PDF - In This Issue

Defining the scientific method - p237

doi:10.1038/nmeth0409-237

The rise of 'omics' methods and data-driven research presents new possibilities for discovery but also stimulates disagreement over how science should be conducted and even how it should be defined.

Abstract - | Full Text - Defining the scientific method | PDF (101 KB) - Defining the scientific method

The UCSC Cancer Genomics Browser - pp239 - 240

Jingchun Zhu, J Zachary Sanborn, Stephen Benz, Christopher Szeto, Fan Hsu, Robert M Kuhn, Donna Karolchik, John Archie, Marc E Lenburg, Laura J Esserman, W James Kent, David Haussler & Ting Wang

doi:10.1038/nmeth0409-239

Full Text - The UCSC Cancer Genomics Browser | PDF (1,706 KB) - The UCSC Cancer Genomics Browser | Supplementary information

mzAPI: a new strategy for efficiently sharing mass spectrometry data - pp240 - 241

Manor Askenazi, Jignesh R Parikh & Jarrod A Marto

doi:10.1038/nmeth0409-240

Full Text - mzAPI: a new strategy for efficiently sharing mass spectrometry data | PDF (910 KB) - mzAPI: a new strategy for efficiently sharing mass spectrometry data

PALM reading - p243

Wayne Peng

doi:10.1038/nmeth0409-243

Super-resolution fluorescence microscopy gets a boost in axial resolution from two groups of optics wizards.

Abstract - | Full Text - PALM reading | PDF (400 KB) - PALM reading

Cheap third-generation sequencing - p244

Nicole Rusk

doi:10.1038/nmeth0409-244a

By covalently attaching cyclodextrin to a hemolysin nanopore, researchers show single-molecule, label-free sequencing at very high accuracy.

Abstract - | Full Text - Cheap third-generation sequencing | PDF (408 KB) - Cheap third-generation sequencing

Deep sequencing of ribosome footprints - p244

Natalie de Souza

doi:10.1038/nmeth0409-244b

Combining ribosome profiling and deep sequencing, researchers present a method to monitor protein translation genome-wide.

Abstract - | Full Text - Deep sequencing of ribosome footprints | PDF (408 KB) - Deep sequencing of ribosome footprints

News in brief - p245

doi:10.1038/nmeth0409-245

Full Text - News in brief | PDF (131 KB) - News in brief

Snapshots of proteins at work - p246

Allison Doerr

doi:10.1038/nmeth0409-246

Two groups extend the boundaries of in-cell nuclear magnetic resonance spectroscopy.

Abstract - | Full Text - Snapshots of proteins at work | PDF (138 KB) - Snapshots of proteins at work

Don't just stand there - p248

Michael Eisenstein

doi:10.1038/nmeth0409-248

A long-range magnetic resonance imaging platform promises unprecedented capabilities for whole-organ visualization and high-throughput sample analysis.

Abstract - | Full Text - Don't just stand there | PDF (394 KB) - Don't just stand there

QPCR without the 'P' - p250

Irene Kaganman

doi:10.1038/nmeth0409-250

With the addition of a ligand-sensing aptamer sequence, a self-replicating RNA enzyme system enables general molecular detection, analogous to that of quantitative PCR.

Abstract - | Full Text - QPCR without the 'P' | PDF (134 KB) - QPCR without the 'P'

Questioning standardization in science - pp253 - 254

Richard Paylor

doi:10.1038/nmeth0409-253

Some scientists suggest that environmental standardization may lead to spurious findings. The implication from this hypothesis will likely be controversial.

Abstract - | Full Text - Questioning standardization in science | PDF (2,384 KB) - Questioning standardization in science

See also: Perspective by Richter et al.

Footprints by deep sequencing - pp254 - 255

Gordon Hager

doi:10.1038/nmeth0409-254

Deep sequencing of DNase I–treated yeast DNA yields genome-wide information on chromatin transitions as well as protein binding in these regions.

Abstract - | Full Text - Footprints by deep sequencing | PDF (562 KB) - Footprints by deep sequencing

See also: Article by Hesselberth et al.

Environmental standardization: cure or cause of poor reproducibility in animal experiments? - pp257 - 261

S Helene Richter, Joseph P Garner & Hanno Würbel

doi:10.1038/nmeth.1312

Abstract - | Full Text - Environmental standardization: cure or cause of poor reproducibility in animal experiments? | PDF (440 KB) - Environmental standardization: cure or cause of poor reproducibility in animal experiments?

See also: News and Views by Paylor

Quantification of rare allelic variants from pooled genomic DNA - pp263 - 265

Todd E Druley, Francesco L M Vallania, Daniel J Wegner, Katherine E Varley, Olivia L Knowles, Jacqueline A Bonds, Sarah W Robison, Scott W Doniger, Aaron Hamvas, F Sessions Cole, Justin C Fay & Robi D Mitra

doi:10.1038/nmeth.1307

The base-calling algorithm SNPSeeker detects single-nucleotide polymorphisms with frequencies that are below the error rate of the sequencing platform. It is thus well suited to analyze data from large pooled samples and find rare variants that may contribute to diseases or complex traits.

Abstract - | Full Text - Quantification of rare allelic variants from pooled genomic DNA | PDF (197 KB) - Quantification of rare allelic variants from pooled genomic DNA | Supplementary information

Hematopoietic stem cell transplantation without irradiation - pp267 - 269

Claudia Waskow, Vikas Madan, Susanne Bartels, Céline Costa, Rosel Blasig & Hans-Reimer Rodewald

doi:10.1038/nmeth.1309

Long-term engraftment of hematopoietic stem cells into the bone marrow of a recipient depends on immunological compatibility between donor and host, or ablation of the host's immune system by irradiation. A 'universal recipient' mouse model now shows that mice that lack T, B and NK cells and bear mutations in the tyrosine kinase Kit accept any donor HSC without irradiation.

Abstract - | Full Text - Hematopoietic stem cell transplantation without irradiation | PDF (267 KB) - Hematopoietic stem cell transplantation without irradiation | Supplementary information

Neonatal desensitization allows long-term survival of neural xenotransplants without immunosuppression - pp271 - 273

Claire M Kelly, Sophie V Precious, Caroline Scherf, Richard Penketh, Nazar N Amso, Alysia Battersby, Nicholas D Allen, Stephen B Dunnett & Anne E Rosser

doi:10.1038/nmeth.1308

Rats are desensitized to xenografts of human neural or embryonic stem cell–derived cells by exposure to the xenogeneic cells during the neonatal period. Brain grafts survive in immunocompetent rats without chronic immunosuppression, allowing long-term studies.

Abstract - | Full Text - Neonatal desensitization allows long-term survival of neural xenotransplants without immunosuppression | PDF (238 KB) - Neonatal desensitization allows long-term survival of neural xenotransplants without immunosuppression | Supplementary information

SUnSET, a nonradioactive method to monitor protein synthesis - pp275 - 277

Enrico K Schmidt, Giovanna Clavarino, Maurizio Ceppi & Philippe Pierre

doi:10.1038/nmeth.1314

As an alternative to the use of radioactively labeled amino acids, incorporation of puromycin into proteins allows evaluation of translation in heterogenous cell populations by flow cytometry analysis after staining with an antibody to puromycin.

Abstract - | Full Text - SUnSET, a nonradioactive method to monitor protein synthesis | PDF (214 KB) - SUnSET, a nonradioactive method to monitor protein synthesis | Supplementary information

Nanoscale live-cell imaging using hopping probe ion conductance microscopy - pp279 - 281

Pavel Novak, Chao Li, Andrew I Shevchuk, Ruben Stepanyan, Matthew Caldwell, Simon Hughes, Trevor G Smart, Julia Gorelik, Victor P Ostanin, Max J Lab, Guy W J Moss, Gregory I Frolenkov, David Klenerman & Yuri E Korchev

doi:10.1038/nmeth.1306

Complex three-dimensional structures on cellular surfaces are often damaged during high-resolution imaging of live cells. Now, hopping probe scanning ion conductance microscopy—which uses a hopping nanopipette that 'hops' instead of 'sliding'—protects surface structures from probe-induced damage.

Abstract - | Full Text - Nanoscale live-cell imaging using hopping probe ion conductance microscopy | PDF (472 KB) - Nanoscale live-cell imaging using hopping probe ion conductance microscopy | Supplementary information

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting - pp283 - 289

Jay R Hesselberth, Xiaoyu Chen, Zhihong Zhang, Peter J Sabo, Richard Sandstrom, Alex P Reynolds, Robert E Thurman, Shane Neph, Michael S Kuehn, William S Noble, Stanley Fields & John A Stamatoyannopoulos

doi:10.1038/nmeth.1313

Dense mapping of DNase I cleavage sites across the whole yeast genome by next-generation sequencing reveals a global view of the binding of regulatory proteins to genomic DNA. The high resolution allows the identification of new binding sites for known factors as well as the de novo derivation of factor binding motifs.

Abstract - | Full Text - Global mapping of protein-DNA interactions in vivo by digital genomic footprinting | PDF (804 KB) - Global mapping of protein-DNA interactions in vivo by digital genomic footprinting | Supplementary information

See also: News and Views by Hager

Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes - pp291 - 295

Iwanka Kozarewa, Zemin Ning, Michael A Quail, Mandy J Sanders, Matthew Berriman & Daniel J Turner

doi:10.1038/nmeth.1311

The PCR step in the preparation of sequencing libraries for the Illumina Genome Analyzer can introduce coverage bias, especially in very (A+T)-rich genomes. By directly annealing template DNA to adapters with sequences needed for attachment in the flow cell, PCR can be omitted as cluster amplification in the flow cell enriches for fully ligated templates.

Abstract - | Full Text - Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes | PDF (323 KB) - Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes | Supplementary information

Automated monitoring and analysis of social behavior in Drosophila - pp297 - 303

Heiko Dankert, Liming Wang, Eric D Hoopfer, David J Anderson & Pietro Perona

doi:10.1038/nmeth.1310

An automated system to measure aggression and courtship in pairs of interacting Drosophila is presented and should allow large-scale screens of these behaviors in the future.

Abstract - | Full Text - Automated monitoring and analysis of social behavior in Drosophila | PDF (461 KB) - Automated monitoring and analysis of social behavior in Drosophila | Supplementary information

Journeys across the membrane - pp305 - 309

Nathan Blow

doi:10.1038/nmeth0409-305

From high-throughput electroporation platforms capable of transfecting thousands of different cells in a day, to nanowires that puncture and deliver DNA to just a single cell, new technology is emerging to help researchers with their changing gene delivery needs.

Abstract - | Full Text - Journeys across the membrane | PDF (1,933 KB) - Journeys across the membrane

Erratum: Photoactivatable mCherry for high-resolution two-color fluorescence microscopy - p311

Fedor V Subach, George H Patterson, Suliana Manley, Jennifer M Gillette, Jennifer Lippincott-Schwartz & Vladislav V Verkhusha

doi:10.1038/nmeth0409-311

Full Text - Erratum: Photoactivatable mCherry for high-resolution two-color fluorescence microscopy | PDF (62 KB) - Erratum: Photoactivatable mCherry for high-resolution two-color fluorescence microscopy

Visualizing signal transduction pathways by quantifying protein-protein interactions in native cells and tissue

Simon Fredriksson

Abstract - | Full Text - Visualizing signal transduction pathways by quantifying protein-protein interactions in native cells and tissue | PDF (1,534 KB) - Visualizing signal transduction pathways by quantifying protein-protein interactions in native cells and tissue

Chromatin immunoprecipitation sequencing (ChIP-Seq) on the SOLiD^™ system

Anjali Shah

Abstract - | Full Text - Chromatin immunoprecipitation sequencing (ChIP-Seq) on the SOLiD™ system | PDF (821 KB) - Chromatin immunoprecipitation sequencing (ChIP-Seq) on the SOLiD™ system