Nature Methods Contents: June 2012 Volume 9 pp 517 - 626

Advertisement QuickExtract™ DNA and RNA Extraction Kits Extract DNA or RNA in minutes for PCR. There's a QuickExtract kit for virtually any sample type, from apples to zebrafish! Two simple heating steps: ideal for genotyping, microbial screening, GMO testing, and more. Learn more: http://www.epicentre.com/quickextract TABLE OF CONTENTS June 2012 Volume 9, Issue 6 In This Issue Editorial This Month Correspondence Research Highlights Methods in Brief Tools in Brief Technology Feature News and Views Review Perspective Brief Communications Articles Corrigenda Application Note Advertisement Light Lab by Carl Zeiss Microscopy is a free fluorescence microscopy app for your iPad, iPhone or iPod touch. With Light Lab, you have a fully interactive spectra configuration tool at your hands. The recently introduced update to Version 1.1 includes native support for the new Retina iPad and direct access to our registration web pages for ZEISS on Your Campus. For more information and download visit www.zeiss.com/micro-apps Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Events @ EMBL The 2012 EMBL Autumn Course and Conference Programme is now available online! To view complete listing visit www.embl.org/events   Advertisement Don't waste your time.... ....with complicated cloning strategies, and long protein expression optimization ! Use StarGate the shortcut and easy to handle protein expression cloning system enabling the convenient evaluation of the best expression features for recombinant protein expression right from the start of your project. For further information please click here    Advertisement The Gel Doc EZ imager from Bio-Rad delivers high-quality gel images and analysis with ease and accuracy. Simply slide in the sample tray, press a single button, and you’ll get publication-ready images in just seconds. Its compact size also frees up bench space. Click here to learn more.   In This Issue Top PDF Editorial Top fMRI: a tree with fuzzy roots p517 doi:10.1038/nmeth.2070 A deeper understanding of the mechanisms underlying functional magnetic resonance imaging signals is crucial for maximizing the return on human fMRI research. Full Text | PDF This Month Top The author file: Oliver Brustle p519 Monya Baker doi:10.1038/nmeth.2035 Making direct conversion pure and efficient Full Text | PDF Points of view: Managing deep data in genome browsers p521 Cydney Nielsen and Bang Wong doi:10.1038/nmeth.2049 Techniques are at hand for taming the ever-growing number of data tracks. Full Text | PDF Correspondence Top Mitochondrial genomes gleaned from human whole-exome sequencing pp523 - 524 Ernesto Picardi and Graziano Pesole doi:10.1038/nmeth.2029 Full Text | PDF Protease bias in absolute protein quantitation pp524 - 525 Mao Peng, Nadia Taouatas, Salvatore Cappadona, Bas van Breukelen, Shabaz Mohammed, Arjen Scholten and Albert J R Heck doi:10.1038/nmeth.2031 Full Text | PDF Improved linear mixed models for genome-wide association studies pp525 - 526 Jennifer Listgarten, Christoph Lippert, Carl M Kadie, Robert I Davidson, Eleazar Eskin and David Heckerman doi:10.1038/nmeth.2037 Full Text | PDF Research Highlights Top Drosophila's outdoor schedule p529 Fly rhythms under natural light and temperature differ from those in the lab. Understudies of DNA and RNA pp530 - 531 With the help of engineered polymerases and reverse transcriptases, synthetic nucleic acids can encode and pass on genetic information. Refined siRNA screens pp530 - 531 Bioinformatic discrimination of siRNAs that perturb cells via direct versus indirect effects can improve data quality and change hit lists in image-based screens. Capturing sequences for bioprospecting p532 Recombineering between two linear molecules enables long sequences to be efficiently cloned from a genomic mixture. Controlling biology by radio p535 Radio waves and iron nanoparticles could hold the key to targeted perturbation of cells deep inside living tissue. Improving gene-editing nucleases p536 A flurry of recent papers report refinements to the activity and the assembly of engineered nucleases. Probing epigenetic cross-talk p538 Bisulfite sequencing of chromatin-immunoprecipitated material allows a direct assessment of cytosine methylation in histone-modified regions of DNA. Methods JOBS of the week Molecular Magnetism and Giant Spin. Implementation of mathematical methods in Physics Università Politecnica delle Marche Development of methods of analysis and design strategies for energy saving, environmental sustainability and integrated conservation of the Architectural Heritage CNR Post-doctoral Position in Neuroimaging Methods Medical Research Council Stochastic methods for geophysics MINES ParisTech Application of molecular methods to pathogen detection from various matrices Università degli Studi di Urbino Carlo Bo - Dip. Scienze Biomolecolari More Science jobs from Methods EVENT T2012 AACR/ASCO Workshop: Methods in Clinical Cancer Research 28th July - 3rd August 2012 US More science events from Methods in Brief Top Gene expression regulation using nanohorns  | A window into the synapse  | Joining forces to find microRNA targets  | Sequencing 5-hydroxymethylcytosine  Tools in Brief Top Sequencing the end  | Probes to detect strain  | Rapamycin's sister  | Tag, you're orange  Technology Feature Top Digital PCR hits its stride pp541 - 544 Monya Baker doi:10.1038/nmeth.2027 As the less familiar cousin of quantitative PCR moves mainstream, researchers have more options to choose from. Full Text | PDF News and Views Top Shedding light on the BOLD fMRI response pp547 - 549 Serge Charpak and Bojana Stefanovic doi:10.1038/nmeth.2039 Fluorescence recording of neural activity in the magnetic resonance scanner is a new strategy for examining the cellular underpinnings of blood oxygenation level-dependent (BOLD) functional magnetic resonance imaging (fMRI). Full Text | PDF See also: Article by Schulz et al. Predicting microbial distributions in space and time pp549 - 551 Noah Fierer and Joshua Ladau doi:10.1038/nmeth.2041 Researchers describe an approach to predict microbial-community composition across broad spatial and temporal gradients, an important step to bringing microbial ecology into the 21st century. Full Text | PDF See also: Article by Larsen et al. Rendering RNA in 3D pp552 - 553 Reza Behrouzi and Sarah A Woodson doi:10.1038/nmeth.2045 Integrating biochemical footprinting data with molecular dynamics yields more accurate RNA three-dimensional structure predictions. Full Text | PDF See also: Article by Ding et al. Review Top Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions pp555 - 566 Paola Picotti and Ruedi Aebersold doi:10.1038/nmeth.2015 In this Review, the authors provide a guide through to the different steps involved in selected reaction monitoring as well as discuss its applications. Abstract | Full Text | PDF Perspective Top Counting stem cells: methodological constraints pp567 - 574 Leonid V Bystrykh, Evgenia Verovskaya, Erik Zwart, Mathilde Broekhuis and Gerald de Haan doi:10.1038/nmeth.2043 Abstract | Full Text | PDF Brief Communications Top Small molecules enable highly efficient neuronal conversion of human fibroblasts pp575 - 578 Julia Ladewig, Jerome Mertens, Jaideep Kesavan, Jonas Doerr, Daniel Poppe, Finnja Glaue, Stefan Herms, Peter Wernet, Gesine Kögler, Franz-Josef Müller, Philipp Koch and Oliver Brüstle doi:10.1038/nmeth.1972 To increase the efficiency of direct neuronal conversion of postnatal human fibroblasts, the authors combine two-factor neuronal programming with small molecules. This method increases the yield and purity of functional neuron-like cells by more than 15-fold. Abstract | Full Text | PDF Accurate identification of human Alu and non-Alu RNA editing sites pp579 - 581 Gokul Ramaswami, Wei Lin, Robert Piskol, Meng How Tan, Carrie Davis and Jin Billy Li doi:10.1038/nmeth.1982 A computational framework is reported for the accurate and sensitive identification of RNA editing sites from whole-genome DNA and RNA sequences from the same individual. Abstract | Full Text | PDF A simple, versatile method for GFP-based super-resolution microscopy via nanobodies pp582 - 584 Jonas Ries, Charlotte Kaplan, Evgenia Platonova, Hadi Eghlidi and Helge Ewers doi:10.1038/nmeth.1991 Nanobodies that bind to fluorescent proteins with high affinity and are coupled to bright organic dyes allow simple efficient labeling of fusion proteins for super-resolution microscopy. Abstract | Full Text | PDF Automated whole-cell patch-clamp electrophysiology of neurons in vivo  pp585 - 587 Suhasa B Kodandaramaiah, Giovanni Talei Franzesi, Brian Y Chow, Edward S Boyden and Craig R Forest doi:10.1038/nmeth.1993 A robot, algorithm and software for automated in vivo intracellular electrophysiology are reported that can automatically perform whole-cell patch clamping in the living mouse brain with quality comparable to that for a trained human experimenter. Abstract | Full Text | PDF An optimized two-finger archive for ZFN-mediated gene targeting pp588 - 590 Ankit Gupta, Ryan G Christensen, Amy L Rayla, Abirami Lakshmanan, Gary D Stormo and Scot A Wolfe doi:10.1038/nmeth.1994 The range of genomic sequences accessible by zinc-finger nucleases is expanded by this archive of validated two-finger modules. Abstract | Full Text | PDF Genome-scale promoter engineering by coselection MAGE pp591 - 593 Harris H Wang, Hwangbeom Kim, Le Cong, Jaehwan Jeong, Duhee Bang and George M Church doi:10.1038/nmeth.1971 The use of marker coselection in combination with multiplex automated genome engineering (MAGE) is reported to improve the efficiency of engineered changes in bacterial genomes. The authors use the method to insert twelve 20-base-pair T7 promoters to control indirubin and indigo production. Abstract | Full Text | PDF M-Track: detecting short-lived protein-protein interactions in vivo  pp594 - 596 Aurora Zuzuarregui, Thomas Kupka, Bhumika Bhatt, Ilse Dohnal, Ingrid Mudrak, Christina Friedmann, Stefan Schüchner, Ingrid E Frohner, Gustav Ammerer and Egon Ogris doi:10.1038/nmeth.2017 A proximity assay based on methylation of interacting 'prey' proteins by a 'bait' fused to the histone lysine methyltransferase permits the detection of enzyme-substrate protein-protein interactions in yeast. Abstract | Full Text | PDF Advertisement Enhanced biological safety for flow cytometry Biosafety cabinets developed for BD flow cytometry instruments provide a high standard of safety, protecting people, products, and the environment. Learn more about the innovations from BD that can improve your workflow, results, and provide the highest level of safety in your lab. bdbiosciences.com/go/biosafety   Articles Top Simultaneous BOLD fMRI and fiber-optic calcium recording in rat neocortex pp597 - 602 Kristina Schulz, Esther Sydekum, Roland Krueppel, Christoph J Engelbrecht, Felix Schlegel, Aileen Schröter, Markus Rudin and Fritjof Helmchen doi:10.1038/nmeth.2013 Simultaneous functional magnetic resonance imaging (fMRI) and fiber-optic-based calcium recordings in rats allow investigation of the relationship between blood oxygen level-dependent (BOLD) fMRI signals and the underlying neural activity. The study uncovers prolonged BOLD signal components involving glial activation. Abstract | Full Text | PDF See also: News and Views by Charpak & Stefanovic Three-dimensional RNA structure refinement by hydroxyl radical probing pp603 - 608 Feng Ding, Christopher A Lavender, Kevin M Weeks and Nikolay V Dokholyan doi:10.1038/nmeth.1976 Hydroxyl radical probing measurements of large RNA molecules drive molecular dynamics simulations to generate three-dimensional structural models. Abstract | Full Text | PDF See also: News and Views by Behrouzi & Woodson Systematic evaluation of factors influencing ChIP-seq fidelity pp609 - 614 Yiwen Chen, Nicolas Negre, Qunhua Li, Joanna O Mieczkowska, Matthew Slattery, Tao Liu, Yong Zhang, Tae-Kyung Kim, Housheng Hansen He, Jennifer Zieba, Yijun Ruan, Peter J Bickel, Richard M Myers, Barbara J Wold, Kevin P White, Jason D Lieb and X Shirley Liu doi:10.1038/nmeth.1985 The authors analyze how sequencing depth, choice of control sample, paired-end versus single-end reads and the selection of peak-calling algorithm influence the interpretation of chromatin immunoprecipitation-sequencing (ChIP-seq) experiments. Abstract | Full Text | PDF FMT-XCT: in vivo animal studies with hybrid fluorescence molecular tomography-X-ray computed tomography pp615 - 620 Angelique Ale, Vladimir Ermolayev, Eva Herzog, Christian Cohrs, Martin Hrabé de Angelis and Vasilis Ntziachristos doi:10.1038/nmeth.2014 A hybrid fluorescence molecular tomography-X ray computed tomography system is applied for in vivo imaging of multiple mouse models, and its performance is validated on post-mortem cryosection data. Abstract | Full Text | PDF Predicting bacterial community assemblages using an artificial neural network approach pp621 - 625 Peter E Larsen, Dawn Field and Jack A Gilbert doi:10.1038/nmeth.1975 Microbial Assemblage Prediction is a predictive model for the climate-dependent abundance of microbial taxa in space and time. It takes potential interactions between taxa into account and is used on longitudinal metagenomic and climate data from the Western English Channel. Abstract | Full Text | PDF See also: News and Views by Fierer & Ladau Advertisement Easy Cell Culture Scale Up with 100X Greater Productivity FiberCell® Systems Inc. hollow fiber bioreactors are an easy way to scale up cell culture in any laboratory and provide more in vivo like culture conditions. Click on the link for our new video that describes hollow fiber cell culture for in vivo-like 3-D cell culture and the production of monoclonal antibodies, recombinant proteins and cell co-cultivation. Website: www.fibercellsystems.com New Video - Hollow Fiber Cell Culture Overview: www.fibercellsystems.com/video Free Hollow Fiber Video Instructions Manual: www.fibercellsystems.com/cd.php   Corrigenda Top Corrigendum: Protein interaction data curation: the International Molecular Exchange (IMEx) consortium p626 Sandra Orchard, Samuel Kerrien, Sara Abbani, Bruno Aranda, Jignesh Bhate, Shelby Bidwell, Alan Bridge, Leonardo Briganti, Fiona Brinkman, Gianni Cesareni, Andrew Chatr-aryamontri, Emilie Chautard, Carol Chen, Marine Dumousseau, Johannes Goll, Robert Hancock, Linda I Hannick, Igor Jurisica, Jyoti Khadake, David J Lynn, Usha Mahadevan, Livia Perfetto, Arathi Raghunath, Sylvie Ricard-Blum, Bernd Roechert, Lukasz Salwinski, Volker Stumpflen, Mike Tyers, Peter Uetz, Ioannis Xenarios and Henning Hermjakob doi:10.1038/nmeth0612-626a Full Text | PDF Corrigendum: Enhanced photostability of cyanine fluorophores across the visible spectrum p626 Roger B Altman, Qinsi Zheng, Zhou Zhou, Daniel S Terry, J David Warren and Scott C Blanchard doi:10.1038/nmeth0612-626b Full Text | PDF Application Note Top A transposable approach to RNA-seq from total RNA  Scott Kuersten Abstract | Full Text | PDF Top Advertisement Nurture your career with the new-look Naturejobs As the world's largest dedicated jobs boards for the scientific community, Naturejobs is the ideal resource to build your career. Our new and improved functionality enables you to search, save and apply for jobs quickly and easily. Search over 10,000 vacancies to find exactly the right job for you at http://www.naturejobs.com   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 More Nature Events

You have been sent this Table of Contents Alert because you have opted in to receive it. You can change or discontinue your e-mail alerts at any time, by modifying your preferences on your nature.com account at: www.nature.com/myaccount (You will need to log in to be recognised as a nature.com registrant) For further technical assistance, please contact our registration department For print subscription enquiries, please contact our subscription department For other enquiries, please contact our customer feedback department Nature Publishing Group | 75 Varick Street, 9th Floor | New York | NY 10013-1917 | USA Nature Publishing Group's worldwide offices: London - Paris - Munich - New Delhi - Tokyo - Melbourne San Diego - San Francisco - Washington - New York - Boston Macmillan Publishers Limited is a company incorporated in England and Wales under company number 785998 and whose registered office is located at Brunel Road, Houndmills, Basingstoke, Hampshire RG21 6XS. © 2012 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.