Nature Methods Contents: May 2015 Volume 12 pp 373 - 471

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Advertisement Determine the Metabolic Phenotype of Your Cells Seahorse Bioscience Webinar: The XFp Cell Energy Phenotype Test determines the metabolic phenotype of live cells under both basal and stressed conditions, to reveal their metabolic potential. Presented by David Ferrick, Ph.D., CSO. Register: www.seahorsebio.com TABLE OF CONTENTS May 2015 Volume 12, Issue 5 In This Issue Editorial This Month Correspondence Research Highlights Technology Feature News and Views Brief Communications Articles Advertisement New One-Touch Templates Simplify Gel/Blot Imaging See how ChemiDoc-ItTS2 Imagers simplify gel and blot image capture with new one-touch templates and capture modes. Imagers feature large touch interface and ultra-sensitive gel/blot detection. UVP offers life science workflow solutions including nucleic acid isolation kits. UVP LLC (800) 452-6788 Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement RNA biomarker discovery, from sample to insight RNA biomarkers are revolutionizing disease studies, but how can you analyze all the RNA species in a sample? Your comprehensive workflow starts with isolation of total RNA, including miRNA, with miRNeasy. Then detect RNA with miScript (miRNA) or RT2 (mRNA and lncRNA) arrays, which include the most comprehensive and curated miRNA and mRNA pathways available.  Start your biomarker discovery journey today!   Advertisement Embarking on a genome editing project using CRISPR/Cas9? Powerful tools for successful CRISPR/Cas9 genome editing: An optimized in vitro assay to estimate sgRNA-directed Cas9 cleavage efficiency A quick and easy method to confirm mutations/indels Plasmid- and viral-based expression systems A sensitive Cas9 antibody Learn how Guide-it™ technologies can improve your CRISPR workflow>>   In This Issue Top In This Issue    Editorial Top Protein binder woes   p373 doi:10.1038/nmeth.3397 The biology research landscape is littered with antibodies that perform poorly for many applications. Two publicly funded academic efforts to explore high-quality binder generation are coming to an end. What have we learned[mdash]and what happens next? This Month Top The Author File: Erin Margaret Schuman   p375 Vivien Marx doi:10.1038/nmeth.3374 Birth-dating proteins and shaping an institute from the first building block. Points of significance: Bayesian statistics   pp377 - 378 Jorge López Puga, Martin Krzywinski and Naomi Altman doi:10.1038/nmeth.3368 Today's predictions are tomorrow's priors. Correspondence Top Whole-brain functional imaging with two-photon light-sheet microscopy   pp379 - 380 Sébastien Wolf, Willy Supatto, Georges Debrégeas, Pierre Mahou, Sergei G Kruglik et al. doi:10.1038/nmeth.3371 MiXCR: software for comprehensive adaptive immunity profiling   pp380 - 381 Dmitriy A Bolotin, Stanislav Poslavsky, Igor Mitrophanov, Mikhail Shugay, Ilgar Z Mamedov et al. doi:10.1038/nmeth.3364 Research Highlights Top RNA structure served in vivo Two transcriptome-scale sequencing methods provide a more complete view of RNA structure in its native context. Deep views into living mice Tool development facilitates deep-tissue photoacoustic imaging. Splitting Cas9 Two research groups show that the CRISPR system can be regulated by heterodimerizing a split Cas9. Shape-shifting MRI probes Tiny, environmentally responsive, magnetic resonance active nanostructures serve as shape-changing MRI sensors. Protein dynamics for the masses Automation tools make large-scale fluor-escence correlation spectroscopy experiments feasible for a wide range of users. Neurons pick up the heat Non-invasive neuronal stimulation deep within the brain is possible by tapping into an alternating magnetic field using magnetic nanoparticles. Solving XFEL's image problem Improved XFEL crystallography data processing methods enable structure determination from limited samples. Methods in Brief Mass spectrometry imaging with MALDI-2 | ChIP-nexus detects transcription factor binding sites | A TRICK for studying translation | Fast reaction kinetics with time-resolved mass spectrometry Tools in Brief Improving CRISPR-induced homologous recombination | Intersectional tools for mouse neuroscience | Photocages activated by green light | Lung organoids Methods JOBS of the week Predictive Modeling – Assistant Professor Ohio State University Postdoc in albumin-based drug delivery Aarhus University Postdoctoral positions in Bioinformatics University of Michigan Bioinformatician / Postdoc German Cancer Research Center (DKFZ) 2 postdoc positions (bioinformatics) European Institute of Oncology More Science jobs from Methods EVENT 2015 Educational Workshop - AACR / ASCO Methods in Clinical Cancer Research Workshop 25th July - 31st July 2015 Colorado, USA More science events from Technology Feature Top PCR heads into the field   pp393 - 397 Vivien Marx doi:10.1038/nmeth.3369 News and Views Top Non-invasive nuclear imaging for localization of viral reservoirs   pp399 - 400 Ekaterina Dadachova and Joan W Berman doi:10.1038/nmeth.3373 Antibody-targeted positron emission tomography (immunoPET) can visualize sites of HIV replication that are difficult to access by traditional means such as tissue biopsies. See also: Article by Santangelo et al. Brief Communications Top Functional annotation of native enhancers with a Cas9-histone demethylase fusion   pp401 - 403 Nicola A Kearns, Hannah Pham, Barbara Tabak, Ryan M Genga, Noah J Silverstein et al. doi:10.1038/nmeth.3325 Targeting a histone demethylase to specific enhancers with Cas9 allows modification of epigenetic marks at the enhancers. CIDRE: an illumination-correction method for optical microscopy   pp404 - 406 Kevin Smith, Yunpeng Li, Filippo Piccinini, Gabor Csucs, Csaba Balazs et al. doi:10.1038/nmeth.3323 A retrospective method to correct for uneven illumination in microscopy is reported in this paper. High-speed label-free functional photoacoustic microscopy of mouse brain in action   pp407 - 410 Junjie Yao, Lidai Wang, Joon-Mo Yang, Konstantin I Maslov, Terence T W Wong et al. doi:10.1038/nmeth.3336 Photoacoustic microscopy is a hybrid imaging technology based on the conversion of absorbed light into ultrasound emission. A single-wavelength pulse-width-based method allows fast functional imaging of the brain. Direct visualization of newly synthesized target proteins in situ   pp411 - 414 Susanne tom Dieck, Lisa Kochen, Cyril Hanus, Maximilian Heumüller, Ina Bartnik et al. doi:10.1038/nmeth.3319 Two assays reveal the birthplace of target proteins. In both, an antibody against a protein is used alongside an antibody that marks recent translation. The close proximity of both antibodies indicates the newly synthesized target protein. Quantifying cellular capacity identifies gene expression designs with reduced burden   pp415 - 418 Francesca Ceroni, Rhys Algar, Guy-Bart Stan and Tom Ellis doi:10.1038/nmeth.3339 Measuring the expression of a GFP-based capacity monitor in E. coli enables assessment of the burden heterologous gene expression exerts on the cell and allows for forward design of constructs with improved growth. Correlation Map, a goodness-of-fit test for one-dimensional X-ray scattering spectra   pp419 - 422 Daniel Franke, Cy M Jeffries and Dmitri I Svergun doi:10.1038/nmeth.3358 A new metric, Correlation Map (CorMap), which provides a goodness-of-fit test for comparing one-dimensional spectra without the need of estimating experimental errors, is developed and applied to evaluate small-angle X-ray scattering (SAXS) data from biological macromolecules. Sequencing small genomic targets with high efficiency and extreme accuracy   pp423 - 425 Michael W Schmitt, Edward J Fox, Marc J Prindle, Kate S Reid-Bayliss, Lawrence D True et al. doi:10.1038/nmeth.3351 Targeted enrichment and duplex sequencing yield extremely efficient, accurate and sensitive sequencing of rare subclonal mutations in small genomic target regions. Articles Top Whole-body immunoPET reveals active SIV dynamics in viremic and antiretroviral therapy-treated macaques   pp427 - 432 Philip J Santangelo, Kenneth A Rogers, Chiara Zurla, Emeline L Blanchard, Sanjeev Gumber et al. doi:10.1038/nmeth.3320 ImmunoPET/CT imaging using a labeled SIV-specific antibody can identify sites of viralinfection in SIV-infected macaques without the need for tissue biopsies, even if viral load in the blood is below the detection limit. Identification of active transcriptional regulatory elements from GRO-seq data   pp433 - 438 Charles G Danko, Stephanie L Hyland, Leighton J Core, Andre L Martins, Colin T Waters et al. doi:10.1038/nmeth.3329 Using data from global run-on and sequencing (GRO-seq) or related methods, the dREG software identifies a new class of transcriptional regulatory elements with strong evidence for directing active transcription. Massively parallel delivery of large cargo into mammalian cells with light pulses   pp439 - 444 Yi-Chien Wu, Ting-Hsiang Wu, Daniel L Clemens, Bai-Yu Lee, Ximiao Wen et al. doi:10.1038/nmeth.3357 The biophotonic laser-assisted surgery tool (BLAST) enables the delivery of nearly any cargo type, including micrometer-sized live bacteria, into a wide variety of cell types with high efficiency, throughput and cell viability. Catchup: a mouse model for imaging-based tracking and modulation of neutrophil granulocytes   pp445 - 452 Anja Hasenberg, Mike Hasenberg, Linda Männ, Franziska Neumann, Lars Borkenstein et al. doi:10.1038/nmeth.3322 Cre recombinase and tdTomato expressed from a neutrophil-specific promoter allow highly specific genetic manipulation and labeling of neutrophils. Robust enumeration of cell subsets from tissue expression profiles   pp453 - 457 Aaron M Newman, Chih Long Liu, Michael R Green, Andrew J Gentles, Weiguo Feng et al. doi:10.1038/nmeth.3337 A computational method to identify cell types within a complex tissue, based on analysis of gene expression profiles, is described in this paper. Sensitive detection of chromatin-altering polymorphisms reveals autoimmune disease mechanisms   pp458 - 464 Ricardo Cruz-Herrera del Rosario, Jeremie Poschmann, Sigrid Laure Rouam, Eileen Png, Chiea Chuen Khor et al. doi:10.1038/nmeth.3326 The combination of deep chromatin immunoprecipitation-sequencing with a statistical test that scores the correlation of peak height and allelic imbalance allows de novo discovery of histone acetylation quantitative trait loci without prior genotyping or genome sequencing. Improved specificity of TALE-based genome editing using an expanded RVD repertoire   pp465 - 471 Jeffrey C Miller, Lei Zhang, Danny F Xia, John J Campo, Irina V Ankoudinova et al. doi:10.1038/nmeth.3330 This study extends the natural code by which transcription activation-like effector nucleases (TALENs) recognize DNA and uses the resulting expanded repertoire of repeat divariable residues (RVDs) to improve TALEN performance. See also: News and Views by Dadachova & Berman Advertisement Sort Smarter with the S3e™ Cell Sorter.   Maximize the sorting capacity of your flow cytometry core with the S3e, an automated benchtop instrument that does not require a dedicated operator. From software-driven setup and real-time sort monitoring to an intuitive interface and small footprint, the S3e makes 1- to 4-color sorts simple and efficient. It's time to start sorting smarter. 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