Volume 20 Issue 5, May 2023

Members of a lab often have a varied language background. This rich language diversity leads to lab dynamics that take mindful handling.

A microscope objective inspired by the Schmidt telescope offers a large field of view, high numerical aperture, long working distance and compatibility with all homogeneous immersion media for versatile bioimaging.

Chemical modifications to DNA, histones and RNA make changes happen. Scientists are exploring ways to track these modifications and how they interact.

Integration of single-cell molecular profiling with cellular spatial localization has remained an elusive goal. Image-seq leverages high-resolution microscopy to spatially resolve and isolate viable bone marrow and leukemia cells for subsequent state-of-the art, single-cell transcriptomics.

DISCOVER-seq+ enables the efficient detection of CRISPR–Cas off-target breaks in primary cells and tissues.

Two new Brillouin microscopes leverage line-scanning to overcome previous limitations of the technique, enabling fast imaging, with low phototoxicity, of mechanical properties in living embryos of model organisms and tumor spheroids.

Light-activated drugs and signaling molecules have therapeutic potential and are valuable experimental tools. Photoactivation of a mu opioid receptor agonist in the mouse brain rapidly triggered pain relief and locomotion, demonstrating that in vivo photopharmacology can drive dynamic studies into animal behavior.

Photoselective sequencing is a new method for genomic and epigenomic profiling within specific regions of a biological specimen that are chosen using light microscopy. This combination of spatial and sequencing information preserves the connections between genomic and environmental properties and deepens our understanding of structure–function relationships in cells and tissues.

Simultaneous maximization of sensitivity, data completeness and throughput in mass-spectrometry proteomics often necessitates trade-offs. To mitigate these trade-offs, we introduce a prioritization algorithm that achieves high sensitivity and data completeness while maximizing throughput. With prioritized single-cell proteomics (pSCoPE), we consistently and accurately quantify proteins and their post-translational modifications in single macrophages and link them to endocytic activity.

Unlike cell surface proteins, secreted proteins are difficult to quantify and trace back to individual cells. We show that the capture of secreted proteins onto their source cell surfaces using an affinity matrix enables simultaneous measurement of protein secretion, cell surface proteins and transcriptomics in thousands of cells at single-cell resolution.

Cells exchange information with one another using secreted chemicals as data carriers. We developed an all-optogenetic synaptic transmission system that replaced a chemical neurotransmitter with emitted photons. This system enabled synthetic signaling between unconnected neurons and the generation of prosthetic synaptic circuits.

This Perspective introduces biologists interested in computational approaches to the benefits of the Julia programming language for meeting current and future computational demands.

This paper compares different transformation approaches for analysis of single-cell RNA-sequencing data and provides recommendations for method selection.

Crowdsourcing condensate database and encyclopedia is a community-editable platform for verified biomolecular condensates and their protein constituents. It also provides an encyclopedia for the scientific terms used in condensate biology and a crowdsourcing web application.

A dual line-scanning approach increases imaging speed and reduces illumination levels in Brillouin microscopy, which is demonstrated on spheroids.

CNV-Y-DAMGO enables photopharmacological manipulations of mu opioid receptor signaling in behaving mice with high temporal resolution.

Photoselective sequencing combines targeted illumination and photocaged fragment libraries to enable the spatial analysis of genomic sequence and chromatin accessibility profiles with subcellular resolution in the context of complex tissues.

TEMPOmap combines pulse-chase metabolic labeling with multiplexed three-dimensional in situ sequencing to simultaneously profile the age and subcellular location of individual RNA molecules from thousands of genes to reveal RNA kinetic landscapes.

DISCOVER-Seq+ is a high-sensitivity method for the detection of off-target effects of CRISPR genome editing.

Prioritized Single-Cell ProtEomics (pSCoPE) introduces the concept of using priority levels that define the temporal order of peptide analysis for single-cell proteomic analysis. Prioritized data acquisition aims to simultaneously optimize the consistency, sensitivity, depth and accuracy of protein quantification.

TRAPS-seq is a sequencing-based method to profile dynamic protein secretion in single cells.

Virtual-scanning light-field microscopy (VsLFM) uses a physics-based deep learning model to improve the quality and speed of LFM, reducing motion artifacts and enabling challenging demonstrations such as fast 3D voltage imaging in Drosophila.

DeepWonder removes background signals from widefield calcium recordings and enables accurate and efficient neuronal segmentation with high throughput.

Line-scan Brillouin microscopy enables fast 3D imaging of mechanical properties with low phototoxicity, as shown for Drosophila and mouse embryos, as well as ascidians.

PhAST is a technology for establishing de novo or modulating synaptic transmission in a light-dependent manner in C. elegans. By combining a calcium-dependent luciferase on pre-synapses with channelrhodopsin on post-synapses, light serves as a synthetic neurotransmitter.