PDF - In This Issue

Elective affinities - p851

doi:10.1038/nmeth1008-851

A feasibility study for the systematic generation of affinity reagents to human proteins provides an opportunity to test the merits of recombinant affinity reagents.

Abstract - | Full Text - Elective affinities | PDF (65 KB) - Elective affinities

Large-scale evaluation of protein reductive methylation for improving protein crystallization - pp853 - 854

Youngchang Kim, Pearl Quartey, Hui Li, Lour Volkart, Catherine Hatzos, Changsoo Chang, Boguslaw Nocek, Marianne Cuff, Jerzy Osipiuk, Kemin Tan, Yao Fan, Lance Bigelow, Natalia Maltseva, Ruiying Wu, Maria Borovilos, Erika Duggan, Min Zhou, T Andrew Binkowski, Rong-guang Zhang & Andrzej Joachimiak

doi:10.1038/nmeth1008-853

Full Text - Large-scale evaluation of protein reductive methylation for improving protein crystallization | PDF (234 KB) - Large-scale evaluation of protein reductive methylation for improving protein crystallization | Supplementary information

A pilot project to generate affinity reagents to human proteins - pp854 - 855

Mathias Uhlen, Susanne Gräslund & Michael Sundström

doi:10.1038/nmeth1008-854

Full Text - A pilot project to generate affinity reagents to human proteins | PDF (228 KB) - A pilot project to generate affinity reagents to human proteins | Supplementary information

Microbes right on target - p857

Michelle Pflumm

doi:10.1038/nmeth1008-857

Researchers use a targeted metagenomic approach to functionally characterize complex microbial communities.

Abstract - | Full Text - Microbes right on target | PDF (145 KB) - Microbes right on target

New twists on photoswitchable proteins - pp858 - 859

Natalie de Souza

doi:10.1038/nmeth1008-858a

Fluorescent proteins with new photoswitching properties allow multilabel imaging at a single detection wavelength and dual-color superresolution microscopy.

Abstract - | Full Text - New twists on photoswitchable proteins | PDF (147 KB) - New twists on photoswitchable proteins

Phosphorylation and the cell cycle - pp858 - 859

Allison Doerr

doi:10.1038/nmeth1008-858b

Two groups used quantitative mass spectrometry to look at changes in protein phosphorylation across the cell cycle.

Abstract - | Full Text - Phosphorylation and the cell cycle | PDF (147 KB) - Phosphorylation and the cell cycle

News in brief - p859

doi:10.1038/nmeth1008-859

Full Text - News in brief | PDF (92 KB) - News in brief

Antibodypedia - p860

Veronique Kiermer

doi:10.1038/nmeth1008-860

A web portal to share antibody validation data.

Abstract - | Full Text - Antibodypedia | PDF (92 KB) - Antibodypedia

A surrogate scaffold tested - p861

Irene Kaganman

doi:10.1038/nmeth1008-861

Researchers tested an alternate antibody scaffold, creating so-called Surrobodies.

Abstract - | Full Text - A surrogate scaffold tested | PDF (95 KB) - A surrogate scaffold tested

Classical genetics goes high-tech - pp863 - 864

David S Fay

doi:10.1038/nmeth1008-863

A combination of automated screening and next-generation sequencing makes it possible to identify Caenorhabditis elegans mutants at unprecedented speed and scale.

Abstract - | Full Text - Classical genetics goes high-tech | PDF (562 KB) - Classical genetics goes high-tech

See also: Brief Communication by Sarin et al. | Brief Communication by Doitsidou et al.

Caenorhabditis elegans mutant allele identification by whole-genome sequencing - pp865 - 867

Sumeet Sarin, Snehit Prabhu, M Maggie O'Meara, Itsik Pe'er & Oliver Hobert

doi:10.1038/nmeth.1249

Identifying the molecular lesions in mutants isolated in forward genetic screens can be a laborious process. A proof-of-principle study in Caenorhabditis elegans now shows that this can be achieved rapidly by whole-genome deep sequencing.

Abstract - | Full Text - Caenorhabditis elegans mutant allele identification by whole-genome sequencing | PDF (225 KB) - Caenorhabditis elegans mutant allele identification by whole-genome sequencing | Supplementary information

See also: News and Views by Fay

Automated screening for mutants affecting dopaminergic-neuron specification in C. elegans - pp869 - 872

Maria Doitsidou, Nuria Flames, Albert C Lee, Alexander Boyanov & Oliver Hobert

doi:10.1038/nmeth.1250

An automated sorting method using the COPAS Biosort machine allows the isolation of mutant C. elegans displaying differences in GFP expression in small numbers of cells. Compared to manual methods this increases the efficiency of the phenotypic selection step in cell-fate screens.

Abstract - | Full Text - Automated screening for mutants affecting dopaminergic-neuron specification in C. elegans | PDF (416 KB) - Automated screening for mutants affecting dopaminergic-neuron specification in C. elegans | Supplementary information

See also: News and Views by Fay

Building consensus spectral libraries for peptide identification in proteomics - pp873 - 875

Henry Lam, Eric W Deutsch, James S Eddes, Jimmy K Eng, Stephen E Stein & Ruedi Aebersold

doi:10.1038/nmeth.1254

Spectral searching, based on matching experimental peptide spectra to reference spectral libraries, is gaining interest as an alternative to traditional sequence-database searching in mass spectrometry–based proteomics. A software tool, SpectraST, now allows users to build their own high-quality spectral libraries from raw data.

Abstract - | Full Text - Building consensus spectral libraries for peptide identification in proteomics | PDF (173 KB) - Building consensus spectral libraries for peptide identification in proteomics | Supplementary information

Imaging individual mRNA molecules using multiple singly labeled probes - pp877 - 879

Arjun Raj, Patrick van den Bogaard, Scott A Rifkin, Alexander van Oudenaarden & Sanjay Tyagi

doi:10.1038/nmeth.1253

A strategy using 48 or more singly labeled fluorescent oligonucleotide probes targeted to individual mRNA molecules allows the simultaneous localization and quantification of three mRNA species in fixed cells. mRNA visualization in whole animals and other organisms is also demonstrated.

Abstract - | Full Text - Imaging individual mRNA molecules using multiple singly labeled probes | PDF (331 KB) - Imaging individual mRNA molecules using multiple singly labeled probes | Supplementary information

Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering - pp881 - 886

Marco Cammarata, Matteo Levantino, Friedrich Schotte, Philip A Anfinrud, Friederike Ewald, Jungkweon Choi, Antonio Cupane, Michael Wulff & Hyotcherl Ihee

doi:10.1038/nmeth.1255

Time-resolved wide-angle X-ray scattering (TR-WAXS) using synchrotron radiation can be used to observe dynamic protein structural changes with nanosecond time resolution in solution, complementing time-resolved optical spectroscopy and Laue crystallography methods.

Abstract - | Full Text - Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering | PDF (497 KB) - Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering | Supplementary information

Identification of genetic variants using bar-coded multiplexed sequencing - pp887 - 893

David W Craig, John V Pearson, Szabolcs Szelinger, Aswin Sekar, Margot Redman, Jason J Corneveaux, Traci L Pawlowski, Trisha Laub, Gary Nunn, Dietrich A Stephan, Nils Homer & Matthew J Huentelman

doi:10.1038/nmeth.1251

Targeted regions of the human genome are resequenced in multiplex with Illumina technology, and the pipeline is evaluated for polymorphism discovery and genotyping.

Abstract - | Full Text - Identification of genetic variants using bar-coded multiplexed sequencing | PDF (687 KB) - Identification of genetic variants using bar-coded multiplexed sequencing | Supplementary information

Optogenetic analysis of synaptic function - pp895 - 902

Jana F Liewald, Martin Brauner, Greg J Stephens, Magali Bouhours, Christian Schultheis, Mei Zhen & Alexander Gottschalk

doi:10.1038/nmeth.1252

Using both behavioral and electrophysiological readouts, Channelrhodopsin-2, a light-gated cation channel, is applied to the study of synaptic function in Caenorhabditis elegans.

Abstract - | Full Text - Optogenetic analysis of synaptic function | PDF (592 KB) - Optogenetic analysis of synaptic function | Supplementary information

Scientific software: seeing the SNPs between us - pp903 - 908

Steven David Buckingham

doi:10.1038/nmeth1008-903

The results of large genome-wide association studies (GWASs) are being deposited in public databases with increasing frequency. But the software to analyze and interpret GWAS datasets can be difficult to use. Could a new generation of user-friendly programs fill the gap?

Abstract - | Full Text - Scientific software: seeing the SNPs between us | PDF (603 KB) - Scientific software: seeing the SNPs between us

Erratum: Mass spectrometry and proteomics: hitting the mark - p910

Nathan Blow

doi:10.1038/nmeth1008-910

Full Text - Erratum: Mass spectrometry and proteomics: hitting the mark | PDF (50 KB) - Erratum: Mass spectrometry and proteomics: hitting the mark

Development of an Eg5 assay using the HTRF® Transcreener® ADP kit

Laurence Jacquemart, Marion De Decker & Bastien Caumes

Abstract - | Full Text - Development of an Eg5 assay using the HTRF® Transcreener® ADP kit | PDF (376 KB) - Development of an Eg5 assay using the HTRF® Transcreener® ADP kit

Rapid, on-demand protein stabilization and destabilization using the ProteoTuner™ systems

Michael Haugwitz, Tatiana Garachtchenko, Omar Nourzaie, Suvarna Gandlur & Hiroaki Sagawa

Abstract - | Full Text - Rapid, on-demand protein stabilization and destabilization using the ProteoTuner™ systems | PDF (467 KB) - Rapid, on-demand protein stabilization and destabilization using the ProteoTuner™ systems