Nature Protocols Contents: Volume 11 Number 4, pp 617-833

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TABLE OF CONTENTS
April 2016, Volume 11 No 4
	In this issue Protocols
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PROTOCOLS Top Interferometric scattering microscopy and its combination with single-molecule fluorescence imaging pp617 - 633 Interferometric scattering microscopy (iSCAT) enables ultrasensitive label-free imaging and high-speed single-particle tracking. This protocol describes how to construct an iSCAT microscope with single-molecule TIRF capabilities. Jaime Ortega Arroyo, Daniel Cole and Philipp Kukura Published online: 03 March 2016 | doi:10.1038/nprot.2016.022 Abstract | Full Text | PDF (4,144K) Assembly and operation of the autopatcher for automated intracellular neural recording in vivo  pp634 - 654 This protocol describes how to set up and use the autopatcher, a robot that automatically obtains intracellular neural recordings from intact mammalian mouse brains. Suhasa B Kodandaramaiah et al. Published online: 03 March 2016 | doi:10.1038/nprot.2016.007 Abstract | Full Text | PDF (4,754K) Monitoring the progression of cell death and the disassembly of dying cells by flow cytometry pp655 - 663 Annexin A5 and TO-PRO-3 (a nucleic acid-binding dye that stains early apoptotic and necrotic cells differentially) are used to distinguish six types of particles in a sample, including apoptotic bodies and cells at various stages of cell death. Lanzhou Jiang et al. Published online: 03 March 2016 | doi:10.1038/nprot.2016.028 Abstract | Full Text | PDF (1,353K) Using Raman spectroscopy to characterize biological materials pp664 - 687 Raman microspectroscopy is useful for the analysis of biological samples, because chemical and structural information can be obtained without using labels. This protocol brings together practical guidelines from expert research groups. Holly J Butler et al. Published online: 10 March 2016 | doi:10.1038/nprot.2016.036 Abstract | Full Text | PDF (2,932K) Near-IR photoactivation using mesoporous silica-coated NaYF4:Yb,Er/Tm upconversion nanoparticles pp688 - 713 Upconversion nanoparticles (UCNs) have the extraordinary ability to emit light with UV-visible wavelengths on illumination in the near-IR region. This protocol describes the preparation of UCNs with potential therapeutic applications. Muthu Kumara Gnanasammandhan et al. Published online: 10 March 2016 | doi:10.1038/nprot.2016.035 Abstract | Full Text | PDF (6,941K) Microfluidic differential immunocapture biochip for specific leukocyte counting pp714 - 726 This protocol from Hassan et al. describes a microfluidic chip that uses an immunocapture chamber to count CD4 and CD8 cells in whole blood for HIV/AIDS diagnostics. The chip can be adapted for different cell types and research applications. Umer Hassan et al. Published online: 10 March 2016 | doi:10.1038/nprot.2016.038 Abstract | Full Text | PDF (1,429K) Functionalization, preparation and use of cell-laden gelatin methacryloyl–based hydrogels as modular tissue culture platforms pp727 - 746 This protocol describes how to make semisynthetic gelatin methacryloyl (GelMA)-based hydrogels for use in 3D cell culture models for cancer research, stem cell research and tissue engineering. Daniela Loessner et al. Published online: 17 March 2016 | doi:10.1038/nprot.2016.037 Abstract | Full Text | PDF (2,931K) A LC-MS–based workflow for measurement of branched fatty acid esters of hydroxy fatty acids pp747 - 763 Branched fatty acid esters of hydroxy fatty acids (FAHFAs) are a recently discovered class of biological lipids. This protocol describes their extraction from serum and tissue samples, followed by enrichment and analysis by LC-MS. Tejia Zhang et al. Published online: 17 March 2016 | doi:10.1038/nprot.2016.040 Abstract | Full Text | PDF (1,613K) Automated screening for small organic ligands using DNA-encoded chemical libraries pp764 - 780 This protocol describes an approach for screening DNA-encoded chemical libraries (DECLs) to identify molecules that bind to proteins of interest. After isolating binding library members, DNA barcodes are amplified and identified by high-throughput sequencing. Willy Decurtins et al. Published online: 17 March 2016 | doi:10.1038/nprot.2016.039 Abstract | Full Text | PDF (2,730K) Design, synthesis and evaluation of molecularly targeted hypoxia-activated prodrugs pp781 - 794 Many solid tumors contain an aggressive hypoxic region that is difficult to treat. This protocol describes how to prepare bioreductive prodrugs that are biologically inactive until they are converted to an active drug by enzymatic reduction in hypoxia. Liam J O'Connor et al. Published online: 24 March 2016 | doi:10.1038/nprot.2016.034 Abstract | Full Text | PDF (644K) Label-free quantification in ion mobility–enhanced data-independent acquisition proteomics pp795 - 812 This protocol describes a data-independent acquisition workflow for label-free quantitative proteomics that integrates ion mobility separation and applies drift time–specific collision energies to improve precursor fragmentation efficiency. Ute Distler, Jorg Kuharev, Pedro Navarro and Stefan Tenzer Published online: 24 March 2016 | doi:10.1038/nprot.2016.042 Abstract | Full Text | PDF (5,310K) Genome-wide profiling of RNA polymerase transcription at nucleotide resolution in human cells with native elongating transcript sequencing pp813 - 833 Human NET-seq enables DNA strand–specific mapping of RNA polymerase (RNAP) activity at single-nucleotide resolution. A cell fractionation approach is used to isolate transcribing RNAP and associated RNAs, avoiding immunoprecipitation or RNA labeling. Andreas Mayer and L Stirling Churchman Published online: 24 March 2016 | doi:10.1038/nprot.2016.047 Abstract | Full Text | PDF (1,558K) Nature Protocols JOBS of the week Postdoctoral Associate- Neurobiology / Stem Cell - Stanley Center Broad Institute Marie Curie Early Stage Researchers University of Birmingham CAGI Lead Scientist University of California - Berkeley More Science jobs from

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