificities. Phage-displayed oligonucleotide libraries encoding peptidomes are immunoprecipitated and analyzed by high-throughput DNA-Seq.

 

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Fit-free analysis of fluorescence lifetime imaging data using the phasor approach    pp1979 - 2004
Suman Ranjit, Leonel Malacrida, David M. Jameson & Enrico Gratton
doi:10.1038/s41596-018-0026-5

This protocol describes fit-free analysis of fluorescence lifetime imaging microscopy (FLIM) data using the phasor approach. Pixel-by-pixel decays are transformed to the phasor space, and then the clusters can be connected to the image by the reciprocity rules of the phasor plots.

 

Accessing crystal–crystal interaction forces with oriented nanocrystal atomic force microscopy probes    pp2005 - 2030
Xin Zhang, Yang He, Jia Liu, Mark E. Bowden, Libor Kovarik et al.
doi:10.1038/s41596-018-0027-4

This protocol describes focused ion beam–milling approaches for fabricating oriented single-nanocrystal atomic force microscopy probes, as well as how to measure direction-specific interaction forces between nanocrystals in solution and in vacuum.

 

Configuration of electrical spinal cord stimulation through real-time processing of gait kinematics     pp2031 - 2061
Marco Capogrosso, Fabien B. Wagner, Jerome Gandar, Eduardo Martin Moraud, Nikolaus Wenger et al.
doi:10.1038/s41596-018-0030-9

This protocol describes how to configure targeted spinal cord stimulation using electromyographic recordings and real-time processing of gait kinematics to enable voluntary control of specific leg movements in rats and nonhuman primates.

 

Generation and assembly of human brain region–specific three-dimensional cultures    pp2062 - 2085
Steven A. Sloan, Jimena Andersen, Anca M. Paşca, Fikri Birey & Sergiu P. Paşca
doi:10.1038/s41596-018-0032-7

Neural differentiation and self-organization of hPSCs are induced by culture in suspension. Neural spheroids are then differentiated into dorsal or ventral forebrain spheroids that can be combined to obtain functionally integrated human assembloids.

 

Preparation of asymmetric phospholipid vesicles for use as cell membrane models    pp2086 - 2101
Milka Doktorova, Frederick A. Heberle, Barbara Eicher, Robert F. Standaert, John Katsaras et al.
doi:10.1038/s41596-018-0033-6

Improved and robust procedures for a cyclodextrin-mediated preparation of asymmetric large unilamellar vesicles of diverse lipid compositions and the characterization of their degree of asymmetry and individual leaflet compositions with NMR and GC.

 

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PEG-4MAL hydrogels for human organoid generation, culture, and in vivo delivery    pp2102 - 2119
Ricardo Cruz-Acuña, Miguel Quirós, Sha Huang, Dorothée Siuda, Jason R. Spence et al.
doi:10.1038/s41596-018-0036-3

This protocol describes how to use a fully defined, synthetic hydrogel to support the in vitro generation and culture of human organoids derived from pluripotent stem cells and the in vivo delivery of hydrogel-encapsulated organoids into mouse colon.

 

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