Nature Protocols Contents: Volume 11 Number 8, pp 1327 - 1571

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TABLE OF CONTENTS
August 2016, Volume 11 No 8
	In this issue Editorial Protocols
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EDITORIAL Top Ten years of Nature Protocols  p1327 On 27th June 2006, ten years ago this week, Nature Protocols officially published its first batch of protocols. In celebration of this fact, we are breaking with tradition to publish our first non-protocol articles: this editorial, as well as an upcoming series of Perspectives that showcase methodological developments over the last decade. Published online: 30 June 2016 | doi:10.1038/nprot.2016.115 Full Text | PDF (432K) PROTOCOLS Top Solid-phase microextraction to determine micropollutant-macromolecule partition coefficients pp1328 - 1344 Interaction with macromolecules affects the environmental availability of a micropollutant. With solid-phase microextraction of radiolabeled micropollutants, the partition coefficient can be determined at environmentally relevant concentrations. Helen L Bridle, Minne B Heringa and Andrea I Schafer Published online: 30 June 2016 | doi:10.1038/nprot.2016.068 Abstract | Full Text | PDF (1,146K) In vivo monitoring of cellular energy metabolism using SoNar, a highly responsive sensor for NAD+/NADH redox state pp1345 - 1359 SoNar is a fluorescent biosensor that is able to monitor NAD+/NADH redox state in living cells and in vivo. This protocol describes how to use SoNar for single cell imaging, high-throughput chemical screening, and in vivo imaging in mice. Yuzheng Zhao et al. Published online: 30 June 2016 | doi:10.1038/nprot.2016.074 Abstract | Full Text | PDF (2,645K) Single-cell in vivo imaging of adult neural stem cells in the zebrafish telencephalon pp1360 - 1370 This protocol describes the labeling and imaging of single adult neural stem cells and their progeny in zebrafish in vivo to investigate their contribution to neurogenesis in the intact and regenerating brain. Joana S Barbosa, Rossella Di Giaimo, Magdalena Gotz and Jovica Ninkovic Published online: 30 June 2016 | doi:10.1038/nprot.2016.077 Abstract | Full Text | PDF (5,359K) Preparative scale and convenient synthesis of a water-soluble, deep cavitand pp1371 - 1387 Cavitands are container molecules that have diverse applications from synthetic chemistry to molecular recognition. Deep, water-soluble cavitands based on a resorcinarene framework are prepared using this protocol. Simone Mosca, Yang Yu and Julius Rebek, Jr Published online: 07 July 2016 | doi:10.1038/nprot.2016.078 Abstract | Full Text | PDF (2,168K) Rapid and simple isolation of vascular, epidermal and mesophyll cells from plant leaf tissue pp1388 - 1395 Endo et al. describe a protocol for the isolation of mesophyll, vascular and epidermal tissues from Arabidopsis leaves. The protocol can be applied to tissue-specific transcriptome, methylome and proteome studies in a number of crop plants. Motomu Endo, Hanako Shimizu and Takashi Araki Published online: 07 July 2016 | doi:10.1038/nprot.2016.083 Abstract | Full Text | PDF (2,506K) Laboratory breeding of the short-lived annual killifish Nothobranchius furzeri  pp1396 - 1413 Nothobranchius furzeri is an important new model organism. This Protocol aims to help laboratories establish healthy breeding colonies of this species and to standardize husbandry methods, which differ from those for other model fish because of dry incubation of the eggs. Matej Polacik, Radim Blazek and Martin Reichard Published online: 07 July 2016 | doi:10.1038/nprot.2016.080 Abstract | Full Text | PDF (3,385K) Protein-observed 19F-NMR for fragment screening, affinity quantification and druggability assessment pp1414 - 1427 Labeling of proteins with fluorinated amino acids and using fluorine-19 NMR greatly simplifies the NMR spectrum. Changes in the spectrum on interaction with ligands makes protein-observed fragment-based drug screening possible. Clifford T Gee et al. Published online: 14 July 2016 | doi:10.1038/nprot.2016.079 Abstract | Full Text | PDF (1,666K) High-mass-resolution MALDI mass spectrometry imaging of metabolites from formalin-fixed paraffin-embedded tissue pp1428 - 1443 Formalin-fixed paraffin embedding (FFPE) of tissues has been assumed to alter the metabolite content or chemical state, hampering metabolomics studies. Here, Ly et al. describe reproducible metabolomic analysis of FFPE samples by mass spectrometry imaging. Alice Ly et al. Published online: 14 July 2016 | doi:10.1038/nprot.2016.081 Abstract | Full Text | PDF (3,738K) A real-time fluorometric method for the simultaneous detection of cell death type and rate pp1444 - 1454 This protocol describes a fluorescence-based assay to measure cell death rate and type (either caspase-dependent apoptosis or caspase-independent necrosis). The method allows for the detection of modality switches between apoptosis and necrosis over time. Sasker Grootjans et al. Published online: 14 July 2016 | doi:10.1038/nprot.2016.085 Abstract | Full Text | PDF (722K) Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq) pp1455 - 1476 Mahat et al. describe how to map the genome-wide positions of active RNA polymerases using a modified nuclear run-on approach called PRO-seq. Details for PRO-cap, a modification that identifies transcription start sites, are also included. Dig Bijay Mahat et al. Published online: 21 July 2016 | doi:10.1038/nprot.2016.086 Abstract | Full Text | PDF (1,415K) A highly multiplexed and sensitive RNA-seq protocol for simultaneous analysis of host and pathogen transcriptomes pp1477 - 1491 This protocol enables simultaneous analysis of host and bacterial transcripts by RNA-seq. It includes procedures for efficient host and bacterial cell lysis, barcoding of samples and analysis of both mammalian and microbial reads from mixed host-pathogen RNA-seq data. Roi Avraham et al. Published online: 21 July 2016 | doi:10.1038/nprot.2016.090 Abstract | Full Text | PDF (804K) A strategy for co-translational folding studies of ribosome-bound nascent chain complexes using NMR spectroscopy pp1492 - 1507 Cassaignau et al. provide a strategy for large-scale production and analysis of translationally arrested, isotopically labelled ribosome-bound nascent chains, enabling high-resolution co-translational protein folding studies using NMR spectroscopy. Anais M E Cassaignau et al. Published online: 28 July 2016 | doi:10.1038/nprot.2016.101 Abstract | Full Text | PDF (1,616K) Single cell-resolution western blotting pp1508 - 1530 Single-cell-resolution western blotting concatenates an electrophoretic separation to downstream immunoprobing of unfixed mammalian cells to detect proteins, isoforms, and interactions that are not discernable by immunoreactivity alone. Chi-Chih Kang et al. Published online: 28 July 2016 | doi:10.1038/nprot.2016.089 Abstract | Full Text | PDF (3,949K) Analysis of bacterial-surface-specific antibodies in body fluids using bacterial flow cytometry pp1531 - 1553 This protocol for bacterial flow cytometry incubates bacterial cells with an antibody-containing bodily fluid, visualizes bound antibody with secondary reagents and quantifies bacteria using flow cytometry, with numerous advantages over standard ELISA and western blotting techniques. Kathrin Moor et al. Published online: 28 July 2016 | doi:10.1038/nprot.2016.091 Abstract | Full Text | PDF (2,040K) A mutagenesis and screening strategy to generate optimally thermostabilized membrane proteins for structural studies pp1554 - 1571 Magnani et al. describe a protocol to generate thermostable membrane proteins for structural analysis. This approach combines mutagenesis with a rapid, radioligand-based thermostability assay to screen and identify mutants with optimal stability. Francesca Magnani et al. Published online: 28 July 2016 | doi:10.1038/nprot.2016.088 Abstract | Full Text | PDF (1,400K) Protocols JOBS of the week Postdoctoral Researcher (m / f) University Hospital Heidelberg Faculty Positions in Chemistry Ecole Polytechnique Fédérale de Lausanne (EPFL) Postdoctoral Fellowships Cleveland Clinic Lerner Research Institute Director of the Institute Institute of Experimental Medicine of ASCR, v.v.i, More Science jobs from Protocols EVENT More science events from
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