Nature Methods Contents: December 2014 Volume 11 pp 1183 - 1266

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Advertisement The Next Generation Biometra Thermal Cycler: TAdvanced   With the TAdvanced, Analytik Jena is offering a new high quality Biometra thermal cycler. It provides a wide-ranging functionality thanks to superior sample block temperature, low noise emission of max. 45 dB, individual rights settings, defined pressure control for highly reproducible results and easy gradient programming.  Learn more > TABLE OF CONTENTS December 2014 Volume 11, Issue 12 In This Issue Editorial This Month Correspondence Research Highlights Historical Commentary Technology Feature News and Views Perspective Brief Communications Articles Application Note Advertisement   Doing Western Blots, ELISA, IF Microscopy, Flow Cytometry or ChIP? Let Rockland's scientists help you with your most critical experiments. We provide free tips monthly and offer technical service by our own in-house experts. Know where your antibodies are coming from and get the support you deserve with Rockland's antibodies. Click here for Rockland Technical Tips!  Register for a free 2015 Game of Clones Calendar. Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Poster & Webcast on CRISPR-Cas technology from Nature Publishing Group Nature Reviews Microbiology  FREE POSTER CRISPR-CAS: EXTRAORDINARY EDITING  Presented by Nature Biotechnology  WEBCAST AND LIVE Q&A: A PRACTICAL GUIDE TO CRISPR TECHNOLOGY  Date: November 25, 2014 Produced with support from OriGene, Your Gene Company     In This Issue Top In This Issue    Editorial Top Seeing in super-resolution   p1183 doi:10.1038/nmeth.3206 The 2014 Nobel Prize in Chemistry has been awarded in recognition of super-resolution fluorescence microscopy. To fully realize the tremendous promise of these methods for biological discovery, there are still challenges to be overcome. This Month Top The Author File: David Kleinfeld   p1185 Vivien Marx doi:10.1038/nmeth.3184 Measuring neurotransmitter concentration, letting lab meetings run free, and why biology does not own neuroscience. Points of Significance: Two-factor designs   pp1187 - 1188 Martin Krzywinski and Naomi Altman doi:10.1038/nmeth.3180 When multiple factors can affect a system, allowing for interaction can increase sensitivity. Correspondence Top bam.iobio: a web-based, real-time, sequence alignment file inspector   p1189 Chase A Miller, Yi Qiao, Tonya DiSera, Brian D'Astous and Gabor T Marth doi:10.1038/nmeth.3174 Research Highlights Top Light microscopy with lattices Thin optical lattices can be used to generate light sheets in order to image dynamic processes at high spatial and temporal resolution. De novo-designed riboregulators RNA-based toggle switches designed from first principles show high dynamic range and orthogonality. Using evolution to predict structure Researchers use sequence coevolution information to predict the structures of protein complexes. It's porin' CNTs Lipid-coated carbon nanotubes can insert themselves spontaneously into lipid bilayers and live-cell membranes. Flies give wings to human disease studies Chemically induced mutations on the fruit fly X chromosome reveal the genetic basis of certain human neurologic disorders. Short reads join hands A transposase can link sequence fragments together for accurate haplotyping and genome assembly. Unwinding to measure tension Two independent groups develop tension probes based on molecular beacons to measure mechanical stimuli in live cells. Methods in Brief Finding noncoding RNA partners | Electrophysiology in a virtual world | Profiling the N-myristoylated proteome | Bow ties for mammalian cells Tools in Brief A Cas9 knock-in mouse | Getting a read on structural variation in cancer | Activity-based RNA probes | Sunny prospects for imaging and gene expression Methods JOBS of the week Development and application of image-processing methods for studies of behavioral effects in aquatic organisms Umeå University PhD position in Biophysics University of Gothenburg (GU) Post-doctoral position in Biomedical Research Case Western Reserve University Program Associate, Data-Driven Discovery Initiative Gordon and Betty Moore Foundation Postdoctoral fellow in computational biology and cancer genomics Albert Einstein College of Medicine of Yeshiva University (AECOM) More Science jobs from Methods EVENT Hybrid Methods in Structural Biology 4th March - 8th March 2015 Tahoe City, USA More science events from Historical Commentary Top The yeast two-hybrid assay: still finding connections after 25 years   pp1203 - 1206 Marc Vidal and Stanley Fields doi:10.1038/nmeth.3182 The idea of using hybrid proteins containing transcription factor domains to analyze protein-protein interactions was described in 1989. Over the past 25 years, this method has begun to reveal the complex protein networks that underlie cellular behavior. Technology Feature Top Microscopy: seeing through tissue   pp1209 - 1214 Vivien Marx doi:10.1038/nmeth.3181 Tissue samples scatter light and shut out a deeper gaze. Tissue-clearing agents have changed that, but scientists must consider optimizing the optics when using these methods. News and Views Top Animal identification with robot rovers   pp1217 - 1218 Philip N Trathan and Louise Emmerson doi:10.1038/nmeth.3195 Robots can be used to detect marked animals with less disturbance when assessing ecological drivers of population change. See also: Brief Communication by Le Maho et al. Perspective Top Live-cell mass profiling: an emerging approach in quantitative biophysics   pp1221 - 1228 Thomas A Zangle and Michael A Teitell doi:10.1038/nmeth.3175 This Perspective discusses methods to measure single-cell mass and their relative strengths and weaknesses for different applications. Brief Communications Top A DNA-based molecular probe for optically reporting cellular traction forces   pp1229 - 1232 Brandon L Blakely, Christoph E Dumelin, Britta Trappmann, Lynn M McGregor, Colin K Choi et al. doi:10.1038/nmeth.3145 DNA hairpins with a conjugated fluorophore-quencher pair are attached to surfaces to monitor cellular traction forces at high spatial resolution. An improved surface passivation method for single-molecule studies   pp1233 - 1236 Boyang Hua, Kyu Young Han, Ruobo Zhou, Hajin Kim, Xinghua Shi et al. doi:10.1038/nmeth.3143 Avoiding nonspecific binding is essential for performing fluorescence microscopy-based analyses of single molecules tethered to surfaces. A dichlorodimethylsilane-Tween-20-passivated surface provides a useful alternative to the standard poly(ethylene glycol) surface for single-molecule studies. Quantum dot-based multiphoton fluorescent pipettes for targeted neuronal electrophysiology   pp1237 - 1241 Bertalan K Andrásfalvy, Gregorio L Galiñanes, Daniel Huber, Mladen Barbic, John J Macklin et al. doi:10.1038/nmeth.3146 Quantum dot-coated pipettes facilitate targeted electrophysiological recordings in deep brain tissue because they are readily visible owing to the strong two-photon fluorescence of the quantum dots. Rovers minimize human disturbance in research on wild animals   pp1242 - 1244 Yvon Le Maho, Jason D Whittington, Nicolas Hanuise, Louise Pereira, Matthieu Boureau et al. doi:10.1038/nmeth.3173 This paper investigates the stress levels and behavior of wild animals when approached by remote-operated vehicles versus humans for data collection in field research See also: News and Views by Trathan & Emmerson Advertisement News Alert: FREE SAMPLES with FREE SHIPPING. Empirical Bioscience provides the purest reagents, assayed for the right concentrations and components and vigorously tested. Their products are manufactured using proprietary technology and rigorous lot controls. Click for a FREE SAMPLE and Observe the Difference.   Articles Top Cell-based reporters reveal in vivo dynamics of dopamine and norepinephrine release in murine cortex   pp1245 - 1252 Arnaud Muller, Victory Joseph, Paul A Slesinger and David Kleinfeld doi:10.1038/nmeth.3151 Cell-based reporters for dopamine and norepinephrine allow real-time measurements of these neurotransmitters in vivo with high specificity. They can address the temporal and spatial dynamics of volume neurotransmission in behaving animals. A robust pipeline for rapid production of versatile nanobody repertoires   pp1253 - 1260 Peter C Fridy, Yinyin Li, Sarah Keegan, Mary K Thompson, Ilona Nudelman et al. doi:10.1038/nmeth.3170 This paper presents an efficient method for generating nanobodies with high affinity and high specificity. In addition, a collection of nanobodies specific for GFP or mCherry that resulted from this work is described. Permanent genetic memory with >1-byte capacity   pp1261 - 1266 Lei Yang, Alec A K Nielsen, Jesus Fernandez-Rodriguez, Conor J McClune, Michael T Laub et al. doi:10.1038/nmeth.3147 Thirty-four integrases and their recognition sites form the basis of permanently recording 2,048 combinations of events. Application Note Top QuantSeq 3′ mRNA sequencing for RNA quantification    Pamela Moll, Michael Ante, Alexander Seitz and Torsten Reda Top Advertisement nature.com webcasts Nature Publishing Group presents a custom webcast on: Complementing the genome: Epigenome wide studies to advance Wednesday, December 3, 2014 8AM PST, 11AM EST, 4PM GMT, 5PM CET  Register for the webcast and live Q and A session. Sponsored by:     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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