Volume 11 Issue 11, November 2014

An avian backpack for discerning individual zebra finches' songs and studying cognition comes to Switzerland via Novosibirsk, Russia.

As a tool for light-dependent protein clustering, cryptochrome offers many opportunities to manipulate and query processes in the cell.

Imaging of electrical activity in vivo in Caenorhabditis elegans is possible with the improved genetically encoded voltage sensors Archer1 and Archer2.

Protein structure changes can be charted on a global scale with a method that couples limited proteolysis with mass spectrometry–based proteomics.

CRISPR-Cas9 is not just for DNA anymore: RNA targeting is also achievable.

A twist on the MAPPIT method enables studying protein-protein interactions within living mammalian cells.

Two surveys of the transcriptome hint at unexpected diversity in the breadth of mRNA modifications.

Researchers grow genetically stable organoids from mouse and human prostate cells in the lab and establish patient-derived lines that model prostate cancer.

Electrodes and electrode arrays to record from neurons come in an increasing number of shapes and sizes, and engineers are continuously adding capabilities.

Protein-responsive ribozymes generated by a streamlined design process will expand the plug-and-play toolbox for synthetic biologists.

Tumor-specific peptides missed in standard mass spectrometry–based workflows can be identified by integrating genomic information to interpret proteomic data. As discussed in this Perspective, an onco-proteogenomic approach to study tumor biology could have a substantial impact on cancer research. Also in this issue, Nesvizhskii reviews proteogenomic technology.

A proteogenomic approach to analyzing mass spectrometry–based proteomic data enables the discovery of novel peptides, provides peptide-level evidence of gene expression, and assists in refining gene models. Strategies for building custom sequence databases, applications benefitting from a proteogenomic approach, and challenges in interpreting data are discussed in this Review. Also in this issue, Alfaro et al. discuss the use of proteogenomic approaches for studying cancer biology.

A microfluidic chip is used to construct a microarray of proteins, each labeled with a dockerin tag, for high-throughput single-molecule force spectroscopy experiments using a single cohesin-modified cantilever.

A method based on the Hadamard transform is shown to enable time-resolved X-ray crystallography measurements of protein dynamics at standard synchrotron sources.

Communications between animals such as zebra finches can be discriminated with back-attached acceleration recorders. In contrast to microphones, these devices record the carrier's signals only, allowing a more precise analysis of individual vocalizations during social interactions.

RnBeads facilitates user-friendly analysis of large-scale DNA methylation data and fosters reproducibility and data sharing.

ShRec3D (shortest-path reconstruction in 3D) converts sparse chromosome contact maps into spatial distances followed by 3D reconstruction.

The CONCOCT software performs unsupervised binning of metagenomic contigs across multiple samples to allow better genome reconstruction from microbial communities.

A model that incorporates the quantitative relationship between microRNA and the expression of its target gene achieves predictable and robust genetic circuits.

Designer ribozymes show protein-responsive translational control and can be combined with transcriptional control elements to program complex gene circuits.

This paper reports an autofluorescent signal in cancer stem cells within epithelial tumors and describes its use as a marker to isolate and study these cells.

This paper reports a combination of two small molecules for very efficient mouse cell reprogramming to induced pluripotency, achieving close to 100% reprogramming within a few days for some cell types.

Quantum dots sequentially loaded into cells are used to generate barcodes that can identify thousands of individual cells within a population and that can be used to track cells over many hours.