Nature Methods Contents: February 2016 Volume 14 pp 97 - 207

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Advertisement High Titer Purified Lentivirus  (Guaranteed >10^8 TU/ml) Fast turnaround 70+ lentiviral vectors Available for CRISPR, ORF cDNA, Promoter, shRNA, miRNA Learn more >> TABLE OF CONTENTS February 2017 Volume 14, Issue 2 In This Issue Editorial This Month Correspondence Research Highlights Commentary Technology Feature News and Views Review Analysis Brief Communications Articles Advertisement Say goodbye to sore thumbs with a $3,000 pipetting robot!  Join the hundreds of labs, including Stanford, Harvard, and Mayo Clinic using Opentrons liquid-handling robots for workflow automation. It is as easy as downloading a protocol, loading your deck, and hitting run.  Click here to learn more about our personal pipetting robots, starting at $3,000. Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement All of your valuable samples deserve the best treatment. With continuous quality assurance throughout the entire production process, you are guaranteed the highest quality consumables for ultimate reliability and reproducibility of your precious experiments. Eppendorf consumables - quality beyond measure.   Advertisement Nature Milestones: Antibodies Nature Milestones: Antibodies chronicles the history of antibodies from their earliest description in antisera, their structure, generation and function, right through to their recent application in cancer immunotherapy. It also includes a timeline and a collection of seminal papers reproduced from Springer Nature.  Access the Milestone free online Produced with support from:  BioLegend  UCB   Advertisement nature.com webcasts Pixels to data: Quantitative cell biology using high-content imaging and analysis. Date: Tuesday 28 February 2017 Time: 8AM PST, 11AM EST, 4PM GMT, 5PM CET  Register Sponsor:  PerkinElmer   In This Issue Top In This Issue    Editorial Top Stand up for science   p97 doi:10.1038/nmeth.4180 Uncertainty reigns in many domains as the Trump administration takes power. Science is no exception. Federal support for biological research must continue. And scientists must not be silenced by political pressure. This Month Top The Author File: Hyongbum (Henry) Kim   p99 doi:10.1038/nmeth.4157 Swimming to a way of testing thousands of guide RNAs at once. Correspondence Top Multicut brings automated neurite segmentation closer to human performance   pp101 - 102 Thorsten Beier, Constantin Pape, Nasim Rahaman, Timo Prange, Stuart Berg et al. doi:10.1038/nmeth.4151 eC-CLEM: flexible multidimensional registration software for correlative microscopies   pp102 - 103 Perrine Paul-Gilloteaux, Xavier Heiligenstein, Martin Belle, Marie-Charlotte Domart, Banafshe Larijani et al. doi:10.1038/nmeth.4170 Research Highlights Top Native chromosome conformation Isolation of nuclei in an isotonic buffer retains chromosome loops and allows the probing of intrinsic loop conformation. Designer proteases for post-translational modifications Researchers have engineered a protease specific for a post-translational modification. Stem cells from the young and old Donor age impacts the epigenetic state and mutational burden of induced pluripotent stem cells. Putting the brakes on CRISPR-Cas9 Researchers identify biological inhibitors of Cas9 nuclease activity and block genome editing in cultured human cells. Genetic tools for magnetic resonance imaging Genetically encoded reporters can be used for noninvasive cell tracking or molecular imaging with magnetic resonance imaging technologies. Methods in Brief A functional assay for promoters | Count on FRET for stoichiometry | Probing protein mechanics with an electric field | Optimized optical recordings of voltage sensors Tools in Brief Special delivery for live-cell imaging | Stretchable multichannel wireless implants | Many models of microbial metabolism | Nanopore-based protein fingerprinting Methods JOBS of the week Postdoctoral Researchers Institute of Animal Physiology and Genetics, Czech Academy of Sciences Associate Research Scientist Columbia University Postdoctoral Position at USC University of Southern California Professorship in Biological Sciences University of Southampton Interdisciplinary Postdoctoral Fellowship in Tumor Biology Johns Hopkins University More Science jobs from Methods EVENT Methods in Computational Neuroscience 30.07.17 Woods Hole, USA More science events from Commentary Top Win-win data sharing in neuroscience   pp112 - 116 Giorgio A Ascoli, Patricia Maraver, Sumit Nanda, Sridevi Polavaram and Rubén Armañanzas doi:10.1038/nmeth.4152 In this Commentary, Ascoli et al. discuss recipes for setting up public data sharing initiatives based on their experiences with NeuroMorpho.Org. Technology Feature Top Pursuing the simple life   pp117 - 121 Michael Eisenstein doi:10.1038/nmeth.4158 Efforts to pare away cellular genomes are yielding streamlined biosynthetic factories and deeper insights into the core processes of biology. News and Views Top Cool and dynamic: single-molecule fluorescence-based structural biology   pp123 - 124 Timothy D Craggs doi:10.1038/nmeth.4159 New methods exploit single-molecule measurements to study protein structure and dynamics. See also: Brief Communication by Weisenburger et al. | Article by Hellenkamp et al. Review Top How best to identify chromosomal interactions: a comparison of approaches   pp125 - 134 James O J Davies, A Marieke Oudelaar, Douglas R Higgs and Jim R Hughes doi:10.1038/nmeth.4146 In this Review, the authors compare commonly used chromosome conformation capture techniques, describing their respective strengths and weaknesses, and provide advice for the end user on which approach and analysis method to use. Analysis Top Simulation-based comprehensive benchmarking of RNA-seq aligners   pp135 - 139 Giacomo Baruzzo, Katharina E Hayer, Eun Ji Kim, Barbara Di Camillo, Garret A FitzGerald et al. doi:10.1038/nmeth.4106 Benchmarking on synthetic data reveals differences between common RNA-seq alignment software tools, particularly for complex genomic regions. Brief Communications Top Cryogenic optical localization provides 3D protein structure data with Angstrom resolution   pp141 - 144 Siegfried Weisenburger, Daniel Boening, Benjamin Schomburg, Karin Giller, Stefan Becker et al. doi:10.1038/nmeth.4141 The positions of fluorophores can be localized in single proteins with Angstrom-scale resolution using Cryogenic Optical Localization in 3D (COLD), a complementary approach to traditional structural biology techniques. See also: News and Views by Craggs cGAL, a temperature-robust GAL4-UAS system for Caenorhabditis elegans   pp145 - 148 Han Wang, Jonathan Liu, Shahla Gharib, Cynthia M Chai, Erich M Schwarz et al. doi:10.1038/nmeth.4109 Standardized driver and effector lines that use optimized GAL4 from a cryophilic yeast species enable bipartite control of transgene expression in Caenorhabditis elegans. Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging   pp149 - 152 Francesco Cutrale, Vikas Trivedi, Le A Trinh, Chi-Li Chiu, John M Choi et al. doi:10.1038/nmeth.4134 Hyper-Spectral Phasors allow unmixing of multiple signals even under conditions with low signal-to-noise ratios, and they enable highly multiplexed 5D imaging of live zebrafish embryos labeled with conventional fluorophores. Advertisement Focus on the neuroscience toolbox  Nature Neuroscience presents a special focus issue on the neuroscience toolbox highlighting recent technological advances, approaches and collaborative initiatives that are enabling new avenues of research.  Access the Focus free online for six months Produced with support from:  The Kavli Foundation   Articles Top In vivo high-throughput profiling of CRISPR-Cpf1 activity   pp153 - 159 Hui K Kim, Myungjae Song, Jinu Lee, A Vipin Menon, Soobin Jung et al. doi:10.1038/nmeth.4104 A lentiviral library expressing Cpf1 guide RNAs and containing target sequences allows high-throughput profiling of highly active guide RNAs and is the basis for cindel, a webtool to predict the activity at any given target sequence. Control of cerebral ischemia with magnetic nanoparticles   pp160 - 166 Jie-Min Jia, Praveen D Chowdary, Xiaofei Gao, Bo Ci, Wenjun Li et al. doi:10.1038/nmeth.4105 Stroke is often modeled in rodents by surgically occluding vessels. SIMPLE is an alternative approach that involves the magnet-induced accumulation of nanoparticles. Because of its reversible nature, this method can be used to study both occlusion and subsequent reperfusion of blood vessels. Scalable whole-genome single-cell library preparation without preamplification   pp167 - 173 Hans Zahn, Adi Steif, Emma Laks, Peter Eirew, Michael VanInsberghe et al. doi:10.1038/nmeth.4140 Direct library preparation (DLP) is a robust and economic method for preparing large numbers of single-cell whole-genome sequencing libraries without preamplification, to study copy-number heterogeneity at the cell level and other variant types at the clone or population level. Multidomain structure and correlated dynamics determined by self-consistent FRET networks   pp174 - 180 Björn Hellenkamp, Philipp Wortmann, Florian Kandzia, Martin Zacharias and Thorsten Hugel doi:10.1038/nmeth.4081 A hybrid approach merges networks of time-correlated distances determined by single-molecule FRET to uncover local and global dynamics of the multidomain protein Hsp90 in solution at multiple timescales. See also: News and Views by Craggs In vivo quantification of spatially varying mechanical properties in developing tissues   pp181 - 186 Friedhelm Serwane, Alessandro Mongera, Payam Rowghanian, David A Kealhofer, Adam A Lucio et al. doi:10.1038/nmeth.4101 The mechanical properties of tissues can be measured by deforming magnetically responsive microdroplets that are implanted in the tissue. Serwane et al. apply this method to study the mechanical properties of tissues in the living zebrafish embryo. Nontargeted in vitro metabolomics for high-throughput identification of novel enzymes in Escherichia coli   pp187 - 194 Daniel C Sévin, Tobias Fuhrer, Nicola Zamboni and Uwe Sauer doi:10.1038/nmeth.4103 A method to screen proteins for enzymatic activity by incubating purified or overexpressed proteins with a metabolite extract and measuring changes in metabolite abundance using mass spectrometry enables high-throughput characterization of functionally uncharacterized proteins in Escherichia coli. Rapidly evolving homing CRISPR barcodes   pp195 - 200 Reza Kalhor, Prashant Mali and George M Church doi:10.1038/nmeth.4108 Homing guide RNAs that target Cas9 to their own loci generate diverse barcodes that can trace the lineage of cells. RESA identifies mRNA-regulatory sequences at high resolution   pp201 - 207 Valeria Yartseva, Carter M Takacs, Charles E Vejnar, Miler T Lee and Antonio J Giraldez doi:10.1038/nmeth.4121 The RNA-element selection assay (RESA) probes regulatory elements in vivo and identifies protein binding partners and the nucleotides that contribute most to the regulation. Advertisement Nature Biomedical Engineering - NOW LIVE The first issue of Nature Biomedical Engineering is now live and available for free.  Click here to access the issue. Remember to follow us on Twitter @NatBME or sign up to receive the e-alert.   Top Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. The contents of the Natureevents Directory are now live. The digital version is available here. Find the latest scientific conferences, courses, meetings and symposia on natureevents.com. 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