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TABLE OF CONTENTS
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July 2017 Volume 14, Issue 7 |
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| In This Issue Editorial This Month Correspondence Research Highlights Commentaries Technology Feature News and Views Analysis Brief Communications Articles Errata Corrigendum | |
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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.
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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 | | | |
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In This Issue | Top |
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In This Issue |
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Editorial | Top |
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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. |
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This Month | Top |
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The Author File: Alexis Battle p639 Vivien Marx doi:10.1038/nmeth.4345 Calculating gene-environment interactions, and the role of a 'why' machine. |
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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. |
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Correspondence | Top |
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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 |
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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. |
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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 |
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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 |
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Research Highlights | Top |
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Commentaries | Top |
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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. |
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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. |
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Technology Feature | Top |
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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. |
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News and Views | Top |
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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. |
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Analysis | Top |
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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. |
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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. |
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Brief Communications | Top |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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Advanced Imaging with Proven Optics
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Articles | Top |
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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. |
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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 |
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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. |
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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. |
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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. |
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Errata | Top |
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Erratum: In vivo imaging of neural activity p752 Weijian Yang and Rafael Yuste doi:10.1038/nmeth0717-752a |
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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 |
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Erratum: Optoacoustic imaging at multiple spatiotemporal scales p752 Rita Strack doi:10.1038/nmeth0717-752d |
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Corrigendum | Top |
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Corrigendum: In vivo imaging of neural activity p752 Weijian Yang and Rafael Yuste doi:10.1038/nmeth0717-752b |
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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 | | | |
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| | | | | | 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 | | | | | |
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