PDF - In This Issue

Lines of communication - p181

doi:10.1038/nmeth0309-181

The increasing impact of science on society calls for improved communication between scientists and the public via dedicated science media centers as well as nontraditional personal blogs.

Abstract - | Full Text - Lines of communication | PDF (93 KB) - Lines of communication

Uncoupling diffusion and binding in FRAP experiments - p183

Nevin A Lambert

doi:10.1038/nmeth0309-183a

Full Text - Uncoupling diffusion and binding in FRAP experiments | PDF (545 KB) - Uncoupling diffusion and binding in FRAP experiments

Reply to "Uncoupling diffusion and binding in FRAP experiments" - pp183 - 184

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

doi:10.1038/nmeth0309-183b

Full Text - Reply to "Uncoupling diffusion and binding in FRAP experiments" | PDF (545 KB) - Reply to "Uncoupling diffusion and binding in FRAP experiments"

A computational approach to correct arginine-to-proline conversion in quantitative proteomics - pp184 - 185

Sung Kyu Park, Lujian Liao, Jin Young Kim & John R Yates, III

doi:10.1038/nmeth0309-184

Full Text - A computational approach to correct arginine-to-proline conversion in quantitative proteomics | PDF (522 KB) - A computational approach to correct arginine-to-proline conversion in quantitative proteomics | Supplementary information

Reverse ChIP - p187

Nicole Rusk

doi:10.1038/nmeth0309-187

The combination of a DNA probe and mass spectrometric analysis allows the unbiased identification of chromatin-associated proteins.

Abstract - | Full Text - Reverse ChIP | PDF (203 KB) - Reverse ChIP

Mimicking a pore - pp188 - 189

Amy Donner

doi:10.1038/nmeth0309-188a

A functionalized polycarbonate nanosorter mimics fundamental properties of the nuclear pore complex.

Abstract - | Full Text - Mimicking a pore | PDF (255 KB) - Mimicking a pore

The many ages of a protein - pp188 - 189

Natalie de Souza

doi:10.1038/nmeth0309-188b

Monomeric fluorescent timers determine protein age within the cell.

Abstract - | Full Text - The many ages of a protein | PDF (255 KB) - The many ages of a protein

News in brief - p189

doi:10.1038/nmeth0309-189

Full Text - News in brief | PDF (121 KB) - News in brief

Setting a nanoparticle trap - p190

Allison Doerr

doi:10.1038/nmeth0309-190

Researchers developed a hybrid microfluidic–optical trapping device to trap and transport very small nanoparticles and DNA molecules.

Abstract - | Full Text - Setting a nanoparticle trap | PDF (242 KB) - Setting a nanoparticle trap

Good vibrations - p192

Michael Eisenstein

doi:10.1038/nmeth0309-192

A microscopy platform that brings magnetic resonance imaging to the nanometer scale offers a promising new tool for three-dimensional molecular visualization.

Abstract - | Full Text - Good vibrations | PDF (310 KB) - Good vibrations

Microfluidics for the people - p194

Allison Doerr

doi:10.1038/nmeth0309-194

A simple approach for making multilayer microfluidic devices should make this technology more accessible to biologists.

Abstract - | Full Text - Microfluidics for the people | PDF (119 KB) - Microfluidics for the people

Faster is better: improving the sensitivity of solid-state NMR - pp197 - 198

Stanley J Opella

doi:10.1038/nmeth0309-197

A method to improve the sensitivity of solid-state nuclear magnetic resonance spectroscopy promises to extend this technology to larger and more biologically interesting systems than previously feasible.

Abstract - | Full Text - Faster is better: improving the sensitivity of solid-state NMR | PDF (214 KB) - Faster is better: improving the sensitivity of solid-state NMR

See also: Brief Communication by Wickramasinghe et al.

Direct determination of haplotypes from single DNA molecules - pp199 - 201

Ming Xiao, Eunice Wan, Catherine Chu, Wen-Chi Hsueh, Yang Cao & Pui-Yan Kwok

doi:10.1038/nmeth.1301

A map of single nucleotide polymorphisms (SNPs), also called a haplotype map, is very informative for mapping complex trait loci, but obtaining haplotypes over long genomic distances is very challenging. The combination of dye-labeling each SNP on PCR fragments with total internal reflection microscopy will allow the reading of long-range haplotypes with relative ease.

Abstract - | Full Text - Direct determination of haplotypes from single DNA molecules | PDF (303 KB) - Direct determination of haplotypes from single DNA molecules | Supplementary information

Quantitative interaction proteomics using mass spectrometry - pp203 - 205

Alexander Wepf, Timo Glatter, Alexander Schmidt, Ruedi Aebersold & Matthias Gstaiger

doi:10.1038/nmeth.1302

Absolute quantitative information about the stoichiometry of protein complex components can be obtained with a modified affinity purification–mass spectrometry method, as demonstrated for the human protein phosphatase 2A network.

Abstract - | Full Text - Quantitative interaction proteomics using mass spectrometry | PDF (177 KB) - Quantitative interaction proteomics using mass spectrometry | Supplementary information

High-efficiency labeling of sialylated glycoproteins on living cells - pp207 - 209

Ying Zeng, T N C Ramya, Anouk Dirksen, Philip E Dawson & James C Paulson

doi:10.1038/nmeth.1305

Sialic acid–containing cell-surface glycoproteins can be chemically labeled with a biotin tag under mild conditions. The method is highly efficient and uses commercially available reagents; it should be useful for studying glycoprotein trafficking as well as in glycoproteomics applications.

Abstract - | Full Text - High-efficiency labeling of sialylated glycoproteins on living cells | PDF (290 KB) - High-efficiency labeling of sialylated glycoproteins on living cells | Supplementary information

Programmed subcellular release for studying the dynamics of cell detachment - pp211 - 213

Bridget Wildt, Denis Wirtz & Peter C Searson

doi:10.1038/nmeth.1299

As cells move over a substrate, they need to first sever their contact with the matrix by detaching focal adhesions. A setup that allows spatially and temporally controlled release of focal adhesions now facilitates the quantitative measurement of cell movement across a substrate.

Abstract - | Full Text - Programmed subcellular release for studying the dynamics of cell detachment | PDF (319 KB) - Programmed subcellular release for studying the dynamics of cell detachment | Supplementary information

Nanomole-scale protein solid-state NMR by breaking intrinsic ¹H T₁ boundaries - pp215 - 218

Nalinda P Wickramasinghe, Sudhakar Parthasarathy, Christopher R Jones, Chhavi Bhardwaj, Fei Long, Mrignayani Kotecha, Shahila Mehboob, Leslie W-M Fung, Jaan Past, Ago Samoson & Yoshitaka Ishii

doi:10.1038/nmeth.1300

Solid-state NMR spectroscopy is used to elucidate structural details about proteins that cannot be easily studied by X-ray crystallography, but because the technique is not very sensitive, large sample amounts are required, limiting its biological application. A combination of optimizations now increases the sensitivity of solid-state NMR spectroscopy by up to 5-fold.

Abstract - | Full Text - Nanomole-scale protein solid-state NMR by breaking intrinsic 1H T1 boundaries | PDF (648 KB) - Nanomole-scale protein solid-state NMR by breaking intrinsic 1H T1 boundaries | Supplementary information

See also: News and Views by Opella

Automated light-based mapping of motor cortex by photoactivation of channelrhodopsin-2 transgenic mice - pp219 - 224

Oliver G S Ayling, Thomas C Harrison, Jamie D Boyd, Alexander Goroshkov & Timothy H Murphy

doi:10.1038/nmeth.1303

Optical stimulation of channelrhodopsin-2 expressed in neurons of the motor cortex is combined with electromyogram recordings or motion-sensing of limb muscles to achieve fast motor mapping in the mouse.

Abstract - | Full Text - Automated light-based mapping of motor cortex by photoactivation of channelrhodopsin-2 transgenic mice | PDF (559 KB) - Automated light-based mapping of motor cortex by photoactivation of channelrhodopsin-2 transgenic mice | Supplementary information

Analysis of receptor oligomerization by FRAP microscopy - pp225 - 230

Sandra Dorsch, Karl-Norbert Klotz, Stefan Engelhardt, Martin J Lohse & Moritz Bünemann

doi:10.1038/nmeth.1304

Dual-color fluorescence recovery after photobleaching (FRAP) is used to investigate dimerization and higher-order complex formation of receptors at the surface of live cells. A defined fraction of receptors is immobilized with antibodies, and the mobility of the nonimmobilized fraction is measured by FRAP.

Abstract - | Full Text - Analysis of receptor oligomerization by FRAP microscopy | PDF (394 KB) - Analysis of receptor oligomerization by FRAP microscopy | Supplementary information

Small RNAs: biology's brave new world - pp231 - 235

Nathan Blow

doi:10.1038/nmeth0309-231

Small RNA discovery and profiling efforts are dramatically reshaping fundamental concepts of how genes are regulated and are leading to new tools for studying gene function.

Abstract - | Full Text - Small RNAs: biology's brave new world | PDF (949 KB) - Small RNAs: biology's brave new world

Antibody signatures defined by high-content peptide microarray analysis

Mike Schutkowski, Johannes Zerweck, Antonia Masch & Holger Wenschuh

Abstract - | Full Text - Antibody signatures defined by high-content peptide microarray analysis | PDF (262 KB) - Antibody signatures defined by high-content peptide microarray analysis