PDF - In This Issue

Looking back and moving forward - p911

doi:10.1038/nmeth1108-911

The fourth anniversary of Nature Methods' arrival on the publishing scene and a change in leadership offer an opportunity for reflection and editorial fine-tuning.

Abstract - | Full Text - Looking back and moving forward | PDF (71 KB) - Looking back and moving forward

A database of mass spectrometric assays for the yeast proteome - pp913 - 914

Paola Picotti, Henry Lam, David Campbell, Eric W Deutsch, Hamid Mirzaei, Jeff Ranish, Bruno Domon & Ruedi Aebersold

doi:10.1038/nmeth1108-913

Full Text - A database of mass spectrometric assays for the yeast proteome | PDF (121 KB) - A database of mass spectrometric assays for the yeast proteome | Supplementary information

Finding copy-number variants - p917

Nicole Rusk

doi:10.1038/nmeth1108-917

Several studies evaluate high-density single-nucleotide polymorphism (SNP) arrays for the detection of copy-number variations in human genomes.

Abstract - | Full Text - Finding copy-number variants | PDF (273 KB) - Finding copy-number variants

SNPing away at anonymity - pp918 - 919

Natalie de Souza

doi:10.1038/nmeth1108-918a

New findings challenge the assumption that aggregate genotype data, in which the single-nucleotide polymorphism (SNP) profiles of many people are pooled, conceal the identity of the individuals within that pool.

Abstract - | Full Text - SNPing away at anonymity | PDF (1,172 KB) - SNPing away at anonymity

Evolving a better-expressing GPCR - pp918 - 919

Allison Doerr

doi:10.1038/nmeth1108-918b

Researchers describe a method for evolving G protein–coupled receptors (GPCRs) with greater stability and enhanced expression.

Abstract - | Full Text - Evolving a better-expressing GPCR | PDF (1,172 KB) - Evolving a better-expressing GPCR

News in brief - p919

doi:10.1038/nmeth1108-919

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

Fighting fire with fire - p920

Nicole Rusk

doi:10.1038/nmeth1108-920

A co-infection model of two pathogens in a nematode yields insights into the complex interaction between the microbes.

Abstract - | Full Text - Fighting fire with fire | PDF (128 KB) - Fighting fire with fire

Microfluidics, microscopy and modeling - p922

Allison Doerr

doi:10.1038/nmeth1108-922

Researchers use microfluidics, a fluorescent reporter and modeling to quantify yeast's response to glucose availability.

Abstract - | Full Text - Systems biologyMicrofluidics, microscopy and modeling | PDF (94 KB) - Systems biologyMicrofluidics, microscopy and modeling

New views into the brain of mice on the move - pp925 - 926

Fritjof Helmchen & Carl C H Petersen

doi:10.1038/nmeth1108-925

A portable fiber-optic epifluorescence microscope allows real-time imaging of brain function with cellular spatial resolution in freely moving mice.

Abstract - | Full Text - New views into the brain of mice on the move | PDF (849 KB) - New views into the brain of mice on the move

See also: Brief Communication by Flusberg et al.

Native mass spectrometry: a bridge between interactomics and structural biology - pp927 - 933

Albert J R Heck

doi:10.1038/nmeth.1265

Abstract - | Full Text - Native mass spectrometry: a bridge between interactomics and structural biology | PDF (733 KB) - Native mass spectrometry: a bridge between interactomics and structural biology

High-speed, miniaturized fluorescence microscopy in freely moving mice - pp935 - 938

Benjamin A Flusberg, Axel Nimmerjahn, Eric D Cocker, Eran A Mukamel, Robert P J Barretto, Tony H Ko, Laurie D Burns, Juergen C Jung & Mark J Schnitzer

doi:10.1038/nmeth.1256

A miniature epifluorescence microscope that can be carried by a freely-moving adult mouse allows cellular-level imaging of neuronal spiking or measurement of microcirculation during normal behavioral activities.

Abstract - | Full Text - High-speed, miniaturized fluorescence microscopy in freely moving mice | PDF (387 KB) - High-speed, miniaturized fluorescence microscopy in freely moving mice | Supplementary information

See also: News and Views by Helmchen & Petersen

Directed enzyme evolution via small and effective neutral drift libraries - pp939 - 942

Rinkoo D Gupta & Dan S Tawfik

doi:10.1038/nmeth.1262

Directed evolution experiments usually rely on high-throughput screening of very large libraries of mutants, but most of the mutants do not even yield stable, functional proteins. The concept of neutral drift can be used to generate small but highly polymorphic and stable mutant libraries as a starting point for further evolution.

Abstract - | Full Text - Directed enzyme evolution via small and effective neutral drift libraries | PDF (203 KB) - Directed enzyme evolution via small and effective neutral drift libraries | Supplementary information

Fluorescence nanoscopy by ground-state depletion and single-molecule return - pp943 - 945

Jonas Fölling, Mariano Bossi, Hannes Bock, Rebecca Medda, Christian A Wurm, Birka Hein, Stefan Jakobs, Christian Eggeling & Stefan W Hell

doi:10.1038/nmeth.1257

A simple yet powerful super-resolution imaging approach based on switching off ordinary fluorophores and localizing those remaining or regaining fluorescence is illustrated using continuous widefield illumination and imaging of fixed and living cells labeled with rhodamine-derived dyes or fluorescent proteins. Biteen et al., also in this issue, describe related work using the ordinary fluorophore of EYFP for super-resolution imaging.

Abstract - | Full Text - Fluorescence nanoscopy by ground-state depletion and single-molecule return | PDF (543 KB) - Fluorescence nanoscopy by ground-state depletion and single-molecule return | Supplementary information

Super-resolution imaging in live Caulobacter crescentus cells using photoswitchable EYFP - pp947 - 949

Julie S Biteen, Michael A Thompson, Nicole K Tselentis, Grant R Bowman, Lucy Shapiro & W E Moerner

doi:10.1038/nmeth.1258

Previous work showed that the commonly used fluorescent protein EYFP can be bleached and reactivated. Exploiting this property allows super-resolution in vivo imaging of EYFP-labeled structures in living bacteria. Fölling et al., also in this issue, describe a related approach for super-resolution imaging using other ordinary fluorophores.

Abstract - | Full Text - Super-resolution imaging in live Caulobacter crescentus cells using photoswitchable EYFP | PDF (316 KB) - Super-resolution imaging in live Caulobacter crescentus cells using photoswitchable EYFP | Supplementary information

Linking SNPs to CAG repeat length in Huntington's disease patients - pp951 - 953

Wanzhao Liu, Lori A Kennington, H Diana Rosas, Steven Hersch, Jang-Ho Cha, Phillip D Zamore & Neil Aronin

doi:10.1038/nmeth.1261

To determine long-range linkage between single-nucleotide polymorphisms (SNPs) and the repeat-containing region of a disease-related gene, Liu et al. develop SNP linkage by circularization (SLiC) and lay the groundwork for using allele-specific RNA interference to target insertion or deletion mutations in disease-associated genes.

Abstract - | Full Text - Linking SNPs to CAG repeat length in Huntington's disease patients | PDF (450 KB) - Linking SNPs to CAG repeat length in Huntington's disease patients | Supplementary information

A noncytotoxic DsRed variant for whole-cell labeling - pp955 - 957

Rita L Strack, Daniel E Strongin, Dibyendu Bhattacharyya, Wen Tao, Allison Berman, Hal E Broxmeyer, Robert J Keenan & Benjamin S Glick

doi:10.1038/nmeth.1264

Many different red fluorescent proteins display cytotoxicity substantially higher than EGFP when used for whole-cell labeling of bacterial and mammalian cells with standard high-level expression systems. An improved tetrameric red fluorescent protein called DsRed-Express2 allows high-level labeling with minimal cytotoxicity comparable to that of EGFP.

Abstract - | Full Text - A noncytotoxic DsRed variant for whole-cell labeling | PDF (236 KB) - A noncytotoxic DsRed variant for whole-cell labeling | Supplementary information

Decision tree–driven tandem mass spectrometry for shotgun proteomics - pp959 - 964

Danielle L Swaney, Graeme C McAlister & Joshua J Coon

doi:10.1038/nmeth.1260

The two major mechanisms for peptide fragmentation by mass spectrometry, collision-activated dissociation (CAD) or a newer method, electron transfer dissociation (ETD), display different efficacies for different peptide chemistries. A decision tree algorithm, which can be embedded into instruments with both CAD and ETD capabilities, selects the optimal fragmentation method to improve the chances of successful peptide identification.

Abstract - | Full Text - Decision tree–driven tandem mass spectrometry for shotgun proteomics | PDF (404 KB) - Decision tree–driven tandem mass spectrometry for shotgun proteomics | Supplementary information

A nano-positioning system for macromolecular structural analysis - pp965 - 971

Adam Muschielok, Joanna Andrecka, Anass Jawhari, Florian Brückner, Patrick Cramer & Jens Michaelis

doi:10.1038/nmeth.1259

The combination of single-molecule fluorescence resonance energy transfer measurements of multiple dye pairs with probabilistic data analysis allows quantitative measurement of the position of flexible domains in macro-molecular complexes. The method was used to determine the three-dimensional probability density of the position of RNA exiting the transcription elongation complex.

Abstract - | Full Text - A nano-positioning system for macromolecular structural analysis | PDF (649 KB) - A nano-positioning system for macromolecular structural analysis | Supplementary information

Correlative light-electron microscopy (CLEM) combining live-cell imaging and immunolabeling of ultrathin cryosections - pp973 - 980

Carolien van Rijnsoever, Viola Oorschot & Judith Klumperman

doi:10.1038/nmeth.1263

Full Text - Correlative light-electron microscopy (CLEM) combining live-cell imaging and immunolabeling of ultrathin cryosections | PDF (446 KB) - Correlative light-electron microscopy (CLEM) combining live-cell imaging and immunolabeling of ultrathin cryosections | Supplementary information

Neuroscience tools: brain insights - pp981 - 987

Nathan Blow

doi:10.1038/nmeth1108-981

Researchers at two Boston–based neuroscience centers are working to develop new imaging tools and technology with the hope of discovering the secrets behind how the brain functions.

Abstract - | Full Text - Neuroscience tools: brain insights | PDF (545 KB) - Neuroscience tools: brain insights

Erratum: Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering - p988

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

doi:10.1038/nmeth1108-988

Full Text - Erratum: Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering | PDF (51 KB) - Erratum: Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering

Transiently produced recombinant proteins to speed up the decision-making process and limit risks

André Sobczyk, Flavien Carpentier & Sébastien Paris

Abstract - | Full Text - Transiently produced recombinant proteins to speed up the decision-making process and limit risks | PDF (177 KB) - Transiently produced recombinant proteins to speed up the decision-making process and limit risks

Harnessing multimodality to enhance quantification and reproducibility of in vivo molecular imaging data

Gilbert D Feke, W Matthew Leevy, Sean Orton, Benjamin Geldhof, M Catherine Muenker, Manisha Patel, Rao Papineni, Douglas Wood, Douglas Vizard & William McLaughlin

Abstract - | Full Text - Harnessing multimodality to enhance quantification and reproducibility of in vivo molecular imaging data | PDF (380 KB) - Harnessing multimodality to enhance quantification and reproducibility of in vivo molecular imaging data

Bioluminescence microscopy for cellular level circadian analysis in the suprachiasmatic nucleus

Werner Kammerloher

Abstract - | Full Text - Bioluminescence microscopy for cellular level circadian analysis in the suprachiasmatic nucleus | PDF (251 KB) - Bioluminescence microscopy for cellular level circadian analysis in the suprachiasmatic nucleus