Nature Methods 5, 577 (2008). doi:10.1038/nmeth0708-577

With access to high-throughput technologies, researchers struggle to store their raw data. Many just give up.

Nature Methods 5, 579 (2008). doi:10.1038/nmeth0708-579

Author: Veronique Kiermer

Zebrafish researchers rejoice! Reverse genetics is now on the menu, thanks to zinc-finger nucleases.

Nature Methods 5, 580 (2008). doi:10.1038/nmeth0708-580a

Author: Daniel Evanko

Tiny droplets of water in oil can serve as miniature culture vessels for living single cells and multicellular organisms.

Nature Methods 5, 580 (2008). doi:10.1038/nmeth0708-580b

Author: Michelle Pflumm

Recently discovered electrophilic probes open the door to activity-based protein profiling (ABPP) studies of a broader range of proteins.

Nature Methods 5, 582 (2008). doi:10.1038/nmeth0708-582

Author: Irene Kaganman

A high-resolution interactome map that describes how proteins interact in living yeast cells is an invaluable reference for the research community.

Nature Methods 5, 585 (2008). doi:10.1038/nmeth0708-585

Author: Jay Shendure

Two complementary approaches, both using next-generation sequencing, have successfully tackled the scale and the complexity of mammalian transcriptomes, at once revealing unprecedented detail and allowing better quantification.

Nature Methods 5, 587 (2008). doi:10.1038/nmeth0708-587

Author: Piero Carninci

Strategies for the comprehensive identification of transcript isoforms produced from specific genomic loci make use of and expand existing tools and resources.

Nature Methods 5, 589 (2008). doi:10.1038/nmeth0708-589

Authors: S Elizabeth Hulme, Sergey S Shevkoplyas & Aravinthan Samuel

Advances in the application of microfluidics technology to biological assays using the model organism Caenorhabditis elegans help to automate otherwise time-consuming experiments.

Nature Methods 5, 597 (2008). doi:10.1038/nmeth.1224

Authors: Kourosh Salehi-Ashtiani, Xinping Yang, Adnan Derti, Weidong Tian, Tong Hao, Chenwei Lin, Kathryn Makowski, Lei Shen, Ryan R Murray, David Szeto, Nadeem Tusneem, Douglas R Smith, Michael E Cusick, David E Hill, Frederick P Roth & Marc Vidal

Describing the 'ORFeome' of an organism, including all major isoforms, is essential for a system-level understanding of any species; however, conventional cloning and sequencing approaches are prohibitively costly and labor-intensive. We describe a potentially genome-wide methodology for efficiently capturing new coding isoforms using reverse transcriptase (RT)-PCR recombinational cloning, 'deep-well' pooling and a next-generation sequencing platform. This ORFeome discovery pipeline will be applicable to any eukaryotic species with a sequenced genome.

Nature Methods 5, 601 (2008). doi:10.1038/nmeth.1225

Authors: Suveera Dhup & Subeer S Majumdar

Current techniques for making transgenic mice are cumbersome, requiring trained personnel, costly infrastructure and collection of many zygotes from mice that are then killed. We developed a reproducible nonterminal technique for transfecting genes in undifferentiated spermatogonia through in vivo electroporation of the testis; about 94% of male mice electroporated with different transgenes successfully sired transgenic pups. Such electroporated males provide a valuable resource for continuous production of transgenic founders for more than a year.

Nature Methods 5, 605 (2008). doi:10.1038/nmeth.1220

Authors: Julia Riedl, Alvaro H Crevenna, Kai Kessenbrock, Jerry Haochen Yu, Dorothee Neukirchen, Michal Bista, Frank Bradke, Dieter Jenne, Tad A Holak, Zena Werb, Michael Sixt & Roland Wedlich-Soldner

Live imaging of the actin cytoskeleton is crucial for the study of many fundamental biological processes, but current approaches to visualize actin have several limitations. Here we describe Lifeact, a 17-amino-acid peptide, which stained filamentous actin (F-actin) structures in eukaryotic cells and tissues. Lifeact did not interfere with actin dynamics in vitro and in vivo and in its chemically modified peptide form allowed visualization of actin dynamics in nontransfectable cells.

Nature Methods 5, 609 (2008). doi:10.1038/nmeth.1219

Authors: Marit J Boot, C Henrik Westerberg, Juanjo Sanz-Ezquerro, James Cotterell, Ronen Schweitzer, Miguel Torres & James Sharpe

Quantitative mapping of the normal tissue dynamics of an entire developing mammalian organ has not been achieved so far but is essential to understand developmental processes and to provide quantitative data for computational modeling. We developed a four-dimensional (4D) imaging technique that can be used to quantitatively image tissue movements and dynamic GFP expression domains in a growing transgenic mouse limb by time-lapse optical projection tomography (OPT).

Nature Methods 5, 613 (2008). doi:10.1038/nmeth.1223

Authors: Nicole Cloonan, Alistair R R Forrest, Gabriel Kolle, Brooke B A Gardiner, Geoffrey J Faulkner, Mellissa K Brown, Darrin F Taylor, Anita L Steptoe, Shivangi Wani, Graeme Bethel, Alan J Robertson, Andrew C Perkins, Stephen J Bruce, Clarence C Lee, Swati S Ranade, Heather E Peckham, Jonathan M Manning, Kevin J McKernan & Sean M Grimmond

Nature Methods 5, 621 (2008). doi:10.1038/nmeth.1226

Authors: Ali Mortazavi, Brian A Williams, Kenneth McCue, Lorian Schaeffer & Barbara Wold

Nature Methods 5, 637 (2008). doi:10.1038/nmeth.1227

Authors: Kwanghun Chung, Matthew M Crane & Hang Lu

Nature Methods 5, 645 (2008). doi:10.1038/nmeth.1222

Authors: Kristin Alberti, Ryan E Davey, Kento Onishi, Sophia George, Katrin Salchert, F Philipp Seib, Martin Bornhäuser, Tilo Pompe, Andras Nagy, Carsten Werner & Peter W Zandstra

Nature Methods 5, 651 (2008). doi:10.1038/nmeth0708-651

Author: Kelly Rae Chi

In designing microscopy software to take advantage of better hardware, developers are facing challenges of accessibility, functionality and usability.