Volume 14 Issue 10, October 2017

Why it's fun to be a 'dye Santa,' how to fine-tune in vivo probes, what to name your firstborn.

Many heads are better than one.

As more phage-derived Cas9 inhibitors are discovered, their detailed characterization is a prerequisite to using them as research tools.

A recombinase-based barcoding approach enables fate mapping in the hematopoietic system under physiological conditions.

An integrated workflow allows the quantitative interrogation of the impact of alternative splicing at the proteome level.

Single-particle reconstruction algorithms can be used to obtain 3D structures from 2D localization microscopy images.

A method to detect highly reactive lysine residues in the proteome helps spot those ripe for targeting by covalent ligands.

DNA and chromatin structures can be visualized in situ with electron tomography.

Trial, error and the art of optimizing 'molecular rulers' that sense molecules or interactions.

DroNc-seq enables low-cost, high-throughput single-nucleus RNA-seq of tissues that are archived or difficult to dissociate, such as post-mortem human brain.

The Omni-ATAC protocol improves the signal-to-background ratio in chromatin accessibility profiles and is suitable for a range of cell lines and primary cell types, as well as frozen tissue.

Blue-light-inducible CRISPR-based transcriptional activation systems achieve high enough endogenous gene expression to trigger the differentiation of iPSCs.

A data-driven strategy is used to estimate the sampling depth required to faithfully capture the true heterogeneity of cellular populations.

Red-shifted luciferins and corresponding mutants of NanoLuc enable brighter bioluminescence imaging in vitro, in cells, and in deep tissues of living mice alone and in the context of the newly developed Antares2 BRET reporter.

ChromVar infers transcription-factor-associated accessibility from low-coverage or single-cell chromatin-accessibility data, thus enabling the clustering of cells and analysis of regulatory sequence motifs from sparse data sets.

Monocle 2 uses reversed graph embedding to automatically learn complex, branched pseudotime trajectories of differentiation or cellular state changes from single-cell expression data.

Monocle 2 uses reversed graph embedding to automatically learn complex, branched pseudotime trajectories of differentiation or cellular state changes from single-cell expression data.

An algorithm and software tool automating the annotation of subcellular features in cryo-electron tomography data is presented.

Guidelines for fine-tuning spectral and chemical properties of fluorophore are introduced, resulting in four new Janelia Fluor dyes, JF₅₀₃, JF₅₂₅, JF₅₈₅ and JF₆₃₅, that span the visible region and align well with standard laser lines.

FreemoVR is a virtual reality system for freely moving animals. The versatile platform is demonstrated in various experiments with Drosophila, zebrafish, and mice.

The genetically encoded GEVAL sensors allow ratiometric imaging of the spatiotemporal dynamics of cellular GTP levels in living cells.

Negative feedback and incoherent feed-forward loops are the only circuit motifs that can adapt in response to stimuli. Rahi et al. describe signatures that allow discriminating between these two motifs and demonstrate the approach in yeast cell cycle timing and C. elegans olfaction.