Volume 19 Issue 3, March 2022

Hiking his way to a well-engineered translational future for tissue-based imaging.

The imminent release of tissue atlases combining multichannel microscopy with single-cell sequencing and other omics data from normal and diseased specimens creates an urgent need for data and metadata standards to guide data deposition, curation and release. We describe a Minimum Information about Highly Multiplexed Tissue Imaging (MITI) standard that applies best practices developed for genomics and for other microscopy data to highly multiplexed tissue images and traditional histology.

Two groups report improved variants of the channelrhodopsins ChRmine and ChroME, respectively.

A metagenomic approach to identifying the sources of N⁶-methyldeoxyadenine (6mA) in eukaryotic DNA found no evidence of high 6mA abundances in sampled eukaryotes.

Comprehensive modeling of cellular networks of cells with a minimal genome.

Live imaging enables temporal tracking of immune cell behavior.

Ultra-high-throughput sequence alignment enables identification of >130,000 novel RNA viruses.

Labs are stacking techniques to disentangle the chemical influences of microbiomes.

A droplet microfluidic system enables deterministic capture and subsequent sequencing and analysis of single-cell transcriptomes from organoids and other small, individual tissue samples.

Global profiling of changes in the reactivity of cysteine residues in response to phosphorylation during mitosis identifies cysteine residues as potential regulatory and drug binding sites on proteins.

This Perspective offers guidance for robust and reproducible antibody-based highly multiplexed tissue imaging.

This resource presents an in silico generated DNA methylation atlas that can be used for cell-type deconvolution of human tissues.

The Splicing Z Score (SpliZ) provides single-cell-level quantification of alternative splicing with improved statistical power.

MCMICRO is a modular and open-source computational pipeline for transforming highly multiplexed whole-slide images of tissues into single-cell data. MCMICRO is versatile and can be used with CODEX, mxIF, CyCIF, mIHC and H&E staining data.

Alevin-fry accurately quantifies single-cell and single-nucleus RNA-seq data with high speed and memory efficiency.

DisCo is a deterministic droplet microfluidics tool for single-cell analysis on low cell input samples, which is demonstrated to profile individual intestinal organoids and in vivo-derived small tissues.

GRAND editing employs a pair of prime editing guide RNAs to enable efficient DNA insertion up to 250 bp without the need of a DNA donor.

This article describes a chemical proteomic approach to quantitatively relate serine/threonine phosphorylation to changes in the reactivity of cysteine residues, thereby affecting their potential to be post-translationally modified and/or targeted by electrophilic small molecules.

Rational design was used to develop a suite of red-shifted, bioconjugatable heptamethine cyanine dyes for multiplexed in vivo imaging in the shortwave-infrared/near-infrared-II region.

Combining a double-ring modulated SPIM with reduced side lobes and a sectionalized deep-learning based super-resolution algorithm enables fast, high-resolution, volumetric imaging of organelle interactions and dynamics in live cells.