Volume 8 Issue 2, February 2011

Practical microsystems are used to monitor flies and worms.

Two approaches using either fosmid clones or a microfluidic device are used to tackle the challenge of a haplotype-resolved human genome.

RNA-based regulatory systems control the behavior of cells in response to endogenous proteins.

In-depth mass spectrometric analysis reveals how cells survive stress by coordinating various enzymes that modify RNAs involved in protein synthesis.

Pluripotent stem cells form intestine-like structures in vitro.

Caenorhabditis elegans can be used to probe the mechanistic basis for cell-fate conversion.

Next-generation sequencing platforms provide both high-throughput sequencing and DNA production.

The focus of metabolomic studies is shifting from cataloging chemical structures to finding biological stories.

In recent years, single-molecule force spectroscopy techniques have been used to study how inter- and intramolecular interactions control the assembly and functional state of biomolecular machinery in vitro. Here we discuss the problems and challenges that need to be addressed to bring these technologies into living cells and to learn how cellular machinery is controlled in vivo.

Two systems allow precise optogenetic stimulation of specific neurons in freely behaving nematodes.

Combining rule-based descriptions of biochemical reactions with agent-based computer simulation opens new avenues for exploring complex cellular processes.

Stimulated Raman scattering (SRS) microscopy is used to directly visualize lipids in cells and model organisms, and facilitates screening for genes involved in fat storage.

Stimulated Raman scattering (SRS) microscopy is a quantitative, label-free imaging method to map fat distribution and accumulation with high spatial resolution and sensitivity at both cellular and organism levels.

In vivo calcium imaging at multiple depths simultaneously is shown using multifocal two-photon microscopy and spatiotemporal multiplexing. This technique involves scanning the sample with multiple beams in parallel at different axial planes and is applied to monitor neuronal network activity in multiple cortical layers of an anesthetized mouse.

Single-molecule fluorescence experiments with microsecond time resolution are made possible using a photoprotection cocktail that reduces dye blinking and bleaching with a combination of dissolved oxygen, a triplet quencher and a free-radical scavenger.

An optogenetic illumination system based on the use of a digital micromirror device and video tracking software is reported, which allows real-time light delivery with high spatial resolution to specified targets in freely moving Caenorhabditis elegans. Also in this issue, Stirman et al. report a similar illumination system using a liquid crystal display projector. Both methods allow optogenetic perturbation of a variety of neural circuits in the behaving worm.

An optogenetic illumination system based on the use of a liquid crystal display projector and video tracking software is reported, which allows real-time multispectral light delivery with high spatial resolution to specified targets in freely moving Caenorhabditis elegans. Also in this issue, Leifer et al. report a similar illumination system using a digital micromirror device. Both methods allow optogenetic perturbation of a variety of neural circuits in the behaving worm.

By individually replacing 16 yeast genes encoding ABC transporters by GFP, mating and selecting for strains with accumulated mutations the authors create a Green Monster, a strain with deletions in all 16 genes.

Tagging the endogenous beta-actin locus with an MS2-binding cassette allows live-cell imaging of mRNA in real time.

A microfluidic embryo-trap array for large-scale end-on imaging of Drosophila melanogaster embryos permits quantitative analysis of dorsoventral gradients during development.

The Network-Free Stochastic Simulator (NFsim) allows the representation of complex biological systems as rule-based models and facilitates coarse-graining of the reaction mechanisms.