Nature Methods Contents: October 2018, Volume 15 No 10

Advertisement Download our IHC e-book for tips & tricks on: Tissue preparation Tissue fixation Antigen retrieval Choosing the right chromogen Picking your detection system And more... TABLE OF CONTENTS October 2018 Volume 15, Issue 10 Editorial This Month Correspondence Research Highlights Technology Feature News & Views Brief Communications Articles Amendments & Corrections Advertisement Nikon's new A1R HD25 confocal system features the largest field of view on the market, enabling you to capture twice the data in a single shot. Increase your imaging throughput and gain better statistics with A1R HD25.  Learn more Advertisement Nature Index 2018 Rising Stars  Creative minds drive the scientific enterprise. This supplement profiles up-and-coming researchers in the natural sciences who have achieved excellence in the Nature Index, and have demonstrated the passion, ambition and resilience to rise even higher in the competitive world of academia.  Read the full supplement    Editorial Phototoxicity revisited    p751 doi:10.1038/s41592-018-0170-4 This Month Bridget Carragher    p753 Vivien Marx doi:10.1038/s41592-018-0147-3 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   Correspondence Assessing photodamage in live-cell STED microscopy    pp755 - 756 Nicole Kilian, Alexander Goryaynov, Mark D. Lessard, Giles Hooker, Derek Toomre et al. doi:10.1038/s41592-018-0145-5 Mutation frequency is not increased in CRISPR–Cas9-edited mice    pp756 - 758 Michaela Willi, Harold E. Smith, Chaochen Wang, Chengyu Liu & Lothar Hennighausen doi:10.1038/s41592-018-0148-2 Research Highlights Raising the game in image classification    p759 Nina Vogt doi:10.1038/s41592-018-0162-4 A tissue-to-organelle view of cellular proteins    p760 Vesna Todorovic doi:10.1038/s41592-018-0163-3 Does the number of chromosomes matter?    p761 Lei Tang doi:10.1038/s41592-018-0164-2 A model for tumor–immune interaction    p762 Natalie de Souza doi:10.1038/s41592-018-0165-1 Better base editors    p763 Nicole Rusk doi:10.1038/s41592-018-0154-4 Modeling temperature during optogenetic illumination    p763 Nina Vogt doi:10.1038/s41592-018-0155-3 Lighting up proteins    p763 Rita Strack doi:10.1038/s41592-018-0156-2 Evolving proteins with improved solubility    p763 Allison Doerr doi:10.1038/s41592-018-0157-1 Proximity labeling with TurboID    p764 Allison Doerr doi:10.1038/s41592-018-0158-0 Gentler super-resolution microscopy    p764 Rita Strack doi:10.1038/s41592-018-0159-z Engineering wild bacteria    p764 Nicole Rusk doi:10.1038/s41592-018-0160-6 Large-sized bilayer nanodiscs    p764 Lei Tang doi:10.1038/s41592-018-0161-5 Coloring electron microscopy connectomes    p765 Ada Yee doi:10.1038/s41592-018-0166-0 Technology Feature Base editing a CRISPR way    pp767 - 770 Vivien Marx doi:10.1038/s41592-018-0146-4 News & Views Single-particle analysis for fluorescence nanoscopy    pp771 - 772 Mark Bates doi:10.1038/s41592-018-0151-7 Deep learning reaches the motor system    pp772 - 773 Aaron P. Batista & James J. DiCarlo doi:10.1038/s41592-018-0152-6 A detector for the sources    pp774 - 775 Henry N. Chapman doi:10.1038/s41592-018-0150-8 Brief Communications Multicolor single-particle reconstruction of protein complexes    pp777 - 780 Christian Sieben, Niccolò Banterle, Kyle M. Douglass, Pierre Gönczy & Suliana Manley doi:10.1038/s41592-018-0140-x A computational and analytical framework enables multicolor 3D particle reconstruction of protein complexes from 2D images. The authors demonstrate the power of the approach by reconstructing native proteins within the human centriole. Template-free 2D particle fusion in localization microscopy    pp781 - 784 Hamidreza Heydarian, Florian Schueder, Maximilian T. Strauss, Ben van Werkhoven, Mohamadreza Fazel et al. doi:10.1038/s41592-018-0136-6 An all-to-all registration approach allows for improved, high-resolution, template-free single-particle reconstruction from localization microscopy data under realistic experimental conditions such as low labeling density. COMRADES determines in vivo RNA structures and interactions    pp785 - 788 Omer Ziv, Marta M. Gabryelska, Aaron T. L. Lun, Luca F. R. Gebert, Jessica Sheu-Gruttadauria et al. doi:10.1038/s41592-018-0121-0 In vivo probing of RNA structures with COMRADES yields insight into RNA folding of the ZIKA virus genome and its interaction with host RNAs. Three-photon imaging of mouse brain structure and function through the intact skull    pp789 - 792 Tianyu Wang, Dimitre G. Ouzounov, Chunyan Wu, Nicholas G. Horton, Bin Zhang et al. doi:10.1038/s41592-018-0115-y Wang et al. demonstrate that the effects of aberrations and scattering caused by the mouse skull can be reduced with three-photon microscopy. Their approach allows structural and functional imaging of the brain through an intact skull. Reducing effects of particle adsorption to the air–water interface in cryo-EM    pp793 - 795 Alex J. Noble, Hui Wei, Venkata P. Dandey, Zhening Zhang, Yong Zi Tan et al. doi:10.1038/s41592-018-0139-3 Reducing the length of time that protein particles spend on a sample grid prior to freezing mitigates deleterious effects caused by particle adsorption to the air–water interface in single-particle cryo-EM. Qiita: rapid, web-enabled microbiome meta-analysis    pp796 - 798 Antonio Gonzalez, Jose A. Navas-Molina, Tomasz Kosciolek, Daniel McDonald, Yoshiki Vázquez-Baeza et al. doi:10.1038/s41592-018-0141-9 The Qiita web platform provides access to large amounts of public microbial multi-omic data and enables easy analysis and meta-analysis of standardized private and public data. Articles Fast and accurate data collection for macromolecular crystallography using the JUNGFRAU detector    pp799 - 804 Filip Leonarski, Sophie Redford, Aldo Mozzanica, Carlos Lopez-Cuenca, Ezequiel Panepucci et al. doi:10.1038/s41592-018-0143-7 A charge-integrating pixel-array detector called JUNGFRAU enables the collection of highly accurate X-ray crystallography data at synchrotron sources at unprecedented speeds. Inferring single-trial neural population dynamics using sequential auto-encoders    pp805 - 815 Chethan Pandarinath, Daniel J. O'Shea, Jasmine Collins, Rafal Jozefowicz, Sergey D. Stavisky et al. doi:10.1038/s41592-018-0109-9 LFADS, a deep learning method for analyzing neural population activity, can extract neural dynamics from single-trial recordings, stitch separate datasets into a single model, and infer perturbations, for example, from behavioral choices to these dynamics. Deep generative models of genetic variation capture the effects of mutations    pp816 - 822 Adam J. Riesselman, John B. Ingraham & Debora S. Marks doi:10.1038/s41592-018-0138-4 DeepSequence is an unsupervised deep latent-variable model that predicts the effects of mutations on the basis of evolutionary sequence information. All-optical synaptic electrophysiology probes mechanism of ketamine-induced disinhibition    pp823 - 831 Linlin Z. Fan, Ralda Nehme, Yoav Adam, Eun Sun Jung, Hao Wu et al. doi:10.1038/s41592-018-0142-8 The synOptopatch approach enables all-optical access to synaptic communication via mutually exclusive expression of an optogenetic actuator and a voltage sensor in pre- and postsynaptic neurons, respectively. Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms    pp832 - 836 Andreas J. Gruber, Foivos Gypas, Andrea Riba, Ralf Schmidt & Mihaela Zavolan doi:10.1038/s41592-018-0114-z TECtool identifies terminal exons from RNA-seq data, uncovering novel isoforms, many of which are translated. Amendments & Corrections Publisher Correction: Calling cell biologists to try cryo-ET    p837 Vivien Marx doi:10.1038/s41592-018-0135-7 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. 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