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donderdag 23 februari 2017

Nature Protocols Contents: Volume 12 Number 3, pp 453-637

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Nature Protocols

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TABLE OF CONTENTS


March 2017, Volume 12 No 3
In this issue
Perspective
Protocols
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PERSPECTIVE

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Turning single-molecule localization microscopy into a quantitative bioanalytical tool pp453 - 460
In the last decade, super-resolution microscopy has enabled us to image cells with unprecedented detail. This Perspective discusses how the field can move beyond images to extract quantitative biological information from multidimensional SMLM data.
Philip R Nicovich, Dylan M Owen and Katharina Gaus
Published online: 02 February 2017 | doi:10.1038/nprot.2016.166
Abstract | Full Text | PDF (1,627K)

PROTOCOLS

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Synthesis of a highly Mg2+-selective fluorescent probe and its application to quantifying and imaging total intracellular magnesium pp461 - 471
Specific and sensitive tools for quantifying intracellular magnesium cations are needed in biochemical research. This protocol describes the synthesis and use of a fluorescent Mg2+ probe based on diaza-18-crown-6-hydroxyquinoline.
Azzurra Sargenti et al.
Published online: 02 February 2017 | doi:10.1038/nprot.2016.183
Abstract | Full Text | PDF (1,180K)


Preparation of visible-light-activated metal complexes and their use in photoredox/nickel dual catalysis pp472 - 492
This protocol describes the synthesis of two photoredox catalysts, [Ir{dF(CF3)2ppy}2(bpy)]PF6 and [Ru(bpy)3](PF6)2, that are activated by visible light. These single-electron transfer agents are used to facilitate diverse synthetic transformations.
Christopher B Kelly et al.
Published online: 02 February 2017 | doi:10.1038/nprot.2016.176
Abstract | Full Text | PDF (2,930K)


Cu-catalyzed enantioselective allylic alkylation with organolithium reagents pp493 - 505
Cu-catalyzed asymmetric allylic alkylation (AAA) is used in the synthesis of pharmaceuticals and natural products. This protocol uses organolithium reagents in the Cu-catalyzed AAA of allylic substrates with Taniaphos or phosphoramidites as ligands.
Valentin Hornillos et al.
Published online: 02 February 2017 | doi:10.1038/nprot.2016.179
Abstract | Full Text | PDF (2,290K)


Using connectome-based predictive modeling to predict individual behavior from brain connectivity pp506 - 518
This protocol describes how to develop linear models to predict individual behavior from brain connectivity data with proper cross-validation, and how to use an online tool to visualize the most predictive features of the models.
Xilin Shen et al.
Published online: 09 February 2017 | doi:10.1038/nprot.2016.178
Abstract | Full Text | PDF (3,129K)


A modular approach to the design, fabrication, and characterization of muscle-powered biological machines pp519 - 533
This protocol describes steps to design and generate biological machines. Ring-shaped skeletal muscle actuators are cultured and coupled to a 3D-printed skeleton. Contraction of muscle rings can be controlled by optical or electrical stimulation.
Ritu Raman, Caroline Cvetkovic and Rashid Bashir
Published online: 09 February 2017 | doi:10.1038/nprot.2016.185
Abstract | Full Text | PDF (2,851K)


Genome-wide base-resolution mapping of DNA methylation in single cells using single-cell bisulfite sequencing (scBS-seq) pp534 - 547
Single-cell bisulfite sequencing (scBS-seq) is a cost-effective method for surveying CpG methylation across genomes of single cells. It gives higher coverage than other methods, is automatable and is compatible with parallel RNA-seq from the same cell.
Stephen J Clark et al.
Published online: 09 February 2017 | doi:10.1038/nprot.2016.187
Abstract | Full Text | PDF (680K)


Detecting natural adaptation of the Streptococcus thermophilus CRISPR-Cas systems in research and classroom settings pp547 - 565
The authors describe here a core protocol with three variants, in which S. thermophilus cells are challenged with phages to study the adaptive nature of this bacterial CRISPR system. In addition, they elaborate on the use of this protocol in undergraduate education.
Alexander P Hynes et al.
Published online: 16 February 2017 | doi:10.1038/nprot.2016.186
Abstract | Full Text | PDF (1,910K)


Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq pp566 - 580
Geo-seq combines laser capture microdissection and single-cell RNA-seq technology to enable transcriptome analysis of small quantities of cells from defined geographical locations.
Jun Chen et al.
Published online: 16 February 2017 | doi:10.1038/nprot.2017.003
Abstract | Full Text | PDF (2,967K)


Genome editing using FACS enrichment of nuclease-expressing cells and indel detection by amplicon analysis pp581 - 603
This protocol provides a pipeline for increasing and evaluating the efficiency of genome editing by ZFNs, TALENs or CRISPR-Cas9 that includes enrichment of nuclease-expressing cells by FACS, followed by Indel Detection by Amplicon Analysis (IDAA).
Lindsey A Lonowski et al.
Published online: 16 February 2017 | doi:10.1038/nprot.2016.165
Abstract | Full Text | PDF (1,997K)


Metal- and additive-free photoinduced borylation of haloarenes pp604 - 610
This protocol describes a simple, metal- and additive-free method to convert haloarenes directly to boronic acids and esters. These can be used to synthesize organic compounds for applications including drug discovery and materials science.
Adelphe M Mfuh, Brett D Schneider, Westley Cruces and Oleg V Larionov
Published online: 23 February 2017 | doi:10.1038/nprot.2016.184
Abstract | Full Text | PDF (390K)


Using hiCLIP to identify RNA duplexes that interact with a specific RNA-binding protein pp611 - 637
hiCLIP is an NGS-based method for identifying RNA duplexes that interact with an RNA-binding protein of interest. A unique feature is the inclusion of a linker that allows both parts of the duplex to be identified with certainty.
Yoichiro Sugimoto, Anob M Chakrabarti, Nicholas M Luscombe and Jernej Ule
Published online: 23 February 2017 | doi:10.1038/nprot.2016.188
Abstract | Full Text | PDF (1,535K)

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