Volume 20 Issue 10, October 2023

Science needs diversity, but barriers such as housing insecurity can hinder access to education and training. To lobby for change, students put their own experiences to work.

The green alga Chlamydomonas reinhardtii is a useful reference organism for studying photosynthesis, cilia and the cell cycle. Like many other algae, it exhibits daily rhythms in gene expression and behavior that are in sync with the rising and setting of the sun.

Miniaturized power sources consisting of a few droplets can generate enough power to modulate neuronal activity.

Making biological research more sustainable requires an accurate assessment of its environmental impact, both at the bench and on the computer.

A new chemically induced dimerization (CID) pair exhibits fluorescence upon dimerization for the first time. Moreover, the CID pair is small and offers easily reversible dimerization that can be repeated multiple times.

Leveraging nanopore long-read sequencing, scNanoHi-C identifies multiway interactions between enhancers and their target promoters within a single cell. Compared with short-read-based single-cell Hi-C or population-based multiway sequencing methods, scNanoHi-C offers new opportunities to investigate the heterogeneities of single-cell gene regulation networks mediated by high-order 3D chromatin structures.

To capture expansive, seamless fields of view from frozen hydrated specimens by cryo-electron tomography, we developed methods for the collection and processing of montage data. This approach enables rapid acquisition of contiguous regions of specimens using a montaged tilt series collection scheme.

We introduce GelMap, a flexible workflow for reporting deformations and anisotropy in expansion microscopy. By intrinsically calibrating the expansion hydrogel using a fluorescent grid that scales with expansion and deforms with anisotropy, GelMap enables the reliable quantification of expansion factors and correction of deformations.

This Review discusses statistical and computational strategies for analyzing various spatial and temporal omics data types, with an emphasis on the common modeling principles.

Flash entropy speeds up mass spectral similarity searches 10,000-fold, including for open search, hybrid search and neutral loss search.

Droplet-based microfluidics enable rapid mixing with millisecond dead times and allow single-molecule measurements of non-equilibrium binding kinetics on even challenging, strongly adsorptive samples, such as intrinsically disordered proteins.

This work introduces a wet lab and computational pipeline, Napu, for small variant calling and de novo assembly of Nanopore sequencing data, which leads to comparable performances to short-read sequencing and allows for large-scale long-read sequencing projects.

scNanoHi-C combines Nanopore long-read sequencing with a proximity-ligation-based Hi-C protocol to profile high-order genome structures in individual cells, enabling the capture of multiway interactions among enhancers and promoters.

This paper presents an improved approach for mapping single-cell RNA-seq reads with optimized transcriptomic references, which markedly recovers previously missing gene expression data.

EzMechanism is a tool for automated prediction of the catalytic mechanisms of enzymes using their three-dimensional structures and chemical reactions as input.

AlteredPQR is a software tool, available as an R package, to infer remodeling of protein functional modules from whole-cell or tissue lysate proteomic measurements.

Single-cell Deep Visual Proteomics integrates imaging, cell segmentation, laser microdissection and multiplexed mass spectrometry for spatial single-cell proteomics measurements in complex tissues.

Montage parallel array cryo-tomography adopts principles of montage tomography via regular array beam-image-shift montage acquisition and is robust for imaging large fields of view while retaining high-resolution structural information in cryo-electron tomography.

A workflow combining optogenetic perturbations with spatial transcriptomics to program spatiotemporal gene expression patterns in organoids.

CATCHFIRE (chemically assisted tethering of chimera by fluorogenic-induced recognition) tools are small tags that can chemically dimerize with turn-on fluorescence, enabling simultaneous control and visualization of protein proximity.

The Clivias are a series of small, monomeric fluorescent RNAs that emit with a large Stokes shift in the orange–red. They enable multiplexed RNA imaging in live cells and BRET-based detection of protein–RNA interactions in mice.

The GelMap workflow adds a fluorescent grid into samples before expansion, allowing for precise determination of expansion factor and subsequent deformation correction in ExM. GelMap works with diverse samples and expansion methods.

Statistically unbiased prediction utilizing spatiotemporal information in imaging data (SUPPORT) is a self-supervised deep learning approach to accurately denoise voltage and calcium imaging data while preserving true dynamic signals.

D-LMBmap is a fully automated pipeline for mesoscale connectomics including deep-learning modules for axon segmentation, brain region segmentation and whole-brain registration. D-LMBmap works accurately across cell types and modalities.

This Registered Report describes an extensive comparison of 22 near-infrared fluorescent proteins in vitro, in cultured mammalian cells, and in model animals, clarifying top performers in diverse biological settings.