Nature Methods Contents: September 2012 Volume 9 pp 847 - 929

Advertisement Specialty enzymes for sequencing workflows Epicentre's unique enzymes are becoming standard tools in sequencing-based applications. CircLigase™ ssDNA Ligase is a key component of ribosomal profiling workflows, while RNase R is being used to study RNA processing. Visit Epicentre's online Enzyme Guide for information. TABLE OF CONTENTS September 2012 Volume 9, Issue 9 In This Issue Editorial This Month Correspondence Research Highlights Methods in Brief Tools in Brief Technology Feature News and Views Commentary Perspective Brief Communications Articles Corrigendum Application Notes Advertisement Light sheet microscopy is a powerful alternative to established fluorescence imaging methods, especially when it comes to 3D imaging deep within tissue or whole living organisms. Recently a panel of experts introduced this technique in a webinar. If you want to know more about the advantages of light sheet microscopy, register here to receive a free offline copy of the webinar and related documentation. Subscribe   Facebook   RSS   Recommend to library   Twitter   In This Issue Top In This Issue Editorial Top Moving bottom-up science closer to the top   p847 doi:10.1038/nmeth.2168 To secure Europe's leadership in research and innovation, the European Union should prioritize its investment in researcher-originated projects. This Month Top The author file: Scott Manalis   p849 Vivien Marx doi:10.1038/nmeth.2140 Musical microfluidics to watch and weigh growing cells Points of view: Into the third dimension   p851 Nils Gehlenborg and Bang Wong doi:10.1038/nmeth.2151 Three-dimensional visualizations are effective for spatial data but rarely for other data types. Correspondence Top Prevention of overfitting in cryo-EM structure determination   pp853 - 854 Sjors H W Scheres and Shaoxia Chen doi:10.1038/nmeth.2115 The Coherent X-ray Imaging Data Bank   pp854 - 855 Filipe R N C Maia doi:10.1038/nmeth.2110 Evolutionary diagnosis method for variants in personal exomes   pp855 - 856 Sudhir Kumar, Maxwell Sanderford, Vanessa E Gray, Jieping Ye and Li Liu doi:10.1038/nmeth.2147 Neonatal desensitization does not universally prevent xenograft rejection   pp856 - 858 Miroslaw Janowski, Anna Jablonska, Hanna Kozlowska, Inema Orukari, Segun Bernard, Jeff WM Bulte, Barbara Lukomska and Piotr Walczak doi:10.1038/nmeth.2146 See also: Correspondence by Kelly et al. Reply to "Neonatal desensitization does not universally prevent xenograft rejection"   p858 Claire M Kelly, Victoria H Roberton, Stephen B Dunnett and Anne E Rosser doi:10.1038/nmeth.2144 See also: Correspondence by Janowski et al. Research Highlights Top Life, simulated A computer model of a bacterium accounts for gene function and predicts unexpected emergent properties. Making PTMs a priority Researchers describe an approach to zero in on post-translational modifications likely to have important regulatory functions. DNA: stretch for the camera Using a special nanochannel chip, genome maps can be constructed from single DNA molecules in any laboratory. When pathogens come in handy Bacterial proteins are used to rewire signaling pathways in yeast and mammalian cells. Moved by sound Acoustic tweezers nudge cells or particles with sound waves. Cancer gene discovery goes viral Examining how proteins from tumor viruses affect their cellular targets helps researchers zero in on the human genes that drive cancer. A sensor that makes sense A 'neutralizer displacement assay' provides a general platform for electrochemistry-based sensing of any class of analyte molecule. Methods JOBS of the week Manager, Methods Development Allen Institute for Brain Science Postdoctoral Postdoctoral position in unconvential methods of modification of carbon nanotubes IMDEA Nanoscience PhD Positions in Unconvential Methods of Modification of Carbon Nanotubes IMDEA Nanoscience Senior Bioinformatics Postdoctoral Research Assistant University of Dundee Postdoctoral Position in Medicinal Chemistry at the University of Southern Denmark Department of Physics, Chemistry and Pharmacy, University of Southern Denmark More Science jobs from Methods EVENT Sterilization Procedures Technology, Equipment & Validation 14th Nov - 15th Nov 2012 PA, US More science events from Methods in Brief Top The apoptotic phosphoproteome | Single-cell transcriptome sequencing | Glycosyltransferase discovery | Profiling chromatin at specific loci Tools in Brief Top Cis-regulatory annotation in the mouse | Functional single-cell screening | Rapid neuronal differentiation | Enhanced personal genomes Technology Feature Top Pulling on single molecules   pp873 - 877 Natalie de Souza doi:10.1038/nmeth.2149 Single-molecule methods to apply and measure force and displacement are expanding mechanobiology. News and Views Top Evaluating protein interactions through cross-linking mass spectrometry   pp879 - 881 David L Tabb doi:10.1038/nmeth.2139 New bioinformatics tools enable the recognition of neighboring amino acids in protein complexes. See also: Brief Communication by Yang et al. | Brief Communication by Walzthoeni et al. Deconstructing myelination: it all comes down to size   pp883 - 884 Ragnhildur Thóra Káradóttir and John Henry Stockley doi:10.1038/nmeth.2145 Through a collaborative effort, engineers and neuroscientists have created a method, using electrospun nanofibers as surrogate neuronal axons, to piece together the complexities of myelination. See also: Article by Lee et al. Commentary Top Biobanks, consent and claims of consensus   pp885 - 888 Zubin Master, Erin Nelson, Blake Murdoch and Timothy Caulfield doi:10.1038/nmeth.2142 Many scholars claim there is a consensus on broad consent for biobanking. We analyzed the literature in PubMed and found no evidence for consensus. Public perception studies report mixed findings on consent, but many biobanks adopt broad consent. A belief in consensus may stem from knowledge of biobank consent practices. Perspective Top Imaging without lenses: achievements and remaining challenges of wide-field on-chip microscopy   pp889 - 895 Alon Greenbaum, Wei Luo, Ting-Wei Su, Zoltán Göröcs, Liang Xue, Serhan O Isikman, Ahmet F Coskun, Onur Mudanyali and Aydogan Ozcan doi:10.1038/nmeth.2114 In this perspective, the authors present the basic features of lens-free computational imaging tools and report performance comparisons with conventional microscopy methods. They also discuss the challenges that these computational on-chip microscopes face for their wide-scale biomedical application. Brief Communications Top A mouse model to identify cooperating signaling pathways in cancer   pp897 - 900 Monica Musteanu, Leander Blaas, Rainer Zenz, Jasmin Svinka, Thomas Hoffmann, Beatrice Grabner, Daniel Schramek, Hans-Peter Kantner, Mathias Müller, Thomas Kolbe, Thomas Rülicke, Richard Moriggl, Lukas Kenner, Dagmar Stoiber, Josef Martin Penninger, Helmut Popper, Emilio Casanova and Robert Eferl doi:10.1038/nmeth.2130 The mouse cancer model 'Multi-Hit' allows for the evaluation of oncogene cooperativities in tumor development based on stochastic Cre-recombination events. Cells with cooperating oncogenes are positively selected and give rise to tumors. The approach is used to study Ras downstream effector pathways in tumorigenesis. False discovery rate estimation for cross-linked peptides identified by mass spectrometry   pp901 - 903 Thomas Walzthoeni, Manfred Claassen, Alexander Leitner, Franz Herzog, Stefan Bohn, Friedrich Förster, Martin Beck and Ruedi Aebersold doi:10.1038/nmeth.2103 xProphet, a tool using a target-decoy strategy, determines false discovery rate in mass-spectrometry data of chemically cross-linked peptides. See also: News and Views by Tabb Identification of cross-linked peptides from complex samples   pp904 - 906 Bing Yang, Yan-Jie Wu, Ming Zhu, Sheng-Bo Fan, Jinzhong Lin, Kun Zhang, Shuang Li, Hao Chi, Yu-Xin Li, Hai-Feng Chen, Shu-Kun Luo, Yue-He Ding, Le-Heng Wang, Zhiqi Hao, Li-Yun Xiu, She Chen, Keqiong Ye, Si-Min He and Meng-Qiu Dong doi:10.1038/nmeth.2099 pLink, software for data analysis of cross-linked proteins coupled with mass spectrometry, estimates false discovery rate and enables analysis of protein complexes without extensive purification. See also: News and Views by Tabb A high-throughput approach for measuring temporal changes in the interactome   pp907 - 909 Anders R Kristensen, Joerg Gsponer and Leonard J Foster doi:10.1038/nmeth.2131 A combination of protein correlation profiling-stable isotope labeling by amino acids in cell culture and size-exclusion chromatography allows stoichiometric analysis of changes in the human interactome in response to a growth factor. Direct observation of mammalian cell growth and size regulation   pp910 - 912 Sungmin Son, Amit Tzur, Yaochung Weng, Paul Jorgensen, Jisoo Kim, Marc W Kirschner and Scott R Manalis doi:10.1038/nmeth.2133 Precise mass measurement on single mammalian cells is combined with imaging to monitor changes in cellular mass during the cell cycle over many generations. Accurate gene synthesis with tag-directed retrieval of sequence-verified DNA molecules   pp913 - 915 Jerrod J Schwartz, Choli Lee and Jay Shendure doi:10.1038/nmeth.2137 Gene synthesis is currently limited by the need to use error-prone oligonucleotide building blocks. Dial-out PCR overcomes the sequence verification bottleneck by using unique sequence tags and massively parallel sequencing to identify and selectively retrieve error-free DNA molecules of interest from complex mixtures. Advertisement The New BD FACSJazz™ Cell Sorter Perfectly tuned cell sorting is now available with the new BD FACSJazz. Built on a proven, dependable platform, it may change the way you'll think of cell sorting with ease of operation, affordability, and a benchtop fit. Exceedingly capable performance whether as a soloist or part of your core lab ensemble. bdbiosciences.com/jazz   Articles Top A culture system to study oligodendrocyte myelination processes using engineered nanofibers   pp917 - 922 Seonok Lee, Michelle K Leach, Stephanie A Redmond, S Y Christin Chong, Synthia H Mellon, Samuel J Tuck, Zhang-Qi Feng, Joseph M Corey and Jonah R Chan doi:10.1038/nmeth.2105 Primary rat oligodendocytes were cultured in the presence of electron-spun nanofibers of varying sizes as a model to study myelination processes in the mammalian central nervous system. The authors study the role of fiber diameter on the initiation of concentric wrapping by oligodendrocytes. See also: News and Views by Karadottir & Stockley Fractional proliferation: a method to deconvolve cell population dynamics from single-cell data   pp923 - 928 Darren R Tyson, Shawn P Garbett, Peter L Frick and Vito Quaranta doi:10.1038/nmeth.2138 A method is presented to model cell proliferation from tracked automated time-lapse imaging of cell populations. The resulting fractional proliferation graphs permit visualization of dynamic changes in the dividing and nondividing subsets of the population. Advertisement   Corrigendum Top Drosophila Brainbow: a recombinase-based fluorescence labeling technique to subdivide neural expression patterns   p929 Stefanie Hampel, Phuong Chung, Claire E McKellar, Donald Hall, Loren L Looger and Julie H Simpson doi:10.1038/nmeth1566-929a Application Notes Top Long-span, mate-pair scaffolding and other methods for faster next-generation sequencing library creation    Cheng-Cang Wu, Rosa Ye, Svetlana Jasinovica, Megan Wagner, Ronald Godiska, Amy Hin-Yan Tong, Si Lok, Amanda Krerowicz, Curtis Knox, David Mead and Michael Lodes High-content analysis of biomarker intensity and distribution in 3D microtissues    Marcel Waschow, Stefan Letzsch, Karin Boettcher and Jens Kelm Top 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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