Volume 12 Issue 1, January 2015

An illustrator drops the barriers between work and play with software to model and explore cells.

Recent improvements in tissue 'clearing' techniques permit their application to a variety of tissues and their combination with immunohistochemistry.

One of the first genome sequences produced on a handheld nanopore sequencer shows the platform's potential as well as its challenges.

Bacterial populations get outfitted with stable analog genetic memory.

A 'bump-and-hole' strategy probes individual BET bromodomains.

Proximity-specific ribosome profiling reveals the exquisite specificity of translation at the endoplasmic reticulum and mitochondrial outer membrane.

Light-sheet fluorescence microscopy techniques are enabling researchers to achieve dynamic, long-term imaging and three-dimensional reconstruction of specimens ranging from single cells to whole embryos.

In light sheet–based fluorescence microscopy (LSFM), optical sectioning in the excitation process minimizes fluorophore bleaching and phototoxic effects. Because biological specimens survive long-term three-dimensional imaging at high spatiotemporal resolution, LSFM has become the tool of choice in developmental biology.

Developments in electrical and optical recording technology are scaling up the size of neuronal populations that can be monitored simultaneously. Light-sheet imaging is rapidly gaining traction as a method for optically interrogating activity in large networks and presents both opportunities and challenges for understanding circuit function.

Ten years of development in light-sheet microscopy have led to spectacular demonstrations of its capabilities. The technology is ready to assist biologists in tackling scientific problems, but are biologists ready for it? Here we discuss the interdisciplinary challenges light-sheet microscopy presents for biologists and highlight available resources.

Data-independent acquisition (DIA) mass spectrometry may change how proteomic data are generated.

Methods to profile and characterize the function of noncoding RNAs will emerge.

Genetically encoded voltage indicators are on the brink of allowing neuronal activity to be directly imaged in vivo.

As the CRISPR-Cas system matures, specificity, efficacy and maybe even a eukaryotic nuclease are being considered.

Protein structures can be determined from microcrystals using X-ray and electron diffraction.

Correlated light and electron microscopy (CLEM) is particularly powerful when applied in super-resolution.

Nanopores hold promise for single-protein characterization.

A closer look into the depths of organs such as the brain is within reach.

Moving and sorting cells with sound are a few of the possible applications for this no-contact technique.

Two high-throughput single-molecule force spectroscopy platforms expand the reach of this technology for biomechanical molecular phenotyping.

Acoustic force spectroscopy applies acoustic forces across a large dynamic range for highly multiplexed single-molecule measurements in a simple, compact setup.

A genetically encoded peroxidase with improved sensitivity, APEX2, is reported for electron microscopy and proximity labeling at low expression levels.

The Archaea metalloproteinase LysargiNase increases proteome coverage, identifies more C-terminal peptides from proteins and improves methylated peptide identification.

The open-source DIAMOND software provides protein alignment that is 20,000 times faster on short reads than BLASTX at similar sensitivity, for rapid analysis of large metagenomics data sets on a desktop computer.

Serial femtosecond crystallography experiments with diverse protein microcrystal suspensions are facilitated using a grease matrix as a carrier medium for sample injection.

An improved genetically encoded red calcium sensor enables the monitoring of neuronal activity in cell culture and in vivo. R-CaMP2 has fast kinetics and a high affinity to calcium and can follow action potentials up to 40 Hz.

Targeted DNase Hi-C uses DNase I instead of restriction enzymes for chromatin fragmentation and improves the resolution of chromatin interaction maps.

This paper presents FpClass, a prediction method for physical protein-protein interactions. The method is benchmarked against experimental data and is used to predict, among others, partners of interactome 'orphans'.

Software to model, pack and integrate biological structures at the scale of macromolecular complexes and cellular organelles is described. It is applied in several contexts, including hypothesis generation and testing.

Our Method of the Year 2014 goes to light-sheet fluorescence microscopy. This series of papers discusses how this technology, in combination with increasingly sophisticated cameras and powerful computing, is dramatically changing and enabling the imaging of living biological samples from developing embryos to functioning brains. We also highlight methods worth watching in the upcoming years.