Structural biology

Improving molecular replacement

Molecular replacement is a standard approach for reconstructing three-dimensional protein structures from crystallography data, but this method usually fails for proteins with less than 30% sequence identity to the nearest homologous structure. DiMaio et al. show that the Rosetta structural modeling program, used in combination with algorithms for crystallographic structure determination, could generate high-resolution structures for several proteins that could not be solved using traditional methods.

DiMaio, F. et al. Nature 473, 540–543 (2011).

Biophysics

Mapping cell shear stress

Krieger et al. describe cysteine shotgun mass spectrometry, a method to map how cysteines are exposed in proteins in cells by mechanical, thermal or drug-based stress. Exposed cysteine residues are labeled with fluorescent thiol probes; the labeled proteins can be imaged and also analyzed for site-specific cysteine modifications by shotgun mass spectrometry. The authors applied the approach to look at the cytoskeletal proteins spectrin, actin and ankyrin in red blood cells that are exposed to shear stress.

Krieger, C.C. et al. Proc. Natl. Acad. Sci. USA 108, 8269–8274 (2011).

Genomics

Trinity assembles transcripts

To fully exploit the potential of high-throughput transcript sequencing (RNA-seq), analysis algorithms are essential. Grabherr et al. now add Trinity, a de novo assembler, to the toolbox. First, the Inchworm module assembles short reads into contigs, then Chrysalis clusters overlapping contigs and constructs de Bruijn graphs, and finally, Butterfly reconstructs full-length transcripts for each isoform. The authors used Trinity to analyze RNA-seq data from fission yeast, mouse and whitefly.

Grabherr, M.G. et al. Nat. Biotechnol. advance online publication (15 May 2011).

Neuroscience

Visualizing neuronal connections by MRI

Wu et al. report a new compound that can be used to trace neuronal connections in the in vivo rat brain using magnetic resonance imaging (MRI). They conjugated the anatomical tracer cholera-toxin subunit-B with gadolinium-chelate to generate a magnetic resonance–visible compound. The tracer is transported monosynaptically, whereas manganese chloride—a tracer currently used to trace neuronal connections with MRI—is transported multisynaptically, which can make the interpretation of connectivity experiments more difficult.

Wu, C.W.-H. et al. Neuron 70, 229–243 (2011).

Biophysics

Minimum information about a simulation experiment

Minimum information guidelines are written with the aim to improve scientific reporting in a number of fields by providing clear instructions to researchers for providing sufficient information in publications to allow others to reproduce the work. Waltemath et al. now present the minimum information about a simulation experiment (MIASE). These guidelines describe the minimal set of information that is needed to describe a computational simulation experiment in a publication.

Waltemath, D. et al. PLoS Comp. Biol. 7, e1001122 (2011).