Articles in 2012

Animations of biological processes are superb tools for science outreach and communication and can be useful in research too. But we need better ways to tell which parts of an animation are based on data.

A new toolbox for structural biology that combines single-molecule fluorescence and molecular modeling is used to generate high-precision structures of protein complexes.

The Genome Multitool (GEM) mapper rapidly and accurately provides all alignments of a read within a user-defined number of mismatches.

Microscopy without fluorescence to peek under the tissue surface

Physical modeling is increasingly important for generating insights into intracellular processes. We describe situations in which combined spatial and stochastic aspects of chemical reactions are needed to capture the relevant dynamics of biochemical systems.

Instruments maximize the yield in high-content single-cell imaging, which calls for carefully planned experiments and data analysis.

Widely used behavioral assays need re-evaluation and validation against their intended use. We focus here on measures of chronic anxiety in mouse models and posit that widely used assays such as the open-field test are performed at the wrong time, for inadequate durations and using inappropriate mouse strains. We propose that behavioral assays be screened for usefulness on the basis of their replicability across laboratories.

Binding studies with systematically mutagenized RNA and RNA-binding proteins allow insight into the relationship between an RNA sequence, its structure and its function.

Integration of transcriptomic and proteomic data allows more detailed annotation of proteomes of model and non-model species.

Using the red shifted opsin C1V1_T and simple raster-scanning illumination, this work shows two-photon optogenetic stimulation of single cells, dendrites and spines. The method is also applied to map synaptic circuits in mouse brain slices and, using holographic photostimulation, for the simultaneous activation of two neurons located in different planes. Also online, Prakash et al. present a collection of opsins for two-photon excitation, inhibition and bistable control of neuronal activity in vitro and in vivo.

A collection of simulation tools and workflow for single-molecule Förster resonance energy transfer (smFRET) allows highly quantitative structural modeling. This hybrid approach yields a model of reverse-transcriptase binding to DNA at sub-angstrom accuracy when benchmarked against a crystal structure and can resolve a flexible single-stranded template overhang.

The structure of the membrane anchor domain of the bacterial autotransporter YadA is solved by a solid-state NMR spectroscopy approach using a uniformly ¹³C- and ¹⁵N-labeled microcrystalline sample.

A collection of opsins for two-photon modulation of neuronal activity in vitro and in vivo is presented in this resource. The opsins have kinetic, expression and spectral properties ideally suited to typical raster-scanning two-photon microscopy. Also online, Packer et al. use the red-shifted opsin C1V1_T and simple raster-scanning illumination to stimulate individual spines and dendrites and map synaptic circuits.

Researchers describe a multifunctional reagent for identifying extracellular interactions.