Nature Methods 6, 471 (2009). doi:10.1038/nmeth0709-471

Though somewhat rare, there are a few good fiction books to be found with refreshingly realistic biologists as central characters in laboratory settings.

Nature Methods 6, 481 (2009). doi:10.1038/nmeth0709-481

Author: Natalie de Souza

Two groups report culture conditions for long-term in vitro growth of intestinal tissue from the mouse.

Nature Methods 6, 482 (2009). doi:10.1038/nmeth0709-482a

Author: Allison Doerr

An engineered infrared fluorescent protein is the first member of a new class of genetically encodable probes, with special advantages over visible-wavelength fluorescent proteins for in vivo imaging.

Nature Methods 6, 482 (2009). doi:10.1038/nmeth0709-482b

Author: Wayne Peng

Computational and experimental biologists teamed up to develop a new software tool to analyze the rich data generated by new and powerful flow cytometers.

Nature Methods 6, 484 (2009). doi:10.1038/nmeth0709-484

Author: Nicole Rusk

Grafting two transgenic plants triggers lateral gene transfer at the graft site but does not elicit long-distance transport of DNA into the scion or root of the graft.

Nature Methods 6, 486 (2009). doi:10.1038/nmeth0709-486

Author: Daniel Evanko

A fluorescent probe designed to incorporate a fluorophore into the structure of a neurotransmitter finds activity-dependent heterogeneity in dopamine release at individual synapses.

Nature Methods 6, 487 (2009). doi:10.1038/nmeth0709-487

Author: Michael Eisenstein

Optical signatures from organic chemicals may help scientists detect traces of life on other planets.

Nature Methods 6, 489 (2009). doi:10.1038/nmeth0709-489

Authors: Katherine Kedzierska, John Stambas & Peter C Doherty

An approach using multiple fluorochrome combinations allows the simultaneous detection of many T-cell populations within a single blood sample.

Nature Methods 6, 490 (2009). doi:10.1038/nmeth0709-490

Author: Victor Muñoz

Sub-microsecond, downhill-reaction protein folding can be investigated by a method to generate large and fast pressure drops. The approach is complementary to nanosecond temperature-jump methods and could provide new insights into the biophysics of protein folding.

Nature Methods 6, 493 (2009). doi:10.1038/nmeth.1342

Authors: Stephen J Pettitt, Qi Liang, Xin Y Rairdan, Jennifer L Moran, Haydn M Prosser, David R Beier, Kent C Lloyd, Allan Bradley & William C Skarnes

We report the characterization of a highly germline competent C57BL/6N mouse embryonic stem cell line, JM8. To simplify breeding schemes, the dominant agouti coat color gene was restored in JM8 cells by targeted repair of the C57BL/6 nonagouti mutation. These cells provide a robust foundation for large-scale mouse knockout programs that aim to provide a public resource of targeted mutations in the C57BL/6 genetic background.

Nature Methods 6, 497 (2009). doi:10.1038/nmeth.1344

Authors: Evan W Newell, Lawrence O Klein, Wong Yu & Mark M Davis

The direct detection of antigen-specific T cells using tetramers of soluble peptide–major histocompatibilty complex (pMHC) molecules is widely used in both basic and clinical immunology. However, the number of specificities that can be assessed simultaneously has been a major limitation. Here we describe and validate a method using combinations of fluorescent pMHC tetramers to simultaneously detect and enrich for many (≥15) T-cell specificities in a single human blood sample.

Nature Methods 6, 500 (2009). doi:10.1038/nmeth.1337

Authors: Alexa M Schmitz, Monica F Morrison, Akochi O Agunwamba, Max L Nibert & Cammie F Lesser

Here we describe the protein interaction platform assay, a method for identifying interacting proteins in Saccharomyces cerevisiae. This assay relies on the reovirus scaffolding protein μNS, which forms large focal inclusions in living cells. When a query protein is fused to μNS and potential interaction partners are fused to a fluorescent reporter, interactors can be identified by screening for yeast that display fluorescent foci.

Nature Methods 6, 503 (2009). doi:10.1038/nmeth.1338

Authors: Kiyomi Taniguchi, Tomoharu Kajiyama & Hideki Kambara

We developed a quantitative PCR method featuring a reusable single-cell cDNA library immobilized on beads for measuring the expression of multiple genes in a single cell. We used this method to analyze multiple cDNA targets (from several copies to several hundred thousand copies) with an experimental error of 15.9% or less. This method is sufficiently accurate to investigate the heterogeneity of single cells.

Nature Methods 6, 507 (2009). doi:10.1038/nmeth.1343

Authors: Daniel S Herman, G Kees Hovingh, Oleg Iartchouk, Heidi L Rehm, Raju Kucherlapati, J G Seidman & Christine E Seidman

To exploit contemporary sequencing technologies for targeted genetic analyses, we developed a hybridization enrichment strategy for DNA capture that uses PCR products as subgenomic traps. We applied this strategy to 115 kilobases of the human genome encompassing 47 genes implicated in cardiovascular disease. Massively parallel sequencing of captured subgenomic libraries interrogated 99.8% of targeted nucleotides ≥20 times (∼40,000-fold enrichment), enabling sensitive and specific detection of sequence variation and copy-number variation.

Nature Methods 6, 511 (2009). doi:10.1038/nmeth.1339

Authors: Robert P J Barretto, Bernhard Messerschmidt & Mark J Schnitzer

Micro-optics are increasingly used for minimally invasive in vivo imaging, in miniaturized microscopes and in lab-on-a-chip devices. Owing to optical aberrations and lower numerical apertures, a main class of microlens, gradient refractive index lenses, has not achieved resolution comparable to conventional microscopy. Here we describe high-resolution microlenses, and illustrate two-photon imaging of dendritic spines on hippocampal neurons and dual-color nonlinear optical imaging of neuromuscular junctions in live mice.

Nature Methods 6, 513 (2009). doi:10.1038/nmeth.1335

Authors: Daniel Riveline & Paul Nurse

Yeast is a powerful genetic model system, but its rigid cell wall has prohibited microinjection. Using microfabricated channels to constrain the fission yeast Schizosaccharomyces pombe, we sheared local regions of individual cells with a piezoelectric unit. The cells remained viable, we detected actin patches in the cell after introduction of fluorescent phalloidin into the medium, and the cytokinetic ring was disrupted after injection of the myosin II inhibitor blebbistatin.

Nature Methods 6, 515 (2009). doi:10.1038/nmeth.1336

Authors: Charles Dumont, Tryggvi Emilsson & Martin Gruebele

Nature Methods 6, 520 (2009). doi:10.1038/nmeth.1345

Authors: Sine Reker Hadrup, Arnold H Bakker, Chengyi J Shu, Rikke S Andersen, Jerre van Veluw, Pleun Hombrink, Emilie Castermans, Per thor Straten, Christian Blank, John B Haanen, Mirjam H Heemskerk & Ton N Schumacher

Nature Methods 6, 527 (2009). doi:10.1038/nmeth.1340

Authors: Sidney B Cambridge, Daniel Geissler, Federico Calegari, Konstantinos Anastassiadis, Mazahir T Hasan, A Francis Stewart, Wieland B Huttner, Volker Hagen & Tobias Bonhoeffer

Nature Methods 6, 532 (2009). doi:10.1038/nmeth.1341

Authors: Justin W Taraska, Michael C Puljung, Nelson B Olivier, Galen E Flynn & William N Zagotta

Nature Methods 6, 539 (2009). doi:10.1038/nmeth0709-539

Author: Nathan Blow

Next-generation sequencing has made decoding entire genomes cheaper and faster. But what about those researchers who only want to sequence a small section of a genome or focus on a couple thousand specific exons? A wave of new technologies has recently emerged that should help these scientists target their sequencing efforts to sequences of interest.