Nature Protocols Contents: Volume 11 Number 5, pp 835-1020

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TABLE OF CONTENTS
May 2016, Volume 11 No 5
	In this issue Protocols
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PROTOCOLS Top Library design and screening protocol for artificial metalloenzymes based on the biotin-streptavidin technology pp835 - 852 This protocol describes a mutagenesis screening method for the optimization of artificial streptavidin-based metalloenzymes. Hendrik Mallin, Martina Hestericova, Raphael Reuter and Thomas R Ward Published online: 31 March 2016 | doi:10.1038/nprot.2016.019 Abstract | Full Text | PDF (1,844K) Detecting DNA double-stranded breaks in mammalian genomes by linear amplification-mediated high-throughput genome-wide translocation sequencing pp853 - 871 This protocol describes a genome-wide method to detect and to quantify DNA double-stranded breaks (DSBs). The approach is applicable to endogenous DSBs, but it can also be used to characterize the activity of engineered nucleases, including Cas9. Jiazhi Hu et al. Published online: 31 March 2016 | doi:10.1038/nprot.2016.043 Abstract | Full Text | PDF (1,657K) Explant culture of adult zebrafish hearts for epicardial regeneration studies pp872 - 881 This protocol describes how to establish explant cultures of intact zebrafish hearts. The explants can be used to study the regeneration of cardiac tissues such as the epicardium, can be maintained for up to 30 d and are amenable to live imaging. Jingli Cao and Kenneth D Poss Published online: 07 April 2016 | doi:10.1038/nprot.2016.049 Abstract | Full Text | PDF (3,454K) Integration and global analysis of isothermal titration calorimetry data for studying macromolecular interactions pp882 - 894 This protocol from Brautigam et al. describes methods for baseline correction and global analysis of isothermal titration calorimetry data using NITPIC and SEDPHAT. Publication-quality graphs of resulting data can then be created and visualized using GUSSI. Chad A Brautigam et al. Published online: 07 April 2016 | doi:10.1038/nprot.2016.044 Abstract | Full Text | PDF (2,010K) The collection of MicroED data for macromolecular crystallography pp895 - 904 MicroED is a cryo-EM technique for collecting electron diffraction data from microcrystals and nanocrystals. This protocol from Gonen and colleagues describes how to prepare the protein crystal samples, how to set up the electron microscope for MicroED, and diffraction data collection. Dan Shi et al. Published online: 14 April 2016 | doi:10.1038/nprot.2016.046 Abstract | Full Text | PDF (1,573K) Computational protein-ligand docking and virtual drug screening with the AutoDock suite pp905 - 919 This protocol describes the use of the AutoDock suite for computational docking in the study of protein-ligand interactions. A number of methods are described ranging from basic docking of drug molecules to virtual screening using a large ligand library of chemical compounds. Stefano Forli et al. Published online: 14 April 2016 | doi:10.1038/nprot.2016.051 Abstract | Full Text | PDF (2,646K) 3D printing of versatile reactionware for chemical synthesis pp920 - 936 This protocol from Kitson et al. describes an approach to create bespoke 3D-printed chemical reactors known collectively as "reactionware". Philip J Kitson et al. Published online: 14 April 2016 | doi:10.1038/nprot.2016.041 Abstract | Full Text | PDF (3,731K) Quantification of cancer cell extravasation in vivo  pp937 - 948 This protocol describes a rapid (<24 h), reproducible and cheap technique for evaluating cancer cell invasiveness by quantifying in vivo rates of cancer cell extravasation in the chorioallantoic membrane (CAM) of chicken embryos. Yohan Kim et al. Published online: 21 April 2016 | doi:10.1038/nprot.2016.050 Abstract | Full Text | PDF (3,089K) Genetic engineering of untransformable coagulase-negative staphylococcal pathogens pp949 - 959 This protocol provides a method for genetically engineering untransformable coagulase-negative staphylococci (CoNS), using bacteriophage Φ187-mediated plasmid transfer. This is a major technical advancement that enables research on CoNS-mediated infections. Volker Winstel, Petra Kuhner, Holger Rohde and Andreas Peschel Published online: 21 April 2016 | doi:10.1038/nprot.2016.058 Abstract | Full Text | PDF (1,506K) Targeted isolation and cloning of 100-kb microbial genomic sequences by Cas9-assisted targeting of chromosome segments pp960 - 975 Here the authors provide the procedural details of a new approach to clone large (up to 100 kb) microbial genomic sequences using Cas9-assisted targeting of chromosome segments (CATCH). The Cas9 cleavage is achieved in agarose gel, and the cleaved product can be ligated into a cloning vector. Wenjun Jiang and Ting F Zhu Published online: 21 April 2016 | doi:10.1038/nprot.2016.055 Abstract | Full Text | PDF (1,498K) Large-scale production of Plasmodium falciparum gametocytes for malaria drug discovery pp976 - 992 This protocol for the induction and isolation of Plasmodium falciparum gametocytes combines seven parameters that have been shown to facilitate the optimum induction of gametocytogenesis in vitro to obtain highly synchronous gametocyte stages on a large scale. Sandra Duffy, Sasdekumar Loganathan, John P Holleran and Vicky M Avery Published online: 28 April 2016 | doi:10.1038/nprot.2016.056 Abstract | Full Text | PDF (1,957K) Six alternative proteases for mass spectrometry-based proteomics beyond trypsin pp993 - 1006 The use of a single enzyme such as trypsin for shotgun proteomics limits the ability to cover the whole proteome and all protein post-translational modifications. This protocol describes the use of six alternative proteases that complement trypsin to increase the coverage of the proteome. Piero Giansanti, Liana Tsiatsiani, Teck Yew Low and Albert J R Heck Published online: 28 April 2016 | doi:10.1038/nprot.2016.057 Abstract | Full Text | PDF (813K) Ex vivo tools for the clonal analysis of zebrafish hematopoiesis pp1007 - 1020 This protocol describes the cultivation and differentiation of zebrafish hematopoietic stem and progenitor cells ex vivo for use in colony assays. Ondrej Svoboda et al. Published online: 28 April 2016 | doi:10.1038/nprot.2016.053 Abstract | Full Text | PDF (1,701K) Nature Protocols JOBS of the week Chief Scientific Officer Baylor College of Medicine (BCM) Postdoc for New Magnetic Resonance Methods in Oncology German Cancer Research Center (DKFZ). More Science jobs from

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