Volume 7 Issue 10, October 2010

Yeast two-hybrid screens plus RNA interference assays are used to identify functionally relevant interactions.

Harmonic-generation microscopy takes the stage to provide biologists with a useful adjunct to fluorescence imaging.

A nanoscale field-effect transistor with a three-dimensional probe-presentation design can record intracellular potentials from single cells.

A haplotype map based on 11 global populations will provide a better understanding of human genome architecture.

A noise-reduction algorithm decreases the amount of light needed for live-cell fluorescence microscopy by orders of magnitude.

Using real-time labeling with fluorescent ligands, researchers track thousands of endogenous proteins at the surface of living cells.

A split protease under small-molecule control selectively activates the executioner caspases involved in apoptosis.

Creating effective screens requires time, skepticism and astute trade-offs.

A software tool based on gene model profiling improves analysis of alternative splice events in RNA sequencing (RNA-seq) data.

A targeted mass spectrometry method, selected reaction monitoring, is applied to validate predicted microRNA targets in Caenorhabditis elegans.

Optogenetic stimulation by ultrashort laser pulses could allow neural circuits in the living brain to be probed with cellular resolution, despite pervasive light scattering. Now sophisticated new multiphoton stimulation systems that strike a better balance between lateral and axial resolution help realize this potential by matching the illumination volume to the soma's dimensions.

This resource describes a human MAP kinase interactome. Yeast two hybrid-derived protein interaction maps of MAP kinase pathway members are refined using multiple criteria, tested against reference sets, and functionally validated using knockdown with siRNA.

Compared in this Analysis are two widely used procedures for ribosomal RNA removal in metatranscriptomic samples, and the authors present recommendations to prevent misleading analyses of microbial communities.

A comparison of ordination analysis methods used to reveal gradients or clusters in sequence data from microbial communities reveals which methods are best suited for which community structure at different sequencing depth.

Adaptations to total internal reflection microscopy permit visualization of the 'footprint' of rolling cells. Applied to neutrophils rolling in whole blood at physiological levels of shear stress, this approach reveals previously unappreciated features of rolling cell biology.

Mice handled by their tails show high levels of anxiety and stress compared to mice handled in cupped hands or in a transparent tunnel.

Random and targeted mutagenesis of the far-red fluorescent protein Katushka followed by screening for low toxicity and red-shifted emission resulted in two near-infrared fluorescent proteins, eqFP650 and eqFP670, that display desirable properties for in vivo imaging compared to existing near-infrared fluorescent proteins.

Single-molecule fluorescence resonance energy transfer (FRET) is a useful technique for monitoring biomolecular dynamics. A new method, termed switchable FRET, facilitates monitoring of multiple distances in single molecules, using a single donor and multiple spectrally identical acceptors that are switched on and off between a fluorescent state and a dark state.

MicroRNA targets predicted by a variety of computational tools can be validated using a quantitative targeted proteomics approach, using stable isotope labeling and selected reaction monitoring mass spectrometry. The authors used this method to confirm predicted let-7 and miR-58 targets in Caenorhabditis elegans.

Alternative expression analysis by sequencing (ALEXA-seq) aligns RNA-seq reads from different cell types to a database of alternative expression sequence features and quantifies isoforms that are differentially expressed between samples.

Generalized phase contrast and temporal focusing are combined to shape two-photon excitation patterns that elicit large photocurrents in ChR2-expressing neurons in culture and slices. This method allows precise aiming of the stimulating light at single neuronal processes, neurons or groups of neurons and can elicit simultaneous excitation of multiple cells using optogenetics.