Nature Methods Contents: February 2013 Volume 10 pp 91 - 177

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Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Fluorescent proteins and sensors: A practical discussion Fluorescent proteins have become invaluable tools for fluorescent microscopy in the life sciences but researchers still have many practical questions about using them. Three experts in the development and use of fluorescent proteins and sensors discuss these challenges and provide practical advice to users. Register for FREE   In This Issue Top In This Issue Editorial Top Beyond the PDF   p91 doi:10.1038/nmeth.2363 The online versions of published research articles can challenge the prevalence of the offline PDF but will require added effort by authors and journals. This Month Top The author file: Loren L. Looger   p93 Vivien Marx doi:10.1038/nmeth.2334 Engineering protein sensors to light up split-second signals in the brain Correspondence Top PRIDE Cluster: building a consensus of proteomics data   pp95 - 96 Johannes Griss, Joseph M Foster, Henning Hermjakob and Juan Antonio Vizcaino doi:10.1038/nmeth.2343 Accelerating 3B single-molecule super-resolution microscopy with cloud computing   pp96 - 97 Ying S Hu, Xiaolin Nan, Prabuddha Sengupta, Jennifer Lippincott-Schwartz and Hu Cang doi:10.1038/nmeth.2335 ImageJ plug-in for Bayesian analysis of blinking and bleaching   pp97 - 98 Edward Rosten, Gareth E Jones and Susan Cox doi:10.1038/nmeth.2342 Research Highlights Top A next-gen ontology An approach to cluster and organize systems biology data yields NeXO, a data-driven ontology. Bessel beams beyond the limit Bessel plane imaging achieves super-resolution performance and proves its value for fast three-dimensional imaging of thick fluorescent living specimens. How parasitic pathogens do it A combination of mutagenesis in a pathogen and RNA interference in its host cell reveals the role of non-essential bacterial genes. Nano-lantern lights the way The bright luminescent protein Nano-lantern is easily modified to create functional sensors. Catching the tsetse fly before it bites Researchers recapitulate in the lab how an infectious parasite gains its ferociousness. Partners in time, partners in crime Phylogenetic profiling implicates diverse genes in small-RNA pathways. Methods JOBS of the week Assistant Professor Louisiana State University Senior Scientific Research & Project Leader University of Sussex, UK Research Associate (Bioinformatician) - 2 Posts Available University of Leicester Postdoctoral Scientist US MHRP, Henry M. Jackson Foundation Postdoctoral Research Associate University of Liverpool More Science jobs from Methods EVENT International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2013) 11th Feb - 14th Feb 2013 Barcelona, Spain More science events from Methods in Brief Top DNA nanostructures built from bricks | Differentiating stem cells in vivo | Soft ionization with vacuum alone | An earthworm QD factory Tools in Brief Top The ups and downs of transcripts | A mouse model to study SUMOylation | TAL effectors on demand | RNA SHAPEs up Technology Feature Top Where stem cells call home   pp111 - 115 Vivien Marx doi:10.1038/nmeth.2336 By building engineered microenvironments, scientists probe the many talents of stem cells. News and Views Top A ligand's-eye view of protein similarity   pp116 - 117 Gerard J P van Westen and John P Overington doi:10.1038/nmeth.2339 Classification of proteins by ligand binding similarity offers an alternative approach to evolutionary methods for organizing and understanding biology, allowing new insights into protein function and physiological signal transduction. See also: Article by Lin et al. A third-generation method reveals cell lineage ancestry   pp117 - 118 Andrew P Feinberg doi:10.1038/nmeth.2338 A combination of proximity ligation and in situ hybridization enables visualization of epigenetic marks in single cells. See also: Article by Gomez et al. Brief Communications Top Single-molecule analysis of gene expression using two-color RNA labeling in live yeast   pp119 - 121 Sami Hocine, Pascal Raymond, Daniel Zenklusen, Jeffrey A Chao and Robert H Singer doi:10.1038/nmeth.2305 Tagging of single transcripts with two fluorescent markers can be used to study many aspects of gene expression, including intrinsic noise in transcription or polymerase dynamics at a single gene. A versatile genome-scale PCR-based pipeline for high-definition DNA FISH   pp122 - 124 Magda Bienko, Nicola Crosetto, Leonid Teytelman, Sandy Klemm, Shalev Itzkovitz and Alexander van Oudenaarden doi:10.1038/nmeth.2306 A primer database covering the mouse and human genomes allows easy and flexible generation of FISH probes covering any desired locus. Conditional genome engineering in Toxoplasma gondii uncovers alternative invasion mechanisms   pp125 - 127 Nicole Andenmatten, Saskia Egarter, Allison J Jackson, Nicolas Jullien, Jean-Paul Herman and Markus Meissner doi:10.1038/nmeth.2301 A nonleaky and efficient DiCre-based conditional knockout system enables the study of essential genes in Toxoplasma gondii, revealing that the actin-myosin motor is not required for host invasion by the parasite. Identifying RNA editing sites using RNA sequencing data alone   pp128 - 132 Gokul Ramaswami, Rui Zhang, Robert Piskol, Liam P Keegan, Patricia Deng, Mary A O'Connell and Jin Billy Li doi:10.1038/nmeth.2330 Highly accurate and sensitive predictions of RNA editing sites can be obtained using RNA sequencing data from multiple individuals or species, without relying on matched genomic DNA sequence. Reanalyzing existing RNA sequencing data in this way greatly expands the catalog of human protein recoding events. Articles Top Analysis of alternative cleavage and polyadenylation by 3[prime; region extraction and deep sequencing   pp133 - 139 Mainul Hoque, Zhe Ji, Dinghai Zheng, Wenting Luo, Wencheng Li, Bei You, Ji Yeon Park, Ghassan Yehia and Bin Tian doi:10.1038/nmeth.2288 The 3′ region extraction and deep sequencing (3′READS) method accurately identifies cleavage and polyadenylation sites, avoiding common artifacts and detecting sites in A-rich contexts. It was used to greatly expand the number of characterized sites in the mouse genome, including those in long noncoding RNAs. A pharmacological organization of G protein-coupled receptors   pp140 - 146 Henry Lin, Maria F Sassano, Bryan L Roth and Brian K Shoichet doi:10.1038/nmeth.2324 Classifying G protein-coupled receptors by ligand binding similarity leads to unexpected links between receptors unrelated by sequence or structure, possibly revealing insights into receptor evolution. See also: News and Views by van Westen & Overington iGLuc: a luciferase-based inflammasome and protease activity reporter   pp147 - 154 Eva Bartok, Franz Bauernfeind, Maria G Khaminets, Christopher Jakobs, Brian Monks, Katherine A Fitzgerald, Eicke Latz and Veit Hornung doi:10.1038/nmeth.2327 A reporter of caspase-1 activity based on Gaussia luciferase—iGLuc—reveals inflammasome activation in mouse cells and in vivo. iGLuc forms nonluminescent aggregates in cells that can be cleaved by specific proteases and, consequently, lead to luciferase activity. The design principle is applied to build reporters for several other proteases. Lentiviral vector-based insertional mutagenesis identifies genes associated with liver cancer   pp155 - 161 Marco Ranzani, Daniela Cesana, Cynthia C Bartholomae, Francesca Sanvito, Mauro Pala, Fabrizio Benedicenti, Pierangela Gallina, Lucia Sergi Sergi, Stefania Merella, Alessandro Bulfone, Claudio Doglioni, Christof von Kalle, Yoon Jun Kim, Manfred Schmidt, Giovanni Tonon, Luigi Naldini and Eugenio Montini doi:10.1038/nmeth.2331 Replication-deficient lentiviral vectors are used as insertional mutagens for cancer gene discovery in the mouse. They are applied to identify oncogenes in hepatocellular carcinoma. An optimized fluorescent probe for visualizing glutamate neurotransmission   pp162 - 170 Jonathan S Marvin, Bart G Borghuis, Lin Tian, Joseph Cichon, Mark T Harnett, Jasper Akerboom, Andrew Gordus, Sabine L Renninger, Tsai-Wen Chen, Cornelia I Bargmann, Michael B Orger, Eric R Schreiter, Jonathan B Demb, Wen-Biao Gan, S Andrew Hires and Loren L Looger doi:10.1038/nmeth.2333 A single-wavelength genetically encoded sensor of extracellular glutamate is reported. The sensor—iGluSnFR—is bright and photostable under both one- and two-photon illumination and is shown to work for in vivo imaging in worms, zebrafish and mice. Detection of histone modifications at specific gene loci in single cells in histological sections   pp171 - 177 Delphine Gomez, Laura S Shankman, Anh T Nguyen and Gary K Owens doi:10.1038/nmeth.2332 A combination of in situ hybridization and a proximity ligation assay allows the visualization of histone modifications at single genomic loci with single-cell resolution in fixed tissue. See also: News and Views by Feinberg 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

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