Volume 10 Issue 4, April 2013

A large-scale comparative study of techniques to localize proteins leads to paths through cells and forests.

Figure labels require the same consistency and alignment in their layout as text.

RNA interference (RNAi)-based genetic interaction screens in mammalian cells show how genes affect each other.

A digital atlas of enhancers active in the developing mammalian brain is available for exploration.

Developing tools to detect the rare mutations found in tumors demands a lot of data and rigorous benchmarking.

An in vivo protein-labeling strategy could enable more comprehensive surveys of organelle proteomic contents.

Researchers study the structure of the metalloenzyme photosystem II by applying femtosecond X-ray pulses to simultaneously record X-ray diffraction and X-ray emission spectroscopy data.

A systematic comparison of gene expression patterns in human inflammatory conditions and in their corresponding mouse models raises troubling questions.

Unusual properties of a diamond defect are exploited to achieve progress toward nanometer-scale magnetic resonance imaging (MRI).

Paving roads through data mountains, consortia are developing workflows and tools for widespread use.

A two-laboratory study of the reproducibility of affinity purification–mass spectrometry shows that a standardized protocol results in highly reproducible interactome data.

Classic gene targeting and gene replacement can now be achieved in zebrafish after cleaving the genome with engineered nucleases in the presence of donor DNA. This simple-to-implement method enables new classes of biological study in this important model organism.

A systematic study of the intra- and interlaboratory reproducibility of a standardized affinity purification–mass spectrometry protocol demonstrates the high reproducibility of this technique and hints at the feasibility of a large-scale human interactome project through interlaboratory efforts.

In this analysis, the authors directly compared immunofluorescence and fluorescent-protein tagging of 506 human proteins and studied their subcellular localization. They conclude that the two methodologies are highly complementary and propose an integrative strategy for the characterization of newly identified proteins.

A statistical method and software yields accurate predictions of sequencing library complexity on the basis of initial shallow sequencing surveys, allowing robust estimates of how deep to sequence for adequate coverage.

Gene targeting via homologous recombination is achieved in the zebrafish with TALENs and double-stranded DNA donors, expanding the range of experimental possibilities in this organism.

A method called neutron-encoding SILAC will enable higher-order multiplexing with high accuracy in quantitative proteomics experiments.

An imaging modality that restricts the number of photons detected in each pixel of an electron-multiplying CCD to an average of <1 allows single-fluorophore localization accuracies that approach the ultimate limit.

A high-sensitivity, high-quality yeast two-hybrid screen using short-read sequencing as its readout is used to map the interactome of human methyltransferases.

Combining a method to label newly synthesized proteins and a strategy to distinguish two populations in cell culture allows quantitative assessment of intracellular protein dynamics.

This linear ANOVA-based method quantifies the activity of different combinations of genetic elements and assigns a score that indicates the variation in performance across changing contexts.

By using a bicistronic design, with a leader peptide that overlaps with and contains the Shine-Dalgarno site for a downstream gene of interest, the authors demonstrate reliable, context-independent gene expression.

Biotinylated tags bind double-strand breaks in genomic DNA; after enrichment and sequencing, this allows precise, genome-wide mapping of the breaks.