Nature Methods Contents: May 2018, Volume 15 No 5 pp 299 - 394

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Advertisement Nikon's new CFI90 20XC Glyc objective is designed for ultra-deep, large-format imaging of whole, cleared brain tissues. With an 8.2mm working distance and high numerical aperture, the new objective lens ensures superior clarity and contrast in every image. Learn more TABLE OF CONTENTS May 2018 Volume 15, Issue 5 Editorial This Month Correspondence Research Highlights Technology Feature News and Views Resources Brief Communications Articles Retraction Corrigenda Application Note   Advertisement Nominations now open! Who are the future leading women in science? The Nature Research Awards for Inspiring Science and Innovating Science are now open for nominations.  Find out more about these awards and nominate your inspiration >>  In partnership with The Estee Lauder Companies.     Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Basic flow cytometry training course (July 26–27, 2018) This 2-day hands-on training course at Miltenyi Biotec/Germany gives a profound introduction to flow cytometry. In lectures and practical lab sessions, participants will be introduced to the basics of instrument setup, sample staining, compensation, and measurement, as well as the analysis of flow cytometry data.   Advertisement nature.com webcasts Nature Research Custom presents a webcast on: Highly multiplexed transcriptome and protein immune profiling in single cells with CITE-seq Date: Wednesday, May 23, 2018 Peter Smibert, Ph.D. from New York Genome Center, will present an overview of CITE-seq and Cell Hashing and discuss methods compatible with 10x Genomics single cell platforms for enhanced cellular phenotyping and sample multiplexing. This webcast has been produced on behalf of the sponsor who retains sole responsibility for content  Register for FREE  Sponsored by: 10x Genomics    Editorial Top Mapping the human   p299 doi:10.1038/nmeth.4685 The Human Cell Atlas, driven by a collaborative spirit and rapid advances in single-cell methods, is poised to advance both biological understanding and technical development.   This Month Top Harris Wang   p301 Vivien Marx doi:10.1038/nmeth.4676 A regulatory vocabulary for synthetic biology and why baby diapers matter.   Correspondence Top What's in a sample? Increasing transparency in biospecimen procurement methods   pp303 - 304 Joshua LaBaer, Joseph F Miceli III and Leonard P Freedman doi:10.1038/nmeth.4684   ATAC Primer Tool for targeted analysis of accessible chromatin   pp304 - 305 Kathryn E Yost, Ava C Carter, Jin Xu, Ulrike Litzenburger and Howard Y Chang doi:10.1038/nmeth.4663   Computational correction of index switching in multiplexed sequencing libraries   pp305 - 307 Anton J M Larsson, Geoff Stanley, Rahul Sinha, Irving L Weissman and Rickard Sandberg doi:10.1038/nmeth.4666   Research Highlights Top AI transforms image reconstruction A deep-learning-based approach improves the speed, accuracy, and robustness of biomedical image reconstruction. A nontoxic rabies virus for neural circuit mapping A double-deletion rabies virus variant overcomes the cytotoxicity that has previously limited long-term applications for retrograde labeling of projection neurons. Correlation analysis in single-molecule localization microscopy A coordinate-based framework quantifies the correlation and interaction of biomolecules in images acquired with super-resolution microscopy techniques. CRISPR-Cas goes RNA CasRx is a programmable CRISPR-Cas system that targets RNA for efficient knockdown and splicing modulation. A MACnificent view of the cellular protein landscape The multipurpose MAC-tag enables integrative interaction proteomics to localize proteins with sub-organelle precision. Methods in Brief Following fitness after mutations in single cells    | Chronic imaging of the fruit fly brain    | Clearing the way for imaging of the human brain    | Extracting neuronal activity from microendoscopy videos      Tools in Brief Expanding the range of base editors    | cisTEM software for cryo-EM    | GFP goes sour    | Metabolomes from metagenomics and modeling      Methods JOBS of the week Staff scientist - Proteomics Weizmann Institute of Science AOI Biosensing Chair Position University of Missouri (MU) College of Engineering Bioinformatics Specialist Massachusetts General Hospital Systems Biologist Columbia University Medical Center Postdoctoral Scholar Oregon Health & Science University and Knight Cancer Institute More Science jobs from Methods EVENT G19 Statistics for Non Statisticians 12.06.18 Maidenhead, UK More science events from Technology Feature Top Microbiology: making the best of PCR bias   pp317 - 320 Michael Eisenstein doi:10.1038/nmeth.4683 Many factors can skew the results of a widely used amplification technique for microbiome analysis, but researchers are finding strategies for getting at the truth.   News and Views Top Sorting apples from oranges in single-cell expression comparisons   pp321 - 322 Fiona K Hamey and Berthold Gottgens doi:10.1038/nmeth.4675 Two methods for comparing single-cell expression data sets help address the challenge of integrating data across conditions and experiments.   Resources Top Metagenomic mining of regulatory elements enables programmable species-selective gene expression   pp323 - 329 Nathan I Johns, Antonio L C Gomes, Sung Sun Yim, Anthony Yang, Tomasz Blazejewski et al. doi:10.1038/nmeth.4633 Metagenomic mining generates a rich resource of regulatory sequences with species-selective and universal activity, making it possible to engineer synthetic circuits with tunable gene expression across diverse bacterial hosts.   A toolbox of immunoprecipitation-grade monoclonal antibodies to human transcription factors   pp330 - 338 Anand Venkataraman, Kun Yang, Jose Irizarry, Mark Mackiewicz, Paolo Mita et al. doi:10.1038/nmeth.4632 A collection of 1,406 high-quality, immunoprecipitation- and immunoblotting-grade monoclonal antibodies to 737 human transcription factors is made available as a community resource, along with all validation data.   Brief Communications Top Identification of spatial expression trends in single-cell gene expression data   pp339 - 342 Daniel Edsgard, Per Johnsson and Rickard Sandberg doi:10.1038/nmeth.4634 trendsceek identifies genes with significant spatial trends in single-cell spatial expression data, as well as in low-dimensional projections of dissociated single-cell RNA-seq data.   SpatialDE: identification of spatially variable genes   pp343 - 346 Valentine Svensson, Sarah A Teichmann and Oliver Stegle doi:10.1038/nmeth.4636 SpatialDE identifies genes with significant spatial expression patterns from multiplexed imaging or spatial RNA-sequencing data, and can cluster genes with similar spatial patterns as a form of expression-based tissue histology.   Photoactivatable drugs for nicotinic optopharmacology   pp347 - 350 Sambashiva Banala, Matthew C Arvin, Nicholas M Bannon, Xiao-Tao Jin, John J Macklin et al. doi:10.1038/nmeth.4637 Optopharmacological manipulation with /`caged/' glutamate and GABA has enabled the study of these ligands/' cognate receptors, but other ligands such as tertiary amine drugs have not been amenable to caging. A new strategy yields a photoactivatable nicotine, PA-Nic, which allows manipulation of nicotinic acetylcholine receptors.   NAMD goes quantum: an integrative suite for hybrid simulations   pp351 - 354 Marcelo C R Melo, Rafael C Bernardi, Till Rudack, Maximilian Scheurer, Christoph Riplinger et al. doi:10.1038/nmeth.4638 The integration of quantum chemistry and molecular dynamics programs coupled with a graphical user interface provides a streamlined tool for powerful simulations of biomolecular reaction mechanisms.   Real-time fluorescence and deformability cytometry   pp355 - 358 Philipp Rosendahl, Katarzyna Plak, Angela Jacobi, Martin Kraeter, Nicole Toepfner et al. doi:10.1038/nmeth.4639 RT-FDC combines the specificity of fluorescent probes with functional readout of a cell's mechanical properties. The resulting correlation of fluorescence-based cell identity with mechanical measurements in real time allows the development of label-free, mechanical cell sorting.   scmap: projection of single-cell RNA-seq data across data sets   pp359 - 362 Vladimir Yu Kiselev, Andrew Yiu and Martin Hemberg doi:10.1038/nmeth.4644 scmap enables the comparison of disparate single-cell RNA-seq data sets by projecting individual cells or clusters from a query sample onto a reference sample or cell atlas.   Improved Ribo-seq enables identification of cryptic translation events   pp363 - 366 Florian Erhard, Anne Halenius, Cosima Zimmermann, Anne L'Hernault, Daniel J Kowalewski et al. doi:10.1038/nmeth.4631 PRICE uses Ribo-seq data to predict ORFs and start codons with high accuracy by computationally eliminating experimental noise and dissecting overlapping translation events.   Real-time 3D single-molecule localization using experimental point spread functions   pp367 - 369 Yiming Li, Markus Mund, Philipp Hoess, Joran Deschamps, Ulf Matti et al. doi:10.1038/nmeth.4661 An open-source, real-time fitter for 3D single-molecule localization microscopy uses experimental point spread functions. This enables accurate 3D super-resolution microscopy on standard microscopes without dedicated 3D optics.   Advertisement   Advanced Imaging with Proven Optics Olympus is dedicated to your work, vision, and science. Through innovation and service, we seek to aide in your discoveries, advance your research, and inspire you to explore new possibilities. Our wide range of microscopes are built with the optical excellence and proven application expertise you can depend on. Your Science Matters™. > Learn more about Olympus microscopes   Articles Top Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics   pp371 - 378 Ryan Peckner, Samuel A Myers, Alvaro Sebastian Vaca Jacome, Jarrett D Egertson, Jennifer G Abelin et al. doi:10.1038/nmeth.4643 Data-independent-acquisition-based mass spectrometry enables highly reproducible proteome analysis, but results interpretation is challenging owing to the complex nature of the spectral data. A software tool, Specter, effectively resolves spectra for highly similar peptides.   FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data   pp379 - 386 Josip S Herman,  Sagar and Dominic Grun doi:10.1038/nmeth.4662 FateID identifies fate biases in early multipotent progenitor populations from single-cell RNA-seq data.   Burden-driven feedback control of gene expression   pp387 - 393 Francesca Ceroni, Alice Boo, Simone Furini, Thomas E Gorochowski, Olivier Borkowski et al. doi:10.1038/nmeth.4635 In this CRISPR-based feedback control system, sgRNA expression is triggered by the burden of protein overexpression, and the sgRNA directs repression of the exogenous gene promoter to reduce burdensome expression and restore growth of the cell.   Advertisement Animation on CRISPR: Gene editing and beyond The CRISPR-Cas9 system has revolutionised gene editing, but cutting DNA isn't all it can do. This Animation, from Nature Methods, explores where CRISPR might be headed next. Watch the Animation here>> Produced with support from:  Dharmacon     Retraction Top Retraction: Unexpected mutations after CRISPR-Cas9 editing in vivo   p394 Kellie A Schaefer, Wen-Hsuan Wu, Diana F Colgan, Stephen H Tsang, Alexander G Bassuk et al. doi:10.1038/nmeth0518-394a   Application Note Top TwistAmp[reg] Liquid: a versatile amplification method to replace PCR    Oliver W Stringer, Jennifer M Andrews, Hazel L Greetham and Matthew S Forrest   Corrigenda Top Corrigendum: RNA-protein interaction detection in living cells   p394 Muthukumar Ramanathan, Karim Majzoub, Deepti S Rao, Poornima H Neela, Brian J Zarnegar et al. doi:10.1038/nmeth0518-394b   Corrigendum: CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets   p394 Shengdar Q Tsai, Nhu T Nguyen, Jose Malagon-Lopez, Ved V Topkar, Martin J Aryee et al. doi:10.1038/nmeth0518-394c   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. For event advertising opportunities across the Nature Publishing Group portfolio please contact natureevents@nature.com More Nature Events

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