Nature Protocols Contents: Volume 9 Number 6, pp 1213-1531

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TABLE OF CONTENTS
June 2014, Volume 9 No 6
	In this issue Protocols Addendum
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Immune system modeling and analysis  Frontiers in T Cell Biology : Frontiers in B Cell Biology The rapid development of new methods for immunological data collection presents us now, for the first time, with the ability to analyze and compare large amounts of immunological data in health, aging and disease. This RT provides a comprehensive snapshot of the current state of the art on immune system modeling and analysis. Research Topics are a great opportunity for you to highlight your research focus - find out more!
PROTOCOLS Top Deep brain optical measurements of cell type–specific neural activity in behaving mice pp1213 - 1228 A description of how to use a time-correlated single-photon counting–based fiber optics system to measure the intensity, emission spectra and lifetime of fluorescent biosensors expressed in deep brain structures in freely moving mice. Guohong Cui et al. Published online: 01 May 2014 | doi:10.1038/nprot.2014.080 Abstract | Full Text | PDF (1,709K) 3D mouse embryonic stem cell culture for generating inner ear organoids pp1229 - 1244 This protocol describes a culture system, in which inner ear sensory tissue is produced in vitro from mouse embryonic stem cells under chemically defined conditions. Karl R Koehler and Eri Hashino Published online: 01 May 2014 | doi:10.1038/nprot.2014.100 Abstract | Full Text | PDF (2,392K) Synthesis of a highly Zn2+-selective cyanine-based probe and its use for tracing endogenous zinc ions in cells and organisms pp1245 - 1254 A detailed procedure for the synthesis of a zinc ion–selective, cyanine-based fluorescent probe and for the probe’s use for the detection of Zn2+ in cells and in living zebrafish. Zhiqian Guo, Gun-Hee Kim, Juyoung Yoon and Injae Shin Published online: 01 May 2014 | doi:10.1038/nprot.2014.086 Abstract | Full Text | PDF (836K) Using TRIP for genome-wide position effect analysis in cultured cells pp1255 - 1281 A detailed protocol for analyzing thousands of reporters integrated in parallel (TRIP) at a genome-wide level to study the influence of local chromatin context on gene expression. Waseem Akhtar et al. Published online: 08 May 2014 | doi:10.1038/nprot.2014.072 Abstract | Full Text | PDF (1,517K) Cell type–specific mRNA purification by translating ribosome affinity purification (TRAP) pp1282 - 1291 Translating ribosome affinity purification (TRAP) combines cell type–specific transgene expression with affinity purification of translating ribosomes and can be used to study the cell type–specific mRNA profiles of any genetically defined cell type. Myriam Heiman et al. Published online: 08 May 2014 | doi:10.1038/nprot.2014.085 Abstract | Full Text | PDF (691K) Engineering genetic circuits that compute and remember pp1292 - 1300 A protocol describing how to construct a platform for two-input Boolean logic functions with concomitant DNA-based memory that enables the straightforward assembly of integrated logic-and-memory circuits that implement desired behaviors within a couple of weeks. Piro Siuti, John Yazbek and Timothy K Lu Published online: 08 May 2014 | doi:10.1038/nprot.2014.089 Abstract | Full Text | PDF (646K) Monitoring protein conformational changes and dynamics using stable-isotope labeling and mass spectrometry pp1301 - 1319 CDSiL-MS involves labeling cysteine and lysine side chains in proteins with N-ethylmaleimide and succinic anhydride, respectively. Information about the conformational state of the protein is inferred from the labeling kinetics as determined by mass spectrometry. Alem W Kahsai, Sudarshan Rajagopal, Jinpeng Sun and Kunhong Xiao Published online: 08 May 2014 | doi:10.1038/nprot.2014.075 Abstract | Full Text | PDF (1,438K) Engineering complex biological systems in bacteria through recombinase-assisted genome engineering pp1320 - 1336 A protocol enabling the production of biofuels and renewable chemicals via the design and construction of complex biological systems in microbial organisms. Christine Nicole S Santos and Yasuo Yoshikuni Published online: 15 May 2014 | doi:10.1038/nprot.2014.084 Abstract | Full Text | PDF (794K) Ultrastructural readout of functional synaptic vesicle pools in hippocampal slices based on FM dye labeling and photoconversion pp1337 - 1347 This protocol provides the means to characterize the relationship between the nanoscale organization of synaptic vesicles and their functional properties during synaptic transmission. Vincenzo Marra, Jemima J Burden, Freya Crawford and Kevin Staras Published online: 15 May 2014 | doi:10.1038/nprot.2014.088 Abstract | Full Text | PDF (1,095K) Application of a robustness screen for the evaluation of synthetic organic methodology pp1348 - 1353 In this protocol from Frank Glorius and colleagues, analysis of gas chromatography data from a reaction conducted in the presence of various additives provides information on each additive's effect on the progress of the reaction and on the additive’s stability under the reaction conditions. Karl D Collins, Andreas Rühling and Frank Glorius Published online: 15 May 2014 | doi:10.1038/nprot.2014.076 Abstract | Full Text | PDF (392K) Semiautomated correlative 3D electron microscopy of in vivo–imaged axons and dendrites pp1354 - 1366 The authors describe an approach that can be used after in vivo imaging of dendrites and axons in adult mouse brains to prepare and image fluorescent structures of interest using focussed ion beam scanning electron microscopy. Bohumil Maco et al. Published online: 15 May 2014 | doi:10.1038/nprot.2014.101 Abstract | Full Text | PDF (2,245K) DNA origami–based standards for quantitative fluorescence microscopy pp1367 - 1391 A procedure for the preparation and use of DNA origami microscopy standards with fluorescent groups that have known fluorescent yields and are positioned at defined mutual distances. Jürgen J Schmied et al. Published online: 15 May 2014 | doi:10.1038/nprot.2014.079 Abstract | Full Text | PDF (2,346K) Experimental determination of invasive fitness in Caenorhabditis elegans  pp1392 - 1400 In this protocol, the author describes an approach to specifically estimate how evolutionarily successful new alleles are in invading populations of the nematode model Caenorhabditis elegans. Ivo M Chelo Published online: 22 May 2014 | doi:10.1038/nprot.2014.098 Abstract | Full Text | PDF (602K) Complementary X-ray tomography techniques for histology-validated 3D imaging of soft and hard tissues using plaque-containing blood vessels as examples pp1401 - 1415 This protocol describes how to analyze post-mortem artery specimens using X-ray CT and overcomes some of the difficulties relating to the different photon energy requirements for analyzing soft and hard tissues. Margaret N Holme et al. Published online: 22 May 2014 | doi:10.1038/nprot.2014.091 Abstract | Full Text | PDF (2,239K) Bayesian deconvolution and quantification of metabolites in complex 1D NMR spectra using BATMAN pp1416 - 1427 BATMAN is an R package developed to analyze one-dimensional NMR spectra of complex metabolite mixtures using a user-defined template library. Jie Hao et al. Published online: 22 May 2014 | doi:10.1038/nprot.2014.090 Abstract | Full Text | PDF (1,379K) Motif-based analysis of large nucleotide data sets using MEME-ChIP pp1428 - 1450 This protocol enables users to perform de novo motif discovery, motif enrichment analysis, motif location analysis, and motif clustering, providing a comprehensive picture of the DNA or RNA motifs that are enriched in the input sequences. Wenxiu Ma, William S Noble and Timothy L Bailey Published online: 22 May 2014 | doi:10.1038/nprot.2014.083 Abstract | Full Text | PDF (3,799K) Perfusion decellularization of whole organs pp1451 - 1468 A Protocol for performing pressure-controlled perfusion decellularization of whole organs, which enables users to prepare acellular 3D scaffolds with preserved extracellular membrane protein content, organ architecture and perfusable vascular conduits. Jacques P Guyette et al. Published online: 29 May 2014 | doi:10.1038/nprot.2014.097 Abstract | Full Text | PDF (1,794K) Antibiotic resistance–mediated isolation of scaffold-specific natural product producers pp1469 - 1479 This Protocol describes the isolation of scaffold-specific antibacterial producers in the presence of a selective antibiotic, an approach that overcomes two major bottlenecks in the drug discovery pipeline: low hit frequency and rediscovery of known molecules. Maulik N Thaker, Nicholas Waglechner and Gerry D Wright Published online: 29 May 2014 | doi:10.1038/nprot.2014.093 Abstract | Full Text | PDF (686K) Capture of activity-induced ultrastructural changes at synapses by high-pressure freezing of brain tissue pp1480 - 1495 This Protocol provides directions on using high-pressure freezing to prepare tissue samples for electron microscopy, avoiding the need for aldehyde fixation and ethanol dehydration. Daniel Studer et al. Published online: 29 May 2014 | doi:10.1038/nprot.2014.099 Abstract | Full Text | PDF (1,840K) Resolving genomic disorder–associated breakpoints within segmental DNA duplications using massively parallel sequencing pp1496 - 1513 An approach to localizing breakpoints with sequence-level precision employing massively parallel sequencing performed on libraries generated from haplotype-resolved chromosomes, genomic DNA, or molecular inversion probe–captured informative regions harboring paralog-distinguishing variants. Xander Nuttle, Andy Itsara, Jay Shendure and Evan E Eichler Published online: 29 May 2014 | doi:10.1038/nprot.2014.096 Abstract | Full Text | PDF (1,039K) Generation, expansion and functional analysis of endothelial cells and pericytes derived from human pluripotent stem cells pp1514 - 1531 The authors of this Protocol describe how to generate endothelial cells and pericytes and how to functionally evaluate the cells' ability to generate primary vascular plexus and incorporate it into the zebrafish vasculature. Valeria V Orlova et al. Published online: 29 May 2014 | doi:10.1038/nprot.2014.102 Abstract | Full Text | PDF (2,498K) ADDENDUM Top Addendum: A reproducible and well-tolerated method for 2/3 partial hepatectomy in mice  Claudia Mitchell and Holger Willenbring Published online: 29 May 2014 | doi:10.1038/nprot.2014.122 Full Text | PDF (443K) Nature Protocols JOBS of the week Life Science Research Assistant Standford University More Science jobs from
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