Nature Methods Contents: July 2017 Volume 14 pp 637 - 752

If you are unable to see the message below, click here to view.

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 July 2017 Volume 14, Issue 7 In This Issue Editorial This Month Correspondence Research Highlights Commentaries Technology Feature News and Views Analysis Brief Communications Articles Errata Corrigendum Advertisement   Detect and Modulate T Cell Activation in Real Time. See for yourself how it can be used to optimize CAR T durability. The Agilent Seahorse XFp analyzer detects real-time T cell activation response within minutes with CD3/CD28 immunogenic beads by measuring discrete changes in cellular glycolysis. Accelerate you analysis with XF technology. Watch the webinar to learn more Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Inspiration does not obey speed limits. Announcing the ORCA-Lightning from Hamamatsu. Our new 12MP sCMOS camera engineered for high speed and low noise and ready for Lightsheet microscopy.  hamamatsucameras.com   Advertisement Nature Index China 2017 China continues to increase its global share of research papers, but publication numbers are just one indicator that a country's science is thriving. Read the full supplement free for six months   Advertisement MEDTECH DEALMAKERS A supplement to Nature Biotechnology | Nature Medicine | Nature Reviews Drug Discovery Medtech Dealmakers explores the dealmaking strategies of the growing medical technology industry, and provides in-depth analysis of emerging technologies, as well as showcase innovative companies seeking partners. Check out the latest issue for medtech dealmaking and financing trends in 2016, and diagnostics deals from the past year- particularly for immuno oncology applications. Download the issue for FREE     In This Issue Top In This Issue      Editorial Top Seeing red   p637 doi:10.1038/nmeth.4363 The growing advantages of red to near-infrared fluorescent probes should move them beyond being a 'second color' in biological imaging.   This Month Top The Author File: Alexis Battle   p639 Vivien Marx doi:10.1038/nmeth.4345 Calculating gene-environment interactions, and the role of a 'why' machine.   Points of Significance: Principal component analysis   pp641 - 642 Jake Lever, Martin Krzywinski and Naomi Altman doi:10.1038/nmeth.4346 PCA helps you interpret your data, but it will not always find the important patterns.   Correspondence Top Mass spectrometrists should search for all peptides, but assess only the ones they care about   pp643 - 644 Adriaan Sticker, Lennart Martens and Lieven Clement doi:10.1038/nmeth.4338 See also: Correspondence by Noble & Keich Response to “Mass spectrometrists should search for all peptides, but assess only the ones they care about”   p644 William Stafford Noble and Uri Keich doi:10.1038/nmeth.4339 See also: Correspondence by Sticker et al. ProHits-viz: a suite of web tools for visualizing interaction proteomics data   pp645 - 646 James D R Knight, Hyungwon Choi, Gagan D Gupta, Laurence Pelletier, Brian Raught et al. doi:10.1038/nmeth.4330   PIQED: automated identification and quantification of protein modifications from DIA-MS data   pp646 - 647 Jesse G Meyer, Sushanth Mukkamalla, Hanno Steen, Alexey I Nesvizhskii, Bradford W Gibson et al. doi:10.1038/nmeth.4334   Research Highlights Top Better tools for Bacteroides Two sets of complementary tools extend our capacity to manipulate the gut microbiome. Charting the subcellular proteome Human protein subcellular locations light up in the Cell Atlas resource. CRISPR kinetics In vitro Cas9-binding assays show the effects of mutations in the target sequence on binding kinetics. Zooming into the larval zebrafish brain A serial-section electron microscopy data set of larval zebrafish brain—imaged at several scales—provides a resource for structure-function analyses of the animals' neural circuitry. Organoid variability examined Single-cell transcriptomics is used to determine what cell types are present in brain organoids and how much these cell types vary across organoids. Methods in Brief Buckets of bacterial genomes | Reconciling small and large scales with FIB-SEM | Ultrafast thermal cycling | Single-protein detection by cryo-EM Tools in Brief Self-limiting Cas9 | Functional blood progenitors for mouse and man | The BioPlex network, 2.0 | Supramolecular assemblies for NIR II imaging Methods JOBS of the week Research Fellow - Data analytics and machine learning (Bioinformatics) University of Birmingham Several PhD positions / one Postdoc position Albert-Ludwigs-Universitaet Freiburg Scientist, Molecular Interaction and Characterization – Bioanalytical Sciences (BAS) Genentech, Inc. Postdoctoral position in bioinformatics / computational biology Stanford University Post-Doctoral Fellow in Bioinformatics / Statistical Genetics Sidra Medical and Research Centre More Science jobs from Methods EVENT NETTAB 2017 Methods, tools & platforms for Personalized Medicine in the Big Data Era 16.10.17 Palermo, Italy More science events from Commentaries Top Assessing phototoxicity in live fluorescence imaging   pp657 - 661 P Philippe Laissue, Rana A Alghamdi, Pavel Tomancak, Emmanuel G Reynaud and Hari Shroff doi:10.1038/nmeth.4344 This Commentary discusses the problem of phototoxicity in live imaging and suggests guidelines to improve its assessment and reporting.   Towards a perceptive understanding of size in cellular biology   pp662 - 665 Monica Zoppè doi:10.1038/nmeth.4300 This piece tackles the question of how to make biological scale more intuitive to human beings, bringing to bear the author's background in scientific visualization.   Technology Feature Top Metabolism: sweeter paths in glycoscience   pp667 - 670 Vivien Marx doi:10.1038/nmeth.4333 Carbohydrates are tough molecules to study, but glycoscientists are developing and democratizing the needed tools.   News and Views Top Illuminating redox biology using NADH- and NADPH-specific sensors   pp671 - 672 Andreas Wiederkehr and Nicolas Demaurex doi:10.1038/nmeth.4336 Genetically encoded NAD and NADP sensors will revolutionize the study of redox biology. See also: Article by Tao et al. Analysis Top FISH-ing for captured contacts: towards reconciling FISH and 3C   pp673 - 678 Geoffrey Fudenberg and Maxim Imakaev doi:10.1038/nmeth.4329 This Analysis explores the relationship between chromosome conformation capture (for example, Hi-C) and FISH datasets, and uses simulations to reconcile measurements from the two technologies.   Comparison of computational methods for Hi-C data analysis   pp679 - 685 Mattia Forcato, Chiara Nicoletti, Koustav Pal, Carmen Maria Livi, Francesco Ferrari et al. doi:10.1038/nmeth.4325 Six tools to call chromatin interactions and seven tools for topologically associating domain calling are systematically compared with real and simulated data. The strengths and weaknesses of each tool are discussed.   Brief Communications Top Differential analysis of RNA-seq incorporating quantification uncertainty   pp687 - 690 Harold Pimentel, Nicolas L Bray, Suzette Puente, Páll Melsted and Lior Pachter doi:10.1038/nmeth.4324 By using bootstraps that estimate inferential variance, the sleuth method and software provide fast and highly accurate differential gene expression analysis in an interactive Shiny app.   webKnossos: efficient online 3D data annotation for connectomics   pp691 - 694 Kevin M Boergens, Manuel Berning, Tom Bocklisch, Dominic Bräunlein, Florian Drawitsch et al. doi:10.1038/nmeth.4331 webKnossos is a browser-based tracing and annotation tool for 3D electron microscopy data sets that is optimized for seamless data viewing. The tool/'s flight-mode view facilitates fast neurite tracing because of its egocentric viewpoint.   Nm-seq maps 2′-O-methylation sites in human mRNA with base precision   pp695 - 698 Qing Dai, Sharon Moshitch-Moshkovitz, Dali Han, Nitzan Kol, Ninette Amariglio et al. doi:10.1038/nmeth.4294 Iterative oxidation, elimination and dephosphorylation steps remove nucleotides from the 3′ end of RNA until a 2′-O-methylated ribose that cannot be oxidized is encountered and brings the process to a stop. High-throughput sequencing of these fragments exposes 2′-O-methyl sites at base resolution.   Allele-specific expression reveals interactions between genetic variation and environment   pp699 - 702 David A Knowles, Joe R Davis, Hilary Edgington, Anil Raj, Marie-Julie Favé et al. doi:10.1038/nmeth.4298 The EAGLE algorithm and software identifies replicable gene-by-environment interactions based on associations between environment and allele-specific expression.   Quantitative mRNA imaging throughout the entire Drosophila brain   pp703 - 706 Xi Long, Jennifer Colonell, Allan M Wong, Robert H Singer and Timothée Lionnet doi:10.1038/nmeth.4309 Improved fluorescence in situ hybridization enables smFISH in cleared whole-mount Drosophila brains with confocal microscopy; a custom Bessel beam structured illumination microscope allows single-mRNA detection across the entire brain.   Testing for differential abundance in mass cytometry data   pp707 - 709 Aaron T L Lun, Arianne C Richard and John C Marioni doi:10.1038/nmeth.4295 A statistical approach makes it possible to detect differentially abundant cell populations across biological conditions from high-dimensional mass cytometry data without relying on cell clustering.   CRISPR-STOP: gene silencing through base-editing-induced nonsense mutations   pp710 - 712 Cem Kuscu, Mahmut Parlak, Turan Tufan, Jiekun Yang, Karol Szlachta et al. doi:10.1038/nmeth.4327 Early STOP codons created with CRISPR base editors leads to gene knockout with high efficiency and does not stress cells with double-strand DNA breaks. CRISPR-STOP can target the majority of human genes and is useful for genetic screens.   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 Fast high-resolution miniature two-photon microscopy for brain imaging in freely behaving mice   pp713 - 719 Weijian Zong, Runlong Wu, Mingli Li, Yanhui Hu, Yijun Li et al. doi:10.1038/nmeth.4305 FHIRM-TPM is a miniature two-photon microscope capable of imaging fluorescently labeled neurons in the brains of freely behaving mice. It allows for imaging of spines or recording of neural activity with a frame rate up to 40 Hz.   Genetically encoded fluorescent sensors reveal dynamic regulation of NADPH metabolism   pp720 - 728 Rongkun Tao, Yuzheng Zhao, Huanyu Chu, Aoxue Wang, Jiahuan Zhu et al. doi:10.1038/nmeth.4306 Genetically encoded iNap sensors allow imaging of NADPH with high spatiotemporal resolution in living systems. The iNaps cover physiologically relevant NADPH concentrations and are demonstrated in mammalian cells and live zebrafish. See also: News and Views by Wiederkehr & Demaurex Biosynthesis and genetic encoding of phosphothreonine through parallel selection and deep sequencing   pp729 - 736 Michael Shaofei Zhang, Simon F Brunner, Nicolas Huguenin-Dezot, Alexandria Deliz Liang, Wolfgang H Schmied et al. doi:10.1038/nmeth.4302 A new approach to evolve novel aminoacyl-tRNA synthetase-tRNA pairs with orthogonal substrate specificity is applied to generate a system to site-specifically incorporate phosphothreonine into proteins, enabling functional studies of this post-translational modification.   A quantitative and multiplexed approach to uncover the fitness landscape of tumor suppression in vivo   pp737 - 742 Zoë N Rogers, Christopher D McFarland, Ian P Winters, Santiago Naranjo, Chen-Hua Chuang et al. doi:10.1038/nmeth.4297 The combination of tumor barcoding with CRISPR-mediated targeting of tumor suppressors allows quantitative analysis of tumor-suppressor function during tumor growth in vivo.   Fused cerebral organoids model interactions between brain regions   pp743 - 751 Joshua A Bagley, Daniel Reumann, Shan Bian, Julie Lévi-Strauss and Juergen A Knoblich doi:10.1038/nmeth.4304 The fusion of patterned cerebral organoids into more complex structures enables modeling of inter-regional processes such as neuronal migration.   Advertisement Focus on Disease models: reproducibility and translation  Lab Animal, a Nature Research journal focusing on in vivo methods, research and technology with model organisms of human health & disease, presents a special Focus on reproducibility and translation of in vivo research with disease models.  Access this Focus > Produced with support from:  Taconic Biosciences, Inc.  Charles River   Errata Top Erratum: In vivo imaging of neural activity   p752 Weijian Yang and Rafael Yuste doi:10.1038/nmeth0717-752a   Erratum: Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput   p752 Todd M Gierahn, Marc H Wadsworth II, Travis K Hughes, Bryan D Bryson, Andrew Butler et al. doi:10.1038/nmeth0717-752c   Erratum: Optoacoustic imaging at multiple spatiotemporal scales   p752 Rita Strack doi:10.1038/nmeth0717-752d   Corrigendum Top Corrigendum: In vivo imaging of neural activity   p752 Weijian Yang and Rafael Yuste doi:10.1038/nmeth0717-752b   Top Advertisement Call for nominations: 2017 John Maddox Prize for Standing up for Science. Recognising the work of individuals who promote science in the face of hostility. Winners will be announced at a reception in London, as well as in Nature, and will receive £2,000. Closing date for nominations is 31st July 2017. Click to learn more   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

You have been sent this Table of Contents Alert because you have opted in to receive it. You can change or discontinue your e-mail alerts at any time, by modifying your preferences on your nature.com account at: www.nature.com/myaccount (You will need to log in to be recognised as a nature.com registrant) For further technical assistance, please contact our registration department For print subscription enquiries, please contact our subscription department For other enquiries, please contact our customer feedback department Springer Nature | One New York Plaza, Suite 4500 | New York | NY 10004-1562 | USA Springer Nature's worldwide offices: London - Paris - Munich - New Delhi - Tokyo - Melbourne San Diego - San Francisco - Washington - New York - Boston Macmillan Publishers Limited is a company incorporated in England and Wales under company number 785998 and whose registered office is located at The Campus, 4 Crinan Street, London, N1 9XW. © 2017 Macmillan Publishers Limited, part of Springer Nature. All Rights Reserved.