Methods & Resources
Deep learning models link local cellular features with whole-animal growth dynamics in zebrafishThe study introduces a deep learning-assisted approach for uncovering the intricate, real-time cross-length scale interactions between individual cells and the entire organism in a vertebrate model.
A fluorescent sensor for real-time monitoring of DPP8/9 reveals crucial roles in immunity and cancerWeiss et al developed a genetically encoded biosensor for real-time monitoring of DPP8/9 activity, an important protease, and revealed roles of DPP8/9 in B-cell maturation and melanoma proliferation.
The RBR E3 ubiquitin ligase HOIL-1 can ubiquitinate diverse non-protein substrates in vitroThe RBR E3 ligase HOIL-1 ubiquitinates Ser/Thr residues and various disaccharides in vitro and can be used to generate ubiquitinated sugars as tools to study non-proteinaceous ubiquitination.
Visualisation of Euglena gracilis organelles and cytoskeleton using expansion microscopyWe applied expansion microscopy to visualise the cytoskeleton, mitochondria, and chloroplasts of Euglena gracilis, which enabled high-resolution imaging, revealing cellular structures and organelle development, demonstrating expansion microscopy’s utility as a complementary method to electron microscopy for studying this protist.
Concatemer-assisted stoichiometry analysis: targeted mass spectrometry for protein quantificationConcatemer-assisted stoichiometry analysis (CASA) addresses a common challenge in cell biology: absolute quantification of protein subunits in native protein complexes.
DICE: fast and accurate distance-based reconstruction of single-cell copy number phylogeniesThis work presents two new computational methods for reconstructing tumor cell lineage trees from single-cell copy number data.
FrozONE: quick cell nucleus enrichment for comprehensive proteomics analysis of frozen tissuesThe authors establish and benchmark a nuclear proteomics workflow that is faster, simpler, and more scalable than classical protocols, while being as efficient, specific, and reproducible.
Systematic assessment of structural variant annotation tools for genomic interpretationThis study benchmarks eight structural variant prioritization tools, highlighting their comparable effectiveness in predicting pathogenicity and providing insights for improved genomic research.
4G cloning: rapid gene assembly for expression of multisubunit protein complexes in diverse hostsTo streamline expression construct preparation for screening in diverse expression hosts, we present vectors and protocols using Golden Gate ligation to guide one-step Gibson assembly.
Mass spectrometry–based proteomic exploration of diverse murine macrophage cellular modelsIn this article, we characterised multiple murine macrophage cell models by proteomics and identified significant differences compared with bone marrow–derived macrophages.