Volume 10 Issue 9, September 2013

RNA sensors lend proteins both specific and bright signals.

Statistics does not tell us whether we are right. It tells us the chances of being wrong.

Optogenetic tools enable light-mediated control over transcription and epigenetic states in specific endogenous loci of the mammalian genome.

A tiny silicon chip internalized by cells measures intracellular pressure changes.

Dissecting the effect of a host's genetic background on circuit performance will allow better design.

Single-cell measurements enable more sophisticated studies of the genetic basis of gene expression phenotypes.

By bundling together receptor domains, researchers identify important extracellular protein-protein interactions that are otherwise too weak to detect.

A handful of new 'GCaMPs' with improved properties for imaging neuronal activity are now available.

Researchers sequence single-cell genomes to target uncharted microbial diversity.

As complements to antibodies, new reagents to target proteins invite broad types of experiments.

An algorithm called CONTACT identifies correlated side-chain motions in proteins from X-ray crystallographic data, providing insights into dynamics and function.

With a flood of new tools for genome engineering, we can benefit from choosing the tool that best fits the job.

Optimism about biomedicine is challenged by the increasingly complex ethical, legal and social issues it raises. Reporting of scientific methods is no longer sufficient to address the complex relationship between science and society. To promote 'ethical reproducibility', we call for transparent reporting of research ethics methods used in biomedical research.

This Review of force-distance curve-based atomic force microscopy highlights the unique capabilities of the technique to simultaneously image the architecture of complex biological systems and map their physical, chemical and biological properties at nanometer resolution.

A method based on in situ sequencing by ligation enables direct reading of short segments of RNA or sequence tags in preserved tissue sections and cells.

Synchrotron-based Fourier transform infrared (FTIR) spectro-microtomography is a nondestructive, label-free imaging technique that allows chemical fingerprinting of intact, three-dimensional biological samples.

A combination of detection probes, targeting a single-nucleotide variant on individual transcripts, and guide probes to diminish the amount of false positives, enables quantification of allele-specific gene expression.

A combination of allele-specific and non–allele-specific probes allows in situ detection and quantification of mRNA transcripts that differ by only a few SNPs.

An RNA aptamer specific for a protein of interest, when fused to an RNA sensor that activates a small-molecule fluorophore, can quantitate protein expression in live bacteria.

A growing collection of segmented and feature-extracted videos recording locomotive behavior in hundreds of C. elegans mutant strains is made available for phenotyping and further analysis.

The specI software automatically and highly accurately delineates and assigns bacterial species based on a set of universal marker genes that it extracts from sequenced genomes.

An unnatural amino acid that forms a covalent bond with a proximal cysteine can be introduced into proteins, facilitating a variety of applications.

The synthetic promoter E-SARE provides a genetic tool to tag neurons in an activity-dependent manner. The authors show the utility of this tool for labeling populations of neurons that respond to specific stimuli in living mice and for tracking the axonal projection patterns.

An algorithm and software tool to uncover contact networks of interacting conformationally heterogeneous protein residues from X-ray crystallography data is described.

Targeting unique variants in highly identical paralogous genes with molecular inversion probes followed by high-throughput sequencing will open a way to associate features in these duplicated genes with human traits.

Single DNA-binding proteins can be tracked on densely covered DNA at high spatial and temporal resolution and in the presence of high protein concentrations by using a technique that combines optical tweezers, confocal fluorescence microscopy and stimulated emission depletion (STED) nanoscopy.