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Small vibrational tags (azide, 13C-edited carbonyl and deuterium-labeled probes) were introduced as metabolic probes for mid-infrared imaging. The tags allow unprecedented in situ visualization of metabolism in cells and animals with high information throughput.
PULSE is an optogenetic tool that consists of two modules with different wavelength sensitivities. Their interplay enables optogenetic access to gene expression in plants independently of ambient light.
Multifocal flat illumination for field-independent imaging (mfFIFI) enables patterned illumination over an extended field of view. Integration with instant structured illumination microscope allowed for high-speed, multicolor, volumetric super-resolution imaging over 100 × 100 µm2.
DeepSTORM3D uses deep learning for accurate localization of point emitters in densely labeled samples in three dimensions for volumetric localization microscopy with high temporal resolution, as well as for optimal point-spread function design.
Targeted sequencing of perturbation effects offers a sensitive approach to capture genes of interest in CRISPR-mediated screens, enabling genome-scale screens at higher scale and lower cost than whole-transcriptome Perturb-seq.
CRISPR-based microraft followed by guide RNA identification (CRaft-ID) combines microraft arrays, microscopy and CRISPR–Cas9 technology for high-content image-based phenotyping. CRaft-ID was used to identify proteins involved in stress granule formation.
In situ point spread function (PSF) retrieval (INSPR) enables precise single-molecule localization in 3D single-molecule localization microscopy of whole cells and tissues. It directly determines PSF from a single-molecule blinking dataset, removing errors associated with sample-induced aberrations.
M-CREATE is an in vivo screening strategy for identifying recombinant AAVs with desired tropism. The approach involves both positive and negative selection and yields vectors with diversified cell-type tropism that can cross the blood–brain barrier in adult mice across strains when delivered intravenously.
3D ATAC-PALM integrates ATAC with super-resolution imaging for nanoscale views of the accessible genome. When combined with FISH, protein fluorescence and genetic perturbation, the method enables investigation of accessible chromatin in situ.
DNA-based FluoroCubes are ~6 nm small, monovalent probes that contain six organic dyes, which confer dramatic photostability relative to single dyes and offer more uniform signal compared to quantum dots for extended biological imaging.
Single-molecule displacement/diffusivity mapping (SMdM) enables nanoscale mapping of freely diffusing molecules in mammalian cells and reveals the structural basis of variations in local diffusivity in both the cytoplasm and nucleus.
The TooManyCells approach to scRNA-seq data facilitates efficient and unbiased identification and visualization of cell clades and rare subpopulations. Application of TooManyCells to drug-resistant leukemia cells identifies a rare resistant-like subpopulation of treatment-naive cells.
Ubiquitous mammalian enzymes can scavenge uracil analogs, leading to non-specific background in cell-type-specific RNA labeling. This work reveals the enzymes involved and describes the uridine/cytidine kinase 2 and 2′-azidouridine pair as a highly specific and non-toxic alternative.
A statistical method called SPARK for analyzing spatially resolved transcriptomic data can efficiently identify spatially expressed genes with effective control of type I errors and high statistical power.
Phenotypic earth mover’s distance (PhEMD) facilitates the comparison of single-cell experimental conditions, each of which is a high-dimensional dataset, and identifies axes of variation among multicellular biospecimens.
Protein–peptide interactions that underpin cell signaling are accurately predicted by wedding the strengths of machine learning with the interpretability of biophysical theory, facilitating detailed mechanistic analyses at the proteome scale.
An optogenetic strategy enables selection of proteases with improved catalytic rates. The developed TEV protease variants are well suited for biotechnology applications, including FLARE assays with substantially improved temporal resolution.
The unique advantages of single-particle cryo-electron microscopy and cryo-electron tomography are combined in a method called TYGRESS, here applied to determine the structure of the intact ciliary axoneme at a resolution of 12 Å.
An approach combining cryo-electron microscopy and mass spectrometry analysis of protein complexes enriched directly from cells enables structure determination of unknown complexes at atomic resolution.
Single-cell isolation following time-lapse imaging (SIFT) enables high-throughput screening of complex and dynamic phenotypes from pooled bacterial libraries. SIFT was used to generate ultraprecise synthetic gene oscillators.
A new method of autophagy measurement is based on the detection of phospho-ATG16L1, a conserved early marker of autophagy. Sensitive detection can be achieved in multiple biological systems and assays with advantages over standard methods.
DuMPLING (dynamic μ-fluidic microscopy phenotyping of a library before in situ genotyping) enables screening of dynamic phenotypes in strain libraries and was used here to study genes that coordinate replication and cell division in Escherichia coli.
Probabilistic cell typing by in situ sequencing (pciSeq), leverages previous single-cell RNA sequencing classification and multiplexed in situ RNA detection to spatially map cell types accurately in the mouse hippocampus and isocortex.
Deep-Z uses deep learning to go from a two-dimensional snapshot to three-dimensional fluorescence images. The method improves imaging speed while reducing light dose, and was shown to be useful for accurate structural and functional imaging of neurons in Caenorhabditis elegans.
mmvec, a neural-network-based algorithm, uses paired multiomics data (microbial sequence counts and metabolite abundances) to compute the conditional probability of observing a metabolite in the presence of a specific microorganism.