Volume 14 Issue 7, July 2017

Calculating gene–environment interactions, and the role of a 'why' machine.

PCA helps you interpret your data, but it will not always find the important patterns.

Two sets of complementary tools extend our capacity to manipulate the gut microbiome.

Human protein subcellular locations light up in the Cell Atlas resource.

In vitro Cas9-binding assays show the effects of mutations in the target sequence on binding kinetics.

A serial-section electron microscopy data set of larval zebrafish brain—imaged at several scales—provides a resource for structure–function analyses of the animals' neural circuitry.

Single-cell transcriptomics is used to determine what cell types are present in brain organoids and how much these cell types vary across organoids.

This Commentary discusses the problem of phototoxicity in live imaging and suggests guidelines to improve its assessment and reporting.

This piece tackles the question of how to make biological scale more intuitive to human beings, bringing to bear the author's background in scientific visualization.

Carbohydrates are tough molecules to study, but glycoscientists are developing and democratizing the needed tools.

Genetically encoded NAD and NADP sensors will revolutionize the study of redox biology.

This Analysis explores the relationship between chromosome conformation capture (for example, Hi-C) and FISH datasets, and uses simulations to reconcile measurements from the two technologies.

Six tools to call chromatin interactions and seven tools for topologically associating domain calling are systematically compared with real and simulated data. The strengths and weaknesses of each tool are discussed.

By using bootstraps that estimate inferential variance, the sleuth method and software provide fast and highly accurate differential gene expression analysis in an interactive Shiny app.

webKnossos is a browser-based tracing and annotation tool for 3D electron microscopy data sets that is optimized for seamless data viewing. The tool’s flight-mode view facilitates fast neurite tracing because of its egocentric viewpoint.

Iterative oxidation, elimination and dephosphorylation steps remove nucleotides from the 3′ end of RNA until a 2′-O-methylated ribose that cannot be oxidized is encountered and brings the process to a stop. High-throughput sequencing of these fragments exposes 2′-O-methyl sites at base resolution.

The EAGLE algorithm and software identifies replicable gene-by-environment interactions based on associations between environment and allele-specific expression.

Improved fluorescence in situ hybridization enables smFISH in cleared whole-mount Drosophila brains with confocal microscopy; a custom Bessel beam structured illumination microscope allows single-mRNA detection across the entire brain.

A statistical approach makes it possible to detect differentially abundant cell populations across biological conditions from high-dimensional mass cytometry data without relying on cell clustering.

Early STOP codons created with CRISPR base editors leads to gene knockout with high efficiency and does not stress cells with double-strand DNA breaks. CRISPR-STOP can target the majority of human genes and is useful for genetic screens.

FHIRM-TPM is a miniature two-photon microscope capable of imaging fluorescently labeled neurons in the brains of freely behaving mice. It allows for imaging of spines or recording of neural activity with a frame rate up to 40 Hz.

Genetically encoded iNap sensors allow imaging of NADPH with high spatiotemporal resolution in living systems. The iNaps cover physiologically relevant NADPH concentrations and are demonstrated in mammalian cells and live zebrafish.

A new approach to evolve novel aminoacyl-tRNA synthetase–tRNA pairs with orthogonal substrate specificity is applied to generate a system to site-specifically incorporate phosphothreonine into proteins, enabling functional studies of this post-translational modification.

The combination of tumor barcoding with CRISPR-mediated targeting of tumor suppressors allows quantitative analysis of tumor-suppressor function during tumor growth in vivo.

The fusion of patterned cerebral organoids into more complex structures enables modeling of inter-regional processes such as neuronal migration.