Volume 12 Issue 12, December 2015

Exploring the extracellular matrix in high throughput and leaping across scientific divides as if they weren't there.

When multiple variables are associated with a response, the interpretation of a prediction equation is seldom simple.

Researchers report that the illumination intensities used in super-resolution imaging can irreversibly damage live cells.

Functional magnetic resonance data are traditionally analyzed on a population level, but new work shows that meaningful information can be extracted from individual subjects.

Researchers develop an approach based on solid-state nuclear magnetic resonance (NMR) to study the structure of an intrinsically disordered protein under near-native conditions.

Spatially targeted optical microproteomics identifies novel amyloid plaque components.

The small, single RNA–guided nuclease Cpf1 is active in human cells.

A nanopore used for sequencing gives a detailed view of how motor proteins behave on DNA.

A growing research community studies autophagy—a process of cellular recycling and maintenance—but there are some hot-button methodological issues.

Thermal profiling in combination with quantitative proteomics makes it possible to identify cellular membrane protein targets of small molecules.

A method for profiling changes in membrane protein thermal stability upon ligand binding using mass spectrometry identifies cellular membrane protein targets of small molecules.

Brillouin microscopy can be used to analyze the mechanical properties of cells in a contact-free fashion. Cells in 2D and 3D environments are accessible to this technology, which provides measurements of longitudinal moduli at optical resolution.

The molecular architecture of protein complexes can be determined using an optimal approach for isolating GFP-tagged complexes at native levels, combined with cross-linking, mass spectrometry analysis, and structure modeling from mass spectrometry-derived distance restraints.

Handling and quantitative image analysis of layered tissues is greatly simplified by cartography with the Image Surface Analysis Environment (ImSAnE), as demonstrated on a variety of specimens, including a beating heart.

A detailed study of the effects of dCas9-KRAB-sgRNA complexes on enhancer activity, gene expression and heterochromatin formation shows high efficacy and specificity.

Fusing a DNA-binding domain to Cas9 with an attenuated, more promiscuous PAM-recognition domain increases the targeting range of Cas9 as well as its specificity.

Transparent micro-optoelectrode arrays enable simultaneous electrical recording and optical stimulation in precise alignment. Depending on the applied light levels, single-unit activity or behavioral responses can be optically evoked.

A fusion of RNA-binding proteins (RBPs) to a poly(U) polymerase allows the tagging of endogenous RNAs bound by the RBPs with a U-tail that can be used to identify the bound RNA by sequencing. RNA tagging is suited to discover RNA-protein networks in vivo.

IsoView microscopy achieves rapid isotropic-resolution imaging of large, nontransparent samples using simultaneous light-sheet illumination and fluorescence detection in four orthogonal directions.

A crosslinking-mass spectrometry strategy, including a new proteome database search engine called XlinkX, enables the identification of inter- and intra-protein cross-links in cell lysates on a proteome-wide scale.

A computational pipeline for analysis and statistical evaluation of quantitative cross-linking–mass spectrometry data facilitates the investigation of protein-complex structural heterogeneity.

Multiplexed hybridization probes are traditionally difficult to design with high sensitivity and specificity. Here Wu et al. present a method for fine, decoupled and on-the-fly tuning of probe behavior based on the stoichiometric formulation of a molecular competitor species.

High-throughput tissue arrays allow for evaluation of in vitro cellular responses and correlation to matrix composition.