Volume 15 Issue 5, May 2018

A regulatory vocabulary for synthetic biology and why baby diapers matter.

A deep-learning-based approach improves the speed, accuracy, and robustness of biomedical image reconstruction.

A double-deletion rabies virus variant overcomes the cytotoxicity that has previously limited long-term applications for retrograde labeling of projection neurons.

A coordinate-based framework quantifies the correlation and interaction of biomolecules in images acquired with super-resolution microscopy techniques.

CasRx is a programmable CRISPR–Cas system that targets RNA for efficient knockdown and splicing modulation.

The multipurpose MAC-tag enables integrative interaction proteomics to localize proteins with sub-organelle precision.

Many factors can skew the results of a widely used amplification technique for microbiome analysis, but researchers are finding strategies for getting at the truth.

Two methods for comparing single-cell expression data sets help address the challenge of integrating data across conditions and experiments.

Metagenomic mining generates a rich resource of regulatory sequences with species-selective and universal activity, making it possible to engineer synthetic circuits with tunable gene expression across diverse bacterial hosts.

A collection of 1,406 high-quality, immunoprecipitation- and immunoblotting-grade monoclonal antibodies to 737 human transcription factors is made available as a community resource, along with all validation data.

trendsceek identifies genes with significant spatial trends in single-cell spatial expression data, as well as in low-dimensional projections of dissociated single-cell RNA-seq data.

SpatialDE identifies genes with significant spatial expression patterns from multiplexed imaging or spatial RNA-sequencing data, and can cluster genes with similar spatial patterns as a form of expression-based tissue histology.

Optopharmacological manipulation with ‘caged’ glutamate and GABA has enabled the study of these ligands’ cognate receptors, but other ligands such as tertiary amine drugs have not been amenable to caging. A new strategy yields a photoactivatable nicotine, PA-Nic, which allows manipulation of nicotinic acetylcholine receptors.

The integration of quantum chemistry and molecular dynamics programs coupled with a graphical user interface provides a streamlined tool for powerful simulations of biomolecular reaction mechanisms.

RT-FDC combines the specificity of fluorescent probes with functional readout of a cell's mechanical properties. The resulting correlation of fluorescence-based cell identity with mechanical measurements in real time allows the development of label-free, mechanical cell sorting.

scmap enables the comparison of disparate single-cell RNA-seq data sets by projecting individual cells or clusters from a query sample onto a reference sample or cell atlas.

PRICE uses Ribo-seq data to predict ORFs and start codons with high accuracy by computationally eliminating experimental noise and dissecting overlapping translation events.

An open-source, real-time fitter for 3D single-molecule localization microscopy uses experimental point spread functions. This enables accurate 3D super-resolution microscopy on standard microscopes without dedicated 3D optics.

Data-independent-acquisition-based mass spectrometry enables highly reproducible proteome analysis, but results interpretation is challenging owing to the complex nature of the spectral data. A software tool, Specter, effectively resolves spectra for highly similar peptides.

FateID identifies fate biases in early multipotent progenitor populations from single-cell RNA-seq data.

In this CRISPR-based feedback control system, sgRNA expression is triggered by the burden of protein overexpression, and the sgRNA directs repression of the exogenous gene promoter to reduce burdensome expression and restore growth of the cell.