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Proximity-based labeling represents a useful approach for mapping protein environment, but current methods for this are limited to application to cell lines. This approach is now extended to primary human tissues with a method that uses antibodies to guide proximity labeling.
Using the ORI of plasmids used in enhancer assays as the sole core promoter and inhibiting the interferon I response triggered by plasmid transfection greatly reduces false positive and negative results in single-candidate and massively parallel enhancer assays and enables genome-wide enhancer screens.
NetSig is a network-based statistic that identifies cancer driver genes with high accuracy and can be combined with gene-based statistical tests; results are validated with a large-scale in vivo tumorigenesis assay.
The window for high-resolution imaging of the lung (WHRIL) enables longitudinal imaging of the same region of murine lung tissue over a period of weeks, and this enables the visualization of spontaneous cancer metastasis from the earliest stages.
Monomeric and homo-oligomeric protein quaternary structure states are predicted on a PDB-wide scale using a method that approaches the accuracy of manual annotation.
An improved MS2-tagging system for live-cell RNA imaging allows faithful monitoring of the mRNA life cycle, overcoming degradation artifacts associated with previous versions and having implications regarding mRNA regulation in yeast.
The high spatial resolution of secondary ion mass spectrometry and the high resolving power of the Orbitrap mass spectrometer are combined in a single imaging platform, the 3D OrbiSIMS. The instrument's capabilities for resolving lipids and neurotransmitters in the brain with subcellular spatial resolution, and a drug in a single cell in three dimensions is demonstrated.
This paper describes methods for the 3D culture of mouse lung progenitor cells that can differentiate in vitro and in vivo along all epithelial lineages.
An automated system for data acquisition and analysis enables high-content screening localization microscopy and increases the throughput and information content of super-resolution microscopy methods such as dSTORM, DNA-PAINT and (spt)PALM.
A reverse two-hybrid approach combined with massively parallel programmed mutagenesis and sequencing allows profiling protein interaction determinants at amino-acid resolution, as demonstrated by identifying interaction-disrupting mutations in a cilia protein complex associated with Bardet–Biedl syndrome.
Combining each sgRNA with a unique molecular identifier in a genome-wide screen increases sensitivity and robustness in both positive and negative selection.
A genetically encoded tension sensor module for measuring molecular forces at 3–5 pN along with tools for multiplexed tension sensing and data analysis reveal an intramolecular tension gradient across talin-1 during cell adhesion.
A tracking microscope for imaging neuronal activity at single-cell resolution in freely swimming zebrafish larvae is described. This technology allows functional imaging during behaviors that have previously been inaccessible to real-time analysis.
Guidelines for fine-tuning spectral and chemical properties of fluorophore are introduced, resulting in four new Janelia Fluor dyes, JF503, JF525, JF585 and JF635, that span the visible region and align well with standard laser lines.
Negative feedback and incoherent feed-forward loops are the only circuit motifs that can adapt in response to stimuli. Rahi et al. describe signatures that allow discriminating between these two motifs and demonstrate the approach in yeast cell cycle timing and C. elegans olfaction.
FreemoVR is a virtual reality system for freely moving animals. The versatile platform is demonstrated in various experiments with Drosophila, zebrafish, and mice.