Volume 16 Issue 6, June 2019

Bioluminescence lights her way to measure glucose uptake in vivo, and why a chemist travels outside her comfort zone.

Quantile regression robustly estimates the typical and extreme values of a response.

Interferometric scattering microscopy enables extended monitoring of gold-nanoparticle-labeled membrane proteins with impressive spatiotemporal resolution.

Phase separation in combination with spatial targeting allows for selective translation of mRNA within synthetic membraneless organelles.

The elimination of all cross-talk in a signaling pathway turns a yeast cell into a model cell that can sense and report on metabolites.

An improved sequential fluorescence in situ hybridization approach allows one to image the expression of 10,000 genes in single cells.

Hybrid multiplexed sculpted light microscopy enables calcium imaging of volumes as large as half a cubic millimeter.

To apply machine learning, labs needn’t have years of computational expertise, but they do need a cautious mind-set.

The interpretation of fragmentation patterns in tandem mass spectrometry is crucial for peptide sequencing, but the relative intensities of these patterns are difficult to predict computationally. Two groups have applied deep neural networks to address this long-standing problem in the proteomics field, extending theoretical spectra with an additional dimension of high-accuracy fragment ion intensities.

Py-EM and SerialEM enable automated microscope control for high-throughput data acquisition in diverse transmission electron microscopy imaging experiments.

A dataset made up of single cancer cells or their mixtures serves as a benchmark for testing almost 4,000 combinations of scRNA-seq data analysis methods.

HiChIRP combines a modified chromosome conformation capture protocol with enrichment of RNA-associated chromosome conformation to visualize genome-wide looping linked to an RNA of interest.

Fluorescence intensity fluctuation spectrometry provides a rapid and accurate measurement of the identity, abundance and stability of protein oligomers.

Iso-LFM enables rapid, instantaneous volumetric imaging of biological processes with isotropic and improved resolution by simultaneously capturing orthogonal light fields.

Epi-illumination SPIM enables fast, volumetric, high-resolution, subcellular imaging of any sample compatible with a standard inverted fluorescence microscope.

CancerMine, a resource based on literature mining, offers a database of drivers, oncogenes and tumor suppressors for gene–cancer associations, updated monthly.

A deep learning–based tool, Prosit, predicts high-quality peptide tandem mass spectra, improving peptide-identification performance compared with that of traditional proteomics analysis methods.

Machine learning and deep learning models are used to predict high-quality tandem mass spectra, providing benefits over traditional analysis methods for interpreting proteomics data.

A bioluminescent glucose-uptake probe enables accurate, real-time, non-invasive longitudinal imaging of d-glucose absorption both in vitro and in vivo.

Using primer-exchange reactions, SABER extends FISH probes with repetitive sequences that can accommodate multiple fluorescent imager strands, resulting in up to 450-fold signal amplification. SABER is showcased in DNA and RNA FISH experiments across a range of complex biological samples.

Light-sheet microscopy in the NIR-II window enables rapid volumetric imaging of tissues at impressive depths in vivo without invasive preparations owing to the reduced light scattering and tissue autofluorescence at these wavelengths.

High-density arrays of optical fibers enable monitoring and manipulation of neural activity at large scale across many brain regions. The multi-fiber arrays can be used in head-fixed tasks, in freely behaving animals and during social interactions.