Nature Methods Contents: June 2013 Volume 10 pp 447 - 590

Advertisement New! TotalScript™ RNA-Seq Kits from Epicentre TotalScript, powered by Nextera™, prepares high complexity and stranded RNA-Seq libraries from only 1-5 ng of intact total RNA, without the need for poly(A) enrichment or ribosomal RNA removal. TABLE OF CONTENTS June 2013 Volume 10, Issue 6 In This Issue Focus Editorial This Month Correspondence Research Highlights Methods in Brief Tools in Brief Technology Feature News and Views Editorial Historical Perspective Commentary Perspectives Reviews Resource Brief Communications Articles Application Note Advertisement Reichert Surface Plasmon Resonance (SPR) systems for protein-protein and small molecule interaction analysis Monitor real-time binding, obtain detailed interaction information: on/off rates, affinity, thermodynamics and concentration. Reichert SPR systems push the detection and sensitivity limits for label-free definitive analysis. ReichertSPR.com Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Better 2-D analysis is now within reach. From sample prep through imaging and analysis, Bio-Rad's new 2-D electrophoresis workflow provides a comprehensive selection of product solutions. Add to that our top-notch support and expertise, and it's easy to see why our 2-D electrophoresis workflow delivers quality and reliability every time. Download the 2-D How-To Guide at bio-rad.com/ad/2d   In This Issue Top In This Issue Focus Top Focus on Mapping the Brain Focus issue: June 2013 Volume 10 No 6 Contents Editorial Historical Perspective Commentary Reviews Resource Sponors NPG Library We are entering a new era in the neurosciences, in which development of technology will be in the spotlight. In this Focus, experts outline the different technologies needed to obtain anatomical and functional brain maps across species, and discuss the importance of assembling these maps and what will be needed beyond them, to understand the functioning of the brain. Editorial Top Focus on Mapping the Brain Why mapping the brain matters   p447 doi:10.1038/nmeth.2513 Obtaining anatomical maps and molecular information of brain circuits and their activity patterns in relation to specific behaviors is instrumental to understanding brain function. This Month Top The author file: Joshua Sanes   p449 Vivien Marx doi:10.1038/nmeth.2487 New features are added to a neuron-painting toolbox that could contribute to the recently announced US brain-mapping initiative. Points of view: Plotting symbols   p451 Martin Krzywinski and Bang Wong doi:10.1038/nmeth.2490 Choose distinct symbols that overlap without ambiguity and communicate relationships in data. Correspondence Top Comprehensive macromolecular conformations mapped by quantitative SAXS analyses   pp453 - 454 Greg L Hura, Helen Budworth, Kevin N Dyer, Robert P Rambo, Michal Hammel, Cynthia T McMurray and John A Tainer doi:10.1038/nmeth.2453 Endrov: an integrated platform for image analysis   pp454 - 456 Johan Henriksson, Jürgen Hench, Yong Guang Tong, Arvid Johansson, David Johansson and Thomas R Bürglin doi:10.1038/nmeth.2478 Research Highlights Top Changing one cell type into another Two independent groups identify factors that drive direct conversion to oligodendrocyte precursor cells in the rodent. Complex logic in a single layer Two independently controlled regulators modulate the output in amplifying Boolean logic gates. Crystallography without crystals Researchers use networked porous metal complexes as crystalline 'sponges' that absorb and orient small molecules for X-ray crystallography. Dream stream decoded Machine learning and imaging show what the dreaming brain sees. Nano-suiting up for SEM A polymer 'nano-suit' allows living organisms to survive the harsh conditions of scanning electron microscopy. Dynamics of DNA demethylation Locating the final oxidation products of methylated cytosine by enrichment and sequencing reveals that DNA demethylation is common across the genome. Magnetic field imaging and more Two reports demonstrate further advances in the use of nitrogen vacancies for very different imaging applications. Methods JOBS of the week Proteomics based analysis of RNA virus entry and exit University of Birmingham - College of Medical and Dental Sciences Bioinformatics Researcher UT Southwestern Medical Center Research Scientist UNIVERSITE DE TECHNOLOGIE DE COMPIEGNE Postdoctoral Scholar in Evolutionary Medicine and Informatics Icahn School of Medicine at Mount Sinai Postdoctoral Scholar Department of Bioengineering, Rice University More Science jobs from Methods EVENT Statistical Methods for Functional Genomics 21st June 2013 New York, USA More science events from Methods in Brief Top Targets of RNA cytosine methyltransferases | Reaction discovery by mass spectrometry | Population genomics without a reference | Polypeptide nanostructures Tools in Brief Top Retinoic acid: now you see it | Wireless, multifunctional optogenetic devices | Measuring cell deformability | Finding function Technology Feature Top Model organisms: beyond the inner circle   pp471 - 473 Vivien Marx doi:10.1038/nmeth.2484 Progress in genomics offers researchers many new reasons to expand the universe of organisms they study. News and Views Top Stroboscopic imaging of macromolecular complexes   pp475 - 476 Robert M. Glaeser doi:10.1038/nmeth.2486 Two reports describing the use of direct-conversion electron detectors and algorithms that correct for beam-induced sample motion in single-particle electron cryomicroscopy demonstrate that this technique can solve structures of macromolecules at near-atomic resolution. See also: Article by Li et al. Panning data for gold: the search for master regulators of cell fate   pp476 - 477 Vanguel Trapkov and Matthias Stadtfeld doi:10.1038/nmeth.2491 An approach for analyzing gene expression data identifies putative lineage-specifying transcription factors that may prove useful in cellular reprogramming. See also: Article by Heinaniemi et al. Editorial Top Focus on Mapping the Brain Focus on Mapping the Brain   p481 Erika Pastrana doi:10.1038/nmeth.2509 Historical Perspective Top Focus on Mapping the Brain From the connectome to brain function   pp483 - 490 Cornelia I Bargmann and Eve Marder doi:10.1038/nmeth.2451 In this Historical Perspective, we ask what information is needed beyond connectivity diagrams to understand the function of nervous systems. Informed by invertebrate circuits whose connectivities are known, we highlight the importance of neuronal dynamics and neuromodulation, and the existence of parallel circuits. The vertebrate retina has these features in common with invertebrate circuits, suggesting that they are general across animals. Comparisons across these systems suggest approaches to study the functional organization of large circuits based on existing knowledge of small circuits. Commentary Top Focus on Mapping the Brain Making sense of brain network data   pp491 - 493 Olaf Sporns doi:10.1038/nmeth.2485 New methods for mapping synaptic connections and recording neural signals generate rich and complex data on the structure and dynamics of brain networks. Making sense of these data will require a concerted effort directed at data analysis and reduction as well as computational modeling. Focus on Mapping the Brain Why not connectomics?   pp494 - 500 Joshua L Morgan and Jeff W Lichtman doi:10.1038/nmeth.2480 Opinions diverge on whether mapping the synaptic connectivity of the brain is a good idea. Here we argue that albeit their limitations, such maps will reveal essential characteristics of neural circuits that would otherwise be inaccessible. Perspectives Top Focus on Mapping the Brain Cellular-resolution connectomics: challenges of dense neural circuit reconstruction   pp501 - 507 Moritz Helmstaedter doi:10.1038/nmeth.2476 Neuronal networks are high-dimensional graphs that are packed into three-dimensional nervous tissue at extremely high density. Comprehensively mapping these networks is therefore a major challenge. Although recent developments in volume electron microscopy imaging have made data acquisition feasible for circuits comprising a few hundreds to a few thousands of neurons, data analysis is massively lagging behind. The aim of this perspective is to summarize and quantify the challenges for data analysis in cellular-resolution connectomics and describe current solutions involving online crowd-sourcing and machine-learning approaches. Focus on Mapping the Brain CLARITY for mapping the nervous system   pp508 - 513 Kwanghun Chung and Karl Deisseroth doi:10.1038/nmeth.2481 With potential relevance for brain-mapping work, hydrogel-based structures can now be built from within biological tissue to allow subsequent removal of lipids without mechanical disassembly of the tissue. This process creates a tissue-hydrogel hybrid that is physically stable, that preserves fine structure, proteins and nucleic acids, and that is permeable to both visible-spectrum photons and exogenous macromolecules. Here we highlight relevant challenges and opportunities of this approach, especially with regard to integration with complementary methodologies for brain-mapping studies. Reviews Top Focus on Mapping the Brain Mapping brain circuitry with a light microscope   pp515 - 523 Pavel Osten and Troy W Margrie doi:10.1038/nmeth.2477 The beginning of the 21st century has seen a renaissance in light microscopy and anatomical tract tracing that together are rapidly advancing our understanding of the form and function of neuronal circuits. The introduction of instruments for automated imaging of whole mouse brains, new cell type-specific and trans-synaptic tracers, and computational methods for handling the whole-brain data sets has opened the door to neuroanatomical studies at an unprecedented scale. We present an overview of the present state and future opportunities in charting long-range and local connectivity in the entire mouse brain and in linking brain circuits to function. Focus on Mapping the Brain Imaging human connectomes at the macroscale   pp524 - 539 R Cameron Craddock, Saad Jbabdi, Chao-Gan Yan, Joshua T Vogelstein, F Xavier Castellanos, Adriana Di Martino, Clare Kelly, Keith Heberlein, Stan Colcombe and Michael P Milham doi:10.1038/nmeth.2482 At macroscopic scales, the human connectome comprises anatomically distinct brain areas, the structural pathways connecting them and their functional interactions. Annotation of phenotypic associations with variation in the connectome and cataloging of neurophenotypes promise to transform our understanding of the human brain. In this Review, we provide a survey of magnetic resonance imaging-based measurements of functional and structural connectivity. We highlight emerging areas of development and inquiry and emphasize the importance of integrating structural and functional perspectives on brain architecture. Resource Top Focus on Mapping the Brain Improved tools for the Brainbow toolbox   pp540 - 547 Dawen Cai, Kimberly B Cohen, Tuanlian Luo, Jeff W Lichtman and Joshua R Sanes doi:10.1038/nmeth.2450 An improved Brainbow toolbox for expression in the mouse is presented in this Resource. The collection includes transgenic lines, plasmids and viral vectors with improved performance and added capabilities relative to the original Brainbow constructs. Brief Communications Top Live mammalian cell arrays   pp550 - 552 Kristina Woodruff, Luis M Fidalgo, Samy Gobaa, Matthias P Lutolf and Sebastian J Maerkl doi:10.1038/nmeth.2473 Contact spotting with standard microarray printing tools can be used to generate high-density arrays of living mammalian cells, permitting the arraying of cell libraries without complex fluid manipulation. A simple tool to improve pluripotent stem cell differentiation   pp553 - 556 Sundari Chetty, Felicia Walton Pagliuca, Christian Honore, Anastasie Kweudjeu, Alireza Rezania and Douglas A Melton doi:10.1038/nmeth.2442 Treatment with DMSO improves the differentiation of multiple human pluripotent stem cell lines into cells of all three germ layers. Advertisement See what nature is hiding BD Horizon™ Brilliant Violet™ polymer conjugates are brighter than traditional dyes and can help identify cell populations with lower receptor density than previously possible. Learn how to resolve rare and dim cell populations with our expanded set of tools and information and request a free sample at bdbiosciences.com/go/brilliant.   Articles Top Measuring image resolution in optical nanoscopy   pp557 - 562 Robert P J Nieuwenhuizen, Keith A Lidke, Mark Bates, Daniela Leyton Puig, David Grunwald, Sjoerd Stallinga and Bernd Rieger doi:10.1038/nmeth.2448 A method for computing the intrinsic resolution of a super-resolution image that accounts for localization uncertainty, labeling density and image anisotropy is described. This work extends and builds on the Fourier ring correlation method used in cryoelectron microscopy. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data   pp563 - 569 Chen-Shan Chin, David H Alexander, Patrick Marks, Aaron A Klammer, James Drake, Cheryl Heiner, Alicia Clum, Alex Copeland, John Huddleston, Evan E Eichler, Stephen W Turner and Jonas Korlach doi:10.1038/nmeth.2474 Unlike hybrid approaches that use multiple libraries for de novo assembly, the hierarchical genome-assembly process uses data from only a single long-read SMRT sequencing library to produce high-quality finished microbial genome or BAC assemblies in an automated workflow. Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics   pp570 - 576 Jovan Simicevic, Adrien W Schmid, Paola A Gilardoni, Benjamin Zoller, Sunil K Raghav, Irina Krier, Carine Gubelmann, Frederique Lisacek, Felix Naef, Marc Moniatte and Bart Deplancke doi:10.1038/nmeth.2441 With a multiplexed, sensitive, selected reaction monitoring-based mass spectrometry approach, transcription factor copy numbers can be accurately quantified during terminal fat cell differentiation. Gene-pair expression signatures reveal lineage control   pp577 - 583 Merja Heinäniemi, Matti Nykter, Roger Kramer, Anke Wienecke-Baldacchino, Lasse Sinkkonen, Joseph Xu Zhou, Richard Kreisberg, Stuart A Kauffman, Sui Huang and Ilya Shmulevich doi:10.1038/nmeth.2445 A method to measure reversals in gene expression between cell types is used to identify transcriptional regulators important for lineage specification. The approach should help identify putative factors for direct fate conversion. See also: News and Views by Trapkov & Stadtfeld Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM   pp584 - 590 Xueming Li, Paul Mooney, Shawn Zheng, Christopher R Booth, Michael B Braunfeld, Sander Gubbens, David A Agard and Yifan Cheng doi:10.1038/nmeth.2472 The combination of a direct electron-detection camera that can count individual electrons and an algorithm for correcting for beam-induced motion in cryo-EM will facilitate determination of three-dimensional structures of smaller, lower-symmetry macromolecular complexes to higher resolution than previously possible. See also: News and Views by Glaeser Advertisement Introducing the S3™ Cell Sorter from Bio-Rad. This state-of-the-art benchtop solution features automated setup and costs up to 50% less than traditional systems. Watch the video to find out how the S3 can make a difference in your lab.   Application Note Top Peggy™: size- or charge-based western blotting at the push of a button    Erik Gentalen, Thayer White and John Proctor Top Advertisement Nature Methods Focus on Mapping the Brain www.nature.com/nmeth/focus/brainmapping Experts discuss the different technologies needed to obtain anatomical and functional brain maps across species, and discuss the importance of assembling these maps and what will be needed beyond them, to understand the functioning of the brain. Produced with support from: Carl Zeiss Microscopy, Hamamatsu Corporation, LaVision BioTec, TissueVision, Inc. and Chroma Technology Corp   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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