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The combination of computational protein design and single-site saturation mutagenesis enables engineering of allosteric transcription factors to respond to new small molecules.
RiboTaper quantifies the three-nucleotide periodicity in Ribo-seq data to find translated open reading frames (ORFs). The de novo inferred set of ORFs comprehensively defines the cellular proteome across a wide expression range and comprises few additional translated noncoding regions.
Measuring the forces generated by cells is not trivial in materials that behave in a nonlinear fashion. An equation that captures this behavior and finite-element modeling can be used to derive these forces from the material deformations around cells.
Addition of a glycan precursor to cells results in the synthesis and secretion of a large variety of O-glycans that can be purified and biochemically analyzed to profile the cellular O-glycome.
Pooling barcoded 3C libraries and simultaneously capturing interactions at many loci of interest generates reproducible cis- and trans-interaction maps at high resolution from low amounts of input material. This allows for the comparison of interactions in different cell types using common software designed for differential analysis of sequence count data, rather than requiring software specifically designed for 3C experiments.
The Fixed and Recovered Intact Single-cell RNA (FRISCR) method enables robust RNA extraction and sequencing from fixed, stained and sorted single cells and allows unprecedented profiling of rare cell types, including two subpopulations of radial glial cells in the developing human cortex.
Combining a reversibly photoswitchable bacteriophytochrome with photoacoustic imaging allows for exceptionally sensitive tomographic imaging deep in living mice, as well as super-resolution photoacoustic microscopy.
A fusion of RNA-binding proteins (RBPs) to a poly(U) polymerase allows the tagging of endogenous RNAs bound by the RBPs with a U-tail that can be used to identify the bound RNA by sequencing. RNA tagging is suited to discover RNA-protein networks in vivo.
A detailed study of the effects of dCas9-KRAB-sgRNA complexes on enhancer activity, gene expression and heterochromatin formation shows high efficacy and specificity.
IsoView microscopy achieves rapid isotropic-resolution imaging of large, nontransparent samples using simultaneous light-sheet illumination and fluorescence detection in four orthogonal directions.
A computational pipeline for analysis and statistical evaluation of quantitative cross-linking–mass spectrometry data facilitates the investigation of protein-complex structural heterogeneity.
Fusing a DNA-binding domain to Cas9 with an attenuated, more promiscuous PAM-recognition domain increases the targeting range of Cas9 as well as its specificity.
Multiplexed hybridization probes are traditionally difficult to design with high sensitivity and specificity. Here Wu et al. present a method for fine, decoupled and on-the-fly tuning of probe behavior based on the stoichiometric formulation of a molecular competitor species.
Transparent micro-optoelectrode arrays enable simultaneous electrical recording and optical stimulation in precise alignment. Depending on the applied light levels, single-unit activity or behavioral responses can be optically evoked.
This paper reports a Bayesian approach for the automatic identification of the optimal clustering proposal in the analysis of single-molecule localization-based super-resolution data.
Single Molecule Cluster Analysis (SiMCAn) is a hierarchical clustering method that enables rapid interpretation of the complex single-molecule dynamic behaviors of cellular machines (such as the spliceosome) from single-molecule fluorescence resonance energy transfer data.
A crosslinking-mass spectrometry strategy, including a new proteome database search engine called XlinkX, enables the identification of inter- and intra-protein cross-links in cell lysates on a proteome-wide scale.