PDF - In This Issue

No fruit fly an island? - p395

doi:10.1038/nmeth0609-395

Methods to study the behavior of Drosophila sp. in the context of a group may deepen our understanding of the neural mechanisms underlying social behavior.

Abstract - | Full Text - No fruit fly an island? | PDF (80 KB) - No fruit fly an island?

Predicting microRNA targets and functions: traps for the unwary - pp397 - 398

William Ritchie, Stephane Flamant & John E J Rasko

doi:10.1038/nmeth0609-397

Full Text - Predicting microRNA targets and functions: traps for the unwary | PDF (104 KB) - Predicting microRNA targets and functions: traps for the unwary | Supplementary information

Snapshots of the cell surface - p401

Allison Doerr

doi:10.1038/nmeth0609-401

Researchers develop an approach to selectively isolate and profile cell-surface proteins by targeting the glycopeptides, a strategy that could be used to generate an atlas of cell-surface protein 'barcodes'.

Abstract - | Full Text - Snapshots of the cell surface | PDF (162 KB) - Snapshots of the cell surface

Micro-reprogramming - pp402 - 403

Natalie de Souza

doi:10.1038/nmeth0609-402a

Researchers use microRNAs to more efficiently generate induced pluripotent stem cells in the mouse.

Abstract - | Full Text - Micro-reprogramming | PDF (187 KB) - Micro-reprogramming

A functional blueprint of E. coli - pp402 - 403

Allison Doerr

doi:10.1038/nmeth0609-402b

Researchers integrate proteomics data with genomic-context analysis and develop a protein-function prediction tool to annotate functional orphans in Escherichia coli.

Abstract - | Full Text - A functional blueprint of E. coli | PDF (188 KB) - A functional blueprint of E. coli

News in brief - p403

doi:10.1038/nmeth0609-403

Full Text - News in brief | PDF (99 KB) - News in brief

Nature's pH meter - p404

Wayne Peng

doi:10.1038/nmeth0609-404

A new pH nanosensor changes color in acidic cell compartments by forming an unusual four-stranded DNA structure.

Abstract - | Full Text - Nature's pH meter | PDF (95 KB) - Nature's pH meter

TACLing rare genetic variants - p406

Nicole Rusk

doi:10.1038/nmeth0609-406

By combining methods for selective genome capture, allele enrichment and array resequencing, researchers create a pipeline for high-throughput variant detection.

Abstract - | Full Text - TACLing rare genetic variants | PDF (97 KB) - TACLing rare genetic variants

Flight patterns - p408

Michael Eisenstein

doi:10.1038/nmeth0609-408

Flying animals ranging from bugs to bats use a common mechanism to maintain control in turns a discovery that reveals hidden advantages of flapping-wing flight.

Abstract - | Full Text - Flight patterns | PDF (92 KB) - Flight patterns

A stress test for mass spectrometry–based proteomics - pp411 - 412

Ruedi Aebersold

doi:10.1038/nmeth.f.255

A multilaboratory study attempts to dispel some of the notions of the irreproducibility of mass spectrometry–based proteomics by pinpointing where the methodological problems are and where challenges remain.

Abstract - | Full Text - A stress test for mass spectrometry–based proteomics | PDF (401 KB) - A stress test for mass spectrometry–based proteomics

See also: Analysis by Bell et al.

The ethomics era? - pp413 - 414

Michael Reiser

doi:10.1038/nmeth0609-413

Applying modern machine-vision techniques to the study of animal behavior, two groups developed systems that quantify many aspects of the complex social behaviors of Drosophila melanogaster. These software tools will enable high-throughput screens that seek to uncover the cellular and molecular underpinnings of behavior.

Abstract - | Full Text - The ethomics era? | PDF (886 KB) - The ethomics era?

See also: Article by Branson et al.

Transposon-mediated genome manipulation in vertebrates - pp415 - 422

Zoltán Ivics, Meng Amy Li, Lajos Mátés, Jef D Boeke, Andras Nagy, Allan Bradley & Zsuzsanna Izsvák

doi:10.1038/nmeth.1332

Abstract - | Full Text - Transposon-mediated genome manipulation in vertebrates | PDF (715 KB) - Transposon-mediated genome manipulation in vertebrates | Supplementary information

A HUPO test sample study reveals common problems in mass spectrometry–based proteomics - pp423 - 430

Alexander W Bell, Eric W Deutsch, Catherine E Au, Robert E Kearney, Ron Beavis, Salvatore Sechi, Tommy Nilsson, John J M Bergeron & HUPO Test Sample Working Group

doi:10.1038/nmeth.1333

A multilaboratory analysis characterized the ability of 27 different labs to identify 20 proteins at equimolar concentrations in a highly purified test sample mixture using mass spectrometry. The results show that while the technology is reproducible, many common experimental problems arise, and improved search engines and databases are still needed.

Abstract - | Full Text - A HUPO test sample study reveals common problems in mass spectrometry–based proteomics | PDF (520 KB) - A HUPO test sample study reveals common problems in mass spectrometry–based proteomics | Supplementary information

See also: News and Views by Aebersold

Versatile P[acman] BAC libraries for transgenesis studies in Drosophila melanogaster - pp431 - 434

Koen J T Venken, Joseph W Carlson, Karen L Schulze, Hongling Pan, Yuchun He, Rebecca Spokony, Kenneth H Wan, Maxim Koriabine, Pieter J de Jong, Kevin P White, Hugo J Bellen & Roger A Hoskins

doi:10.1038/nmeth.1331

Two bacterial artificial chromosome (BAC) libraries, spanning almost the entire D. melanogaster genome in insert sizes of 20 and 80 kb, that allow easy integration into the fruit fly genome at defined docking sites provide a rich resource to study gene expression and function.

Abstract - | Full Text - Versatile P[acman] BAC libraries for transgenesis studies in Drosophila melanogaster | PDF (369 KB) - Versatile P[acman] BAC libraries for transgenesis studies in Drosophila melanogaster | Supplementary information

A toolkit for high-throughput, cross-species gene engineering in Drosophila - pp435 - 437

Radoslaw K Ejsmont, Mihail Sarov, Sylke Winkler, Kamil A Lipinski & Pavel Tomancak

doi:10.1038/nmeth.1334

Genomic fosmid libraries for Drosophila melanogaster and Drosophila pseudoobscura with an average insert size of 36 kilobases can easily be tagged and inserted into the fly genome. These resources will be valuable for evolutionary and developmental studies in the fly.

Abstract - | Full Text - A toolkit for high-throughput, cross-species gene engineering in Drosophila | PDF (503 KB) - A toolkit for high-throughput, cross-species gene engineering in Drosophila | Supplementary information

TU-tagging: cell type–specific RNA isolation from intact complex tissues - pp439 - 441

Michael R Miller, Kristin J Robinson, Michael D Cleary & Chris Q Doe

doi:10.1038/nmeth.1329

Expressing uracil phosphoribosyltransferase in specific tissues in the fly allows the incorporation of 4-thiouracil into newly synthesized RNA in vivo. The thio-labeled RNA can then be isolated and analyzed by routine procedures allowing the cell type–specific measure of RNA synthesis and decay rates.

Abstract - | Full Text - TU-tagging: cell type–specific RNA isolation from intact complex tissues | PDF (354 KB) - TU-tagging: cell type–specific RNA isolation from intact complex tissues | Supplementary information

Rapid creation and quantitative monitoring of high coverage shRNA libraries - pp443 - 445

Michael C Bassik, Robert Jan Lebbink, L Stirling Churchman, Nicholas T Ingolia, Weronika Patena, Emily M LeProust, Maya Schuldiner, Jonathan S Weissman & Michael T McManus

doi:10.1038/nmeth.1330

On-array synthesis of over 20,000 shRNAs at a coverage of 30 shRNAs per gene, followed by cloning into lentiviral shRNA libraries and deconvolution of the complex libraries by deep sequencing, ensures high confidence in the observed knockdown phenotypes with low false-negative rates and few off-target hits.

Abstract - | Full Text - Rapid creation and quantitative monitoring of high coverage shRNA libraries | PDF (380 KB) - Rapid creation and quantitative monitoring of high coverage shRNA libraries | Supplementary information

Automated unrestricted multigene recombineering for multiprotein complex production - pp447 - 450

Christoph Bieniossek, Yan Nie, Daniel Frey, Natacha Olieric, Christiane Schaffitzel, Ian Collinson, Christophe Romier, Philipp Berger, Timothy J Richmond, Michel O Steinmetz & Imre Berger

doi:10.1038/nmeth.1326

A modular, automatable system using recombineering to facilitate multigene assembly, called Acembl, provides a streamlined approach for expressing multiprotein complexes in Escherichia coli.

Abstract - | Full Text - Automated unrestricted multigene recombineering for multiprotein complex production | PDF (480 KB) - Automated unrestricted multigene recombineering for multiprotein complex production | Supplementary information

High-throughput ethomics in large groups of Drosophila - pp451 - 457

Kristin Branson, Alice A Robie, John Bender, Pietro Perona & Michael H Dickinson

doi:10.1038/nmeth.1328

An automated system for tracking large numbers of fruit flies over time and for detecting their behaviors is presented, and should allow high-throughput quantitative studies of fly behavior.

Abstract - | Full Text - High-throughput ethomics in large groups of Drosophila | PDF (1,904 KB) - High-throughput ethomics in large groups of Drosophila | Supplementary information

See also: News and Views by Reiser

Tissue tectonics: morphogenetic strain rates, cell shape change and intercalation - pp458 - 464

Guy B Blanchard, Alexandre J Kabla, Nora L Schultz, Lucy C Butler, Benedicte Sanson, Nicole Gorfinkiel, L Mahadevan & Richard J Adams

doi:10.1038/nmeth.1327

As tissues mature, they undergo shape changes that are the result of individual and collective cell movement triggered by cell-autonomous behavior or external forces. By measuring patterns of strain rates the authors can model these forces and quantify tissue shaping behavior.

Abstract - | Full Text - Tissue tectonics: morphogenetic strain rates, cell shape change and intercalation | PDF (2,001 KB) - Tissue tectonics: morphogenetic strain rates, cell shape change and intercalation | Supplementary information

In vivo molecular imaging: the inside job - pp465 - 469

Nathan Blow

doi:10.1038/nmeth0609-465

In a short period of time, in vivo molecular imaging systems have become indispensable research tools in many clinical and basic research laboratories. But developers are now pushing the technology further in the hopes of making a new generation of platforms with greater accuracy and sensitivity for a wider array of applications.

Abstract - | Full Text - In vivo molecular imaging: the inside job | PDF (545 KB) - In vivo molecular imaging: the inside job

Characterization of phosphoprotein signaling in limited biological samples using the Cell Biosciences CB1000

David W Voehringer & Walter A Ausserer

Abstract - | Full Text - Characterization of phosphoprotein signaling in limited biological samples using the Cell Biosciences CB1000 | PDF (331 KB) - Characterization of phosphoprotein signaling in limited biological samples using the Cell Biosciences CB1000

Automated selection and collection of pluripotent stem cell colonies using the CellCelector^™

Simone Haupt, Jan Grützner, Barbara H Rath, Heike Möhlig & Oliver Brüstle

Abstract - | Full Text - Automated selection and collection of pluripotent stem cell colonies using the CellCelector™ | PDF (452 KB) - Automated selection and collection of pluripotent stem cell colonies using the CellCelector™

Kodak X-Sight 761 Nanospheres effectively label living cells for longitudinal cell tracking in mice

W Matthew Leevy, Sean P Orton, Seth T Gammon, Wenyi Che, Gilbert D Feke, Tao Ji, M Catherine Muenker, Megan Schmidt, Victoria Jacobs, Douglas Vizard & William McLaughlin

Abstract - | Full Text - Kodak X-Sight 761 Nanospheres effectively label living cells for longitudinal cell tracking in mice | PDF (346 KB) - Kodak X-Sight 761 Nanospheres effectively label living cells for longitudinal cell tracking in mice

Mutation profiling in tumor samples using the Sequenom OncoCarta^™ Panel

Marisa Pearce, Amy Cullinan, Grant Hogg, Dana Hosseini & Mathias Ehrich

Abstract - | Full Text - Mutation profiling in tumor samples using the Sequenom OncoCarta™ Panel | PDF (407 KB) - Mutation profiling in tumor samples using the Sequenom OncoCarta™ Panel