Nature Methods Contents: March 2018, Volume 15 No 3 pp 151 - 227

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Advertisement Can you trust your Antibody? Implications for disease research. A recent publication in Scientific Reports rigorously tested nine commercially available antibodies for specificity and sensitivity and found that only one, from Cell Signaling Technology, met all validation criteria. Read this open-access article to explore the potentially serious implications of non-specific antibodies and disease research. Read more now. TABLE OF CONTENTS March 2018 Volume 15, Issue 3 Editorial This Month Correspondence Research Highlights Technology Feature News and Views Perspective Brief Communications Articles Erratum Corrigenda   Advertisement Nikon's all-new A1R HD confocal features a High Definition 1K resonant scanner, which delivers high resolution images at ultra-high speed. The new scanner also provides 4x the field of view at the same resolution usually generated by a normal 512x512 scanner. Learn more    Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Nature Collection: 2017 Nobel Prize in Physiology or Medicine The 2017 Nobel Prize in Physiology or Medicine was awarded to Jeffrey C. Hall, Michael Rosbash and Michael W. Young for their pioneering work in Drosophila that elucidated the molecular mechanisms controlling circadian rhythm.  Access this collection free online>> Produced with support from:  Vanda Pharmaceuticals     Advertisement npj Molecular Phenomics is an online-only, open access journal that provides a forum for cutting-edge scientific advances in the emerging field of phenomics, the study of the physical and chemical characteristics of an individual in quantitative terms. Part of the Nature Partner Journals series, npj Molecular Phenomics is published in partnership with Fudan University. The journal is now open for submissions.   Find out more >>>    Editorial Top Sharing epigenomes globally   p151 doi:10.1038/nmeth.4630 Epigenome reference data are continually being enriched—researchers should explore them, even if raw data access still presents some hurdles.   This Month Top The Author File: Miguel Angel Esteban   p153 Vivien Marx doi:10.1038/nmeth.4626 A way to study the RNA interactome, baby RNA encounters, a sprinkle of poetry.   Correspondence Top hichipper: a preprocessing pipeline for calling DNA loops from HiChIP data   pp155 - 156 Caleb A Lareau and Martin J Aryee doi:10.1038/nmeth.4583   Picky: a simple online PRM and SRM method designer for targeted proteomics   pp156 - 157 Henrik Zauber, Marieluise Kirchner and Matthias Selbach doi:10.1038/nmeth.4607   Research Highlights Top Gas vesicles enable ultrasound imaging Acoustic reporter genes that produce gas vesicles offer a way to image and locate microorganisms in mammalian hosts. Tracking the protein-metabolite interactome A method combining limited proteolysis with mass spectrometry systematically detects protein-metabolite interactions. Gene factories made of droplets How to make large synthetic gene libraries out of some beads, an oligo array and an emulsion. Imaging allelic loci in live cells SNP-CLING enables determining the dynamics of alleles on different chromosomes in live cells. Transcriptomics in the NICHE The combination of photoactivatable fluorescent markers with single-cell RNA-seq allows transcriptome analysis of cells from specific tissue locations. Methods in Brief Top Cas goes rogue | Tilted light-sheet microscopy with 3D point-spread functions | Light-based RNA structure probing | Antibody function revealed in high throughput Tools in Brief Top The Protein Contacts Atlas | A four-armed patch-clamping robot | An expanded set of full-length microbial marker genes | Tracking nanoparticles by eye Methods JOBS of the week Dean of the Faculty of Science The Chinese University of Hong Kong Associate Research Scientist Columbia University Postdoctoral Fellow Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Computational Scientist Celgene CITRE Research Group Leader Opening IGFL More Science jobs from Methods EVENT Computational Methods in Systems Biology (CMSB 2018) 12.09.18 Brno, Czech Republic More science events from Technology Feature Top Putting microfluidics in other people's hands   pp167 - 170 Vivien Marx doi:10.1038/nmeth.4609 In microfluidics, sharing is hard. But practitioners are exploring new ways to share designs, devices and experience.   News and Views Top RNA dynamics revealed by metabolic RNA labeling and biochemical nucleoside conversions   pp171 - 172 Marisa A P Baptista and Lars Dölken doi:10.1038/nmeth.4608 The combination of metabolic RNA labeling with biochemical nucleoside conversion now adds a broadly applicable temporal dimension to RNA sequencing. See also: Article by Schofield et al. Perspective Top STED super-resolved microscopy   pp173 - 182 Giuseppe Vicidomini, Paolo Bianchini and Alberto Diaspro doi:10.1038/nmeth.4593 This Perspective reviews nanoscopy via stimulated emission depletion (STED), focusing on challenges for biologists and how technical advances are helping to meet these challenges.   Brief Communications Top EVIR: chimeric receptors that enhance dendritic cell cross-dressing with tumor antigens   pp183 - 186 Mario Leonardo Squadrito, Chiara Cianciaruso, Sarah K Hansen and Michele De Palma doi:10.1038/nmeth.4579 Chimeric receptors expressed on the surface of antigen-presenting cells enable the uptake of cancer-cell-derived extracellular vesicles and the display of tumor antigens.   Widespread bacterial protein histidine phosphorylation revealed by mass spectrometry-based proteomics   pp187 - 190 Clement M Potel, Miao-Hsia Lin, Albert J R Heck and Simone Lemeer doi:10.1038/nmeth.4580 A twist on a common method used for enriching phosphorylated peptides for mass spectrometry-based proteomics analysis now reveals previously undetected and widespread histidine phosphorylation in Escherichia coli.   Ab initio electron density determination directly from solution scattering data   pp191 - 193 Thomas D Grant doi:10.1038/nmeth.4581 An iterative structure factor retrieval algorithm allows electron densities to be directly calculated from solution scattering data, avoiding assumptions that limit modeling algorithms.   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 Supermultiplexed optical imaging and barcoding with engineered polyynes   pp194 - 200 Fanghao Hu, Chen Zeng, Rong Long, Yupeng Miao, Lu Wei et al. doi:10.1038/nmeth.4578 A class of probes enables highly multiplexed imaging and barcoding applications with Raman microscopy.   Highly parallel direct RNA sequencing on an array of nanopores   pp201 - 206 Daniel R Garalde, Elizabeth A Snell, Daniel Jachimowicz, Botond Sipos, Joseph H Lloyd et al. doi:10.1038/nmeth.4577 Direct sequencing of RNA molecules in real time using nanopores allows for the detection of splice variants and hold promises for profiling RNA modifications.   RNA-protein interaction detection in living cells   pp207 - 212 Muthukumar Ramanathan, Karim Majzoub, Deepti S Rao, Poornima H Neela, Brian J Zarnegar et al. doi:10.1038/nmeth.4601 RaPID uses biotin ligases BirA[ast] and the faster acting BASU to label proteins in the proximity of an RNA motif of interest in living cells.   Capturing the interactome of newly transcribed RNA   pp213 - 220 Xichen Bao, Xiangpeng Guo, Menghui Yin, Muqddas Tariq, Yiwei Lai et al. doi:10.1038/nmeth.4595 Labeling newly transcribed RNA with 5-ethynyluridine and adding biotin via click chemistry allows the analysis of the proteome bound to the various RNA species, including nascent RNA.   TimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding   pp221 - 225 Jeremy A Schofield, Erin E Duffy, Lea Kiefer, Meaghan C Sullivan and Matthew D Simon doi:10.1038/nmeth.4582 TimeLapse-seq chemically recodes labeled s4U nucleosides to a cytidine derivative and monitors transcriptional dynamics. See also: News and Views by Baptista & Dolken Advertisement nature.com webcasts Springer Nature presents a custom webcast on: Sequencing Structural Variants for Disease Gene Discovery and Population Genetics Date: Thursday, March 8, 2018  Register for FREE  Sponsored by: PacBio    Corrigenda Top Corrigendum: Automated structure modeling of large protein assemblies using crosslinks as distance restraints   p226 Mathias Ferber, Jan Kosinski, Alessandro Ori, Umar J Rashid, María Moreno-Morcillo et al. doi:10.1038/nmeth0318-226b   Corrigendum: Nm-seq maps 2'-O-methylation sites in human mRNA with base precision   pp226 - 227 Qing Dai, Sharon Moshitch-Moshkovitz, Dali Han, Nitzan Kol, Ninette Amariglio et al. doi:10.1038/nmeth0318-226c   Erratum Top Erratum: Depleting endogenous proteins   p226 Ada Yee doi:10.1038/nmeth0318-226a   Top Advertisement nature.com webcasts Join us for our upcoming webcast with live Q&A:  FIGHTING INFECTIOUS DISEASES Presented by BioPharma Dealmakers Date: Tuesday, February 27, 2018 Time: 8AM PST, 11AM EST, 4PM GMT, 5PM CET REGISTER FOR FREE Sponsored by: PaxVax, Inc., NovaBiotics Ltd, Wellcome      Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. 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