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vrijdag 28 april 2017

Nature Protocols Contents: Volume 12 Number 5 pp 865-1102

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Nature Protocols

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May 2017, Volume 12 No 5
In this issue
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On-chip human microvasculature assay for visualization and quantification of tumor cell extravasation dynamics pp865 - 880
This protocol describes how to set up and use an in vitro model of the human microcirculation with the capability to recapitulate discrete steps of early metastatic seeding, including tumor cell arrest and transendothelial migration.
Michelle B Chen et al.
Published online: 30 March 2017 | doi:10.1038/nprot.2017.018
Abstract | Full Text | PDF (4,319K)

Analyzing trapped protein complexes by Virotrap and SFINX pp881 - 898
This protocol enables the study of protein complexes by trapping them in virus-like particles and thereby preserving cellular integrity. The Virotrap protocol is complemented by SFINX, an online data analysis tool for interactomics studies.
Kevin Titeca et al.
Published online: 30 March 2017 | doi:10.1038/nprot.2017.014
Abstract | Full Text | PDF (1,897K)

Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions pp899 - 915
Li et al. provide a protocol for long-read ChIA-PET, a technique for mapping chromatin interactions. The longer paired-end tags, which are generated by tagmentation, provide sufficient coverage to determine haplotype-specific chromatin interactions at single-nucleotide resolution.
Xingwang Li et al.
Published online: 30 March 2017 | doi:10.1038/nprot.2017.012
Abstract | Full Text | PDF (1,017K)

Diverse protocols for correlative super-resolution fluorescence imaging and electron microscopy of chemically fixed samples pp916 - 946
Four different techniques for preparing and acquiring super-resolution CLEM data sets on aldehyde-fixed specimens are provided: Tokuyasu cryosectioning; whole-cell mount; cell unroofing and platinum replication; and resin embedding and sectioning.
Benjamin G Kopek et al.
Published online: 06 April 2017 | doi:10.1038/nprot.2017.017
Abstract | Full Text | PDF (9,040K)

Antifungal drug testing by combining minimal inhibitory concentration testing with target identification by gas chromatography-mass spectrometry pp947 - 963
By combining minimal inhibitory concentration testing with GC-MS-based pathway analysis, it is possible to identify which enzymes in the ergosterol biosynthesis pathway are being targeted by potential new antifungal substances.
Christoph Muller, Ulrike Binder, Franz Bracher and Martin Giera
Published online: 06 April 2017 | doi:10.1038/nprot.2017.005
Abstract | Full Text | PDF (1,002K)

Preparation of molecularly imprinted polymers specific to glycoproteins, glycans and monosaccharides via boronate affinity controllable-oriented surface imprinting pp964 - 987
This protocol describes how to produce molecularly imprinted polymers, synthetic receptors that can be produced with antibody-like binding properties. They are easier and cheaper to produce than antibodies and lectins.
Rongrong Xing et al.
Published online: 06 April 2017 | doi:10.1038/nprot.2017.015
Abstract | Full Text | PDF (2,411K)

Nature Milestones: Antibodies

Nature Milestones:Antibodies chronicles the history of antibodies from their earliest description in antisera, their structure, generation and function, right through to their recent application in cancer immunotherapy. It also includes a timeline and a collection of seminal papers reproduced from Springer Nature.

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Strategic and practical guidelines for successful structured illumination microscopy pp988 - 1010
This protocol describes the preparation of calibration bead slides, their use and additional strategies to reduce artifacts of structured illumination microscopy that will allow researchers to exploit the technique's full potential for biological applications.
Justin Demmerle et al.
Published online: 13 April 2017 | doi:10.1038/nprot.2017.019
Abstract | Full Text | PDF (9,001K)

Quantitative 3D structured illumination microscopy of nuclear structures pp1011 - 1028
This protocol describes how to prepare samples for labeling nuclei of cultured mammalian cells for 3D structured illumination microscopy of nuclear structures. Image acquisition, registration and downstream image analysis are also described.
Felix Kraus et al.
Published online: 13 April 2017 | doi:10.1038/nprot.2017.020
Abstract | Full Text | PDF (5,249K)

Generation of multipotent induced cardiac progenitor cells from mouse fibroblasts and potency testing in ex vivo mouse embryos pp1029 - 1054
Expandable and multipotent induced cardiac progenitor cells (iCPCs) are generated from mouse adult fibroblasts using forced expression of Mesp1, Tbx5, Gata4, Nkx2.5 and Baf60c and activation of the Wnt and JAK/STAT signaling pathway. Furthermore, embryonic potency of iCPCs is tested ex vivo.
Pratik A Lalit, Adriana M Rodriguez, Karen M Downs and Timothy J Kamp
Published online: 20 April 2017 | doi:10.1038/nprot.2017.021
Abstract | Full Text | PDF (8,338K)

Modular low-light microscope for imaging cellular bioluminescence and radioluminescence pp1055 - 1076
Bioluminescence and radioluminescence are both dim phenomena that require a highly sensitive microscope for imaging at the cellular level. This protocol describes how to construct a modular low-light microscope for imaging these events.
Tae Jin Kim, Silvan Turkcan and Guillem Pratx
Published online: 20 April 2017 | doi:10.1038/nprot.2017.008
Abstract | Full Text | PDF (4,037K)

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Tissue-engineered 3D human lymphatic microvascular network for in vitro studies of lymphangiogenesis pp1077 - 1088
This protocol describes how to generate a human 3D lymphatic capillary network from primary cells without the use of synthetic scaffolds or exogenous factors. The tissue is stable over many weeks and accurately recapitulates in vivo human dermal lymphatic microvasculature.
Laure Gibot et al.
Published online: 27 April 2017 | doi:10.1038/nprot.2017.025
Abstract | Full Text | PDF (5,663K)

Assessment of engineered cells using CellNet and RNA-seq pp1089 - 1102
CellNet is a computational platform designed to improve cell fate engineering protocols. Here the authors demonstrate how to apply CellNet to RNA-seq data and how to build a completely new CellNet platform applicable to new species or cell types/tissues.
Arthur H Radley et al.
Published online: 27 April 2017 | doi:10.1038/nprot.2017.022
Abstract | Full Text | PDF (1,475K)

Nature Protocols
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