Volume 21 Issue 9, September 2024

Early-career scientists shared some of their plans, hopes and dreams about being a principal investigator at the 2024 annual meeting of the International Society for Stem Cell Research.

Scientific breakthroughs can change how we understand and live in the world, disrupting long-held assumptions and concepts and raising new questions for philosophy and science. To address these challenges, we describe a model for collaboration of scientists with philosophers and ethicists, and its benefits to the research process and outcomes.

Biomaterials are revolutionizing organoid development by offering tunable platforms that provide instructive cues, which enhance cell fate transitions, tissue-level functions and reproducibility. These advances are crucial for harnessing the translational potential of organoids.

DNA origami tension sensors can provide insights into mechanotransduction in a physiological environment.

The global imaging community is pursuing innovative approaches to achieve more equitable access to instruments and expertise.

The capability of high-resolution in situ imaging by electron cryo-tomography (cryo-ET) has now been expanded to large multicellular tissues by newly developed workflows involving lift-out and serial sectioning using focused ion beam milling under cryogenic conditions.

A systematic comparison of 11 sequencing-based spatial transcriptomics methods reveals molecular diffusion as a critical variable that influences the effective resolution and data interpretation across platforms. Our benchmarking study should aid biologists in selecting the most appropriate method for their specific tissue.

We demonstrate CRISPRdelight, a robust CRISPR–Cas12a-based method for imaging non-repetitive genomic DNAs in a highly efficient way. This system is a powerful tool for studying functional links between gene dynamics, localization and regulation, and reveals heterogeneity in the expression of differently localized alleles in the same cells.

SpatialGlue is a tool designed to decipher spatial domains from spatial multi-omics data acquired from a single tissue section. It employes graph neural networks with a dual-attention mechanism to accomplish within-omics integration of measured features and spatial information, followed by cross-omics integration.

Single-cell bisulfite sequencing enables the genome-wide quantification of DNA methylation at single-cell resolution, but methods to analyze the resulting data are lacking. The MethSCAn software accurately distinguishes cell types and states by scanning the genome for informative regions and providing a robust approach to quantifying methylation within these regions.

This Perspective discusses the integration of small-scale datasets with each other or with larger reference atlases, particularly in the context of single-cell approaches.

Scalable tools are needed for the analysis of increasingly large mass spectrometry-based proteomics datasets. quantms offers an open-source, cloud-based pipeline for massively parallel proteomics data analysis.

The MHz repetition rates available at second-generation X-ray free-electron lasers enable the collection of microsecond time-resolved X-ray scattering data with exceptionally low noise, providing insights into protein structural dynamics.

Smart parallel automated cryo-electron tomography (SPACEtomo) uses deep learning to fully automate data collection from lamella detection to tilt series acquisition, driving the future of cryo-ET through improved throughput and statistics.

This work highlights the technical issues in previous approaches and introduces a preprocessing approach along with a software package, MethSCAn, for single-cell bisulfite sequencing data analysis.

EpiChem enables the co-profiling of small molecule–DNA interactions and multiple epigenomic features in single cells.

SwitchSeeker combines computational and experimental techniques to identify functional RNA structural switches. Applied to the human transcriptome, it identified a novel RNA switch in the 3ʹUTR of RORC, linked to nonsense-mediated decay.

This work introduces CRISPRdelight, a dCas12a-based DNA-imaging tool that facilitates the imaging of non-repetitive loci and the tracking of DNA dynamics.

SpatialGlue is a graph neural network-based approach for integrating multimodal spatial omics data. Combining complementary data modalities improves the discovery of spatial domains as well as the identification of cell subpopulations across tissues.

This work presents ORFtag that enables proteome-wide functional screens by tagging and overexpression of endogenously encoded proteins via randomly integrated cassettes.

DeepPBS is a deep-learning model designed to predict the binding specificity of protein–DNA interactions using physicochemical and geometric contexts. DeepPBS functions across protein families and on experimentally determined as well as predicted protein–DNA complex structures.

Serial Lift-Out creates a series of lamellae from one lift-out volume for cryo-ET, increasing the ease and throughput of cryo-lift-out and enabling the study of molecular anatomy in multicellular systems including C. elegans larvae.

Serialized on-grid lift-in sectioning for tomography (SOLIST) improves the throughput of the serial lift-out technique for creating lamellas, addressing a major bottleneck in the use of cryo-electron tomography for in situ structural biology.

Super-resolution imaging of reference and target structures enables precise determination of the labeling efficiency of high-affinity binding proteins in cells for improved quantitative assessment of protein organization at the single-molecule level.

Protein-tag degree of labeling (ProDOL) is a versatile reference-based approach for experimentally determining the degree of target labeling for improved protein counting and quantification and for optimizing labeling protocols in fixed and live cells.

Bayesian nonparametric Track (BNP-Track) simultaneously determines emitter numbers and their tracks alongside uncertainty, extending the superresolution paradigm from static samples to single-particle tracking even in dense environments.

CaST is a Ca²⁺-activated version of split-TurboID. The tool allows labeling active neurons quickly, simply by administration of exogenous biotin, thus enabling the study of behaviors that would be impaired by hardware required for the use of other, light-dependent tools.

Onavg is a surface template of the human cortex. In contrast to existing templates, the cortical surface is uniformly sampled, which has advantages in numerous applications.

This analysis presents a systematic comparison of 11 sequencing-based spatial transcriptomics methods using well-characterized references, which offers insights into performance variations in spatial transcriptomic techniques.

The dyes chosen for DNA-PAINT microscopy are pivotal for data quality. This Analysis shows a comprehensive comparison of 18 fluorescent dyes in DNA-PAINT and offers guidance for optimum dye selection in single-color and multiplexed imaging.