Nature Methods Contents: October 2016 Volume 13 pp 799 - 890

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Discover how the Fast mode for Airyscan compares to traditional confocal detection and download our free white paper with more information TABLE OF CONTENTS October 2016 Volume 13, Issue 10 In This Issue Editorials This Month Correspondence Research Highlights Commentary Technology Feature Brief Communications Articles Corrigenda Application Notes Advertisement   Determine the Metabolic Phenotype of Your Cells The Agilent Seahorse XF Cell Energy Phenotype Test uses as few as 15,000 cells, and the Agilent Seahorse XFp Analyzer, to identify your cells' metabolic phenotype, as well as their metabolic potential - the relative utilization of mitochondrial respiration and glycolysis.  http://bit.ly/1Caw9Eq Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Fluorescence-Based Cell Biology Assays Cell Proliferation & Viability Assays - iClick™ EdU assays, AlamarBlue cell viability assays, LIVE-or-DIE™ cell viability/cytotoxicity assays, cell generation analysis, and more Cell Apoptosis Assays - TUNEL assays, caspase activity assays, annexin V binding assays, mitochondrial membrane potential assays, and more Cell Structure Probes - Cytoskeleton, nucleus, golgi complex, membrane, cytosol, mitochondria, lysosome, endoplasmic Learn more >>   Advertisement Get +Together. Experience the new Eppendorf Centrifuge 5920 R and its seamless integration with Eppendorf Conical Tubes and Eppendorf DWP/MTP Plates. Spin tubes and plates in the same bucket. No separate plate buckets needed. Your benefit? Save cost! Click here   Advertisement Experimental & Molecular Medicine is an open access journal to communicate experimental and translational research performed using molecular tools. Submit your manuscript.   In This Issue Top In This Issue    Editorials Top Where are the data?   p799 doi:10.1038/nmeth.4026 Nature Methods now requires data availability statements to be supplied with research papers. And are the tools available?   p799 doi:10.1038/nmeth.4039 We take the opportunity to remind our readers of the materials sharing policy at Nature Methods. This Month Top The Author File: Shankar Balasubramanian   p801 Vivien Marx doi:10.1038/nmeth.4002 A chemist intrigued by DNA and RNA structure and two-wheeled mountainous ascents. Points of Significance: Regularization   pp803 - 804 Jake Lever, Martin Krzywinski and Naomi Altman doi:10.1038/nmeth.4014 Constraining the magnitude of parameters of a model can control its complexity Correspondence Top The NIH Protein Capture Reagents Program (PCRP): a standardized protein affinity reagent toolbox   pp805 - 806 Seth Blackshaw, Anand Venkataraman, Jose Irizarry, Kun Yang, Stephen Anderson et al. doi:10.1038/nmeth.4013 DoCM: a database of curated mutations in cancer   pp806 - 807 Benjamin J Ainscough, Malachi Griffith, Adam C Coffman, Alex H Wagner, Jason Kunisaki et al. doi:10.1038/nmeth.4000 Micro-Magellan: open-source, sample-adaptive, acquisition software for optical microscopy   pp807 - 809 Henry Pinkard, Nico Stuurman, Kaitlin Corbin, Ronald Vale and Matthew F Krummel doi:10.1038/nmeth.3991 Research Highlights Top Optogenetics at cellular resolution A combination of restricting channel-rhodopsin to the soma and restricting the excitation volume with temporal focusing enables the mapping of neural circuits with high precision. A nervous system from Mom and a gonad from Dad A simple tweak on the zygote's mitotic spindle generated hybrid Caenorhabditis elegans with certain tissues (such as those of the nervous system) consisting of entirely maternal genomes and others (such as the germline) consisting of entirely paternal genomes. Crowdsourcing for natural products research The Global Natural Products Social Molecular Networking knowledgebase facilitates community sharing and curation of mass spectrometry data from natural products. Simultaneous multicolor localization microscopy Point spread function engineering streamlines multicolor super-resolution imaging and single-particle tracking. Learning the histone language Sequential rounds of immunoprecipitation and barcoding reveal the genome-wide occurrence of paired histone marks. The definition of naive Scientists propose a more human-centric benchmark for assessing naive and primed pluripotency in human embryonic stem cells. Tracking the proteome A combination of quantitative mass spectrometry, subcellular fractionation and stringent statistical analyses allows the description of protein translocation events at the proteome scale. Methods in Brief Fast and easy super-resolution microscopy | A single-cell screen for genetic drivers of leukemia | Faster spinning for better structure resolution | Label-free histopathology Tools in Brief Juicer and Juicebox for chromatin conformation analysis | Wireless recording of neural activity with ultrasound | Expanding known viral diversity | Antigen-receptor sequences captured from single T cells Methods JOBS of the week Research Scientist: Fermentation California Institute for Biomedical Research Senior Scientist: Process Biochemistry California Institute for Biomedical Research Experimental Planetology University of Bayreuth (Germany) Institute Research Investigator - Systems Biology - 108709 The University of Texas MD Anderson Cancer Center Institute Research Scientist - Translational Biomarker Discovery The University of Texas MD Anderson Cancer Center More Science jobs from Commentary Top A proposal for validation of antibodies   pp823 - 827 Mathias Uhlen, Anita Bandrowski, Steven Carr, Aled Edwards, Jan Ellenberg et al. doi:10.1038/nmeth.3995 We convened an ad hoc International Working Group for Antibody Validation in order to formulate the best approaches for validating antibodies used in common research applications and to provide guidelines that ensure antibody reproducibility. We recommend five conceptual 'pillars' for antibody validation to be used in an application-specific manner. Technology Feature Top Genomics in 3D and 4D   pp829 - 832 Vivien Marx doi:10.1038/nmeth.4001 DNA folding shapes gene expression. Emerging techniques promise to reveal the intricacies of this architectural language of chromosomes. Brief Communications Top Single-cell multimodal profiling reveals cellular epigenetic heterogeneity   pp833 - 836 Lih Feng Cheow, Elise T Courtois, Yuliana Tan, Ramya Viswanathan, Qiaorui Xing et al. doi:10.1038/nmeth.3961 sc-GEM enables the dissection of cellular heterogeneity by simultaneously assaying the status of DNA mutations, gene expression and DNA methylation at multiple targeted loci in individual cells. MetaMass, a tool for meta-analysis of subcellular proteomics data   pp837 - 840 Fridtjof Lund-Johansen, Daniel de la Rosa Carrillo, Adi Mehta, Krzysztof Sikorski, Marit Inngjerdingen et al. doi:10.1038/nmeth.3967 A straightforward method and tool, MetaMass, utilizes a list of subcellular markers to analyze and classify subcellular proteomics data from multiple experiments. An accompanying analysis reveals a wide variation in the results of subcellular fractionation protocols. rG4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome   pp841 - 844 Chun Kit Kwok, Giovanni Marsico, Aleksandr B Sahakyan, Vicki S Chambers and Shankar Balasubramanian doi:10.1038/nmeth.3965 rG4-seq enables the mapping of RNA G-quadruplex structures across entire transcriptomes at nucleotide resolution. Diffusion pseudotime robustly reconstructs lineage branching   pp845 - 848 Laleh Haghverdi, Maren Büttner, F Alexander Wolf, Florian Buettner and Fabian J Theis doi:10.1038/nmeth.3971 Diffusion pseudotime (DPT) enables robust and scalable inference of cellular trajectories, branching events, metastable states and underlying gene dynamics from snapshot single-cell gene expression data. Vibrio natriegens as a fast-growing host for molecular biology   pp849 - 851 Matthew T Weinstock, Eric D Hesek, Christopher M Wilson and Daniel G Gibson doi:10.1038/nmeth.3970 A suite of tools and resources for Vibrio natriegens introduces the bacterium as a faster-growing alternative to E. coli for molecular biology and biotechnology applications. Augmenting CRISPR applications in Drosophila with tRNA-flanked sgRNAs   pp852 - 854 Fillip Port and Simon L Bullock doi:10.1038/nmeth.3972 Expressing guide RNAs from a tRNA scaffold enhances mutagenesis by both Cas9 and Cpf1 and allows conditional CRISPR applications in vivo. DSBCapture: in situ capture and sequencing of DNA breaks   pp855 - 857 Stefanie V Lensing, Giovanni Marsico, Robert Hänsel-Hertsch, Enid Y Lam, David Tannahill et al. doi:10.1038/nmeth.3960 Double-strand DNA breaks capture (DSBCapture) identifies in situ DSBs via the ligation of an Illumina adaptor into the break site and shows no bias for chromatin state or base composition. A genome-wide DSB profile shows breaks occurring more frequently in euchromatin and transcriptionally active regions. Advertisement Need access to Nature Plants at your workplace or institution? Site license access offers full online content plus added benefits! Recommend site license access to your librarian.   Articles Top Shrinkage-mediated imaging of entire organs and organisms using uDISCO   pp859 - 867 Chenchen Pan, Ruiyao Cai, Francesca Paola Quacquarelli, Alireza Ghasemigharagoz, Athanasios Lourbopoulos et al. doi:10.1038/nmeth.3964 uDISCO clearing renders whole animals transparent and capitalizes on shrinkage to image them. This method allows the analysis of intact nervous systems and whole-body screens for transplanted cells and human tissue samples after prolonged storage. A multifunctional AAV-CRISPR-Cas9 and its host response   pp868 - 874 Wei Leong Chew, Mohammadsharif Tabebordbar, Jason K W Cheng, Prashant Mali, Elizabeth Y Wu et al. doi:10.1038/nmeth.3993 Packaging split Cas9 into AAVs increases cargo capacity and allows for efficient genome editing and gene activation in vivo. AAV-split-Cas9 activates the host immune system but does not trigger the extensive cellular damage observed with delivery of Cas9 via DNA electroporation. Stable long-term chronic brain mapping at the single-neuron level   pp875 - 882 Tian-Ming Fu, Guosong Hong, Tao Zhou, Thomas G Schuhmann, Robert D Viveros et al. doi:10.1038/nmeth.3969 Flexible mesh electronics facilitate stable long-term recordings of the same single neurons in mouse brains over months, enabling chronic recordings in behaving animals and longitudinal studies to resolve aging-dependent changes in neural activity. An in vivo multiplexed small-molecule screening platform   pp883 - 889 Barbara M Grüner, Christopher J Schulze, Dian Yang, Daisuke Ogasawara, Melissa M Dix et al. doi:10.1038/nmeth.3992 The combination of cellular barcoding and treatment with a library of small molecules before injecting the treated cells into mice allows the screening for compounds that inhibit metastatic seeding. Advertisement Human Genome Variation (HGV) is an online, open access journal with accompanying database. Submit your next manuscript to Human Genome Variation and benefit from: - Quality peer-review and fast decision times - High visibility for your research - Now included within PubMed - Article Processing Charge for Data Reports waived now Learn more.   Application Notes Top Real-time monitoring of cellular metabolic activity: intracellular oxygen    Andrea Krumm and Conn Carey DNA fragmentation and quality control analysis using Diagenode shearing systems and Fragment Analyzer    Wassim Lakha, Irina Panteleeva, Sharon Squazzo, Rini Saxena, Jerome Kroonen et al. Corrigenda Top Corrigendum: A far-red fluorescent protein evolved from a cyanobacterial phycobiliprotein   p890 Erik A Rodriguez, Geraldine N Tran, Larry A Gross, Jessica L Crisp, Xiaokun Shu et al. doi:10.1038/nmeth1016-890a Corrigendum: Classification evaluation   p890 Jake Lever, Martin Krzywinski and Naomi Altman doi:10.1038/nmeth1016-890b Top Advertisement nature.com webcasts Springer Nature presents a custom webcast on: Defining the immune system at single cell resolution with Seurat Date: Tuesday October 4, 2016 Time: 11AM PDT, 2PM EDT Speaker: Dr Rahul Satija, Assistant Professor, NYU Center for Genomics and Systems Biology  Register for FREE at And learn how to control for heterogeneity in sequencing depth and cell cycle. Sponsored by: 10x Genomics, Inc.     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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