Nature Protocols Contents: Volume 10 Number 11, pp 1643-1896

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TABLE OF CONTENTS
November 2015, Volume 10 No 11
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PROTOCOLS Top Selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis pp1643 - 1669 In SHAPE-MaP, reverse transcriptase-induced mutations at SHAPE-modified RNA nucleotides are detected by high-throughput sequencing. ShapeMapper converts sequence data to mutational profiles (MaPs), which can be used by SuperFold for RNA structure modeling. Matthew J Smola et al. Published online: 01 October 2015 | doi:10.1038/nprot.2015.103 Abstract | Full Text | PDF (2,992K) Fabrication of nanopores with ultrashort single-walled carbon nanotubes inserted in a lipid bilayer pp1670 - 1678 When an electric field is applied across a membrane containing nanopores, it induces an ion current that alters upon ligand binding. Single-walled carbon nanotubes form nanopores that can be used as sensors; specificity is a function of pore size. Lei Liu, Jiani Xie, Ting Li and Hai-Chen Wu Published online: 01 October 2015 | doi:10.1038/nprot.2015.112 Abstract | Full Text | PDF (998K) Efficient processing and analysis of large-scale light-sheet microscopy data pp1679 - 1696 The Keller lab describes a detailed protocol for processing large multidimensional imaging datasets obtained from light-sheet microscopy. Fernando Amat et al. Published online: 01 October 2015 | doi:10.1038/nprot.2015.111 Abstract | Full Text | PDF (2,765K) The isolation and culture of endothelial colony-forming cells from human and rat lungs pp1697 - 1708 Rat or human lung samples are enzymatically digested, and CD31-expressing cells are positively selected using magnetic-activated cell sorting before plating in endothelial-specific growth conditions. Rajesh S Alphonse et al. Published online: 08 October 2015 | doi:10.1038/nprot.2015.107 Abstract | Full Text | PDF (1,870K) Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging pp1709 - 1727 This protocol describes how to perform CUBIC (Clear, Unobstructed Brain/Body Imaging Cocktails and Computational analysis), a simple and efficient method for organ clearing, imaging by light-sheet microscopy, and quantitative imaging analysis. Etsuo A Susaki et al. Published online: 08 October 2015 | doi:10.1038/nprot.2015.085 Abstract | Full Text | PDF (3,625K) Determination of the CYP1A-inducing potential of single substances, mixtures and extracts of samples in the micro-EROD assay with H4IIE cells pp1728 - 1741 The micro-EROD assay is a high-throughput screening method used to assess the CYP1A-inducing potential of dioxins and dioxin-like chemicals in rat hepatoma cells. Andreas Schiwy et al. Published online: 08 October 2015 | doi:10.1038/nprot.2015.108 Abstract | Full Text | PDF (1,065K) Preparation of a cyanine-based fluorescent probe for highly selective detection of glutathione and its use in living cells and tissues of mice pp1742 - 1754 Changes in the levels of cellular thiols (e.g., glutathione) are linked to many diseases. This protocol is for the synthesis of CPDSA, a fluorescent turn-on glutathione probe with near-infrared emission. In-cell and in vivo assays are also described. Jun Yin et al. Published online: 15 October 2015 | doi:10.1038/nprot.2015.109 Abstract | Full Text | PDF (2,441K) Using the GEMM-ESC strategy to study gene function in mouse models pp1755 - 1785 This protocol describes a modular approach to modify existing genetically engineered mouse models (GEMMs) by re-derivation of embryonic stem cells (ESCs) and subsequent modification of these cells by recombinase-mediated transgene insertion. Ivo J Huijbers et al. Published online: 15 October 2015 | doi:10.1038/nprot.2015.114 Abstract | Full Text | PDF (2,533K) Mapping ribonucleotides in genomic DNA and exploring replication dynamics by polymerase usage sequencing (Pu-seq) pp1786 - 1801 Pu-seq (polymerase usage sequencing) is an approach for identifying ribonucleotides by high-throughput sequencing to allow the mapping of replicative polymerase usage genome wide. This has been used to define origin efficiencies and replication timing in yeast. Andrea Keszthelyi et al. Published online: 15 October 2015 | doi:10.1038/nprot.2015.116 Abstract | Full Text | PDF (2,069K) Imaging the beating heart in the mouse using intravital microscopy techniques pp1802 - 1819 This protocol enables microscopic imaging of organs in live mice by addressing tissue movement resulting from cardiac and respiratory cycles. Claudio Vinegoni, Aaron D Aguirre, Sungon Lee and Ralph Weissleder Published online: 22 October 2015 | doi:10.1038/nprot.2015.119 Abstract | Full Text | PDF (5,761K) Precision-engineering the Pseudomonas aeruginosa genome with two-step allelic exchange pp1820 - 1841 Here, the authors describe genetically engineering the Pseudomonas genome by two-step allelic exchange. Suicide vector-encoded alleles are used to generate mutations by homologous recombination at the single base pair level. Laura R Hmelo et al. Published online: 22 October 2015 | doi:10.1038/nprot.2015.115 Abstract | Full Text | PDF (1,620K) Efficient delivery of nuclease proteins for genome editing in human stem cells and primary cells pp1842 - 1859 In this protocol, the authors describe methods for the direct delivery of ZFN, TALEN and Cas9 nuclease proteins into cells for efficient and targeted genome editing. Jia Liu et al. Published online: 22 October 2015 | doi:10.1038/nprot.2015.117 Abstract | Full Text | PDF (1,522K) Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping pp1860 - 1896 This protocol describes how to fix, embed, clear and stain excised organs or whole organisms to create optically transparent samples. This versatile protocol is able to process a wide range of sample types for high-resolution imaging. Jennifer B Treweek et al. Published online: 22 October 2015 | doi:10.1038/nprot.2015.122 Abstract | Full Text | PDF (6,789K) Nature Protocols JOBS of the week Staff Clinician – Allergic Diseases National Institute of Allergy and Infectious Diseases (NIAID) Senior Research Scientist California Institute of Technology Director of Operations and Outreach / Assistant Chair Northwestern University Post-doc in neuro-immune interaction KU Leuven Postdoctoral Research Assistant University of Bristol More Science jobs from
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