Volume 19 Issue 5, May 2022

From a physicist who explores biology’s unknowns, greater precision by linking two methods.

Scientists in Ukraine share their current reality and post-war plans.

Perturb-map combines multiplex imaging and spatial transcriptomics to dissect complex biological functions from CRISPR screens in tumor tissues.

The MINI2P is a two-photon miniscope that enables robust calcium imaging during mouse behavior.

Cell-free DNA ‘fragmentomics’ empowers cancer detection and classification.

B_net provides a measure of radiation damage suffered by protein crystals during X-ray crystallography.

A genetic tracing approach follows the division history of cells in vivo.

Securing biodiversity takes many measures, including the involvement of Indigenous peoples.

A novel approach to probabilistically align adjacent multiple tissue slices from spatially resolved transcriptomics data provides unprecedented depth for the investigation of tissue architecture and paves the way for new developments in 3D spatial analytics.

A flexible open-top light-sheet microscope has been developed that can perform deep three-dimensional imaging on all clearing protocols with low and high optical resolution.

Counting of RNA molecules using unique molecular identifiers (UMIs) is ubiquitous in single-cell sequencing. Here, we introduce molecular spikes, a new type of RNA spike-ins with in-built UMIs. These versatile molecular spikes have many uses in experimental and computational method development and routine biological applications.

Neuromechanical simulations enable the study of how interactions between organisms and their physical surroundings give rise to behavior. NeuroMechFly is an open-source neuromechanical model of adult Drosophila, with data-driven morphological biorealism that enables a synergistic cross-talk between computational and experimental neuroscience.

This work presents an overview of the evolution of spatial transcriptomics and highlights recent efforts in method developments in this space.

NEAT-seq offers a tri-omics tool for profiling nuclear protein abundance along with ATAC-seq and RNA-seq in single cells.

Two-color fluorogenic DNA-PAINT introduces self-quenching, kinetics-optimized probe designs. This approach improves imaging speed 26-fold and eliminates the need for optical sectioning.

This work presents an RNA spike-in that can be used to improve RNA counting in single-cell RNA-sequencing (scRNA-seq) analysis, as well as to report the performance of scRNA-seq methods.

PASTE aligns and integrates spatial transcriptomics data generated from adjacent tissue slices by leveraging their transcriptomic similarity and spatial coordinates, which ultimately increases the power for downstream analysis.

ROCK (RNA oligomerization-enabled cryo-EM via installing kissing loops) enables improved single-particle cryo-EM of RNAs. ROCK was used to generate high-quality structures of three diverse RNAs, including the Tetrahymena group I intron.

iNTA combines interferometric detection of scattering with nanoparticle tracking analysis for determining the size and refractive index distributions of nanoparticles in suspension with high sensitivity and precision.

A model-based correction (MBC) algorithm offers fast and accurate correction of multiple-blinking artifacts in PALM data. MBC outperforms other algorithms in both speed and accuracy and improves quantitative downstream image analysis.

A dynamic model of the 4Pi point spread function enables localization microscopy with exceptional three-dimensional resolution and a simpler optical design. 4Pi-STORM images of neurons and mitochondria reveal new details of nanoscale protein and nucleic acid organization.

A ‘hybrid’ open-top light-sheet microscope is described, which can be used for broad multi-scale volumetric imaging of one or more large tissues, cleared with diverse protocols, and conveniently mounted on an array of sample holders.

NeuroMechFly enables simulations of adult Drosophila melanogaster. The platform combines a biomechanical representation of the fly body, models of the muscles, a neural controller and a physics-based simulation of the environment.