Nature Methods 5, 1061 (2008). doi:10.1038/nmeth1208-1061

Author: Nathan Blow

With increasing numbers of well-characterized stem cell lines and improved culture and differentiation technologies, more scientists are testing the waters of stem cell research.

Nature Methods 5, 993 (2008). doi:10.1038/nmeth1208-993

Author: Allison Doerr

Researchers describe a method for protein identification and quantification based on electron-vibration-vibration two-dimensional infrared spectroscopy.

Nature Methods 5, 998 (2008). doi:10.1038/nmeth1208-998

Author: Allison Doerr

A diamond impurity holds great promise for nanoscale magneto-optical resonance imaging.

Nature Methods 5, 996 (2008). doi:10.1038/nmeth1208-996

Author: Michael Eisenstein

An algorithm for identifying allosteric mechanisms allows researchers to assemble a functional multidomain protein and may offer new evolutionary insights.

Nature Methods 5, 1011 (2008). doi:10.1038/nmeth.1273

Authors: Naoki Goshima, Yoshifumi Kawamura, Akiko Fukumoto, Aya Miura, Reiko Honma, Ryohei Satoh, Ai Wakamatsu, Jun-ichi Yamamoto, Kouichi Kimura, Tetsuo Nishikawa, Taichi Andoh, Yuki Iida, Kumiko Ishikawa, Emi Ito, Naoko Kagawa, Chie Kaminaga, Kei-ichi Kanehori, Bunsei Kawakami, Kiyokazu Kenmochi, Rie Kimura, Miki Kobayashi, Toshihiro Kuroita, Hisashi Kuwayama, Yukio Maruyama, Kiyoshi Matsuo, Kazuyoshi Minami, Mariko Mitsubori, Masatoshi Mori, Riyo Morishita, Atsushi Murase, Akira Nishikawa, Shigemichi Nishikawa, Toshihiko Okamoto, Noriko Sakagami, Yutaka Sakamoto, Yukari Sasaki, Tomoe Seki, Saki Sono, Akio Sugiyama, Tsuyoshi Sumiya, Tomoko Takayama, Yukiko Takayama, Hiroyuki Takeda, Takushi Togashi, Kazuhide Yahata, Hiroko Yamada, Yuka Yanagisawa, Yaeta Endo, Fumio Imamoto, Yasutomo Kisu, Shigeo Tanaka, Takao Isogai, Jun-ichi Imai, Shinya Watanabe & Nobuo Nomura

Nature Methods 5, 1001 (2008). doi:10.1038/nmeth1208-1001

Authors: James L Hartley, Kourosh Salehi-Ashtiani & David E Hill

Comprehensive sets of clones and improved high-throughput methods for production of functional proteins now allow proteome-scale in vitro experiments on nearly 15,000 human genes.

Nature Methods 5, 1003 (2008). doi:10.1038/nmeth1208-1003

Authors: Thomas Knorpp & Markus F Templin

Efficient methods to characterize the binding properties of affinity reagents are required. A combination of bacterial surface display, flow cytometry and pyrosequencing is now used for high-speed mapping of the epitopes recognized by antibodies.

Nature Methods 5, 994 (2008). doi:10.1038/nmeth1208-994a

Author: Nicole Rusk

To scale up the production and complexity of DNA nanostructures, researchers enlist the help of Escherichia coli to replicate and assemble them in vivo.

Nature Methods 5, 994 (2008). doi:10.1038/nmeth1208-994b

Author: Natalie de Souza

Chemical-genetic manipulation of enzyme activity allows specific memory erasure in the mouse.

Nature Methods 5, 989 (2008). doi:10.1038/nmeth1208-989

Sequencing technology is now advanced enough to decode individual human genomes. Will it prove to be better than existing methods for discovering the genetic basis of human phenotypic variation?

Nature Methods 5, 1031 (2008). doi:10.1038/nmeth.1266

Authors: Axel B Berger, Ghislain G Cabal, Emmanuelle Fabre, Tarn Duong, Henri Buc, Ulf Nehrbass, Jean-Christophe Olivo-Marin, Olivier Gadal & Christophe Zimmer

Nature Methods 5, 1047 (2008). doi:10.1038/nmeth.1274

Authors: Bo Huang, Sara A Jones, Boerries Brandenburg & Xiaowei Zhuang

Nature Methods 5, 1039 (2008). doi:10.1038/nmeth.1272

Authors: Johan Rockberg, John Löfblom, Barbara Hjelm, Mathias Uhlén & Stefan Ståhl

Nature Methods 5, 1053 (2008). doi:10.1038/nmeth.1268

Authors: Michaela Schwarzenbacher, Martin Kaltenbrunner, Mario Brameshuber, Clemens Hesch, Wolfgang Paster, Julian Weghuber, Bettina Heise, Alois Sonnleitner, Hannes Stockinger & Gerhard J Schütz

Nature Methods 5, 1027 (2008). doi:10.1038/nmeth.1271

Authors: Travis J Gould, Mudalige S Gunewardene, Manasa V Gudheti, Vladislav V Verkhusha, Shu-Rong Yin, Julie A Gosse & Samuel T Hess

Knowledge of the orientation of molecules within biological structures is crucial to understanding the mechanisms of cell function. We present a method to image simultaneously the positions and fluorescence anisotropies of large numbers of single molecules with nanometer lateral resolution within a sample. Based on a simple modification of fluorescence photoactivation localization microscopy (FPALM), polarization (P)-FPALM does not compromise speed or sensitivity. We show results for mouse fibroblasts expressing Dendra2-actin or Dendra2-hemagglutinin.

Nature Methods 5, 1019 (2008). doi:10.1038/nmeth.1269

Authors: Dmitriy Kedrin, Bojana Gligorijevic, Jeffrey Wyckoff, Vladislav V Verkhusha, John Condeelis, Jeffrey E Segall & Jacco van Rheenen

We report a technique to evaluate the same tumor microenvironment over multiple intravital imaging sessions in living mice. We optically marked individual tumor cells expressing photoswitchable proteins in an orthotopic mammary carcinoma and followed them for extended periods through a mammary imaging window. We found that two distinct microenvironments in the same orthotopic mammary tumor affected differently the invasion and intravasation of tumor cells.

Nature Methods 5, 1023 (2008). doi:10.1038/nmeth.1267

Authors: Stijn van Dongen, Cei Abreu-Goodger & Anton J Enright

Sylamer is a method for detecting microRNA target and small interfering RNA off-target signals in 3′ untranslated regions from a ranked gene list, sorted from upregulated to downregulated, after a microRNA perturbation or RNA interference experiment. The output is a landscape plot that tracks occurrence biases using hypergeometric P-values for all words across the gene ranking. We demonstrated the utility, speed and accuracy of this approach on several datasets.