Microscopy

Advances in label-free chemical imaging

Stimulated Raman scattering is a label-free biomedical imaging technique based on vibrational spectroscopy. In its original implementation, narrow-band laser beams had been used to excite a single Raman-active mode, but molecules with overlapping Raman bands could not be distinguished. Freudiger et al. now introduce spectrally tailored excitation-stimulated Raman scattering (STE-SRS) microscopy, which applies collective excitation of selected vibrational frequencies to allow specific molecules to be imaged, even when interfering species are present.

Freudiger, C.W. et al. Nat. Photonics 5, 103–109 (2011).

Biophysics

Transient time-resolved FRET

The integration of structural and kinetic data is necessary to understand protein function. Nesmelov et al. describe transient time-resolved fluorescence resonance energy transfer (dubbed (TR)2FRET), a method that allows structural kinetics to be resolved on a sub-millisecond timescale, based on the use of a fluorescence instrument with a pulsed laser and direct waveform recording. They applied the method to investigate the real-time structural kinetics of the motor protein myosin.

Nesmelov, Y.E. et al. Proc. Natl. Acad. Sci. USA 108, 1891–1896 (2011).

Genomics

De novo assembly of large genomes

Massively parallel DNA sequencing technologies have revolutionized genomics, but a continuing challenge has been the assembly of high-quality, large mammalian genomes from these short-read technologies. Gnerre et al. describe an algorithm and software package called ALLPATHS-LG, optimized for de novo assembly of large genomes. The quality of human and mouse genome assembly with ALLPATHS-LG is comparable to that of traditional capillary-based sequencing, but at a much lower overall cost.

Gnerre, S. et al. Proc. Natl. Acad. Sci. USA 108, 1513–1518 (2011).

Structural biology

A method to measure water-protein interactions

Hydration water molecules that specifically interact with the protein surface can have an important role in protein dynamics and function, but the extremely short residence times of water molecules make them difficult to study. Nucci et al. describe a way around this. Using ubiquitin as an example, they tightly confine the protein in a reverse micelle, which slows down the water dynamics and allows site-resolved water-protein interactions to be detected by nuclear magnetic resonance spectroscopy.

Nucci, N.V. et al. Nat. Struct. Mol. Biol. 18, 245–249 (2011).

Imaging

Imaging organic-inorganic interfaces in the tooth

Gordon and Joester show that atom probe tomography (APT), a widely used technique in materials research, may be applied to generate three-dimensional chemical maps of organic fibers embedded in biominerals, such as in a marine mollusk tooth. APT is uniquely suited to detecting chemical and structural heterogeneity with its high spatial resolution and sensitivity for all elements.

Gordon, L.M. & Joester, D. Nature 469, 194–197 (2011).