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donderdag 27 juli 2017

Nature Protocols Contents: Volume 12 Number 8, pp 1513 - 1721

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TABLE OF CONTENTS


August 2017, Volume 12 No 8
In this issue
Protocols
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PROTOCOLS

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Murine chronic lymph node window for longitudinal intravital lymph node imaging pp1513 - 1520
This protocol describes the surgical preparation for implantation of a chronic lymph node window in mice. This preparation allows for stable longitudinal intravital imaging of the inguinal lymph node without the need for serial surgeries while preserving lymph node blood and lymph flow.
Eelco F J Meijer et al.
Published online: 06 July 2017 | doi:10.1038/nprot.2017.045
Abstract | Full Text | PDF (4,488K)


Shear-thinning and self-healing hydrogels as injectable therapeutics and for 3D-printing pp1521 - 1541
Hydrogels, networks of water-swollen polymers, are being exploited for the local delivery of cells and biologically relevant molecules. Loebel et al. describe the preparation of supramolecular hydrogels and their characterization.
Claudia Loebel, Christopher B Rodell, Minna H Chen and Jason A Burdick
Published online: 06 July 2017 | doi:10.1038/nprot.2017.053
Abstract | Full Text | PDF (2,188K)


Use of luciferase probes to measure ATP in living cells and animals pp1542 - 1562
This protocol describes how to construct luciferase probes that are targeted to the mitochondrial matrix or the outer surface of the plasma membrane. These probes can be used to measure ATP concentrations in different cellular compartments.
Giampaolo Morciano et al.
Published online: 06 July 2017 | doi:10.1038/nprot.2017.052
Abstract | Full Text | PDF (3,352K)


Capturing suboptical dynamic structures in lipid bilayer patches formed from free-standing giant unilamellar vesicles pp1563 - 1575
Bhatia et al. describe how to prepare giant unilamellar vesicles by using complex lipid mixtures and proteins (Na+/K+-ATPase) at physiological conditions; the protocol includes subsequent imaging of lateral nanoscale structures of the membrane.
Tripta Bhatia, Flemming Cornelius and John H Ipsen
Published online: 13 July 2017 | doi:10.1038/nprot.2017.047
Abstract | Full Text | PDF (4,016K)


A fluorescence-based imaging method to measure in vitro and in vivo mitophagy using mt-Keima pp1576 - 1587
Sun et al. describe how to image and quantify mitophagy in both living cells and tissues, using the pH-sensitive fluorescent reporter mt-Keima. This protocol provides information for analysis by both confocal and super-resolution microscopy.
Nuo Sun et al.
Published online: 13 July 2017 | doi:10.1038/nprot.2017.060
Abstract | Full Text | PDF (5,349K)


Preparation of a Trp-BODIPY fluorogenic amino acid to label peptides for enhanced live-cell fluorescence imaging pp1588 - 1619
Fluorescent peptides with excellent target specificity are useful imaging probes. This protocol describes the synthesis of a tryptophan-based fluorogenic amino acid (Fmoc-Trp(C2-BODIPY)-OH) and its incorporation into peptides for live-cell imaging.
Lorena Mendive-Tapia et al.
Published online: 13 July 2017 | doi:10.1038/nprot.2017.048
Abstract | Full Text | PDF (8,110K)


O2-controllable hydrogels for studying cellular responses to hypoxic gradients in three dimensions in vitro and in vivo  pp1620 - 1638
This protocol describes how to make and use a gelatin-based hypoxia-inducible hydrogel to inject or embed tissue or cells. This enables the cellular responses to controllable hypoxic gradients to be assessed in vitro and in vivo, e.g., in mice.
Daniel M Lewis, Michael R Blatchley, Kyung Min Park and Sharon Gerecht
Published online: 20 July 2017 | doi:10.1038/nprot.2017.059
Abstract | Full Text | PDF (5,275K)


Patch-clamp technique to characterize ion channels in enlarged individual endolysosomes pp1639 - 1658
Chen, Cang and colleagues describe how to characterize intracellular ion channels using a manual patch-clamp technique on enlarged organelles such as endolysosomes.
Cheng-Chang Chen et al.
Published online: 20 July 2017 | doi:10.1038/nprot.2017.036
Abstract | Full Text | PDF (3,840K)


Mapping genome-wide transcription-factor binding sites using DAP-seq pp1659 - 1672
This protocol describes DAP-seq, a transcription-factor binding site discovery assay that can be used to produce cistrome and epicistrome maps for any organism.
Anna Bartlett et al.
Published online: 20 July 2017 | doi:10.1038/nprot.2017.055
Abstract | Full Text | PDF (586K)


Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data pp1673 - 1682
This protocol provides a computational pipeline for accurate detection and grouping of viral sequences from microbiome samples. The approach uses a set of viral protein families as bait for identifying viral sequences directly from metagenomic assemblies.
David Paez-Espino, Georgios A Pavlopoulos, Natalia N Ivanova and Nikos C Kyrpides
Published online: 27 July 2017 | doi:10.1038/nprot.2017.063
Abstract | Full Text | PDF (2,218K)


Quantitative, multiplexed workflow for deep analysis of human blood plasma and biomarker discovery by mass spectrometry pp1683 - 1701
This protocol describes the deep-scale analysis of the blood plasma proteome. By combining abundant protein depletion, sample multiplexing with isobaric labeling and fractionation, this enables rapid quantification of >4,500 plasma proteins.
Hasmik Keshishian et al.
Published online: 27 July 2017 | doi:10.1038/nprot.2017.054
Abstract | Full Text | PDF (961K)


Chemoenzymatic synthesis of glycoengineered IgG antibodies and glycosite-specific antibody-drug conjugates pp1702 - 1721
Glycoengineering of IgG antibodies and glycosite-specific antibody-drug conjugates is an important tool for enhancing their therapeutic efficacy. Tang et al. describe a protocol for efficient and homogeneous chemoenzymatic antibody glycoengineering.
Feng Tang, Lai-Xi Wang and Wei Huang
Published online: 27 July 2017 | doi:10.1038/nprot.2017.058
Abstract | Full Text | PDF (3,371K)

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