We celebrate the 2011 International Year of Chemistry by highlighting the important contributions of chemistry to methods currently used in biology research. Included in the special feature is a Historical Commentary on mass spectrometry, two Commentaries—one on bioorthogonal chemistry and another on fluorescent probes—a Technology Feature on protein engineering, a selection of chemistry papers published in past issues of Nature Methods, and an Editorial. |
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Special Feature: International Year of Chemistry
Editorial |  Top |
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The year of the chemist p607
doi:10.1038/nmeth.1667
The year 2011 has been designated the International Year of Chemistry. Nature Methods joins in the celebration with a special feature in this issue.
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This Month | Top |
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The author file: Carl Hansen p609
Monya Baker
doi:10.1038/nmeth.1655
A million picoliter PCR chambers give quick, precise answers.
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Points of view: Simplify to clarify p611
Bang Wong
doi:10.1038/nmeth.1660
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Correspondence | Top |
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OpenFreezer: a reagent information management software system pp612 - 613
Marina Olhovsky, Kelly Williton, Anna Yue Dai, Adrian Pasculescu, John Paul Lee, Marilyn Goudreault, Clark D. Wells, Jin Gyoon Park, Anne-Claude Gingras, Rune Linding, Tony Pawson and Karen Colwill
doi:10.1038/nmeth.1658
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Research Highlights | Top |
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Technology Feature | Top |
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Special Feature: International Year of Chemistry
Protein engineering: navigating between chance and reason pp623 - 626
Monya Baker
doi:10.1038/nmeth.1654
Researchers use large libraries, focused libraries and rational design to engineer useful proteins.
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News and Views | Top |
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From journal articles to computational models: a new automated tool pp627 - 628
Tom M. Mitchell
doi:10.1038/nmeth.1661
Automated methods can now extract brain-image coordinates appearing in hundreds of publications in targeted topic areas and then integrate these data to form computational models that classify new brain-image data.
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See also: Article by Yarkoni et al.
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Seeing the light: integrating genome engineering with double-strand break repair pp628 - 630
Matthew Porteus
doi:10.1038/nmeth.1656
The two-color traffic light reporter reads out what pathway is used to repair a DNA break and will increase insights into genome engineering.
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See also: Article by Certo et al.
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Simply quantifying ubiquitin complexity pp630 - 631
Eric J Bennett and J Wade Harper
doi:10.1038/nmeth.1651
An absolute quantification approach combined with differential affinity capture provides a means by which to accurately measure distinct pools of ubiquitin in cells or tissues.
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See also: Article by Kaiser et al.
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Historical Commentary | Top |
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Special Feature: International Year of Chemistry
A century of mass spectrometry: from atoms to proteomes pp633 - 637
John R Yates III
doi:10.1038/nmeth.1659
Long before mass spectrometry became an important tool for cell biology, it was yielding scientific insights in physics and chemistry. Here is a brief history of how the technology has expanded from a tool for studying atomic structure and characterizing small molecules to its current incarnation as the most powerful technique for analyzing proteomes.
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Commentary | Top |
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Special Feature: International Year of Chemistry
Bringing chemistry to life pp638 - 642
Michael Boyce and Carolyn R Bertozzi
doi:10.1038/nmeth.1657
Bioorthogonal chemistry allows a wide variety of biomolecules to be specifically labeled and probed in living cells and whole organisms. Here we discuss the history of bioorthogonal reactions and some of the most interesting and important advances in the field.
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Special Feature: International Year of Chemistry
Fluorescent probes for sensing and imaging pp642 - 645
Tasuku Ueno and Tetsuo Nagano
doi:10.1038/nmeth.1663
A diverse array of small molecule-based fluorescent probes is available for many different types of biological experiments. Here we examine the history of these probes and discuss some of the most interesting applications.
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Chemistry Methods | Top |
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Special Feature: International Year of Chemistry
Chemistry Methods pp646 - 647
doi:10.1038/nmeth0811-646
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Brief Communications | Top |
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Megapixel digital PCR pp649 - 651
Kevin A Heyries, Carolina Tropini, Michael VanInsberghe, Callum Doolin, Oleh I Petriv, Anupam Singhal, Kaston Leung, Curtis B Hughesman and Carl L Hansen
doi:10.1038/nmeth.1640
This digital PCR device arrays samples into one million small-volume reactors, achieving a dynamic range of 107, measurement precision better than 1% and the ability to detect single-nucleotide variants present at less than 1:100,000.
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CREST maps somatic structural variation in cancer genomes with base-pair resolution pp652 - 654
Jianmin Wang, Charles G Mullighan, John Easton, Stefan Roberts, Sue L Heatley, Jing Ma, Michael C Rusch, Ken Chen, Christopher C Harris, Li Ding, Linda Holmfeldt, Debbie Payne-Turner, Xian Fan, Lei Wei, David Zhao, John C Obenauer, Clayton Naeve, Elaine R Mardis, Richard K Wilson, James R Downing and Jinghui Zhang
doi:10.1038/nmeth.1628
This algorithm uses the soft-clipped, unaligned parts of a sequence read to map structural variation in cancer genomes with high predictive accuracy.
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Large-scale phosphosite quantification in tissues by a spike-in SILAC method pp655 - 658
Mara Monetti, Nagarjuna Nagaraj, Kirti Sharma and Matthias Mann
doi:10.1038/nmeth.1647
Quantitative, large-scale in vivo phosphoproteomics analyses are made possible with a form of spike-in stable-isotope llabeling with amino acids in cell culture (SILAC), in which SILAC-labeled cell lines act as an internal standard for mass spectrometry-based tissue phosphoproteome analysis.
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A public genome-scale lentiviral expression library of human ORFs pp659 - 661
Xiaoping Yang, Jesse S Boehm, Xinping Yang, Kourosh Salehi-Ashtiani, Tong Hao, Yun Shen, Rakela Lubonja, Sapana R Thomas, Ozan Alkan, Tashfeen Bhimdi, Thomas M Green, Cory M Johannessen, Serena J Silver, Cindy Nguyen, Ryan R Murray, Haley Hieronymus, Dawit Balcha, Changyu Fan, Chenwei Lin, Lila Ghamsari, Marc Vidal, William C Hahn, David E Hill and David E Root
doi:10.1038/nmeth.1638
Two sequence-verified, clonal, publicly available collections of human open reading frames are reported. One collection is in a lentiviral vector for expression in mammalian cells; the other is in the Gateway vector system.
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Functional ultrasound imaging of the brain pp662 - 664
Emilie Macé, Gabriel Montaldo, Ivan Cohen, Michel Baulac, Mathias Fink and Mickael Tanter
doi:10.1038/nmeth.1641
A new method called functional ultrasound (fUS) is reported that allows imaging of transient changes in blood volume in the whole rat brain with a spatiotemporal resolution not attained by other functional brain imaging modalities.
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Western Blotting Peace of Mind
Bio-Rad's Precision Plus Protein™ WesternC™ standards are a useful quality control tool for each step in your western blotting workflow. These dual-colored standards are convenient for easy monitoring of electrophoretic separation, protein transfer, and sizing of target proteins after chemiluminescent or fluorescent blot development. |  |
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Articles | Top |
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Large-scale automated synthesis of human functional neuroimaging data pp665 - 670
Tal Yarkoni, Russell A Poldrack, Thomas E Nichols, David C Van Essen and Tor D Wager
doi:10.1038/nmeth.1635
A framework and web interface for the large-scale and automated synthesis of human neuroimaging data extracted from the literature is presented. It is used to generate a large database of mappings between neural and cognitive states and to address long-standing inferential problems in the neuroimaging literature.
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See also: News and Views by Mitchell
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Tracking genome engineering outcome at individual DNA breakpoints pp671 - 676
Michael T Certo, Byoung Y Ryu, James E Annis, Mikhail Garibov, Jordan Jarjour, David J Rawlings and Andrew M Scharenberg
doi:10.1038/nmeth.1648
A fluorescent reporter, named traffic light, reads out whether repair of a DNA break occurs by nonhomologous end-joining or by homologous recombination. It should enable the identification of factors that affect repair pathway choice and thus improved approaches for genome engineering.
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See also: News and Views by Porteus
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A large-scale method to measure absolute protein phosphorylation stoichiometries pp677 - 683
Ronghu Wu, Wilhelm Haas, Noah Dephoure, Edward L Huttlin, Bo Zhai, Mathew E Sowa and Steven P Gygi
doi:10.1038/nmeth.1636
The functional role of protein phosphorylation is determined not just by whether a particular site is phosphorylated or not but also by the site's stoichiometry. A method to determine the absolute stoichiometries of protein phosphorylation on a proteomic scale is described.
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Two-photon polarization microscopy reveals protein structure and function pp684 - 690
Josef Lazar, Alexey Bondar, Stepan Timr and Stuart J Firestein
doi:10.1038/nmeth.1643
Membrane protein interactions and conformational changes can be sensitively monitored with two-photon polarization microscopy, a method that takes advantage of the anisotropic absorption properties of fluorescent proteins. The authors applied the method to image G-protein activation and changes in intracellular calcium concentration.
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Protein standard absolute quantification (PSAQ) method for the measurement of cellular ubiquitin pools pp691 - 696
Stephen E Kaiser, Brigit E Riley, Thomas A Shaler, R Sean Trevino, Christopher H Becker, Howard Schulman and Ron R Kopito
doi:10.1038/nmeth.1649
Ubiquitin, an important post-translational modification that regulates a variety of biological processes is found in free and conjugated (monoubiquitin and polyubiquitin) forms in the cell. A method for precisely measuring these cellular pools using protein standard absolute quantification mass spectrometry is described; the approach should yield insights into ubiquitin signaling.
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See also: News and Views by Bennett & Harper
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Application Note | Top |
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Robust target labeling from small amounts of RNA for Illumina® Expression BeadChip® arrays
Jim Pease
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