PDF - In This Issue

Next-generation genome - p989

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?

Abstract - | Full Text - Next-generation genome | PDF (88 KB) - Next-generation genome

Much room for improvement in deposition rates of expression microarray datasets - p991

Scott A Ochsner, David L Steffen, Christian J Stoeckert, Jr & Neil J McKenna

doi:10.1038/nmeth1208-991

Full Text - Much room for improvement in deposition rates of expression microarray datasets | PDF (124 KB) - Much room for improvement in deposition rates of expression microarray datasets | Supplementary information

Optical proteomics - p993

Allison Doerr

doi:10.1038/nmeth1208-993

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

Abstract - | Full Text - Optical proteomics | PDF (185 KB) - Optical proteomics

DNA nanostructures go 'live' - pp994 - 995

Nicole Rusk

doi:10.1038/nmeth1208-994a

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

Abstract - | Full Text - DNA nanostructures go 'live' | PDF (190 KB) - DNA nanostructures go 'live'

No sunshine in a spotless mind? - pp994 - 995

Natalie de Souza

doi:10.1038/nmeth1208-994b

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

Abstract - | Full Text - No sunshine in a spotless mind? | PDF (190 KB) - No sunshine in a spotless mind?

News in brief - p995

doi:10.1038/nmeth1208-995

Full Text - News in brief | PDF (125 KB) - News in brief

Hotwiring protein regulation - p996

Michael Eisenstein

doi:10.1038/nmeth1208-996

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

Abstract - | Full Text - Hotwiring protein regulation | PDF (172 KB) - Hotwiring protein regulation

Diamonds are a spectroscopist's best friend - p998

Allison Doerr

doi:10.1038/nmeth1208-998

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

Abstract - | Full Text - Diamonds are a spectroscopist's best friend | PDF (122 KB) - Diamonds are a spectroscopist's best friend

Proteome expression moves in vitro: resources and tools for harnessing the human proteome - pp1001 - 1002

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

doi:10.1038/nmeth1208-1001

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.

Abstract - | Full Text - Proteome expression moves in vitro: resources and tools for harnessing the human proteome | PDF (862 KB) - Proteome expression moves in vitro: resources and tools for harnessing the human proteome

See also: Resource by Goshima et al.

On display on a bug: a systematic approach to characterize antibodies - pp1003 - 1004

Thomas Knorpp & Markus F Templin

doi:10.1038/nmeth1208-1003

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.

Abstract - | Full Text - On display on a bug: a systematic approach to characterize antibodies | PDF (2,876 KB) - On display on a bug: a systematic approach to characterize antibodies

See also: Article by Rockberg et al.

A large genome center's improvements to the Illumina sequencing system - pp1005 - 1010

Michael A Quail, Iwanka Kozarewa, Frances Smith, Aylwyn Scally, Philip J Stephens, Richard Durbin, Harold Swerdlow & Daniel J Turner

doi:10.1038/nmeth.1270

Abstract - | Full Text - A large genome center's improvements to the Illumina sequencing system | PDF (628 KB) - A large genome center's improvements to the Illumina sequencing system | Supplementary information

Human protein factory for converting the transcriptome into an in vitro–expressed proteome - pp1011 - 1017

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

doi:10.1038/nmeth.1273

A collection of 33,275 human Gateway entry clones and complementary in vitro protein expression methodologies are described that allow proteome-scale production of human proteins. This 'human protein factory' was validated by expression of 13,364 human proteins and assessment of activity in a variety of assays.

Abstract - | Full Text - Human protein factory for converting the transcriptome into an in vitro–expressed proteome | PDF (387 KB) - Human protein factory for converting the transcriptome into an in vitro–expressed proteome | Supplementary information

See also: News and Views by Hartley et al.

Intravital imaging of metastatic behavior through a mammary imaging window - pp1019 - 1021

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

doi:10.1038/nmeth.1269

The combination of a glass window placed on top of a mouse mammary gland with photoswitchable fluorescent protein labeling of implanted tumor cells allows tumor-cell tracking over multiple imaging sessions in orthotopic tumors. Results show the existence of two distinct microenvironments with different tumor-cell invasion and intravasation characteristics.

Abstract - | Full Text - Intravital imaging of metastatic behavior through a mammary imaging window | PDF (348 KB) - Intravital imaging of metastatic behavior through a mammary imaging window | Supplementary information

Detecting microRNA binding and siRNA off-target effects from expression data - pp1023 - 1025

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

doi:10.1038/nmeth.1267

The algorithm Sylamer finds over- or underrepresented nucleotide motifs, such as microRNA seeds, in a gene list ranked according to expression levels and thus establishes whether a microRNA is directly affecting gene expression.

Abstract - | Full Text - Detecting microRNA binding and siRNA off-target effects from expression data | PDF (1,024 KB) - Detecting microRNA binding and siRNA off-target effects from expression data | Supplementary information

Nanoscale imaging of molecular positions and anisotropies - pp1027 - 1030

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

doi:10.1038/nmeth.1271

A simple modification to the optical configuration used for fluorescence photoactivation localization microscopy (FPALM) allows the fluorescence anisotropies of each individual molecule in a nanoscale image to be measured. The method was used to obtain position and orientation information for fluorescently labeled actin or hemagglutinin molecules in fixed fibroblasts.

Abstract - | Full Text - Nanoscale imaging of molecular positions and anisotropies | PDF (406 KB) - Nanoscale imaging of molecular positions and anisotropies | Supplementary information

High-resolution statistical mapping reveals gene territories in live yeast - pp1031 - 1037

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

doi:10.1038/nmeth.1266

The spatial organization of the genome within the eukaryotic cell nucleus is not random. Automated imaging of thousands of live yeast is now used to build high-resolution probabilistic maps of the locations occupied by individual loci.

Abstract - | Full Text - High-resolution statistical mapping reveals gene territories in live yeast | PDF (1,112 KB) - High-resolution statistical mapping reveals gene territories in live yeast | Supplementary information

Epitope mapping of antibodies using bacterial surface display - pp1039 - 1045

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

doi:10.1038/nmeth.1272

An efficient pipeline for mapping antibody epitopes is presented. Combining bacterial surface display of peptide libraries, flow cytometric sorting, and pyrosequencing, the approach is amenable to a high-throughput format and should find future application in whole-proteome studies.

Abstract - | Full Text - Epitope mapping of antibodies using bacterial surface display | PDF (569 KB) - Epitope mapping of antibodies using bacterial surface display | Supplementary information

See also: News and Views by Knorpp & Templin

Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution - pp1047 - 1052

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

doi:10.1038/nmeth.1274

Extension of multicolor three-dimensional stochastic optical reconstruction microscopy (STORM) allows super-resolution fluorescence imaging of whole cells and quantitative characterization of subcellular structures and their spatial relationships. This was demonstrated by imaging the entire mitochondrial and tubulin networks in cells.

Abstract - | Full Text - Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution | PDF (717 KB) - Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution | Supplementary information

Micropatterning for quantitative analysis of protein-protein interactions in living cells - pp1053 - 1060

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

doi:10.1038/nmeth.1268

Co-patterning of a membrane protein bait and a fluorescently labeled prey is used to examine protein-protein interactions in a semiautomated fashion in living cells. Photobleaching experiments and single-molecule imaging further allow dynamic studies of the interaction.

Abstract - | Full Text - Micropatterning for quantitative analysis of protein-protein interactions in living cells | PDF (887 KB) - Micropatterning for quantitative analysis of protein-protein interactions in living cells | Supplementary information

Stem cells: finding the right path - pp1061 - 1068

Nathan Blow

doi:10.1038/nmeth1208-1061

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.

Abstract - | Full Text - Stem cells: finding the right path | PDF (762 KB) - Stem cells: finding the right path