Volume 11 Issue 4, April 2014

Traversing biology at multiple scales, a system automates flow cytometry. And a constitution changes lab culture.

When a large number of tests are performed, P values must be interpreted differently.

From single-molecule functional studies to atomic-resolution structures, a windfall of data sheds light on the Cas9 mechanism of targeted DNA scission.

A new device for injecting membrane-protein microcrystals into the path of an X-ray free-electron laser beam improves the efficiency of serial femtosecond crystallography.

Quick-hybridizing probes help scientists image the high-speed events leading up to gene transcription.

Combining 63 annotations provides a unified score for the potential deleteriousness of every possible human mutation.

By pushing throughput, single-cell transcript profiling can replace marker-based sorting and bulk RNA sequencing to redefine tissues from the bottom up.

The power of genetics in the worm, and in the bacteria that worms eat, is harnessed for a systems view of the effect of diet on a host organism.

Tumors impart hints at what drives their progression. Parsing those signals takes old and new approaches.

The combination of mass spectroscopy with immunohistochemistry allows highly multiplexed, directly quantitative imaging of tissue samples for both basic and clinical research.

A comparative analysis of methods for scoring human sleep data, in particular sleep spindles, from encephalographic recordings is reported. The authors develop methods for crowdsourcing the identification of sleep spindles and compare the detection performance of experts, non-experts and automated algorithms.

The synthetic firefly luciferase substrate CycLuc1 offers brighter bioluminescence and improved imaging in mouse models at lower doses than the standard D-luciferin.

The hierarchical Bayesian model identifies and quantifies clonal populations in tumors from deep-sequenced somatic mutations.

This paper describes the use of paired Cas9 nickases to edit the mammalian genome with no detectable off-target effects.

Four types of mass spectrometry (MS) data—label-free quantitative bottom-up proteomics, native MS, ion mobility–MS and cross-linking MS—are used to derive restraints for structural modeling of large protein assemblies.

Multivariate linear mixed models implemented in the GEMMA software package add speed, power and the ability to test for genome-wide associations between genetic polymorphisms and multiple correlated phenotypes.

The combination of stimulated Raman scattering (SRS) microscopy with an alkyne group as a Raman-active tag allows high-contrast, live-cell dynamic imaging of a variety of biomolecules including DNA, RNA, protein, lipids and small-molecule drugs.

CS-Rosetta-RNA is a web tool for determining high-resolution structures of noncoding RNA motifs using ¹H NMR chemical shift data coupled with Rosetta-based modeling.

This paper reports the use of mass cytometry on adherent cells and tissue samples for highly multiplexed imaging at subcellular resolution.

Cryo-scanning transmission electron tomography (CSTET) of unstained, fully hydrated vitrified biological specimens is shown to have advantages over cryo-electron tomography (CET), notably at high sample tilts providing greater depth resolution for thick samples.

High-throughput in vitro analysis of TALE nuclease (TALEN) cleavage specificity gives insight into the mechanism of TALE binding and allows the design of TALENs with lower off-target activity.

This paper reports conditions for the in vitro culture of human leukemia stem cells, which should enable basic studies as well as chemical screens on these cells.

An automated flow cytometry setup is described for dynamic and quantitative measurements of yeast growth and molecular phenotypes at high throughput.

This paper describes optical control of complex and dynamic bacterial gene expression patterns for the study of gene circuits.

Single-molecule structural transitions involving DNA twisting can be measured with substantially greater spatiotemporal resolution than previously possible with a gold rotor bead tracking (AuRBT) method. This approach uses magnetic tweezers and evanescent darkfield microscopy to track a gold nanoparticle probe attached to a DNA molecule.