Volume 21 Issue 4, April 2024

To select the best postdoctoral fellows for their labs, principal investigators assess scientific qualifications and more.

After having been largely neglected for more than a century, the tiny marine animal Trichoplax adhaerens is enjoying a revival and is now poised to become a mainstream model organism for the study of epithelial evolution, diversification and specialization.

All animals are equal, but some animals are more equal than others. —George Orwell

Organoids are an emerging way to model the fraught complexity of tumors.

New condenser aperture designs form square or rectangular beams that match the camera dimensions, which efficiently expands the data acquisition area in cryogenic electron microscopy.

The exceptionally photostable green fluorescent protein StayGold has been monomerized in different laboratories, which has generated three unique monomeric variants that will enable new imaging applications.

Diploid assembly is a difficult task that requires several types of genomic sequencing data, including — but not limited to — HiFi reads and parental sequences. Hypo-assembler, an assembly algorithm, uses high quality solid k-mers extracted from Illumina data alongside Nanopore reads to produce a high-quality diploid assembly using only Nanopore and Illumina data.

A square electron beam improves imaging of large fields of view in transmission electron microscopes by facilitating montage tomography of vitrified specimens with no loss in data quality relative to conventional round beams.

Square and rectangular beams made with new condenser apertures enable more efficient image capture in low-dose transmission electron microscopy with no compromise to image quality in single-particle cryoelectron microscopy.

MINSTED quantifies tiny movements of individual biomolecules with high spatiotemporal precision to successfully resolve the steps of the molecular motor protein kinesin-1 labeled with a single fluorophore as it switches protofilaments.

This work introduces two polishers for refining the draft genome generated from nanopore long reads, as well as an assembler pipeline for producing telomere-to-telomere diploid genome with low error rate.

A CasRx-based screening platform for genome-scale long noncoding RNA transcriptome perturbation is described.

Targeting coalescent analysis (TarCA) is a statistical method that quantifies the number of progenitor cells of a given population using single-cell phylogenetic data.

A copper(II)-functionalized Mycobacterium smegmatis porin A nanopore enables direct identification of all 20 proteinogenic amino acids, one unnatural amino acid and two post-translational modifications, and shows potential for peptide discrimination and sequencing.

Implementation of ultralong transients on an Orbitrap mass spectrometer improves mass resolution, sensitivity and accuracy of charge determination in the analysis of large macromolecular ions.

scPROTEIN is a deep graph contrastive learning framework that can estimate the uncertainty of peptide quantification, denoise protein data, remove batch effects and encode single-cell proteomic-specific embeddings under a unified framework.

Deep interactome profiling by mass spectrometry (DIP-MS) combines affinity purification with native BN-PAGE fractionation and mass spectrometry to resolve protein complexes sharing the same target protein. The paper also presents PPIprophet, a data-driven neural network-based protein complex deconvolution approach.

Monomeric and tandem dimer derivatives of the bright and photostable green fluorescent protein StayGold offer versatile tools for tagging target proteins and membranes in extended live-cell imaging.

mBaoJin is a monomeric derivative of the bright and photostable green fluorescent protein StayGold. mBaoJin offers favorable photophysical properties for use in diverse protein tagging and subcellular labeling applications.

An optogenetic system enables the controlled release of soluble and transmembrane proteins for precise exploration of cellular protein function at the single-molecule level and streamlined single-molecule imaging.

Effortless landmark detection is an unsupervised deep learning-based approach that addresses key challenges in landmark detection and image registration for accurate performance across diverse tissue imaging datasets.

Next-generation red and green G-protein-coupled receptor-based dopamine sensors with improved properties have been developed. Their performance is demonstrated in cell culture, in brain slices and in vivo in the mouse.

Deng et al. expand the toolbox of neurotransmitter sensors with high-sensitivity green and red genetically encoded serotonin sensors. These are suitable for in vivo applications, as demonstrated in a variety of applications in mice.

A-SOiD is a computational platform for behavioral annotation whose training includes elements of supervised and unsupervised learning. The approach is demonstrated on mouse, macaque and human datasets.

A benchmark study compares 13 spatial clustering methods on spatial transcriptomics data.

This analysis provides 108 noncoding CRISPR screens collated by the ENCODE4 consortium and establishes experimental guidelines for future CRISPRi screens characterizing functional cis-regulatory elements.